Citrus Sinensis ID: 044988

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------54
Protein Sequence
MLVEEIIPANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE
Secondary Structure (PSIPRED)
cccccccccccccccccccHHHHHHHHHcccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHccccccccccHHHHHHHHHcccccHHHHHHHHHHHHcccccccEEHHHHHHHHHcccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHcccccHHHHHHHHccccccccHHHHHHHHHHHHcccHHHHHHHHccccccccccHHHHHHHHHHccccHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHcccccccccEEEEHHHHHHHHccccHHHHHHHHHcccccccccHHHHHHHHHcccccccHHHHHHHHHHHcccccHHHHHHHHHHHcHHcccccccccHHHHHHHHHcccccHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHccccHHHHHHHHHHHHcccccccccEEEEEccEEEEEEEcccccccHHHHHHHHHHHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccEEHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHcHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccEHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccEEEEEEccEEEEEEEcccccccHHHHHHHHHHHHHHHHHccccccccEEEEcccc
Coil and Loop (DISEMBL)
mlveeiipanpatsskaltTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKvfektenpstAIWNQMIrgharsetpeKSVYLYKQMIdketepdeyTYSFLLSVCARCglfregeqvHGRVLASGYCSNVFIRTNLMNLYLmsggecgvgcarllfddmparsvVSWNSLLKGYVKRGDIDGAWKIfdemphrnvvSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEEnfsvgrepVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLsacshggfvdeGRQFFECMnqnwgikpriehygCMVDLFSRAGLMDEAFSLvqnmpmkpndaVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKmgvrkppgqswvQINGVLhdfvagdstYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE
Flexible Loop (DISEMBL)
mlveeiipanpatsskalttRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMirgharsetpekSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMgvrkppgqsWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE
Low Complexity Region (SEG)
MLVEEIIPANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQaagylalvanvyaaaKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE
Disordered region (IsUnstruct)
*****************LTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGH********SVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFL****
Disordered Region (DISOPRED)
*************SSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE
Disordered Region (DISEMBL)
MLVEEIIPANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE
Disordered Region (DISPRO)
MLVEEIIPANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIE*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLVEEIIPANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	538	2.2.26 [Sep-21-2011]
Q9FJY7	620	Pentatricopeptide repeat-	yes	no	0.940	0.816	0.388	1e-110
Q9FI80	646	Pentatricopeptide repeat-	no	no	0.933	0.777	0.369	1e-99
A8MQA3	595	Pentatricopeptide repeat-	no	no	0.869	0.786	0.362	4e-97
Q9FND7	612	Putative pentatricopeptid	no	no	0.940	0.826	0.344	5e-96
Q9LSB8	687	Putative pentatricopeptid	no	no	0.905	0.708	0.364	1e-95
Q9SIT7	697	Pentatricopeptide repeat-	no	no	0.907	0.700	0.363	3e-95
Q9FMA1	530	Pentatricopeptide repeat-	no	no	0.892	0.905	0.375	2e-94
Q9SIL5	534	Pentatricopeptide repeat-	no	no	0.910	0.917	0.347	1e-90
Q0WQW5	638	Pentatricopeptide repeat-	no	no	0.918	0.774	0.343	1e-90
P0C8Q7	534	Pentatricopeptide repeat-	no	no	0.901	0.908	0.365	1e-90

>sp|Q9FJY7|PP449_ARATH Pentatricopeptide repeat-containing protein At5g66520 OS=Arabidopsis thaliana GN=PCMP-H61 PE=2 SV=1

 Score =  399 bits (1025), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 207/533 (38%), Positives = 318/533 (59%), Gaps = 27/533 (5%)

Query: 22  QIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTS---GYLINAHKVFEKT 78
           +  S LQ  +  + L QIH++++  G  Q +Y + K L+F ++S    +L  A  VF+  
Sbjct: 16  ETMSCLQRCSKQEELKQIHARMLKTGLMQDSYAITKFLSFCISSTSSDFLPYAQIVFDGF 75

Query: 79  ENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGE 138
           + P T +WN MIRG + S+ PE+S+ LY++M+      + YT+  LL  C+    F E  
Sbjct: 76  DRPDTFLWNLMIRGFSCSDEPERSLLLYQRMLCSSAPHNAYTFPSLLKACSNLSAFEETT 135

Query: 139 QVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYV 198
           Q+H ++   GY ++V+   +L+N Y ++G       A LLFD +P    VSWNS++KGYV
Sbjct: 136 QIHAQITKLGYENDVYAVNSLINSYAVTGN---FKLAHLLFDRIPEPDDVSWNSVIKGYV 192

Query: 199 KRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVA 258
           K G +D A  +F +M  +N +SWTTMISG  Q   +++AL LF+EM+ + V  D V+L  
Sbjct: 193 KAGKMDIALTLFRKMAEKNAISWTTMISGYVQADMNKEALQLFHEMQNSDVEPDNVSLAN 252

Query: 259 ALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKM 318
           ALSACA++G L+ GKWIHSY+ +     R  +   L   LI MYA CGE+EEA  VF+ +
Sbjct: 253 ALSACAQLGALEQGKWIHSYLNKT----RIRMDSVLGCVLIDMYAKCGEMEEALEVFKNI 308

Query: 319 QRRNTVSWTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGR 363
           ++++  +WT++I+G+A  G+ +EA+               +TF  VL+ACS+ G V+EG+
Sbjct: 309 KKKSVQAWTALISGYAYHGHGREAISKFMEMQKMGIKPNVITFTAVLTACSYTGLVEEGK 368

Query: 364 QFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRI 423
             F  M +++ +KP IEHYGC+VDL  RAGL+DEA   +Q MP+KPN  + G+LL  CRI
Sbjct: 369 LIFYSMERDYNLKPTIEHYGCIVDLLGRAGLLDEAKRFIQEMPLKPNAVIWGALLKACRI 428

Query: 424 HNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPG 483
           H N EL  ++ + L+A IDP     Y+   AN++A  K+W   A  R+ M + GV K PG
Sbjct: 429 HKNIELGEEIGEILIA-IDPYHGGRYVH-KANIHAMDKKWDKAAETRRLMKEQGVAKVPG 486

Query: 484 QSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGI 536
            S + + G  H+F+AGD ++ +   I      +  +  + GY P++ E+ L +
Sbjct: 487 CSTISLEGTTHEFLAGDRSHPEIEKIQSKWRIMRRKLEENGYVPELEEMLLDL 539

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FI80|PP425_ARATH Pentatricopeptide repeat-containing protein At5g48910 OS=Arabidopsis thaliana GN=PCMP-H38 PE=2 SV=1

 Score =  364 bits (934), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 203/549 (36%), Positives = 321/549 (58%), Gaps = 47/549 (8%)

Query: 28  QIRN--TTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGY----LINAHKVFEKTENP 81
           QI N  T + L QIH+  I +G  +     A++L F  TS      L  AHK+F +    
Sbjct: 29  QINNCRTIRDLSQIHAVFIKSGQMRDTLAAAEILRFCATSDLHHRDLDYAHKIFNQMPQR 88

Query: 82  STAIWNQMIRGHARSETPEKSVYL---YKQMIDKETEPDEYTYSFLLSVCARCGLFREGE 138
           +   WN +IRG + S+  +  + +   Y+ M D+  EP+ +T+  +L  CA+ G  +EG+
Sbjct: 89  NCFSWNTIIRGFSESDEDKALIAITLFYEMMSDEFVEPNRFTFPSVLKACAKTGKIQEGK 148

Query: 139 QVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLF------DDMPARS------ 186
           Q+HG  L  G+  + F+ +NL+ +Y+M G    +  AR+LF       DM   +      
Sbjct: 149 QIHGLALKYGFGGDEFVMSNLVRMYVMCGF---MKDARVLFYKNIIEKDMVVMTDRRKRD 205

Query: 187 --VVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEM 244
             +V WN ++ GY++ GD   A  +FD+M  R+VVSW TMISG + NG  + A+ +F EM
Sbjct: 206 GEIVLWNVMIDGYMRLGDCKAARMLFDKMRQRSVVSWNTMISGYSLNGFFKDAVEVFREM 265

Query: 245 RRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYAS 304
           ++  +  + V LV+ L A + +G L+LG+W+H Y E++  +  + VL S   ALI MY+ 
Sbjct: 266 KKGDIRPNYVTLVSVLPAISRLGSLELGEWLHLYAEDS-GIRIDDVLGS---ALIDMYSK 321

Query: 305 CGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL---------------LTFLGV 349
           CG IE+A  VF ++ R N ++W++MI GFA  G A +A+               + ++ +
Sbjct: 322 CGIIEKAIHVFERLPRENVITWSAMINGFAIHGQAGDAIDCFCKMRQAGVRPSDVAYINL 381

Query: 350 LSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKP 409
           L+ACSHGG V+EGR++F  M    G++PRIEHYGCMVDL  R+GL+DEA   + NMP+KP
Sbjct: 382 LTACSHGGLVEEGRRYFSQMVSVDGLEPRIEHYGCMVDLLGRSGLLDEAEEFILNMPIKP 441

Query: 410 NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAV 469
           +D +  +LL  CR+  N E+  +VA  L+ ++ P  +  Y+AL +N+YA+   W +V+ +
Sbjct: 442 DDVIWKALLGACRMQGNVEMGKRVANILM-DMVPHDSGAYVAL-SNMYASQGNWSEVSEM 499

Query: 470 RQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDI 529
           R +M +  +RK PG S + I+GVLH+FV  D ++ +A  I   L EI+ +    GY+P  
Sbjct: 500 RLRMKEKDIRKDPGCSLIDIDGVLHEFVVEDDSHPKAKEINSMLVEISDKLRLAGYRPIT 559

Query: 530 SELFLGIEE 538
           +++ L +EE
Sbjct: 560 TQVLLNLEE 568

Arabidopsis thaliana (taxid: 3702)

>sp|A8MQA3|PP330_ARATH Pentatricopeptide repeat-containing protein At4g21065 OS=Arabidopsis thaliana GN=PCMP-H28 PE=2 SV=2

 Score =  355 bits (912), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 192/530 (36%), Positives = 307/530 (57%), Gaps = 62/530 (11%)

Query: 31  NTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTS----GYLINAHKVFEKTENP-STAI 85
           ++   L QIH+  I +G S  +  L K L FY+ S      +  AHKVF K E P +  I
Sbjct: 28  SSITKLRQIHAFSIRHGVSISDAELGKHLIFYLVSLPSPPPMSYAHKVFSKIEKPINVFI 87

