CLUSTALW multiple alignment

Abstract Thompson, J.D., Higgins, D.G. and Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. (1994) Nucleic Acids Research, 22, 4673-4680 

                         10        20        30        40        50        60
                          |         |         |         |         |         |
Homoxx0          -MAAVVALSLRRRLPATTLGG---------ACLQASRGAQTAAATAPRIKKFAIYRWDPD
Gallusg_SDH_IP   MAAAVVGVSLRRGVPARFLRAGLRPVRGLEAVHGICRGAQTAAAATSRIKKFSIYRWDPD
Reclinomas       -----------------------------------------MNTKKEKIMLFKVYRWNPD
Scerev           ----MLNVLLRRKAFCLVTKKG------------MATATTAAATHTPRLKTFKVYRWNPD
Ascaris          --MLRGSTSVCRSLELVTQAAR------------YASAATAAAPTGKRIKTFEIYRFNPE
Ecoli_FRD_IP     -------------------------------------------MAEMKNLKIEVVRYNPE
                                                                :   : : *::*:
Prim.cons.       M2AAVV4VSLRR4LPA4TL4AGLRPVRGLEA2224AR2A22AA22TPRIKKF22YRWNPD

                         70        80        90       100       110       120
                          |         |         |         |         |         |
Homoxx0          KAGDKPHMQTYKVDLNKCGPMVLDALIKIKNEVDSTLTFRRSCREGICGSCAMNINGGNT
Gallusg_SDH_IP   KPGDKPRMQTYEVDLNKCGPMVLDALIKIKNELDSTLTFRRSCREGICGSCAMNIAGGNT
Reclinomas       KK-EKPHISTYSVDLNSCGPMVLDALIKIKNEQDSTLTFRRSCREGVCGSCAMNIDGTNT
Scerev           EPSAKPHLQSYQVDLNDCGPMVLDALLKIKDEQDSTLTFRRSCREGICGSCAMNIGGRNT
Ascaris          EPGAKPKLQKFDVDLDKCGTMVLDALIKIKNEVDPTLTFRRSCREGICGSCAMNIAGENT
Ecoli_FRD_IP     VD-TAPHSAFYEVPYDAT-TSLLDALGYIKDNLAPDLSYRWSCRMAICGSCGMMVNNVPK
                      *:   :.*  :   . :****  **::  . *::* *** .:****.* : .  .
Prim.cons.       KPG2KPH2QTYEVDLNKCGPMVLDALIKIKNE3DSTLTFRRSCREGICGSCAMNI2GGNT

                        130       140       150       160       170       180
                          |         |         |         |         |         |
Homoxx0          LACTRRIDTNLNKVSKIYPLPHMYVIKDLVPDLSNFYAQYKSIEPYLKKKDESQEGKQQY
Gallusg_SDH_IP   LACTKKIDPDLSKTTKIYPLPHMYVVKDLVPDLSNFYAQYKSIEPYLKKKDESKQGKEQY
Reclinomas       LACIKSIDTNK-KEMKIYPLPHMHIIKDLVPDLSNFYAQYKSIEPWMKTTEKKLD--KEF
Scerev           LACICKIDQNESKQLKIYPLPHMFIVKDLVPDLTNFYQQYKSIQPYLQRSSFPKDG-TEV
Ascaris          LACICNIDQNTSKTTKIYPLPHMFVIKDLVPDMNLFYAQYASIQPWLQKKTKINLGEKQQ
Ecoli_FRD_IP     LACKTFLRDYT-DGMKVEALANFPIERDLVVDMTHFIESLEAIKPYIIGNSRTAD-QGTN
                 ***   :     .  *: .*.:: : :*** *:. *  .  :*:*::  .          
Prim.cons.       LACI2KID2N2SKT2KIYPLPHM22IKDLVPDLSNFYAQYKSIEPYLKKK22SKDGKKQY

                        190       200       210       220       230       240
                          |         |         |         |         |         |
Homoxx0          LQSIEEREKLDGLYECILCACCSTSCPSYWWNGDKYLGPAVLMQAYRWMIDSRDDFTEER
Gallusg_SDH_IP   LQSIEDRQKLDGLYECILCACCSTSCPSYWWNGDKYLGPAVLMQAYRWMIDSRDDYTEER
Reclinomas       YQSRNDREKLDGLYECVLCACCSTSCPSYWWNSDKYLGPAVLLQAYRWIVDSRDQGTRER
Scerev           LQSIEDRKKLDGLYECILCACCSTSCPSYWWNQEQYLGPAVLMQAYRWLIDSRDQATKTR
Ascaris          YQSIKEQEKLDGLYECILCACCSASCPSYWWNADKYLGPAVLMQAYRWIIDSRDDSAAER
Ecoli_FRD_IP     IQTPAQMAKYHQFSGCINCGLCYAACPQFGLN-PEFIGPAAITLAHRYNEDSRDHGKKER
                  *:  :  * . :  *: *. * ::**.:  *  :::***.:  *:*:  ****.    *
Prim.cons.       LQSIEDREKLDGLYECILCACCSTSCPSYWWNGDKYLGPAVLMQAYRW2IDSRDDGT2ER

                        250       260       270       280       290
                          |         |         |         |         |
Homoxx0          LAKLQDPFSLYRCHTIMNCTRTCPKGLNPGKAIAEIKKMMATYKEKKASV------
Gallusg_SDH_IP   LAQLQDPFSLYRCHTIMNCTRTCPKGLNPGKAIAEIKKMMATYKEKAAAA------
Reclinomas       LQYLEDPFKLYRCHTILNCTKTCPKHLNPAQAIAKIKQNITLLT------------
Scerev           KAMLNNSMSLYRCHTIMNCTRTCPKGLNPGLAIAEIKKSLAFA-------------
Ascaris          LARMQDGFSAFKCHTIMNCTKTCPKHLNPARAIGEIKMLLTKMKTKPAPLPTPANF
Ecoli_FRD_IP     MAQLNSQNGVWSCTFVGYCSEVCPKHVDPAAAIQQGKVESSKDFLIATLKPR----
                    ::.    : *  :  *:..*** ::*. ** : *   :                   
Prim.cons.       LAQLQDPFSLYRCHTIMNCTRTCPK2LNP2KAIAEIKKM2A2YKEKAA44P2PANF

Alignment data :
Alignment length : 296
Identity (*) : 59 is 19.93 %
Strongly similar (:) : 49 is 16.55 %
Weakly similar (.) : 22 is 7.43 %
Different : 166 is 56.08 %
Sequence 0001 : Homoxx0 ( 280 residues).
Sequence 0002 : Gallusg_SDH_IP ( 290 residues).
Sequence 0003 : Reclinomas ( 239 residues).
Sequence 0004 : Scerev ( 266 residues).
Sequence 0005 : Ascaris ( 282 residues).
Sequence 0006 : Ecoli_FRD_IP ( 244 residues).

CLUSTALW options used :
endgaps=1
gapdist=8
gapext=0.2
gapopen=10.0
hgapresidues=GPSNDQERK
ktuple=1
matrix=gonnet
maxdiv=30
outorder=aligned
pairgap=3
score=percent
topdiags=5
type=PROTEIN
window=5

Result files (text) :
CLUSTALW

Garnier parameters

Auto calculated
Decision constants Helix Sheet Turn Coil
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SOPM parameters

Number of conformational states
Similarity threshold : Window width :
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SOPMA parameters

Number of conformational states
Similarity threshold : Window width :
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Comments. Last modified: Mon May 22 03:04:41 2000. Current time: Mon May 22 03:04:41 2000