Chicken sequences: searching chicken database with homologues.
Underlined is presequence not present in mature complex.
(see separate HTML file for complete results, this is minimal to cover)

SQR FP:
(lowercase region in 3d row is unknown fr chick- beef seq used)
xxMAAVVAASRSLAKCWLRPAARAWPAACQTHARNFHFTVDGKKNASTKVSDSISTQYPV
VDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNMEDD
NWRWHFYDTVKGSDWLGDQDAIHYMTEQapasvvelenygmpfsrtedGKIYQRAFGGQS
LQFGKGGQAHRCCCVADRTGHSLLHTLYGRSLRYDTSYFVEYFALDLLMENGECRGVIAL
CIEDGTIHRFRAKNTVIATGGYGRTYFSCTSAHTSTGDGTAMVTRAGLPCQDLEFVQFHP
TGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTIEIREGRGC
GPEKDHVYLQLHHLPPQQLATRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMGGIPTNY
KGQVITHVNGEDKVVPGLYACGEAASASVHGANRLGANSLLDLVVFGRACALTIAETCKP
GEPVPSIKPNAGEESVANLDKLRFADGTIRTSEARLNMQKTMQSHAAVFRTGSILQEGCE
KLSQIYCDLAHLKTFDRGIVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDY
KFRIDDFDYSKPLQGQQKRPFEEHWRKHTLSYVDVKSGKVTLKYRPVIDRTLNEEDCSSV
PPAIRSY 667

UDELPATPK0054E6F udel.pat.pk0054.e6.f    Frame = +1

Query: 1   MSGVAAVSRLWRARRLALTCTKWSAAWQTGTRSFHFTVDGNKRSSAKVSDAISAQYPVVD 60
           M+ V A SR      L      W AA QT  R+FHFTVDG K +S KVSD+IS QYPVVD
Sbjct: 4   MAAVVAASRSLAKCWLRPAARAWPAACQTHARNFHFTVDGKKNASTKVSDSISTQYPVVD 183

Query: 61  HEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNMEEDNW 120
           HEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNME+DNW
Sbjct: 184 HEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNMEDDNW 363

Query: 121 RWHFYDTVKGSDWLGDQDAIHYMTEQAPASVVELENYGMPFSRTEDGKIYQRAFGGQSLK 180
           RWHFYDTVKGSDWLGDQDAIHYMTEQ        + +     +   G+    AFGGQ + 
Sbjct: 364 RWHFYDTVKGSDWLGDQDAIHYMTEQPQLQ**TGKLWDA--IQ*NRGRKITAAFGGQ-IS 534

Query: 181 FGKGGQAHRC 190
           FGKG     C
Sbjct: 535 FGKGDGXXLC 564
1-145 looks reliable, this is absent in the non-redundant database.

From NR database: gi|3851616|gb|AAC72374.1|  (AF095939)

              130       140       150       160       170       180
                |         |         |         |         |         |
bos2   EDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPASVVELENYGMPFSRTEDGKIYQRAFGG
Gallus --------------------------------------------------GKIYQRAFGG

(underlined is the 20 residue gap between sequence above and this)

        1 gkiyqrafgg qslqfgkggq ahrcccvadr tghsllhtly grslrydtsy fveyfaldll
       61 mengecrgvi alciedgtih rfrakntvia tggygrtyfs ctsahtstgd gtamvtragl
      121 pcqdlefvqf hptgiygagc litegcrgeg gilinsqger fmeryapvak dlasrdvvsr
      181 smtieiregr gcgpekdhvy lqlhhlppqq latrlpgise tamifagvdv tkepipvlpt
      241 vhynmggipt nykgqvithv ngedkvvpgl yacgeaasas vhganrlgan slldlvvfgr
      301 acaltiaetc kpgepvpsik pnageesvan ldklrfadgt irtsearlnm qktmqshaav
      361 frtgsilqeg ceklsqiycd lahlktfdrg ivwntdlvet lelqnlmlca lqtiygaear
      421 kesrgahare dykfriddfd yskplqgqqk rpfeehwrkh tlsyvdvksg kvtlkyrpvi
      481 drtlneedcs svppairsy

UDELPATPK0037G1F udel.pat.pk0037.g1.f             Frame = +3
          GECRGVIALCIEDGSIHRIRARNTVIATGGYGRTYFSCTSAHTSTGDGTAMVTRAGLPC

Query: 231 ECRGVIALCIEERVHPPHQGQEHCHRHRSYGRTYFSCTSAHTSTGDGTAMVTRAGLPCQD 290
           ECRGVIALCIE+                         T   T TGDGTAMVTRAGLPCQD
Sbjct: 3   ECRGVIALCIEDGTIHRFRAKNTVIATG---------------TGDGTAMVTRAGLPCQD 137

Query: 291 LEFVQFHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTL 350
           LEFVQFHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMT+
Sbjct: 138 LEFVQFHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTI 317

Query: 351 EIREGRGCGPEK 362
           EIREGRGCGPEK
Sbjct: 318 EIREGRGCGPEK 353

This is all present in NR database- the deletion doesn't exist

Note the beef sequences used as query has ~15 residues wrong in here.