Query: 86  WNQMIRGHARSETPEKSVYLYKQM-IDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRV 144
           WN +IRG+A       +  LY++M +    EPD +TY FL+         R GE +H  V
Sbjct: 88  WNTLIRGYAEIGNSISAFSLYREMRVSGLVEPDTHTYPFLIKAVTTMADVRLGETIHSVV 147

Query: 145 LASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDID 204
           + SG+ S ++++ +L++LY      CG                              D+ 
Sbjct: 148 IRSGFGSLIYVQNSLLHLY----ANCG------------------------------DVA 173

Query: 205 GAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACA 264
            A+K+FD+MP +++V+W ++I+G A+NGK  +AL+L+ EM    +  D   +V+ LSACA
Sbjct: 174 SAYKVFDKMPEKDLVAWNSVINGFAENGKPEEALALYTEMNSKGIKPDGFTIVSLLSACA 233

Query: 265 EIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTV 324
           +IG L LGK +H Y+     VG    L S +N L+ +YA CG +EEA  +F +M  +N+V
Sbjct: 234 KIGALTLGKRVHVYM---IKVGLTRNLHS-SNVLLDLYARCGRVEEAKTLFDEMVDKNSV 289

Query: 325 SWTSMITGFAKQGYAQEAL----------------LTFLGVLSACSHGGFVDEGRQFFEC 368
           SWTS+I G A  G+ +EA+                +TF+G+L ACSH G V EG ++F  
Sbjct: 290 SWTSLIVGLAVNGFGKEAIELFKYMESTEGLLPCEITFVGILYACSHCGMVKEGFEYFRR 349

Query: 369 MNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAE 428
           M + + I+PRIEH+GCMVDL +RAG + +A+  +++MPM+PN  +  +LL  C +H +++
Sbjct: 350 MREEYKIEPRIEHFGCMVDLLARAGQVKKAYEYIKSMPMQPNVVIWRTLLGACTVHGDSD 409

Query: 429 LASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQ 488
           LA + A+  + +++P  +  Y+ L++N+YA+ +RW DV  +R++M++ GV+K PG S V+
Sbjct: 410 LA-EFARIQILQLEPNHSGDYV-LLSNMYASEQRWSDVQKIRKQMLRDGVKKVPGHSLVE 467

Query: 489 INGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE 538
           +   +H+F+ GD ++ Q+  IY  L E+T +   EGY P IS +++ +EE
Sbjct: 468 VGNRVHEFLMGDKSHPQSDAIYAKLKEMTGRLRSEGYVPQISNVYVDVEE 517

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FND7|PP410_ARATH Putative pentatricopeptide repeat-containing protein At5g40405 OS=Arabidopsis thaliana GN=PCMP-H14 PE=3 SV=1

 Score =  352 bits (903), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 184/534 (34%), Positives = 314/534 (58%), Gaps = 28/534 (5%)

Query: 24  FSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSG--YLINAHKVFEKTENP 81
            +LL    T K + QIH+++ ++G  + ++++   +     S   YL  A+++ +++E P
Sbjct: 10  IALLDSGITFKEVRQIHAKLYVDGTLKDDHLVGHFVKAVALSDHKYLDYANQILDRSEKP 69

Query: 82  STAIWNQMIRGHARSETPEKSVYLYKQMID--KETEPDEYTYSFLLSVCARCGLFREGEQ 139
           +    N MIR H +S  PEKS   Y++++    + +PD YT +FL+  C    +   G Q
Sbjct: 70  TLFALNSMIRAHCKSPVPEKSFDFYRRILSSGNDLKPDNYTVNFLVQACTGLRMRETGLQ 129

Query: 140 VHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVK 199
           VHG  +  G+ ++  ++T L++LY   G  C   C ++ F+ +P    V   +++    +
Sbjct: 130 VHGMTIRRGFDNDPHVQTGLISLYAELG--CLDSCHKV-FNSIPCPDFVCRTAMVTACAR 186

Query: 200 RGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAA 259
            GD+  A K+F+ MP R+ ++W  MISG AQ G+SR+AL++F+ M+   V ++ VA+++ 
Sbjct: 187 CGDVVFARKLFEGMPERDPIAWNAMISGYAQVGESREALNVFHLMQLEGVKVNGVAMISV 246

Query: 260 LSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQ 319
           LSAC ++G L  G+W HSY+E N    +  + V L   L+ +YA CG++E+A  VF  M+
Sbjct: 247 LSACTQLGALDQGRWAHSYIERN----KIKITVRLATTLVDLYAKCGDMEKAMEVFWGME 302

Query: 320 RRNTVSWTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGRQ 364
            +N  +W+S + G A  G+ ++ L               +TF+ VL  CS  GFVDEG++
Sbjct: 303 EKNVYTWSSALNGLAMNGFGEKCLELFSLMKQDGVTPNAVTFVSVLRGCSVVGFVDEGQR 362

Query: 365 FFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIH 424
            F+ M   +GI+P++EHYGC+VDL++RAG +++A S++Q MPMKP+ AV  SLL   R++
Sbjct: 363 HFDSMRNEFGIEPQLEHYGCLVDLYARAGRLEDAVSIIQQMPMKPHAAVWSSLLHASRMY 422

Query: 425 NNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQ 484
            N EL    ++K++ E++      Y+ L++N+YA +  W +V+ VRQ M   GVRK PG 
Sbjct: 423 KNLELGVLASKKML-ELETANHGAYV-LLSNIYADSNDWDNVSHVRQSMKSKGVRKQPGC 480

Query: 485 SWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE 538
           S +++NG +H+F  GD ++ + + I     +I+ +    GYK D + +   I+E
Sbjct: 481 SVMEVNGEVHEFFVGDKSHPKYTQIDAVWKDISRRLRLAGYKADTTPVMFDIDE 534

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LSB8|PP235_ARATH Putative pentatricopeptide repeat-containing protein At3g15930 OS=Arabidopsis thaliana GN=PCMP-E51 PE=3 SV=2

 Score =  350 bits (899), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 187/513 (36%), Positives = 293/513 (57%), Gaps = 26/513 (5%)

Query: 38  QIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSE 97
           ++H  ++  G     Y+   L+  Y   G +  A  VF++        WN MI G+ R +
Sbjct: 156 KLHCHVVKFGLGSNLYVQNALVKMYSLCGLMDMARGVFDRRCKEDVFSWNLMISGYNRMK 215

Query: 98  TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRT 157
             E+S+ L  +M      P   T   +LS C++       ++VH  V       ++ +  
Sbjct: 216 EYEESIELLVEMERNLVSPTSVTLLLVLSACSKVKDKDLCKRVHEYVSECKTEPSLRLEN 275

Query: 158 NLMNLYLMSGGECG-VGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR 216
            L+N Y      CG +  A  +F  M AR V+SW S++KGYV+RG++  A   FD+MP R
Sbjct: 276 ALVNAY----AACGEMDIAVRIFRSMKARDVISWTSIVKGYVERGNLKLARTYFDQMPVR 331

Query: 217 NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIH 276
           + +SWT MI G  + G   ++L +F EM+ A +  D+  +V+ L+ACA +G L++G+WI 
Sbjct: 332 DRISWTIMIDGYLRAGCFNESLEIFREMQSAGMIPDEFTMVSVLTACAHLGSLEIGEWIK 391

Query: 277 SYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQ 336
           +Y+++N  +  +   V + NALI MY  CG  E+A  VF  M +R+  +WT+M+ G A  
Sbjct: 392 TYIDKN-KIKND---VVVGNALIDMYFKCGCSEKAQKVFHDMDQRDKFTWTAMVVGLANN 447

Query: 337 GYAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEH 381
           G  QEA+               +T+LGVLSAC+H G VD+ R+FF  M  +  I+P + H
Sbjct: 448 GQGQEAIKVFFQMQDMSIQPDDITYLGVLSACNHSGMVDQARKFFAKMRSDHRIEPSLVH 507

Query: 382 YGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEI 441
           YGCMVD+  RAGL+ EA+ +++ MPM PN  V G+LL   R+HN+  +A   A+K++ E+
Sbjct: 508 YGCMVDMLGRAGLVKEAYEILRKMPMNPNSIVWGALLGASRLHNDEPMAELAAKKIL-EL 566

Query: 442 DPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDS 501
           +P+  A Y AL+ N+YA  KRW+D+  VR+K++ + ++K PG S +++NG  H+FVAGD 
Sbjct: 567 EPDNGAVY-ALLCNIYAGCKRWKDLREVRRKIVDVAIKKTPGFSLIEVNGFAHEFVAGDK 625

Query: 502 TYKQASLIYKTLGEITMQAMQEGYKPDISELFL 534
           ++ Q+  IY  L E+  ++    Y PD SEL  
Sbjct: 626 SHLQSEEIYMKLEELAQESTFAAYLPDTSELLF 658

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SIT7|PP151_ARATH Pentatricopeptide repeat-containing protein At2g13600 OS=Arabidopsis thaliana GN=PCMP-E76 PE=3 SV=1

 Score =  349 bits (896), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 187/515 (36%), Positives = 293/515 (56%), Gaps = 27/515 (5%)

Query: 38  QIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSE 97
           Q+HS I  + F    YI + L+  Y   G + +A +VF++  + +   WN +I    ++ 
Sbjct: 173 QVHSLIAKSPFLSDVYIGSALVDMYSKCGNVNDAQRVFDEMGDRNVVSWNSLITCFEQNG 232

Query: 98  TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRT 157
              +++ +++ M++   EPDE T + ++S CA     + G++VHGRV+ +    N  I +
Sbjct: 233 PAVEALDVFQMMLESRVEPDEVTLASVISACASLSAIKVGQEVHGRVVKNDKLRNDIILS 292

Query: 158 N-LMNLYLMSGGECG-VGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH 215
           N  +++Y     +C  +  AR +FD MP R+V++  S++ GY        A  +F +M  
Sbjct: 293 NAFVDMY----AKCSRIKEARFIFDSMPIRNVIAETSMISGYAMAASTKAARLMFTKMAE 348

Query: 216 RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWI 275
           RNVVSW  +I+G  QNG++ +ALSLF  ++R  V     +    L ACA++ +L LG   
Sbjct: 349 RNVVSWNALIAGYTQNGENEEALSLFCLLKRESVCPTHYSFANILKACADLAELHLGMQA 408

Query: 276 HSYVEEN---FSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITG 332
           H +V ++   F  G E  +  + N+LI MY  CG +EE Y VFRKM  R+ VSW +MI G
Sbjct: 409 HVHVLKHGFKFQSGEEDDIF-VGNSLIDMYVKCGCVEEGYLVFRKMMERDCVSWNAMIIG 467

