10        20        30        40        50      
                  |         |         |         |         |         |
Bostaurus       ---SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLV--G-V
Gallus          ---GELELHPPAFPWSHGGPLSALDHSSVRRGFQVYKQVCSACHSMDYVAFRNLI--G-V
Saccharocere    MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLV--G-V
RbcapsGA        ------NSNVQDHAFSFEGIFGKFDQAQLRRGFQVYSEVCSTCHGMKFVPIRTLSDDGGP
RbCapsulatus    ------NSNVPDHAFSFEGIFGKYDQAQLRRGFQVYNEVCSACHGMKFVPIRTLADDGGP
Rbsphaeroides   --------HVEDVPFSFEGPFGTFDQHQLQRGLQVYTEVCAACHGMKFVPIRSLSEPGGP
                        :    .:*. * :   *: .::** *** :**::**.:. *. * *   *  
Prim.cons.      ------2LHVPD222S2EGPFG2FD2A2LRRGFQVYKEVCSACH2M2FV2IRTL2--G22

Either:             60         70         80        90       100       110      
                     |          |         |         |         |         |
Bostaurus       CYTEDEAKALAEEVE-VQDGPNEDGEMFMRPGKLSDYFPKPYPNPEAARAANNGALPPDL
Gallus          THTEAEAKALAEEVE-VQDGPDENGELFMRPGKISDYFPKPYPNPEAARADNNGALPPDL
Saccharocere    SHTNEEVRNMAEEFE-YDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDL
RbcapsGA        QLDPTFVREYAAGLDTIID--KDSG--EERDRKETDMFPTRVGD----------GMGPDL
RbCapsulatus    QLDPTFVREYAAGLDTIID--KDSG--EERDRKETDMFPTRVGD----------GMGPDL
Rbsphaeroides   ELPEDQVRAYATQFT-VTD--EETG--EDREGKPTDHFPHSALE-----------NAPDL
                      .:  *  .    *  .: *    *  * :* :*    :             ***
Prim.cons.      QLTE2EVRAYAEE3E-V2D-22ESG--E2RPGK22DYFP2PYPN--2222-2-2ALPPDL

OR:                 60        70        80        90       100       110      
                     |         |         |         |         |         |
Bostaurus       CYTEDEAKALAEEVEVQDGPNEDGEMFMRPGKLSDYFPKPYPNPEAARAANNGALPPDL
Gallus          THTEAEAKALAEEVEVQDGPDENGELFMRPGKISDYFPKPYPNPEAARADNNGALPPDL
Saccharocere    SHTNEEVRNMAEEFEYDDEPDEQGNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDL
RbcapsGA        QLDPTFVREYAAGLD--TIIDKDS-GEERDRKETDMFPTRVGD----------GMGPDL
RbCapsulatus    QLDPTFVREYAAGLD--TIIDKDS-GEERDRKETDMFPTRVGD----------GMGPDL
Rbsphaeroides   ELPEDQVRAYATQFT---VTDEET-GEDREGKPTDHFPHSALE-----------NAPDL
                      .:  *  .    *  .: *    *  * :* :*    :             ***
Prim.cons.      QLTE2EVRAYAEE3E-V2D-22ESG--E2RPGK22DYFP2PYPN--2222-2-2ALPPDL


                    120                        130        140         150   
                      | -----------------        |     -    |    --     |     
Bostaurus       SYIVRARH-----------------GGEDYVFSLLTGY-CEPPTGVSLR--EGLYFNPYF
Gallus          SYIVYARH-----------------GGEDYVFSLLTGY-CDPPAGVVVR--EGLHYNPYF
Saccharocere    SLIVKARH-----------------GGCDYIFSLLTGYPDEPPAGVALP--PGSNYNPYF
RbcapsGA        SVMAKARAGFSGPAGSGMNQLFKGIGGPEYIYRYVTGFPEENPACAPEG-IDGYYYNEVF
RbCapsulatus    SVMAKARAGFSGPAGSGMNQLFKGMGGPEYIYNYVIGF-EENPECAPEG-IDGYYYNKTF
Rbsphaeroides   SLMAKARAGFHGPMGTGISQLFNGIGGPEYIYSVLTGFPEEPPKCAEGHEPDGFYYNRAF
                * :. **                  ** :*::  : *:  : *  .      *  :*  *
Prim.cons.      S322KAR222-22-2-2--222-2-GGP2YI2SLLTG2PEEPPA22P22--DG2YYNPYF