DKFZ426_3N5R1 REFORMAT of: dkfz426_3n5r1.dat   Frame = +1

Query: 353 REGRGCGPEKDHVYLQLHHLPPAQLAMRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMG 412
           REGRGCGPEKDHVYLQLHHLPP QLA RLPGISETAMIFAGVDVTKEPIPVLPTVHYNMG
Sbjct: 1   REGRGCGPEKDHVYLQLHHLPPQQLATRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMG 180

Query: 413 GIPTNYKGQVLRHVNGQDQGVPGLYACGEAACASVHGANRLGANSLLDLVVFGRACALSI 472
           GIPTNYKGQV+ HVNG+D+ VPGLYACGEAA ASVHGANRLGANSLLDLVVFGRACAL+I
Sbjct: 181 GIPTNYKGQVITHVNGEDKVVPGLYACGEAASASVHGANRLGANSLLDLVVFGRACALTI 360

Query: 473 AESCRPGDKVPSIKPNAGEESVMNLDKLRFANGSIRTSELRLNMQKSMQSHAAVFRVGSV 532
           AE+C+PG+ VPSIKPNAGEESV NLDKLRFA+G+IRTSE RLNMQK+MQSHAAVFR GS+
Sbjct: 361 AETCKPGEPVPSIKPNAGEESVANLDKLRFADGTIRTSEARLNMQKTMQSHAAVFRTGSI 540

Query: 533 LQEGCEKISSLYGDLRHLKTFDRGMVWNTDLVETLELQNLMLCALQTIYGAEARKESRG 591
           LQEGCEK+S +Y DL HLKTFDRG+VWNTDLVETLELQNLMLCALQTIYGAEARKESRG
Sbjct: 541 LQEGCEKLSQIYCDLAHLKTFDRGIVWNTDLVETLELQNLMLCALQTIYGAEARKESRG 717

(This is all included in seq from NR database)

SQR IP:

UDELPATPK0036A2F udel.pat.pk0036.a2.f    Frame = +3

Query: 10  LRRGVPARFLRAGLRPVRGLEAVHGICRGAQTAAAATSRIKKFSIYRWDPDKPGDKPRMQ 69
           LRRGVPARFLRAGLRP         ICRGAQTAAAATSRIKKFSIYRWDPDKPGDKPRMQ
Sbjct: 3   LRRGVPARFLRAGLRP---------ICRGAQTAAAATSRIKKFSIYRWDPDKPGDKPRMQ 155

Query: 70  TYEVDLNKCGPMVLDALIKIKNELDSTLTFRRSCREGICGSCAMNIAGGNTLACTKKIDP 129
           TYEVDLNKCGPMVLDALIKIKNELDSTLTFRRSCREGICGSCAMNIAGGNTLACTKKIDP
Sbjct: 156 TYEVDLNKCGPMVLDALIKIKNELDSTLTFRRSCREGICGSCAMNIAGGNTLACTKKIDP 335

Query: 130 DLSKTTKIYPLPHMYVVKDLVPDLSNFYAQYKSIEPYLKKKDESKQGKEQYLQSIEDRQK 189
           DLSKTTKIYPLPHMYVVKDLVPDLSNFY QYKSIEPYLKKKD    GK+     IED   
Sbjct: 336 DLSKTTKIYPLPHMYVVKDLVPDLSNFYXQYKSIEPYLKKKD-XXTGKDS-TSIIED--- 500

Query: 190 LDGLYECILCACCSTSCPSYW 210
           L          CC  +CP  W
Sbjct: 501 LXNWTXXX*SLCCXHNCPVRW 563

xThe rest of the matches from chick EST's have insignificant homology.