Query: 333 FAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP 377
           FA+ GY  EAL               +T +GVLSAC H GFV+EGR +F  M +++G+ P
Sbjct: 468 FAQNGYGNEALELFREMLESGEKPDHITMIGVLSACGHAGFVEEGRHYFSSMTRDFGVAP 527

Query: 378 RIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKL 437
             +HY CMVDL  RAG ++EA S+++ MPM+P+  + GSLL  C++H N  L   VA+KL
Sbjct: 528 LRDHYTCMVDLLGRAGFLEEAKSMIEEMPMQPDSVIWGSLLAACKVHRNITLGKYVAEKL 587

Query: 438 VAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFV 497
           + E++P  +  Y+ L++N+YA   +W+DV  VR+ M K GV K PG SW++I G  H F+
Sbjct: 588 L-EVEPSNSGPYV-LLSNMYAELGKWEDVMNVRKSMRKEGVTKQPGCSWIKIQGHDHVFM 645

Query: 498 AGDSTYKQASLIYKTLGEITMQAMQEGYKPDISEL 532
             D ++ +   I+  L  +  +   E    +I  L
Sbjct: 646 VKDKSHPRKKQIHSLLDILIAEMRPEQDHTEIGSL 680

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FMA1|PP433_ARATH Pentatricopeptide repeat-containing protein At5g56310 OS=Arabidopsis thaliana GN=PCMP-E13 PE=2 SV=1

 Score =  347 bits (889), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 191/509 (37%), Positives = 299/509 (58%), Gaps = 29/509 (5%)

Query: 31  NTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMI 90
           N  KTL Q H  +II G ++ N  +AK +     +G+L  A+ VF     P+T + N MI
Sbjct: 26  NNLKTLKQSHCYMIITGLNRDNLNVAKFIEACSNAGHLRYAYSVFTHQPCPNTYLHNTMI 85

Query: 91  RGHARSETPEK---SVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLAS 147
           R  +  + P     ++ +Y+++     +PD +T+ F+L +  R      G Q+HG+V+  
Sbjct: 86  RALSLLDEPNAHSIAITVYRKLWALCAKPDTFTFPFVLKIAVRVSDVWFGRQIHGQVVVF 145

Query: 148 GYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAW 207
           G+ S+V + T L+ +Y   GG   +G AR +FD+M  + V  WN+LL GY K G++D A 
Sbjct: 146 GFDSSVHVVTGLIQMYFSCGG---LGDARKMFDEMLVKDVNVWNALLAGYGKVGEMDEAR 202

Query: 208 KIFDEMPH--RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAE 265
            + + MP   RN VSWT +ISG A++G++ +A+ +F  M    V  D+V L+A LSACA+
Sbjct: 203 SLLEMMPCWVRNEVSWTCVISGYAKSGRASEAIEVFQRMLMENVEPDEVTLLAVLSACAD 262

Query: 266 IGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVS 325
           +G L+LG+ I SYV+    + R    VSLNNA+I MYA  G I +A  VF  +  RN V+
Sbjct: 263 LGSLELGERICSYVDHR-GMNRA---VSLNNAVIDMYAKSGNITKALDVFECVNERNVVT 318

Query: 326 WTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMN 370
           WT++I G A  G+  EAL               +TF+ +LSACSH G+VD G++ F  M 
Sbjct: 319 WTTIIAGLATHGHGAEALAMFNRMVKAGVRPNDVTFIAILSACSHVGWVDLGKRLFNSMR 378

Query: 371 QNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELA 430
             +GI P IEHYGCM+DL  RAG + EA  ++++MP K N A+ GSLL    +H++ EL 
Sbjct: 379 SKYGIHPNIEHYGCMIDLLGRAGKLREADEVIKSMPFKANAAIWGSLLAASNVHHDLELG 438

Query: 431 SQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQIN 490
            +   +L+ +++P  +  Y+ L+AN+Y+   RW +   +R  M  +GV+K  G+S +++ 
Sbjct: 439 ERALSELI-KLEPNNSGNYM-LLANLYSNLGRWDESRMMRNMMKGIGVKKMAGESSIEVE 496

Query: 491 GVLHDFVAGDSTYKQASLIYKTLGEITMQ 519
             ++ F++GD T+ Q   I++ L E+ +Q
Sbjct: 497 NRVYKFISGDLTHPQVERIHEILQEMDLQ 525

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SIL5|PP165_ARATH Pentatricopeptide repeat-containing protein At2g20540 OS=Arabidopsis thaliana GN=PCMP-E78 PE=2 SV=1

 Score =  334 bits (857), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 179/515 (34%), Positives = 298/515 (57%), Gaps = 25/515 (4%)

Query: 38  QIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSE 97
           +I++ III+G SQ ++++ K++ F      +  A ++F +  NP+  ++N +IR +  + 
Sbjct: 28  KINASIIIHGLSQSSFMVTKMVDFCDKIEDMDYATRLFNQVSNPNVFLYNSIIRAYTHNS 87

Query: 98  TPEKSVYLYKQMIDKETE-PDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIR 156
                + +YKQ++ K  E PD +T+ F+   CA  G    G+QVHG +   G   +V   
Sbjct: 88  LYCDVIRIYKQLLRKSFELPDRFTFPFMFKSCASLGSCYLGKQVHGHLCKFGPRFHVVTE 147

Query: 157 TNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR 216
             L+++Y+          A  +FD+M  R V+SWNSLL GY + G +  A  +F  M  +
Sbjct: 148 NALIDMYMKFDDLVD---AHKVFDEMYERDVISWNSLLSGYARLGQMKKAKGLFHLMLDK 204

Query: 217 NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIH 276
            +VSWT MISG    G   +A+  F EM+ A +  D+++L++ L +CA++G L+LGKWIH
Sbjct: 205 TIVSWTAMISGYTGIGCYVEAMDFFREMQLAGIEPDEISLISVLPSCAQLGSLELGKWIH 264

Query: 277 SYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQ 336
            Y E    + +  V     NALI MY+ CG I +A  +F +M+ ++ +SW++MI+G+A  
Sbjct: 265 LYAERRGFLKQTGVC----NALIEMYSKCGVISQAIQLFGQMEGKDVISWSTMISGYAYH 320

Query: 337 GYAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEH 381
           G A  A+               +TFLG+LSACSH G   EG ++F+ M Q++ I+P+IEH
Sbjct: 321 GNAHGAIETFNEMQRAKVKPNGITFLGLLSACSHVGMWQEGLRYFDMMRQDYQIEPKIEH 380

Query: 382 YGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEI 441
           YGC++D+ +RAG ++ A  + + MPMKP+  + GSLL  CR   N ++A  VA   + E+
Sbjct: 381 YGCLIDVLARAGKLERAVEITKTMPMKPDSKIWGSLLSSCRTPGNLDVA-LVAMDHLVEL 439

Query: 442 DPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDS 501
           +PE    Y+ L+AN+YA   +W+DV+ +R+ +    ++K PG S +++N ++ +FV+GD+
Sbjct: 440 EPEDMGNYV-LLANIYADLGKWEDVSRLRKMIRNENMKKTPGGSLIEVNNIVQEFVSGDN 498

Query: 502 TYKQASLIYKTLGEITMQAMQEGYKPDISELFLGI 536
           +    + I   L   T    Q+    + +  F+GI
Sbjct: 499 SKPFWTEISIVLQLFTSHQDQDVITNNNALAFIGI 533

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WQW5|PPR85_ARATH Pentatricopeptide repeat-containing protein At1g59720, mitochondrial OS=Arabidopsis thaliana GN=PCMP-H51 PE=2 SV=2

 Score =  334 bits (856), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 194/565 (34%), Positives = 315/565 (55%), Gaps = 71/565 (12%)

Query: 1   MLVEEIIPANPATSSKALTT-----RQIFSLLQIRNTTKTLFQIHSQIIINGFSQKN--- 52
           +LV  + P  P  SS + +T     ++IFSL +  +    L Q+H+  +   + ++    
Sbjct: 24  LLVHPLSPHIPPASSPSASTAGNHHQRIFSLAETCSDMSQLKQLHAFTLRTTYPEEPATL 83

Query: 53  YILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSET-PEKSVYLYKQMID 111
           ++  K+L    +   +  A +VF+  EN S+ +WN +IR  A   +  E++  LY++M++
Sbjct: 84  FLYGKILQLSSSFSDVNYAFRVFDSIENHSSFMWNTLIRACAHDVSRKEEAFMLYRKMLE 143

Query: 112 K-ETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGEC 170
           + E+ PD++T+ F+L  CA    F EG+QVH +++  G+  +V++   L++LY    G C
Sbjct: 144 RGESSPDKHTFPFVLKACAYIFGFSEGKQVHCQIVKHGFGGDVYVNNGLIHLY----GSC 199

Query: 171 G-VGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCA 229
           G +  AR +FD+MP RS+VSWNS++   V+ G+ D                         
Sbjct: 200 GCLDLARKVFDEMPERSLVSWNSMIDALVRFGEYDS------------------------ 235

Query: 230 QNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREP 289
                  AL LF EM+R+    D   + + LSACA +G L LG W H+++     V    
Sbjct: 236 -------ALQLFREMQRS-FEPDGYTMQSVLSACAGLGSLSLGTWAHAFLLRKCDVD-VA 286

Query: 290 VLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL------ 343
           + V + N+LI MY  CG +  A  VF+ MQ+R+  SW +MI GFA  G A+EA+      
Sbjct: 287 MDVLVKNSLIEMYCKCGSLRMAEQVFQGMQKRDLASWNAMILGFATHGRAEEAMNFFDRM 346

Query: 344 -----------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRA 392
                      +TF+G+L AC+H GFV++GRQ+F+ M +++ I+P +EHYGC+VDL +RA
Sbjct: 347 VDKRENVRPNSVTFVGLLIACNHRGFVNKGRQYFDMMVRDYCIEPALEHYGCIVDLIARA 406

Query: 393 GLMDEAFSLVQNMPMKPNDAVLGSLLLG-CRIHNNAELASQVAQKLVAEIDPEQA----- 446
           G + EA  +V +MPMKP+  +  SLL   C+   + EL+ ++A+ ++   +  ++     
Sbjct: 407 GYITEAIDMVMSMPMKPDAVIWRSLLDACCKKGASVELSEEIARNIIGTKEDNESSNGNC 466

