Sequence alignment for CL0074

PF02337

GAG_JSRV/1-90MGHTHS--------R.QLFVHMLSVMLKHR-GITVSKTKLINF--LSFIEEVCPWFPREGTVNLETWKKVGEQIRTHYTL
GAG_SMRVH/3-93QASSHS--------ENDLFISHLKESLKVR-RIRVRKKDLVSF--FSFIFKTCPWFPQEGSIDSRVWGRVGDCLNDYYRV
O41288_MPMV/1-91MGQELS--------QHQIYVGQLKEALKIR-GVKVKGNDLFKF--FDFVKDTCPWFPQEGTIDIKRWRRVGDCFQDYYNT
GAG_MMTVB/4-92SGSKGQ--------K..LFVSVLQRLLSER-GLHVKESSAIEF--YQFLIKVSPWFPEEGGLNLQDWKRVGREMKRYAAE
GAG_IPHA/1-84MGSSQS--------V....VTALQTVLKQR-DLKIAPRTLQNF--MKEVDRVAPWYACSGSLTVASWNKLGKELDR...K

PF01140

GAG_MLVAV/2-129-GQTVT....TPLSLTLEHWEDVQRIASNQ-SVDVKKRRWVTFCSAEWPTFGVGW-PQDGTFNLDIILQVKSKVFSPGPH
GAG_WMSV/2-128-GQNNS....TPLSLTLGHWKDVRTRAHNL-SVKIRKEKWQTFCSSEWPTFGVGW-PPEGTFNLSVIFAVKRIVFQET.G
GAG_MLVRD/2-129-GQTVT....TPLSLTLEHWGDVQRIASNQ-SVEVKKRRRVTFCPAEWPTFDVGW-PQDGTFNLDIILQVKSKVFSPGPH
GAG_GALV/2-125-GQDNS....TPISLTLNHWRDVRTRAHNL-SVEIKKGKWQTFCSSEWPTFGVGW-PPEGTFNLSVIFAVKKIVFQEN.G
GAG_FLV/76-201-GQTVT....TPLSLTLDHWSEVRARAHNQ-GVEVRKKKWITLCEAEWVMMNVGW-PREGTFSLDNISQVEKKIFAPGPH
O36448_FOWPV/2-137-GQAGSKGLLTPLECILKNFSDFKKRAGDY-GEDVDSFTLRKLCELEWPTFGVGW-PKEGTLDFRVVAAVRNIVFGNP..
Q67457_MLVFR/2-131-GQTVT....TPLSLTLDHWKDVERTAHNQ-SVEVRKRRWVTLCSAEWPTFNVGW-PQDGTFNPDIITQVKIKVFSPGPH
Q62700_RAT/2-128-GQSLT....TPLSLTLDHWKDVRDRARDQ-SVEIKKGKWQTLCIVRVAHLRCRM-AGERTFNKTTILQVKDLIFRQKPY
Q83378_9GAMR/2-128-GQSLT....TPLSLTLDHLKDVRDRARDQ-SVEIKKGKWQTLCTSEWPTYDVGW-PVNGTFNKTTILQVKDLIFRQKPY

PF02228

GAG_HTL1A/1-92MGQIFS-----------RSASPIPRPPRGL-AAH----HWLNFLQAAYRLE-----PGPSSYDFHQLKKFLKIALETPAR
O12272_9DELA/1-92MGKTYS-----------SPANPIPKAPKGL-AIH----HWLNFLQAAYRLQ-----PGPSEFDFHQLRKFLKLAIKTPVW

PF00540

GAG_HV1A2/2-134-GARAS----VLSGGELDKWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGC---RQILGQLQPSLQTGSE
GAG_SIVCZ/2-140-GARAS----VLTGGKLDRWEKVRLRPGGRKRYMMKHLVWASRELERFACDPGLMESKEGC---TKLLQQLEPALKTGSE
GAG_SIVV1/2-141-GAATS----ALNRRQLDEFEHIRLRPNGKKKYQIKHLIWAGKKMDRFGLHEKLLETEEGC---KKIIEVLSPLEPTGSE

PF02813

Q83009_9RETR/2-84----------------DTVKRVLKTLAQDQ..RTSVRSKDVVSCIERLIAEGAIKRPSD-IFARDIWPHCTATLTQRAMT
Q64992_RSVSR/2-87----------------EAVIKVISSACKTYCGKTSPSKKEIGAMLSLLQKEGLLMSPSD-LYSPGSWDPITAALSQRAMI
Q9QME3_9RETR/2-87----------------DQVIKVLVQFCKDYCGKSTPSRKEIATVLSLLNELGELDSPCH-ILDSSRWDLLTSALCQRAMA