Entire sequence available from NR database:

>gi|3851612|gb|AAC72372.1|   (AF095937)  xxx

        1 maaavvgvsl rrgvparflr aglrpvrgle avhgicrgaq taaaatsrik kfsiyrwdpd
       61 kpgdkprmqt yevdlnkcgp mvldalikik neldstltfr rscregicgs camniaggnt
      121 lactkkidpd lskttkiypl phmyvvkdlv pdlsnfyaqy ksiepylkkk deskqgkeqy
      181 lqsiedrqkl dglyecilca ccstscpsyw wngdkylgpa vlmqayrwmi dsrddyteer
      241 laqlqdpfsl yrchtimnct rtcpkglnpg kaiaeikkmm atykekaaaa

UDELPTR1CPK0002B18 udelptr1cpk0002b18                              29  2.1
DKFZ426_20J5R1 REFORMAT of: dkfz426_20j5r1.dat  check: 5972 ...    28  2.7
UDELPATPK0008D7 udel.pat.pk0008.d7                                 28  3.5
UDELPATPK0071B6F udel.pat.pk0071.b6.f                              27  4.6
DKFZ426_17J15R1 REFORMAT of: dkfz426_17j15r1.dat  check: 143...    27  4.6
DKFZ426_25F19R1 REFORMAT of: dkfz426_25f19r1.dat  check: 251...    27  4.6
UDELPCO1SPK0001F10 udelpco1spk0001f10                              27  4.6

Chicken QPS1

  1 MAALVLRCVARRCLLARLSPGPSVHHVVPMATTAKEEMARFWEKNTKSSRPLSPHISIYKW  61
 62 SLPMAMSITHRGTGVALSLGVSLFSLAALLLPEQFPHYVAVVKSLSLSPALIYSAKFALV 121
122 FPLSYHTWNGIRHLVWDMGKGFKLSQVEQSGVVVLILTLLSSAGIAAIS 170

122 FPLSYHTWNGIRHLVWDMGKGFKLSQVEQSG 152
                     -GKGFKLNQGGSNXGVVVLILTLLSSAGIAAI 169
            NGIRHLVWDMGKGFKLSQVEQSGVVVLILTLLSSAGIAAIS 170
  (this last line is from consensus RNA seq, see qps1rna.doc)

UDELPATPK0079D4F udel.pat.pk0079.d4.f               Frame = +2

Query: 2   AALLLRHVGRHCLRAHLSPQLCIRNAVPLGTTAKEEMERFWSKNTTLNRPLSPHISIYGW 61
           AAL+LR V R CL A LSP   + + VP+ TTAKEEM RFW KNT  +RPLSPHISIY W
Sbjct: 2   AALVLRCVARRCLLARLSPGPSVHHVVPMATTAKEEMARFWEKNTKSSRPLSPHISIYKW 181

Query: 62  SLPMAMSICHRGTGIALSAGVSLFGLSALLVPGSFESHLEFVKSLCLGPALIHTAKFALV 121
           SLPMAMSI HRGTG+ALS GVSLF L+ALL+P  F  ++  VKSL L PALI++AKFALV
Sbjct: 182 SLPMAMSITHRGTGVALSLGVSLFSLAALLLPEQFPHYVAVVKSLSLSPALIYSAKFALV 361

Query: 122 FPLMYHTWNGIRHLMWDLGKGLTISQLHQSG 152
           FPL YHTWNGIRHL+WD+GKG  +SQ+ QSG
Sbjct: 362 FPLSYHTWNGIRHLVWDMGKGFKLSQVEQSG 454

UDELPATPK0076F8F udel.pat.pk0076.f8.f                Frame = +1

Query: 1   MAALLLRHVGRHCLRAHLSPQLCIRNAVPLGTTAKEEMERFWSKNTTLNRPLSPHISIYG 60
           MAAL+LR V R CL A LSP   + + VP+ TTAKEEM RFW KNT  +RPLSPHISIY 
Sbjct: 10  MAALVLRCVARRCLLARLSPGPSVHHVVPMATTAKEEMARFWEKNTKSSRPLSPHISIYK 189

Query: 61  WSLPMAMSICHRGTGIALSAGVSLFGLSALLVPGSFESHLEFVKSLCLGPALIHTAKFAL 120
           WSLPMAMSI HRGTG+ALS GVSLF L+ALL+P  F  ++  VKSL L PALI++AKF  
Sbjct: 190 WSLPMAMSITHRGTGVALSLGVSLFSLAALLLPEQFPHYVAVVKSLSLSPALIYSAKFRP 369

Query: 121 -VFPLMYHTWNGIRHLMWDLGK 141
              P      NGIRHL    G+
Sbjct: 370 GSSPSPTTPGNGIRHLRVGYGE 435

 Frame = +3
Query: 121 VFPLMYHTWN-------GIRHLMWDLGKGLTISQ-LHQSGVAVLVLTVLSSVGLAAM 169
           VFPL YHTW        GI    W  GKG  ++Q     GV VL+LT+LSS G+AA+
Sbjct: 372 VFPLSYHTWERNPTPPCGI----W--GKGFKLNQGGSNXGVVVLILTLLSSAGIAAI 524
If this is significant, and I think it is, it means two frame shift errors
Must be error in sequencing, as udel.pat.pk0079.d4.f above has both regions aligning.