Query: 447 AGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQA 506
           +G   L++ VYA+A RW DV  VR+ M + G+RK PG S ++ING+ H+F AGD+++ Q 
Sbjct: 467 SGAYVLLSRVYASASRWNDVGIVRKLMSEHGIRKEPGCSSIEINGISHEFFAGDTSHPQT 526

Query: 507 SLIYKTLGEITMQAMQEGYKPDISE 531
             IY+ L  I  +    GY PD S+
Sbjct: 527 KQIYQQLKVIDDRLRSIGYLPDRSQ 551

Arabidopsis thaliana (taxid: 3702)

>sp|P0C8Q7|PP369_ARATH Pentatricopeptide repeat-containing protein At5g08305 OS=Arabidopsis thaliana GN=PCMP-E105 PE=2 SV=1

 Score =  334 bits (856), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 191/523 (36%), Positives = 298/523 (56%), Gaps = 38/523 (7%)

Query: 14  SSKALTTRQIFSLLQIRNTTKT---LFQIHSQIIINGFSQKNYILAKLLAFYV--TSGYL 68
           SS +L  + I     +R+  K+   L++IH+ +I  G S++   +++ L+F    +SG +
Sbjct: 4   SSSSLVAKSI-----LRHQCKSMSELYKIHTLLITLGLSEEEPFVSQTLSFSALSSSGDV 58

Query: 69  INAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVC 128
             A+K   K  +P    WN +IRG + S  PEKS+ +Y QM+     PD  TY FL+   
Sbjct: 59  DYAYKFLSKLSDPPNYGWNFVIRGFSNSRNPEKSISVYIQMLRFGLLPDHMTYPFLMKSS 118

Query: 129 ARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVV 188
           +R    + G  +H  V+ SG   ++FI   L+++Y   G       AR LFD+MP +++V
Sbjct: 119 SRLSNRKLGGSLHCSVVKSGLEWDLFICNTLIHMY---GSFRDQASARKLFDEMPHKNLV 175

Query: 189 SWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNE-MRRA 247
           +WNS+L  Y K GD+  A  +FDEM  R+VV+W++MI G  + G+  +AL +F++ MR  
Sbjct: 176 TWNSILDAYAKSGDVVSARLVFDEMSERDVVTWSSMIDGYVKRGEYNKALEIFDQMMRMG 235

Query: 248 RVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGE 307
               ++V +V+ + ACA +G L  GK +H Y+ +       P+ V L  +LI MYA CG 
Sbjct: 236 SSKANEVTMVSVICACAHLGALNRGKTVHRYILDV----HLPLTVILQTSLIDMYAKCGS 291

Query: 308 IEEAYGVFRKMQRRNT--VSWTSMITGFAKQGYAQEAL---------------LTFLGVL 350
           I +A+ VF +   + T  + W ++I G A  G+ +E+L               +TFL +L
Sbjct: 292 IGDAWSVFYRASVKETDALMWNAIIGGLASHGFIRESLQLFHKMRESKIDPDEITFLCLL 351

Query: 351 SACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPN 410
           +ACSHGG V E   FF+ + ++ G +P+ EHY CMVD+ SRAGL+ +A   +  MP+KP 
Sbjct: 352 AACSHGGLVKEAWHFFKSLKES-GAEPKSEHYACMVDVLSRAGLVKDAHDFISEMPIKPT 410

Query: 411 DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVR 470
            ++LG+LL GC  H N ELA  V +KL+ E+ P     Y+ L ANVYA  K+++   ++R
Sbjct: 411 GSMLGALLNGCINHGNLELAETVGKKLI-ELQPHNDGRYVGL-ANVYAINKQFRAARSMR 468

Query: 471 QKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTL 513
           + M K GV+K  G S + ++G  H F+A D T+  +  IY  L
Sbjct: 469 EAMEKKGVKKIAGHSILDLDGTRHRFIAHDKTHFHSDKIYAVL 511

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	538
225457355	553	PREDICTED: pentatricopeptide repeat-cont	0.994	0.967	0.670	0.0
147817753	569	hypothetical protein VITISV_031721 [Viti	0.942	0.891	0.68	0.0
297733949	467	unnamed protein product [Vitis vinifera]	0.834	0.961	0.674	0.0
449487105	555	PREDICTED: pentatricopeptide repeat-cont	0.925	0.897	0.572	1e-172
449439631	555	PREDICTED: pentatricopeptide repeat-cont	0.923	0.895	0.569	1e-171
356565111	478	PREDICTED: pentatricopeptide repeat-cont	0.843	0.949	0.613	1e-169
224097410	554	predicted protein [Populus trichocarpa]	0.842	0.817	0.605	1e-167
225425100	622	PREDICTED: pentatricopeptide repeat-cont	0.923	0.799	0.426	1e-120
147832325	622	hypothetical protein VITISV_030261 [Viti	0.923	0.799	0.426	1e-120
224111954	331	predicted protein [Populus trichocarpa]	0.565	0.918	0.652	1e-119

>gi|225457355|ref|XP_002281803.1| PREDICTED: pentatricopeptide repeat-containing protein At5g66520-like [Vitis vinifera]

 Score =  780 bits (2013), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/555 (67%), Positives = 449/555 (80%), Gaps = 20/555 (3%)

Query: 1   MLVEEIIPANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLA 60
           MLVEE  PAN  T  +AL  +  FSLLQ  +T K L QIH+QII+NGFSQKN++L KLL+
Sbjct: 1   MLVEEASPAN-LTGLRALQ-QHFFSLLQTCDTIKKLKQIHTQIIVNGFSQKNFLLVKLLS 58

Query: 61  FYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYT 120
           FY+TSG L+NAHKVFE+ ENPST +WNQMIRGH++SETP K V LY +M++ E EP+E+T
Sbjct: 59  FYITSGNLLNAHKVFERIENPSTTVWNQMIRGHSQSETPHKLVELYNRMVEAEAEPNEFT 118

Query: 121 YSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFD 180
           YSFL+  CAR  L REGEQVHGRV+A+GYC+NVF+RT+L+NLY ++GG  GV  AR +FD
Sbjct: 119 YSFLIGGCARSRLLREGEQVHGRVVANGYCTNVFVRTSLVNLYAIAGGYDGVRKARRVFD 178

Query: 181 DMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSL 240
           ++  R++VSWNSLL GYV+ GD+DGA +IFDEMP RNVVSWTTMI+GCAQ G+ +QAL L
Sbjct: 179 EIVDRNIVSWNSLLAGYVRCGDVDGARRIFDEMPERNVVSWTTMIAGCAQIGRCKQALHL 238

Query: 241 FNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIH 300
           F+EMRRA V LDQVALVAALSACAE+GDLKLG WIHSY++E    G +P+LVSLNN+LIH
Sbjct: 239 FHEMRRAGVKLDQVALVAALSACAELGDLKLGTWIHSYIDERLHAGNQPLLVSLNNSLIH 298

Query: 301 MYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL----------------- 343
           MYASCG I++AY VF  MQ+R+T+SWTSMITGFAKQG+A+EAL                 
Sbjct: 299 MYASCGVIDKAYKVFIGMQQRSTISWTSMITGFAKQGHAEEALGVFQWMQRLGTDEGRPD 358

Query: 344 -LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLV 402
            +TF+GVL ACSH GFVD+GR FFECMN+ WGI PRIEHYGCMVDL SRAG +DEA  L+
Sbjct: 359 GITFIGVLCACSHAGFVDQGRHFFECMNKKWGIVPRIEHYGCMVDLLSRAGFLDEAHRLI 418

Query: 403 QNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKR 462
           ++MPMKPNDAV G+LL GCRIH NAELAS VAQKL  E+ P+QAAGYL L++NVYA AKR
Sbjct: 419 ESMPMKPNDAVWGALLGGCRIHKNAELASHVAQKLALELKPDQAAGYLVLLSNVYATAKR 478

Query: 463 WQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQ 522
           WQDVA VRQKM+++GVRKP G+SWVQINGV+HDFVAGD T+K AS +Y+ L +IT QA  
Sbjct: 479 WQDVALVRQKMVEIGVRKPAGRSWVQINGVVHDFVAGDWTHKHASSVYEMLSKITRQAKL 538

Query: 523 EGYKPDISELFLGIE 537
           EGYK DISE+ L +E
Sbjct: 539 EGYKLDISEVLLDVE 553

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147817753|emb|CAN66661.1| hypothetical protein VITISV_031721 [Vitis vinifera]

 Score =  761 bits (1966), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/525 (68%), Positives = 431/525 (82%), Gaps = 18/525 (3%)

Query: 31  NTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMI 90
           +T K L QIH+QII+NGFSQKN++L KLL+FY+TSG L+NAHKVFE+ ENPST +WNQMI
Sbjct: 45  DTIKKLKQIHTQIIVNGFSQKNFLLVKLLSFYITSGNLLNAHKVFERIENPSTTVWNQMI 104

Query: 91  RGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYC 150
           RGH++SETP K V LY +M++ E EP+E+TYSFL+  CAR  L REGEQVHGRV+A+GYC
Sbjct: 105 RGHSQSETPHKLVELYNRMVEAEAEPNEFTYSFLIGGCARSXLLREGEQVHGRVVANGYC 164

Query: 151 SNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIF 210
           +NVF+RT+L+NLY ++GG  GV  AR +FD++  R++VSWNSLL GYV+ GD+DGA +IF
Sbjct: 165 TNVFVRTSLVNLYAIAGGYDGVRKARRVFDEIVDRNIVSWNSLLAGYVRCGDVDGARRIF 224

Query: 211 DEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLK 270
           DEMP RNVVSWTTMI+GCAQ G+ +QAL LF+EMRRA V LDQVALVAALSACAE+GDLK
Sbjct: 225 DEMPERNVVSWTTMIAGCAQIGRCKQALHLFHEMRRAGVKLDQVALVAALSACAELGDLK 284

Query: 271 LGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMI 330
           LG WIHSY++E    G +P+LVSLNN+LIHMYASCG I++AY VF  MQ+R+T+SWTSMI
Sbjct: 285 LGTWIHSYIDERLHAGNQPLLVSLNNSLIHMYASCGVIDKAYKVFIGMQQRSTISWTSMI 344

Query: 331 TGFAKQGYAQEAL------------------LTFLGVLSACSHGGFVDEGRQFFECMNQN 372
           TGFAKQG+A+EAL                  +TF+GVL ACSH GFVD+GR FFECMN+ 
Sbjct: 345 TGFAKQGHAEEALGVFQWMQRLGTDEGRPDGITFIGVLCACSHAGFVDQGRHFFECMNKK 404