                                      160       170       180        190     
                                        |         |         |         |      
Bostaurus       P------------------GQAIGMAPPIYNEVLEFDDGTPATMSQVAKDVCTFLRWAAE
Gallus          P------------------GQAIGMAPPIYNEILEYDDGTPATMSQIAKDVCTFLRWAAE
Saccharocere    P------------------GGSIAMARVLFDDMVEYEDGTPATTSQMAKDVTTFLNWCAE
RbcapsGA        QVGGVPDTCKDAAGIKTTHGSWAQMPPALFDDLVTYEDGTPATVDQMGQDVASFLMWAAE
RbCapsulatus    QIGGVPDTCKDAAGVKITHGSWARMPPPLVDDQVTYEDGTPATVDQMAQDVSAFLMWAAE
Rbsphaeroides   QNGSVPDTCKDANGVKTTAGSWIAMPPPLMDDLVEYADGHDASVHAMAEDVSAFLMWAAE
                                   *    *.  : :: : : **  *:   :.:** :** *.**
Prim.cons.      2-2-22222222-2-2-2-GSWI2M2PPL2DDLVEYEDGTPATVSQMAKDV2TFLMWAAE

                  200       210       220       230       240       250  
                    |         |         |         |         |         | 
Bostaurus       PEHDHRKRMGLKMLLMMGLLLPLVYAMKRHKWSVLKSRKLAYRPPK---
Gallus          PEHDQRKRMGLKMLLISALLTSLLYYMKRHKWSVLKSRKMAYRPPK---
Saccharocere    PEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFVFNPPKPRK
RbcapsGA        PKLVARKQMGLVAVVMLGLLSVMLYLTNKRLWAPYKRQKA---------
RbCapsulatus    PKLVARKQMGLVAMVMLGLLSVMLYLTNKRLWAPYKGHKA---------
Rbsphaeroides   PKLMARKQAGFTAVMFLTVLSVLLYLTNKRLWAGVKGKKKTNV------
                *:   **: *:  :::   *  :    ::  *:  * :*                     
Prim.cons.      P22DARK2MGLKAV2MLGLLSVLLYLT2KR2WA32K2RKAAYRPPKPRK

For clustalw:

>Bostaurus
xxxSDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLVxxGxVCYTEDEAKALAEEVExVQDGPNEDGEM
FMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRARHxxxxxxxxxxxxxxxxxGGEDYVFSLLTGYCxEPPTGVSLRx
xEGLYFNPYFPxxxxxxxxxxxxxxxxxxGQAIGMAPPIYNEVLEFDDGTPATMSQVAKDVCTFLRWAAEPEHDHRKRMGLKMLLMMGLLL
PLVYAMKRHKWSVLKSRKLAYRPPK
 >Gallus
xxxGELELHPPAFPWSHGGPLSALDHSSVRRGFQVYKQVCSACHSMDYVAFRNLIxxGxVTHTEAEAKALAEEVExVQDGPDENGEL
FMRPGKISDYFPKPYPNPEAARADNNGALPPDLSYIVYARHxxxxxxxxxxxxxxxxxGGEDYVFSLLTGYCxDPPAGVVVRx
xEGLHYNPYFPxxxxxxxxxxxxxxxxxxGQAIGMAPPIYNEILEYDDGTPATMSQIAKDVCTFLRWAAEPEHDQRKRMGLKMLLISALLT
SLLYYMKRHKWSVLKSRKMAYRPPK
 >Saccharocere
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVxxGxVSHTNEEVRNMAEEFExYDDEPDEQGNP
KKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIVKARHxxxxxxxxxxxxxxxxxGGCDYIFSLLTGYPDEPPAGVALPx
xPGSNYNPYFPxxxxxxxxxxxxxxxxxxGGSIAMARVLFDDMVEYEDGTPATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLY
LLSIWVKKFKWAGIKTRKFVFNPPKPRK
 >Rb.capsGA
xxxxxxNSNVQDHAFSFEGIFGKFDQAQLRRGFQVYSEVCSTCHGMKFVPIRTLSDDGGPQLDPTFVREYAAGLDTIIDxxKDSGxx
EERDRKETDMFPTRVGDxxxxxxxxxxGMGPDLSVMAKARAGFSGPAGSGMNQLFKGIGGPEYIYRYVTGFPEENPACAPEGx
IDGYYYNEVFQVGGVPDTCKDAAGIKTTHGSWAQMPPALFDDLVTYEDGTPATVDQMGQDVASFLMWAAEPKLVARKQMGLVAVVMLGLLS
VMLYLTNKRLWAPYKRQKA
>RbCapsulatus
xxxxxxnsnvpdhafsfegifgkydqaqlrrgfqvynevcsachg
mkfvpirtladdggpqldptfvreyaagldtiidxxkdsgxxeerdrketdmfptrvgdxxxxxxxxxxgmgpd
lsvmakaragfsgpagsgmnqlfkgmggpeyiynyvigfxeenpecapegxidgyyynktfq
iggvpdtckdaagvkithgswarmppplvddqvtyedgtpatvdqmaqdvsaflmwaaep
klvarkqmglvamvmlgllsvmlyltnkrlwapykghka
>Rb.sphaeroides
xxxxxxxxHVEDVPFSFEGPFGTFDQHQLQRGLQVYTEVCAACHGMKFVPIRSLSEPGGPELPEDQVRAYATQFTxVTDxxEETGxx
EDREGKPTDHFPHSALExxxxxxxxxxxNAPDLSLMAKARAGFHGPMGTGISQLFNGIGGPEYIYSVLTGFPEEPPKCAEGHE
PDGFYYNRAFQNGSVPDTCKDANGVKTTAGSWIAMPPPLMDDLVEYADGHDASVHAMAEDVSAFLMWAAEPKLMARKQAGFTAVMFLTVLS
VLLYLTNKRLWAGVKGKKktnv