eother in sequencing or in evolution
FM_ROS050B11-T3-1 REFORMAT of: EST4682-T3-1.seq  check: 2287...    30  0.48
 Frame = +1

Query: 55  HISIYGWSLPMAMSICHRGTGIALSAGVSLFGLSALLVPGSFESHLEFVKSLCLGPAL-- 112
           H+ I  W +P+ + +   G     S   SLF  S L   GS E HL  + S+ + P L  
Sbjct: 193 HLGIMSWIIPVFVGLSCFG-----SVNGSLFTSSRLFFVGSREGHLPSILSM-IHPRLLT 354

Query: 113 -IHTAKFALVFPLMYHTWNGI 132
            + +  F  V  L+Y   N I
Sbjct: 355 PVPSLVFTCVMTLLYAFSNDI 417
FM_ROS066F07-T7-1 REFORMAT of: EST6187-T7-1.seq  check: 9528...    27  2.4
 Frame = -2

Query: 7   RHVGRHCLRAHLSPQLCIRNAVPLGTTAKEEMERFWS 43
           R  G HC+  HLSP  C      LG+T +    R WS
Sbjct: 441 RSPGGHCVGPHLSPSTCGARG-GLGSTRRCHSGRPWS 334
DKFZ426_25P4R1 REFORMAT of: dkfz426_25p4r1.dat  check: 8443 ...    27  3.2
 Frame = -2

Query: 118 FALVFPLMYHTWNGIRHL-MWDLGKGLTISQLHQSGVAVLVLTVLSSVG 165
           F L  PL +       HL MW  G    ++ L Q G  V +  VLS VG
Sbjct: 583 FPLFLPLQHRGRRAKAHLRMW*NGDEFPLAALAQVGDGVAIQAVLSHVG 437
UDELPATPK0061F10F udel.pat.pk0061.f10.f                            27  4.2
 Frame = -2

Query: 4   LLLRHVGRHCLR-------AHLSPQLCIRNAVPLGTTAKEE-----MERFWSKNTTLNRP 51
           L   H GRHC R        H   ++C +   P+G+ A+ E         WS+  T + P
Sbjct: 260 LFFTHYGRHCPR*CQLGFMIHKVLEVCRKLPFPMGSNAQSEG*VCVQRSGWSERCTAS-P 84

Query: 52  LSPHISIYG 60
               + I+G
Sbjct: 83  AQGALPIHG 57

Chicken QPS3:

DKFZ426_16P18R1 REFORMAT of: dkfz426_16p18r1.dat  check: 820...  Frame = +3

Query: 17  ALFLRTPVVRPALVSAFLQDRPAQGWCGTQHIHLSPSHHSGSKAASLHWTGERVVSVLLL 76
           A  LR  ++R + V     DR A      Q    +P  H  SKAASLHWT ER VS LLL
Sbjct: 9   AALLRGTLLRHSAVLTAAADRSAPA---RQSHGGAPQGHGSSKAASLHWTSERAVSALLL 179

Query: 77  GLIPAAYLNPCSAMDYSLAATLTLHSHWGIGQVVTDYVHGDAVQKAAKTGLLVLSAFTFA 136
           GL+PAAYL P  A+DYSLAA LTLH HWG+GQV+TDYVHGD   K A TGL VLSA TF 
Sbjct: 180 GLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVANTGLYVLSAITFT 359

Query: 137 GLCYFNYHDVGICKAVAMLWKL 158
           GLCYFNY+DVGICKAVAMLW +
Sbjct: 360 GLCYFNYYDVGICKAVAMLWSI 425

Sbjct: 9   AALLRGTLLRHSAVLTAAADRSAPA---RQSHGGAPQGHGSSKAASLHWTSERAVSALLL 179
Sbjct: 180 GLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVANTGLYVLSAITFT 359
Sbjct: 360 GLCYFNYYDVGICKAVAMLWSI 425

UDELPATPK0023E8F udel.pat.pk0023.e8.f          Frame = +2

Query: 65  WTGERVVSVLLLGLIPAAYLNPCSAMDYSLAATLTLHSHWGIGQVVTDYVHGDAVQKAAK 124
           WT ER VS LLLGL+PAAYL P  A+DYSLAA LTLH HWG+GQV+TDYVHGD   K A 
Sbjct: 2   WTSERAVSALLLGLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVAN 181