Query: 373 WGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQ 432
           WGI PRIEHYGCMVDL SRAG +DEA  L ++MPMKPNDAV G+LL GCRIH NAELAS 
Sbjct: 405 WGIVPRIEHYGCMVDLLSRAGFLDEAHRLXESMPMKPNDAVWGALLGGCRIHKNAELASH 464

Query: 433 VAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGV 492
           VAQKLV E+ P+QAAGYL L++NVYA AKRWQDVA VRQKM+++GVRKP G+SWVQINGV
Sbjct: 465 VAQKLVLELKPDQAAGYLVLLSNVYATAKRWQDVALVRQKMVEIGVRKPAGRSWVQINGV 524

Query: 493 LHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIE 537
           +HDFVAGD T+K AS +Y+ L +IT QA  EGYK DISE+ L +E
Sbjct: 525 VHDFVAGDWTHKHASSVYEMLSKITRQAKLEGYKLDISEVLLDVE 569

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297733949|emb|CBI15196.3| unnamed protein product [Vitis vinifera]

 Score =  667 bits (1720), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 315/467 (67%), Positives = 380/467 (81%), Gaps = 18/467 (3%)

Query: 89  MIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASG 148
           MIRGH++SETP K V LY +M++ E EP+E+TYSFL+  CAR  L REGEQVHGRV+A+G
Sbjct: 1   MIRGHSQSETPHKLVELYNRMVEAEAEPNEFTYSFLIGGCARSRLLREGEQVHGRVVANG 60

Query: 149 YCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWK 208
           YC+NVF+RT+L+NLY ++GG  GV  AR +FD++  R++VSWNSLL GYV+ GD+DGA +
Sbjct: 61  YCTNVFVRTSLVNLYAIAGGYDGVRKARRVFDEIVDRNIVSWNSLLAGYVRCGDVDGARR 120

Query: 209 IFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGD 268
           IFDEMP RNVVSWTTMI+GCAQ G+ +QAL LF+EMRRA V LDQVALVAALSACAE+GD
Sbjct: 121 IFDEMPERNVVSWTTMIAGCAQIGRCKQALHLFHEMRRAGVKLDQVALVAALSACAELGD 180

Query: 269 LKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTS 328
           LKLG WIHSY++E    G +P+LVSLNN+LIHMYASCG I++AY VF  MQ+R+T+SWTS
Sbjct: 181 LKLGTWIHSYIDERLHAGNQPLLVSLNNSLIHMYASCGVIDKAYKVFIGMQQRSTISWTS 240

Query: 329 MITGFAKQGYAQEAL------------------LTFLGVLSACSHGGFVDEGRQFFECMN 370
           MITGFAKQG+A+EAL                  +TF+GVL ACSH GFVD+GR FFECMN
Sbjct: 241 MITGFAKQGHAEEALGVFQWMQRLGTDEGRPDGITFIGVLCACSHAGFVDQGRHFFECMN 300

Query: 371 QNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELA 430
           + WGI PRIEHYGCMVDL SRAG +DEA  L+++MPMKPNDAV G+LL GCRIH NAELA
Sbjct: 301 KKWGIVPRIEHYGCMVDLLSRAGFLDEAHRLIESMPMKPNDAVWGALLGGCRIHKNAELA 360

Query: 431 SQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQIN 490
           S VAQKL  E+ P+QAAGYL L++NVYA AKRWQDVA VRQKM+++GVRKP G+SWVQIN
Sbjct: 361 SHVAQKLALELKPDQAAGYLVLLSNVYATAKRWQDVALVRQKMVEIGVRKPAGRSWVQIN 420

Query: 491 GVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIE 537
           GV+HDFVAGD T+K AS +Y+ L +IT QA  EGYK DISE+ L +E
Sbjct: 421 GVVHDFVAGDWTHKHASSVYEMLSKITRQAKLEGYKLDISEVLLDVE 467

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449487105|ref|XP_004157498.1| PREDICTED: pentatricopeptide repeat-containing protein At5g66520-like [Cucumis sativus]

 Score =  611 bits (1576), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 297/519 (57%), Positives = 382/519 (73%), Gaps = 21/519 (4%)

Query: 23  IFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPS 82
           IFS+L+   + + L +IH+QI+++GFSQKNYIL  LL+ Y++ G L +A KVFE    PS
Sbjct: 30  IFSVLKSCVSFRNLAKIHAQIVVSGFSQKNYILNHLLSLYISFGSLGSAQKVFEDITAPS 89

Query: 83  TAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHG 142
           T +WNQ+I+GH RS+T +KS+ L+K+M     E + +TYSFLLS C R  LFREGEQ+HG
Sbjct: 90  TTVWNQIIKGHTRSKTSKKSIELFKRMTLAGVEANGFTYSFLLSACVRSRLFREGEQIHG 149

Query: 143 RVLASGYCSNVFIRTNLMNLYLM--SGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKR 200
           RVL +GY SN+++RTNL+NLY     GG+  +  AR LFD+MP  +VV WNSLL GYV+R
Sbjct: 150 RVLVNGYWSNLYVRTNLINLYANGGDGGDFDLKRARYLFDEMPDSNVVGWNSLLAGYVRR 209

Query: 201 GDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAAL 260
           GD DGA K+FDEMP RNV +WT M++G AQNG+ + ALSLF++MRRA V LDQVALVAAL
Sbjct: 210 GDFDGARKVFDEMPERNVRTWTIMVAGFAQNGQCKLALSLFDQMRRAGVELDQVALVAAL 269

Query: 261 SACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR 320
           SACAE+GDL LGKWIH YVE  +     PVLVSLNNALIHMYASCG ++ AY VF ++ +
Sbjct: 270 SACAELGDLTLGKWIHGYVERTWRSRHLPVLVSLNNALIHMYASCGVMDLAYKVFEEIPQ 329

Query: 321 RNTVSWTSMITGFAKQGYAQEAL------------------LTFLGVLSACSHGGFVDEG 362
           RNTVSW+S+ITGFAKQG   EA+                  +TF+G L+ACSH G + +G
Sbjct: 330 RNTVSWSSIITGFAKQGCGVEAIRIFQLMLCSGQNEVRPDEITFIGALTACSHAGLISDG 389

Query: 363 RQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCR 422
            + F+ M++ +G+ P+IEHYGCMVDL SRAGL+ EA SL+++MPMKPN+AV G+LL GCR
Sbjct: 390 IRLFQSMHKTFGVIPQIEHYGCMVDLLSRAGLLTEALSLIESMPMKPNNAVWGALLSGCR 449

Query: 423 IHNNAELASQVAQKLVAEIDP-EQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKP 481
           +H N E+ S VA+ L  EI P  QAAGY  L+ANVYAA  RWQD A VR+ M  +GV+KP
Sbjct: 450 LHKNDEIVSHVAKHLSFEIHPNNQAAGYFMLLANVYAADGRWQDTATVRRNMHDIGVKKP 509

Query: 482 PGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQA 520
            G+SW++INGVL  F+ G+ T+K  +LIY+ LG IT Q 
Sbjct: 510 SGRSWIEINGVLCSFMVGEETHKDVNLIYEMLGNITRQT 548

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449439631|ref|XP_004137589.1| PREDICTED: pentatricopeptide repeat-containing protein At5g66520-like [Cucumis sativus]

 Score =  608 bits (1569), Expect = e-171,   Method: Compositional matrix adjust.
 Identities = 295/518 (56%), Positives = 381/518 (73%), Gaps = 21/518 (4%)

Query: 23  IFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPS 82
           IFS+L+   + + L + H+QI+++GFSQKNYIL  LL+ Y++ G L +A KVFE    PS
Sbjct: 30  IFSVLKSCVSFRNLAKTHAQIVVSGFSQKNYILNHLLSLYISFGSLGSAQKVFEDITAPS 89

Query: 83  TAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHG 142
           T +WNQ+I+GH RS+T +KS+ L+K+M     E + +TYSFLLS C R  LFREGEQ+HG
Sbjct: 90  TTVWNQIIKGHTRSKTSKKSIELFKRMTLAGVEANGFTYSFLLSACVRSRLFREGEQIHG 149

Query: 143 RVLASGYCSNVFIRTNLMNLYLM--SGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKR 200
           RVL +GY SN+++RTNL+NLY     GG+  +  A  LFD+MP  +VV WNSLL GYV+R
Sbjct: 150 RVLVNGYWSNLYVRTNLINLYANGGDGGDFDLKRALYLFDEMPDSNVVGWNSLLAGYVRR 209

Query: 201 GDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAAL 260
           GD DGA K+FDEMP RNV +WT M++G AQNG+ + ALSLF++MRRA V LDQVALVAAL
Sbjct: 210 GDFDGARKVFDEMPERNVRTWTIMVAGFAQNGQCKLALSLFDQMRRAGVELDQVALVAAL 269

Query: 261 SACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR 320
           SACAE+GDL LGKWIH YVE  +     PVLVSLNNALIHMYASCG ++ AY +F ++ +
Sbjct: 270 SACAELGDLTLGKWIHGYVERTWRSRHLPVLVSLNNALIHMYASCGAMDLAYKLFEEIPQ 329

Query: 321 RNTVSWTSMITGFAKQGYAQEAL------------------LTFLGVLSACSHGGFVDEG 362
           RNTVSW+S+ITGFAKQG   EA+                  +TF+G L+ACSH G + +G
Sbjct: 330 RNTVSWSSIITGFAKQGCGVEAIRIFQLMLCSGQNEVRPDEITFIGALTACSHAGLISDG 389

Query: 363 RQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCR 422
            + F+ M++ +G+ P+IEHYGCMVDL SRAGL+ EA SL+++MPMKPN+AV G+LL GCR
Sbjct: 390 IRLFQSMHKTFGVIPQIEHYGCMVDLLSRAGLLTEALSLIESMPMKPNNAVWGALLSGCR 449

Query: 423 IHNNAELASQVAQKLVAEIDP-EQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKP 481
           +H N E+ S VA+ L  EIDP  QAAGY  L+ANVYAA  RWQD A VR+ M  +GV+KP
Sbjct: 450 LHKNDEIVSHVAKHLSFEIDPNNQAAGYFMLLANVYAADGRWQDTATVRRNMHDIGVKKP 509

Query: 482 PGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQ 519
            G+SW++INGVL  F+ G+ T+K  +LIY+ LG IT Q
Sbjct: 510 SGRSWIEINGVLCSFMVGEETHKDVNLIYEMLGNITRQ 547

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356565111|ref|XP_003550788.1| PREDICTED: pentatricopeptide repeat-containing protein At5g66520-like [Glycine max]