for vertalign:

>Bostaurus
-------------------------------------------------------------
---SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLV--G-VCYTEDEAKALAEEVE-VQDGPNEDGEM-
FMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRARH-----------------GGEDYVFSLLTGYC-EPPTGVSLR-
-EGLYFNPYFP------------------GQAIGMAPPIYNEVLEFDDGTPATMSQVAKDVCTFLRWAAEPEHDHRKRMGLKMLLMMGLLL
PLVYAMKRHKWSVLKSRKLAYRPPK----
 >Gallus
-------------------------------------------------------------
---GELELHPPAFPWSHGGPLSALDHSSVRRGFQVYKQVCSACHSMDYVAFRNLI--G-VTHTEAEAKALAEEVE-VQDGPDENGEL-
FMRPGKISDYFPKPYPNPEAARADNNGALPPDLSYIVYARH-----------------GGEDYVFSLLTGYC-DPPAGVVVR-
-EGLHYNPYFP------------------GQAIGMAPPIYNEILEYDDGTPATMSQIAKDVCTFLRWAAEPEHDQRKRMGLKMLLISALLT
SLLYYMKRHKWSVLKSRKMAYRPPK---
 >Saccharocere
-------------------------------------------------------------
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLV--G-VSHTNEEVRNMAEEFE-YDDEPDEQGNP-
KKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIVKARH-----------------GGCDYIFSLLTGYPDEPPAGVALP-
-PGSNYNPYFP------------------GGSIAMARVLFDDMVEYEDGTPATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLY
LLSIWVKKFKWAGIKTRKFVFNPPKPRK-
 >Saccharo-pre
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLV--G-VSHTNEEVRNMAEEFE-YDDEPDEQGNP-
KKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIVKARH-----------------GGCDYIFSLLTGYPDEPPAGVALP-
-PGSNYNPYFP------------------GGSIAMARVLFDDMVEYEDGTPATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLY
LLSIWVKKFKWAGIKTRKFVFNPPKPRK-
 >Rb.capsGA
-------------------------------------------------------------
------NSNVQDHAFSFEGIFGKFDQAQLRRGFQVYSEVCSTCHGMKFVPIRTLSDDGGPQLDPTFVREYAAGLDTIID--KDSG---
EERDRKETDMFPTRVGD----------GMGPDLSVMAKARAGFSGPAGSGMNQLFKGIGGPEYIYRYVTGFPEENPACAPEG-
IDGYYYNEVFQVGGVPDTCKDAAGIKTTHGSWAQMPPALFDDLVTYEDGTPATVDQMGQDVASFLMWAAEPKLVARKQMGLVAVVMLGLLS
VMLYLTNKRLWAPYKRQKA----------
>RbCapsulatus
-------------------------------------------------------------
------nsnvpdhafsfegifgkydqaqlrrgfqvynevcsachg
mkfvpirtladdggpqldptfvreyaagldtiid--kdsg---eerdrketdmfptrvgd----------gmgpd
lsvmakaragfsgpagsgmnqlfkgmggpeyiynyvigf-eenpecapeg-idgyyynktfq
iggvpdtckdaagvkithgswarmppplvddqvtyedgtpatvdqmaqdvsaflmwaaep
klvarkqmglvamvmlgllsvmlyltnkrlwapykghka
>Rb.sphaeroides
-------------------------------------------------------------
--------HVEDVPFSFEGPFGTFDQHQLQRGLQVYTEVCAACHGMKFVPIRSLSEPGGPELPEDQVRAYATQFT-VTD--EETG---
EDREGKPTDHFPHSALE-----------NAPDLSLMAKARAGFHGPMGTGISQLFNGIGGPEYIYSVLTGFPEEPPKCAEGHE
PDGFYYNRAFQNGSVPDTCKDANGVKTTAGSWIAMPPPLMDDLVEYADGHDASVHAMAEDVSAFLMWAAEPKLMARKQAGFTAVMFLTVLS
VLLYLTNKRLWAGVKGKKktnv---