Query: 125 TGLLVLSAFTFAGLCYFNYHDVGICKAVAMLWKL 158
           TGL VLSA TF GLCYFNY+DVGICKAVAMLW +
Sbjct: 182 TGLYVLSAITFTGLCYFNYYDVGICKAVAMLWSI 283

Sbjct: 2   WTSERAVSALLLGLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVAN 181
Sbjct: 182 TGLYVLSAITFTGLCYFNYYDVGICKAVAMLWSI 283

FM_ROS051C11-T3-1 REFORMAT of: EST4779-T3-1.seq  check: 181  Frame = +1

Query: 20  LRTPVVRPALVSAFLQDRPAQGWCGTQHIHLSPSHHSGSKAASLHWTGERVVSVLLLGLI 79
           LR  ++R + V     DR A      Q    +P  H  SKAASLHWT ER VS LLLGL+
Sbjct: 103 LRGTLLRHSAVLTAAADRSAPA---RQSHGGAPQGHGSSKAASLHWTSERAVSALLLGLL 273

Query: 80  PAAYLNPCSAMDYSLAATLTLHSHWGIGQVVTDYVHGDAVQKAAKTGL 127
           PAAYL P  A+DYSLAA LTLH HWG+GQV+TDYV    + K   TGL
Sbjct: 274 PAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVMEILLSKWLNTGL 417

Sbjct: 103 LRGTLLRHSAVLTAAADRSAPA---RQSHGGAPQGHGSSKAASLHWTSERAVSALLLGLL 273
Sbjct: 274 PAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVMEILLSKWLNTGL 417

DKFZ426_11O20R1 REFORMAT of: dkfz426_11o20r1.dat  check: 577.. Frame = +2

Query: 37  RPAQGWCGTQHIHLSPSHHSGSKAASLHWTGERVVSVLLLGLIPAAYLNPCSAMDYSLAA 96
           RP       +   ++P   +   +    WT ER  S LLLG  P  YL P          
Sbjct: 584 RPRDRSAXARQTMVAPRRATAVPSCIPAWTXERAXSALLLGPAPRCYLXPGPLXTTPWCX 763

Query: 97  TLTLHSHWGIGQ 108
            L+    WG+GQ
Sbjct: 764 LLSW--AWGLGQ 793

Sbjct: 584 RPRDRSAXARQTMVAPRRATAVPSCIPAWTXERAXSALLLGPAPRCYLXPGPLXTTPWCX 763
Sbjct: 764 LLSW--AWGLGQ 793

FM_ROS059G10-M13F-1 REFORMAT of: EST5543-M13F-1.seq  check: .. Frame = -1

Query: 34  LQDRPAQGWCGTQHIHLSPSHHSGSKAASLHW 65
           L  R A+G  G+ H  L  SHH   + +  HW
Sbjct: 190 LPARGAEGCAGSAHSSLLRSHHCRHRGSHPHW 95

DKFZ426_16P18R1   AALLRGTLLRHSAVLTAAADRSAPA---RQSHGGAPQGHGSSKAASLHWTSERAVSALLL 179
FM_ROS051C11-T3-1    LRGTLLRHSAVLTAAADRSAPA---RQSHGGAPQGHGSSKAASLHWTSERAVSALLL 273
UDELPATPK0023E8F                                                  WTSERAVSALLL

DKFZ426_16P18R1   GLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVANTGLYVLSAITFT 359
FM_ROS051C11-T3-1 GLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVMEILLSKWLNTGL 417
UDELPATPK0023E8F  GLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVANTGLYVLSAITFT 181

DKFZ426_16P18R1   GLCYFNYYDVGICKAVAMLWSI 425
FM_ROS051C11-T3-1
UDELPATPK0023E8F  GLCYFNYYDVGICKAVAMLWSI 283


consensus (= first sequence):

AALLRGTLLRHSAVLTAAADRSAPA---RQSHGGAPQGHGSSKAASLHWTSERAVSALLL
GLLPAAYLYPGPAVDYSLAAALTLHGHWGLGQVITDYVHGDTPIKVANTGLYVLSAITFT
GLCYFNYYDVGICKAVAMLWSI

Sbjct: 584 RPRDRSAXARQTMVAPRRATAVPSCIPAWTXERAXSALLLGPAPRCYLXPGPLXTTPWCX 763
Sbjct: 764 LLSW--AWGLGQ 793

Sbjct: 190 LPARGAEGCAGSAHSSLLRSHHCRHRGSHPHW 95

xxx