 Score =  600 bits (1548), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 295/481 (61%), Positives = 357/481 (74%), Gaps = 27/481 (5%)

Query: 79  ENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGE 138
           +NP+T +WN +IRG+ARS TP K+V  Y  M+  + EPD +T+S LLS CAR GL +EGE
Sbjct: 2   DNPTTTVWNHVIRGYARSHTPWKAVECYTHMVSSKAEPDGFTHSSLLSACARGGLVKEGE 61

Query: 139 QVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYV 198
           QVH  VL  GYCSNVF+ T+L+  Y    G  GV  AR +FD MP RSVVSWNS+L GYV
Sbjct: 62  QVHATVLVKGYCSNVFVDTSLITFY---AGRGGVERARHVFDGMPQRSVVSWNSMLAGYV 118

Query: 199 KRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVA 258
           +  D DGA ++FD MP RNVVSWTTM++GCA+NGKSRQAL LF EMRRA V LDQVALVA
Sbjct: 119 RCADFDGARRVFDVMPCRNVVSWTTMVAGCARNGKSRQALLLFGEMRRACVELDQVALVA 178

Query: 259 ALSACAEIGDLKLGKWIHSYVEENFSVGR--EPVLVSLNNALIHMYASCGEIEEAYGVFR 316
           ALSACAE+GDLKLG+WIH YV++ F V R  +   V LNNALIHMYASCG + EAY VF 
Sbjct: 179 ALSACAELGDLKLGRWIHWYVQQRF-VARNWQQPSVRLNNALIHMYASCGILHEAYQVFV 237

Query: 317 KMQRRNTVSWTSMITGFAKQGYAQEAL--------------------LTFLGVLSACSHG 356
           KM R++TVSWTSMI  FAKQG  +EAL                    +TF+GVL ACSH 
Sbjct: 238 KMPRKSTVSWTSMIMAFAKQGLGKEALDLFKTMLSDGVKVDGVRPDEITFIGVLCACSHA 297

Query: 357 GFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGS 416
           GFVDEG Q F  M   WGI P IEHYGCMVDL SRAGL+DEA  L++ MP+ PNDA+ G+
Sbjct: 298 GFVDEGHQIFASMKHTWGISPSIEHYGCMVDLLSRAGLLDEARGLIETMPLNPNDAIWGA 357

Query: 417 LLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM 476
           LL GCRIH N+ELASQV  KLV E++ +QAAGYL L++N+YA  +RWQDV  VRQKMI+M
Sbjct: 358 LLGGCRIHRNSELASQVENKLVPELNGDQAAGYLVLLSNIYAFGQRWQDVITVRQKMIEM 417

Query: 477 GVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGI 536
           GV+KPPG+SW+QINGV+H+F+AGD T+K +S IY+TL ++T QA  EGY  +I  +FL +
Sbjct: 418 GVKKPPGRSWIQINGVVHNFIAGDMTHKHSSFIYETLRDVTKQANLEGYDREII-VFLDV 476

Query: 537 E 537
           E
Sbjct: 477 E 477

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224097410|ref|XP_002310922.1| predicted protein [Populus trichocarpa] gi|222850742|gb|EEE88289.1| predicted protein [Populus trichocarpa]

 Score =  595 bits (1534), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 287/474 (60%), Positives = 360/474 (75%), Gaps = 21/474 (4%)

Query: 64  TSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSF 123
           ++ +L++AH VF+  ++PST +WNQMIR HARS+TP KS+  + QM+  ++ PD +TYSF
Sbjct: 72  SAHHLLSAHYVFKDIQSPSTILWNQMIRAHARSQTPAKSIQFFNQMLLTDSRPDAHTYSF 131

Query: 124 LLSVCARCGLFREGEQVHGRVLASGY-CSNVFIRTNLMNLYL-MSGGE-CGVGCARLLFD 180
           LL+ C      REG+QVH +VL +GY  SNVF+ + L+N Y  + GGE   +  AR +FD
Sbjct: 132 LLAACTSSLSLREGQQVHSKVLTNGYYSSNVFLMSKLVNFYAAVVGGEGAALASARKVFD 191

Query: 181 DMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSL 240
           DM  R+VV WNS+L GY++RG++DGA +IF EMP RNVVSWTTMISG A+NGK +QAL+L
Sbjct: 192 DMSERNVVCWNSMLAGYMRRGNLDGARRIFYEMPERNVVSWTTMISGYAKNGKCKQALNL 251

Query: 241 FNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIH 300
           F++MR+A V LDQV L+AAL+ACAE+GDLK+G WIHSY+++ F    + VLVSLNNALIH
Sbjct: 252 FDQMRKAGVELDQVVLLAALTACAELGDLKMGMWIHSYIQDTFVGSNQRVLVSLNNALIH 311

Query: 301 MYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL----------------- 343
           MYASCG I+EAY VFR M  R+ VSWTS+IT FAKQGYAQ  L                 
Sbjct: 312 MYASCGMIDEAYEVFRWMPERSAVSWTSLITAFAKQGYAQAVLEIFRSMQRLGTSEARPD 371

Query: 344 -LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLV 402
            +TF+GVL ACSH G VDEGRQ F+ M Q WGIKPRIEHYGCMVDL SRAG +DEA  L+
Sbjct: 372 GITFIGVLCACSHAGLVDEGRQLFKDMIQRWGIKPRIEHYGCMVDLLSRAGFLDEAQELI 431

Query: 403 QNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKR 462
             MP+KPN+AV G+LL GCR + NAELAS V+QKLVAE DP++AAGYL+L+A VYA+A++
Sbjct: 432 ATMPVKPNNAVWGALLGGCRFYRNAELASLVSQKLVAEPDPDKAAGYLSLLAQVYASAEK 491

Query: 463 WQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEI 516
           WQDVA VRQKM+ MGV+KP GQSWVQIN V HD VAGD T++  S IY+ LG+I
Sbjct: 492 WQDVATVRQKMVAMGVKKPAGQSWVQINEVFHDSVAGDRTHENTSSIYEMLGKI 545

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225425100|ref|XP_002272744.1| PREDICTED: pentatricopeptide repeat-containing protein At5g66520-like [Vitis vinifera]

 Score =  439 bits (1129), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 223/523 (42%), Positives = 322/523 (61%), Gaps = 26/523 (4%)

Query: 22  QIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVT--SGYLINAHKVFEKTE 79
           Q   LLQ  +  + L QIH Q++  G        +KLLAF  +  SG L  A  VF++  
Sbjct: 20  QTLHLLQRCSNMEELRQIHGQMLKTGLILDEIPASKLLAFCASPNSGSLAYARTVFDRIF 79

Query: 80  NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQ 139
            P+T +WN MIRG++ S+ PE+++ LY  M+      + YT+ FLL  C+      E +Q
Sbjct: 80  RPNTFMWNTMIRGYSNSKEPEEALLLYHHMLYHSVPHNAYTFPFLLKACSSMSALEETQQ 139

Query: 140 VHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVK 199
           +H  ++  G+ S ++   +L+N+Y  SG    +  ARLLFD +  R  VSWNS++ GY K
Sbjct: 140 IHAHIIKMGFGSEIYTTNSLLNVYSKSGD---IKSARLLFDQVDQRDTVSWNSMIDGYTK 196

Query: 200 RGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAA 259
            G+I+ A++IF+ MP RN++SWT+MISGC   GK ++AL+LF+ M+ A + LD VALV+ 
Sbjct: 197 CGEIEMAYEIFNHMPERNIISWTSMISGCVGAGKPKEALNLFHRMQTAGIKLDNVALVST 256

Query: 260 LSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQ 319
           L ACA++G L  GKWIH+Y++++  +  +P+   L   LI MYA CG++EEA  VFRKM+
Sbjct: 257 LQACADLGVLDQGKWIHAYIKKH-EIEIDPI---LGCVLIDMYAKCGDLEEAIEVFRKME 312

Query: 320 RRNTVSWTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGRQ 364
            +    WT+MI+G+A  G  +EAL               +TF G+L+ACSH G V E + 
Sbjct: 313 EKGVSVWTAMISGYAIHGRGREALEWFMKMQTAGVEPNQMTFTGILTACSHAGLVHEAKL 372

Query: 365 FFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIH 424
            FE M +  G KP IEHYGCMVDL  RAGL+ EA  L++NMP+KPN A+ G+LL  C IH
Sbjct: 373 LFESMERIHGFKPSIEHYGCMVDLLGRAGLLKEAEELIENMPVKPNAAIWGALLNACHIH 432

Query: 425 NNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQ 484
            N EL  Q+  K++ ++DP     Y+ L A+++AAA  W   A VR++M + GV K PG 
Sbjct: 433 GNLELGKQIG-KILIQVDPGHGGRYIHL-ASIHAAAGEWNQAARVRRQMKEQGVSKLPGC 490

Query: 485 SWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKP 527
           S + +NG  H+F+AGD ++ Q   I   L +I  +  +EGYKP
Sbjct: 491 SVISVNGTAHEFLAGDESHPQIKEIDHMLEQIVERLREEGYKP 533

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147832325|emb|CAN66581.1| hypothetical protein VITISV_030261 [Vitis vinifera]

 Score =  438 bits (1127), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 223/523 (42%), Positives = 322/523 (61%), Gaps = 26/523 (4%)

Query: 22  QIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVT--SGYLINAHKVFEKTE 79
           Q   LLQ  +  + L QIH Q++  G        +KLLAF  +  SG L  A  VF++  
Sbjct: 20  QTLHLLQRCSNMEELRQIHGQMLKTGLILDEIPASKLLAFCASPNSGSLAYARTVFDRIF 79

Query: 80  NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQ 139
            P+T +WN MIRG++ S+ PE+++ LY  M+      + YT+ FLL  C+      E +Q
Sbjct: 80  RPNTFMWNTMIRGYSNSKEPEEALLLYHHMLYHSVPHNAYTFPFLLKACSSMSASEETQQ 139

Query: 140 VHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVK 199
           +H  ++  G+ S ++   +L+N+Y  SG    +  ARLLFD +  R  VSWNS++ GY K
Sbjct: 140 IHAHIIKMGFGSEIYTTNSLLNVYSKSGD---IKSARLLFDQVDQRDTVSWNSMIDGYTK 196

Query: 200 RGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAA 259
            G+I+ A++IF+ MP RN++SWT+MISGC   GK ++AL+LF+ M+ A + LD VALV+ 
Sbjct: 197 CGEIEMAYEIFNHMPERNIISWTSMISGCVGAGKPKEALNLFHRMQTAGIKLDNVALVST 256