PF02337

GAG_JSRV/1-90HGPEKVPVETLSFWT--------------LIRDCLD----------------------------------
GAG_SMRVH/3-93FGPETIPITTFNYYN--------------LIRDVLT----------------------------------
O41288_MPMV/1-91FGPEKIPVTAFSYWN--------------LIRDLID----------------------------------
GAG_MMTVB/4-92HGTDSIPKQAYPIWL--------------QLREILT----------------------------------
GAG_IPHA/1-84HAEGDLCLGTKAIWK--------------LVKNCLE----------------------------------

PF01140

GAG_MLVAV/2-129GHPDQVPY--IVTWEAIAYEPP------PWVKPFVSPK......LSPSP.TAPILPSGPSTQPPPRSALY
GAG_WMSV/2-128GHPDQVPY--IVVWQDLAQSPP------PWVPPSAKIA....VVSSPENTQGPSAGR.PSAPPRPP..IY
GAG_MLVRD/2-129GHPDQVPY--IVTWEAIAYEPP------SWVKPFVSPK....LSLSPTAPILPSGPS.TQPPPRSA..LY
GAG_GALV/2-125GHPDQVPY--IVVWQDLAQNPP------PWV.....PA..SAKVAVVSDTRRPVAGR.PSAPPRPP..IY
GAG_FLV/76-201GHPDQVPY--ITTWRSLATDPP------SWVRPFLPPP......KPPTPLPQPLSPQ.PSAPLTSS..LY
O36448_FOWPV/2-137GHPDQVIY--ITVWIDITIERP------KYLKDCGCKPTGPSKVLLASQKVNPRRPVLPSAPESPPR.MR
Q67457_MLVFR/2-131GHPEQVPY--IVTWEALAVDPP------PWVKPFVHPKPP..LLLPPSAPSLPPEPP.LSTPPQSS..LY
Q62700_RAT/2-128GHPDQVAY--IVTWESLAFSPP------PWAEPFVDPN......WLPVS.PKPVSPS.PPDPLVASSSLY
Q83378_9GAMR/2-128GHPDQVAY--IVTWESLAFSPP------PWAEPFVDPN......WLPVS.PKPVSPS.PPDPLVASSSLY

PF02228

GAG_HTL1A/1-92ICPINYSLLASLLPKGYPGRVN------EILHILIQTQA-------------------------------
O12272_9DELA/1-92LNPINYSVLAGLIPKNYPGRVH------EIVAILIQETP-------------------------------

PF00540

GAG_HV1A2/2-134ELRSLYNTVATLYCVHQRIDVKDTKEALEKIEEEQNKSKKK.........AQQAAAAAGTGNSSQVSQNY
GAG_SIVCZ/2-140GLRSLFNTLAVLWCIHSDITVEDTQKALEQLKRHHGEQQSK..TESNSGSREGGASQG.ASASAGISGNY
GAG_SIVV1/2-141GMKSLYNLVCVLLCVHQEKKVKDTEEALAIVRQCCHLVDK.EKTAVTPPGGQQKNNTGGTATPGG.SQNF

PF02813

Q83009_9RETR/2-84GS.A----GELRTWG-------------TIMRILQTAKEE------------------------------
Q64992_RSVSR/2-87LGKS----GELKTWG-------------LVLGALKAAREE------------------------------
Q9QME3_9RETR/2-87SQKA----TELKTWG-------------LMLGALKAAREE------------------------------

This alignment is coloured according to the ClustalX colouring scheme:

 
Glycine (G)
 
Proline (P)
 
Small or hydrophobic (C,A,V,L,I,M,F,W)
 
Hydroxyl or amine amino acids (S,T,N,Q)
 
Charged amino-acids (D,E,R,K)
 
Histidine or tyrosine (H,Y)

For UniProt-based alignments, we also add some additional mark-up to the alignments where appropriate. Active site information is shown as follows:

 
Active site (residue annotated in SwissProt as an active site)
 
Predicted active site (residue aligns in a Pfam alignment with a SwissProt active site)
 
Predicted active site (residue annotated in SwissProt as a potential active site)

Some UniProt sequences can be mapped to protein structures, in which case we also show the secondary structure definition. These lines are shown below the sequence to which they apply and are marked (SS). The meaning of each of the symbols is as follows:

C
Random coil
H
Alpha-helix
G
3(10) helix
I
Pi-helix
E
Hydrogen bonded beta-strand (extended strand)
B
Residue in isolated beta-bridge
T
H-bonded turn (3-turn, 4-turn, or 5-turn)
S
Bend (five-residue bend centered at residue i)
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