Query: 260 LSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQ 319
           L ACA++G L  GKWIH+Y++++  +  +P+   L   LI MYA CG++EEA  VFRKM+
Sbjct: 257 LQACADLGVLDQGKWIHAYIKKH-EIEIDPI---LGCVLIDMYAKCGDLEEAIEVFRKME 312

Query: 320 RRNTVSWTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGRQ 364
            +    WT+MI+G+A  G  +EAL               +TF G+L+ACSH G V E + 
Sbjct: 313 EKGVSVWTAMISGYAIHGRGREALEWFMKMQTAGVEPNQMTFTGILTACSHAGLVHEAKL 372

Query: 365 FFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIH 424
            FE M +  G KP IEHYGCMVDL  RAGL+ EA  L++NMP+KPN A+ G+LL  C IH
Sbjct: 373 LFESMERIHGFKPSIEHYGCMVDLLGRAGLLKEAEELIENMPVKPNAAIWGALLNACHIH 432

Query: 425 NNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQ 484
            N EL  Q+  K++ ++DP     Y+ L A+++AAA  W   A VR++M + GV K PG 
Sbjct: 433 GNLELGKQIG-KILIQVDPGHGGRYIHL-ASIHAAAGEWNQAARVRRQMKEQGVSKLPGC 490

Query: 485 SWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKP 527
           S + +NG  H+F+AGD ++ Q   I   L +I  +  +EGYKP
Sbjct: 491 SVISVNGTAHEFLAGDESHPQIKEIDHMLEQIVERLREEGYKP 533

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224111954|ref|XP_002332852.1| predicted protein [Populus trichocarpa] gi|222837177|gb|EEE75556.1| predicted protein [Populus trichocarpa]

 Score =  434 bits (1117), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 210/322 (65%), Positives = 251/322 (77%), Gaps = 18/322 (5%)

Query: 213 MPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLG 272
           MP RNVVSWTTMISG A+NGK +QAL+LF++MR+A V LDQV L+AAL+ACAE+GDLK+G
Sbjct: 1   MPERNVVSWTTMISGYAKNGKCKQALNLFDQMRKAGVELDQVVLLAALTACAELGDLKMG 60

Query: 273 KWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITG 332
            WIHSY+++ F    + VLVSLNNALIHMYASCG I+EAY VFR M  R+ VSWTS+IT 
Sbjct: 61  MWIHSYIQDTFVGSNQRVLVSLNNALIHMYASCGMIDEAYEVFRWMPERSAVSWTSLITA 120

Query: 333 FAKQGYAQEAL------------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWG 374
           FAKQGYAQ  L                  +TF+GVL ACSH G VDEGRQ F+ M Q WG
Sbjct: 121 FAKQGYAQAVLEIFRSMQRLGTSEARPDGITFIGVLCACSHAGLVDEGRQLFKDMIQRWG 180

Query: 375 IKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVA 434
           IKPRIEHYGCMVDL SRAG +DEA  L+  MP+KPN+AV G+LL GCR + NAELAS V+
Sbjct: 181 IKPRIEHYGCMVDLLSRAGFLDEAQELIATMPVKPNNAVWGALLGGCRFYRNAELASLVS 240

Query: 435 QKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLH 494
           QKLVAE DP++AAGYL+L+A VYA+A++WQDVA VRQKM+ MGV+KP GQSWVQIN V+H
Sbjct: 241 QKLVAEPDPDKAAGYLSLLAQVYASAEKWQDVATVRQKMVAMGVKKPAGQSWVQINEVVH 300

Query: 495 DFVAGDSTYKQASLIYKTLGEI 516
           D V+ D T+K  S IY+ LG+I
Sbjct: 301 DSVSVDKTHKNTSSIYEMLGKI 322

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	538
TAIR|locus:2154855	620	AT5G66520 "AT5G66520" [Arabido	0.938	0.814	0.383	1.5e-97
TAIR|locus:1009023396	612	AT5G40405 "AT5G40405" [Arabido	0.938	0.825	0.335	7.2e-84
TAIR|locus:2161018	530	AT5G56310 "AT5G56310" [Arabido	0.892	0.905	0.365	5e-83
TAIR|locus:2093920	687	AT3G15930 "AT3G15930" [Arabido	0.903	0.707	0.352	3.6e-82
TAIR|locus:2054789	534	MEF21 "mitochondrial editing f	0.847	0.853	0.347	8.7e-79
TAIR|locus:2167593	657	AT5G44230 [Arabidopsis thalian	0.949	0.777	0.325	1.8e-78
TAIR|locus:2060640	738	OTP81 "ORGANELLE TRANSCRIPT PR	0.910	0.663	0.317	3e-78
TAIR|locus:2041198	681	SLO1 "SLOW GROWTH 1" [Arabidop	0.821	0.649	0.346	6.2e-78
TAIR|locus:2130354	722	AT4G14820 "AT4G14820" [Arabido	0.886	0.660	0.341	1.6e-77
TAIR|locus:2144143	622	AT5G06540 [Arabidopsis thalian	0.936	0.810	0.319	3.1e-76

TAIR|locus:2154855 AT5G66520 "AT5G66520" [Arabidopsis thaliana (taxid:3702)]

 Score = 969 (346.2 bits), Expect = 1.5e-97, P = 1.5e-97
 Identities = 205/534 (38%), Positives = 317/534 (59%)

Query:    22 QIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTS---GYLINAHKVFEKT 78
             +  S LQ  +  + L QIH++++  G  Q +Y + K L+F ++S    +L  A  VF+  
Sbjct:    16 ETMSCLQRCSKQEELKQIHARMLKTGLMQDSYAITKFLSFCISSTSSDFLPYAQIVFDGF 75

Query:    79 ENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGE 138
             + P T +WN MIRG + S+ PE+S+ LY++M+      + YT+  LL  C+    F E  
Sbjct:    76 DRPDTFLWNLMIRGFSCSDEPERSLLLYQRMLCSSAPHNAYTFPSLLKACSNLSAFEETT 135

Query:   139 QVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYV 198
             Q+H ++   GY ++V+   +L+N Y ++G       A LLFD +P    VSWNS++KGYV
Sbjct:   136 QIHAQITKLGYENDVYAVNSLINSYAVTGN---FKLAHLLFDRIPEPDDVSWNSVIKGYV 192

Query:   199 KRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVA 258
             K G +D A  +F +M  +N +SWTTMISG  Q   +++AL LF+EM+ + V  D V+L  
Sbjct:   193 KAGKMDIALTLFRKMAEKNAISWTTMISGYVQADMNKEALQLFHEMQNSDVEPDNVSLAN 252

Query:   259 ALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKM 318
             ALSACA++G L+ GKWIHSY+ +   +  + VL  +   LI MYA CGE+EEA  VF+ +
Sbjct:   253 ALSACAQLGALEQGKWIHSYLNKT-RIRMDSVLGCV---LIDMYAKCGEMEEALEVFKNI 308

Query:   319 QRRNTVSWTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGR 363
             ++++  +WT++I+G+A  G+ +EA+               +TF  VL+ACS+ G V+EG+
Sbjct:   309 KKKSVQAWTALISGYAYHGHGREAISKFMEMQKMGIKPNVITFTAVLTACSYTGLVEEGK 368

Query:   364 QFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRI 423
               F  M +++ +KP IEHYGC+VDL  RAGL+DEA   +Q MP+KPN  + G+LL  CRI
Sbjct:   369 LIFYSMERDYNLKPTIEHYGCIVDLLGRAGLLDEAKRFIQEMPLKPNAVIWGALLKACRI 428

Query:   424 HNNAELASQVAQKLVAEIDPEQXXXXXXXXXXXXXXXKRWQDVAAVRQKMIKMGVRKPPG 483
             H N EL  ++ + L+A IDP                 K+W   A  R+ M + GV K PG
Sbjct:   429 HKNIELGEEIGEILIA-IDPYHGGRYVHKANIHAMD-KKWDKAAETRRLMKEQGVAKVPG 486

Query:   484 QSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQE-GYKPDISELFLGI 536
              S + + G  H+F+AGD ++ +   I ++   I  + ++E GY P++ E+ L +
Sbjct:   487 CSTISLEGTTHEFLAGDRSHPEIEKI-QSKWRIMRRKLEENGYVPELEEMLLDL 539

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0016556 "mRNA modification" evidence=RCA

TAIR|locus:1009023396 AT5G40405 "AT5G40405" [Arabidopsis thaliana (taxid:3702)]

 Score = 840 (300.8 bits), Expect = 7.2e-84, P = 7.2e-84
 Identities = 179/533 (33%), Positives = 304/533 (57%)

Query:    25 SLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSG--YLINAHKVFEKTENPS 82
             +LL    T K + QIH+++ ++G  + ++++   +     S   YL  A+++ +++E P+
Sbjct:    11 ALLDSGITFKEVRQIHAKLYVDGTLKDDHLVGHFVKAVALSDHKYLDYANQILDRSEKPT 70

Query:    83 TAIWNQMIRGHARSETPEKSVYLYKQMIDK--ETEPDEYTYSFLLSVCARCGLFREGEQV 140
                 N MIR H +S  PEKS   Y++++    + +PD YT +FL+  C    +   G QV
Sbjct:    71 LFALNSMIRAHCKSPVPEKSFDFYRRILSSGNDLKPDNYTVNFLVQACTGLRMRETGLQV 130

Query:   141 HGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKR 200
             HG  +  G+ ++  ++T L++LY   G  C   C ++ F+ +P    V   +++    + 
Sbjct:   131 HGMTIRRGFDNDPHVQTGLISLYAELG--CLDSCHKV-FNSIPCPDFVCRTAMVTACARC 187

Query:   201 GDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAAL 260
             GD+  A K+F+ MP R+ ++W  MISG AQ G+SR+AL++F+ M+   V ++ VA+++ L
Sbjct:   188 GDVVFARKLFEGMPERDPIAWNAMISGYAQVGESREALNVFHLMQLEGVKVNGVAMISVL 247

Query:   261 SACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR 320
             SAC ++G L  G+W HSY+E N    +  + V L   L+ +YA CG++E+A  VF  M+ 
Sbjct:   248 SACTQLGALDQGRWAHSYIERN----KIKITVRLATTLVDLYAKCGDMEKAMEVFWGMEE 303

Query:   321 RNTVSWTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGRQF 365
             +N  +W+S + G A  G+ ++ L               +TF+ VL  CS  GFVDEG++ 
Sbjct:   304 KNVYTWSSALNGLAMNGFGEKCLELFSLMKQDGVTPNAVTFVSVLRGCSVVGFVDEGQRH 363

Query:   366 FECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHN 425
             F+ M   +GI+P++EHYGC+VDL++RAG +++A S++Q MPMKP+ AV  SLL   R++ 
Sbjct:   364 FDSMRNEFGIEPQLEHYGCLVDLYARAGRLEDAVSIIQQMPMKPHAAVWSSLLHASRMYK 423

Query:   426 NAELASQVAQKLVAEIDPEQXXXXXXXXXXXXXXXKRWQDVAAVRQKMIKMGVRKPPGQS 485
             N EL    ++K++ E++                    W +V+ VRQ M   GVRK PG S
Sbjct:   424 NLELGVLASKKML-ELETANHGAYVLLSNIYADSND-WDNVSHVRQSMKSKGVRKQPGCS 481

Query:   486 WVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE 538
              +++NG +H+F  GD ++ + + I     +I+ +    GYK D + +   I+E
Sbjct:   482 VMEVNGEVHEFFVGDKSHPKYTQIDAVWKDISRRLRLAGYKADTTPVMFDIDE 534

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2161018 AT5G56310 "AT5G56310" [Arabidopsis thaliana (taxid:3702)]

 Score = 832 (297.9 bits), Expect = 5.0e-83, P = 5.0e-83
 Identities = 186/509 (36%), Positives = 289/509 (56%)

Query:    31 NTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMI 90
             N  KTL Q H  +II G ++ N  +AK +     +G+L  A+ VF     P+T + N MI
Sbjct:    26 NNLKTLKQSHCYMIITGLNRDNLNVAKFIEACSNAGHLRYAYSVFTHQPCPNTYLHNTMI 85

Query:    91 RGHARSETPEK---SVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLAS 147
             R  +  + P     ++ +Y+++     +PD +T+ F+L +  R      G Q+HG+V+  
Sbjct:    86 RALSLLDEPNAHSIAITVYRKLWALCAKPDTFTFPFVLKIAVRVSDVWFGRQIHGQVVVF 145

Query:   148 GYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAW 207
             G+ S+V + T L+ +Y   GG   +G AR +FD+M  + V  WN+LL GY K G++D A 
Sbjct:   146 GFDSSVHVVTGLIQMYFSCGG---LGDARKMFDEMLVKDVNVWNALLAGYGKVGEMDEAR 202

Query:   208 KIFDEMPH--RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAE 265
              + + MP   RN VSWT +ISG A++G++ +A+ +F  M    V  D+V L+A LSACA+
Sbjct:   203 SLLEMMPCWVRNEVSWTCVISGYAKSGRASEAIEVFQRMLMENVEPDEVTLLAVLSACAD 262

Query:   266 IGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVS 325
             +G L+LG+ I SYV+    + R    VSLNNA+I MYA  G I +A  VF  +  RN V+
Sbjct:   263 LGSLELGERICSYVDHR-GMNRA---VSLNNAVIDMYAKSGNITKALDVFECVNERNVVT 318

Query:   326 WTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMN 370
             WT++I G A  G+  EAL               +TF+ +LSACSH G+VD G++ F  M 
Sbjct:   319 WTTIIAGLATHGHGAEALAMFNRMVKAGVRPNDVTFIAILSACSHVGWVDLGKRLFNSMR 378

Query:   371 QNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELA 430
               +GI P IEHYGCM+DL  RAG + EA  ++++MP K N A+ GSLL    +H++ EL 
Sbjct:   379 SKYGIHPNIEHYGCMIDLLGRAGKLREADEVIKSMPFKANAAIWGSLLAASNVHHDLELG 438

Query:   431 SQVAQKLVAEIDPEQXXXXXXXXXXXXXXXKRWQDVAAVRQKMIKMGVRKPPGQSWVQIN 490
              +   +L+ +++P                  RW +   +R  M  +GV+K  G+S +++ 
Sbjct:   439 ERALSELI-KLEPNNSGNYMLLANLYSNLG-RWDESRMMRNMMKGIGVKKMAGESSIEVE 496

Query:   491 GVLHDFVAGDSTYKQASLIYKTLGEITMQ 519
               ++ F++GD T+ Q   I++ L E+ +Q
Sbjct:   497 NRVYKFISGDLTHPQVERIHEILQEMDLQ 525

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2093920 AT3G15930 "AT3G15930" [Arabidopsis thaliana (taxid:3702)]

 Score = 824 (295.1 bits), Expect = 3.6e-82, P = 3.6e-82
 Identities = 180/510 (35%), Positives = 284/510 (55%)

Query:    38 QIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSE 97
             ++H  ++  G     Y+   L+  Y   G +  A  VF++        WN MI G+ R +
Sbjct:   156 KLHCHVVKFGLGSNLYVQNALVKMYSLCGLMDMARGVFDRRCKEDVFSWNLMISGYNRMK 215

Query:    98 TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRT 157
               E+S+ L  +M      P   T   +LS C++       ++VH  V       ++ +  
Sbjct:   216 EYEESIELLVEMERNLVSPTSVTLLLVLSACSKVKDKDLCKRVHEYVSECKTEPSLRLEN 275

Query:   158 NLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRN 217
              L+N Y   G E  +  A  +F  M AR V+SW S++KGYV+RG++  A   FD+MP R+
Sbjct:   276 ALVNAYAACG-EMDI--AVRIFRSMKARDVISWTSIVKGYVERGNLKLARTYFDQMPVRD 332

Query:   218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHS 277
              +SWT MI G  + G   ++L +F EM+ A +  D+  +V+ L+ACA +G L++G+WI +
Sbjct:   333 RISWTIMIDGYLRAGCFNESLEIFREMQSAGMIPDEFTMVSVLTACAHLGSLEIGEWIKT 392

Query:   278 YVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQG 337
             Y+++N  +  + V+    NALI MY  CG  E+A  VF  M +R+  +WT+M+ G A  G
Sbjct:   393 YIDKN-KIKNDVVV---GNALIDMYFKCGCSEKAQKVFHDMDQRDKFTWTAMVVGLANNG 448

Query:   338 YAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHY 382
               QEA+               +T+LGVLSAC+H G VD+ R+FF  M  +  I+P + HY
Sbjct:   449 QGQEAIKVFFQMQDMSIQPDDITYLGVLSACNHSGMVDQARKFFAKMRSDHRIEPSLVHY 508

Query:   383 GCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEID 442
             GCMVD+  RAGL+ EA+ +++ MPM PN  V G+LL   R+HN+  +A   A+K++ E++
Sbjct:   509 GCMVDMLGRAGLVKEAYEILRKMPMNPNSIVWGALLGASRLHNDEPMAELAAKKIL-ELE 567

Query:   443 PEQXXXXXXXXXXXXXXXKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDST 502
             P+                KRW+D+  VR+K++ + ++K PG S +++NG  H+FVAGD +
Sbjct:   568 PDNGAVYALLCNIYAGC-KRWKDLREVRRKIVDVAIKKTPGFSLIEVNGFAHEFVAGDKS 626

Query:   503 YKQASLIYKTLGEITMQAMQEGYKPDISEL 532
             + Q+  IY  L E+  ++    Y PD SEL
Sbjct:   627 HLQSEEIYMKLEELAQESTFAAYLPDTSEL 656

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2054789 MEF21 "mitochondrial editing factor 21" [Arabidopsis thaliana (taxid:3702)]

 Score = 792 (283.9 bits), Expect = 8.7e-79, P = 8.7e-79
 Identities = 167/481 (34%), Positives = 277/481 (57%)

Query:    38 QIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSE 97
             +I++ III+G SQ ++++ K++ F      +  A ++F +  NP+  ++N +IR +  + 
Sbjct:    28 KINASIIIHGLSQSSFMVTKMVDFCDKIEDMDYATRLFNQVSNPNVFLYNSIIRAYTHNS 87

Query:    98 TPEKSVYLYKQMIDKETE-PDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIR 156
                  + +YKQ++ K  E PD +T+ F+   CA  G    G+QVHG +   G   +V   
Sbjct:    88 LYCDVIRIYKQLLRKSFELPDRFTFPFMFKSCASLGSCYLGKQVHGHLCKFGPRFHVVTE 147

Query:   157 TNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR 216
               L+++Y+          A  +FD+M  R V+SWNSLL GY + G +  A  +F  M  +
Sbjct:   148 NALIDMYMKFDDLVD---AHKVFDEMYERDVISWNSLLSGYARLGQMKKAKGLFHLMLDK 204

Query:   217 NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIH 276
              +VSWT MISG    G   +A+  F EM+ A +  D+++L++ L +CA++G L+LGKWIH
Sbjct:   205 TIVSWTAMISGYTGIGCYVEAMDFFREMQLAGIEPDEISLISVLPSCAQLGSLELGKWIH 264

Query:   277 SYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQ 336
              Y E    + +  V     NALI MY+ CG I +A  +F +M+ ++ +SW++MI+G+A  
Sbjct:   265 LYAERRGFLKQTGVC----NALIEMYSKCGVISQAIQLFGQMEGKDVISWSTMISGYAYH 320

Query:   337 GYAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEH 381
             G A  A+               +TFLG+LSACSH G   EG ++F+ M Q++ I+P+IEH
Sbjct:   321 GNAHGAIETFNEMQRAKVKPNGITFLGLLSACSHVGMWQEGLRYFDMMRQDYQIEPKIEH 380

Query:   382 YGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEI 441
             YGC++D+ +RAG ++ A  + + MPMKP+  + GSLL  CR   N ++A  VA   + E+
Sbjct:   381 YGCLIDVLARAGKLERAVEITKTMPMKPDSKIWGSLLSSCRTPGNLDVAL-VAMDHLVEL 439

Query:   442 DPEQXXXXXXXXXXXXXXXKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDS 501
             +PE                K W+DV+ +R+ +    ++K PG S +++N ++ +FV+GD+
Sbjct:   440 EPEDMGNYVLLANIYADLGK-WEDVSRLRKMIRNENMKKTPGGSLIEVNNIVQEFVSGDN 498

Query:   502 T 502
             +
Sbjct:   499 S 499

GO:0005739 "mitochondrion" evidence=ISM

GO:0080156 "mitochondrial mRNA modification" evidence=IMP

TAIR|locus:2167593 AT5G44230 [Arabidopsis thaliana (taxid:3702)]

 Score = 789 (282.8 bits), Expect = 1.8e-78, P = 1.8e-78
 Identities = 176/541 (32%), Positives = 287/541 (53%)

Query:    13 TSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLIN-- 70
             ++ K L    + S L        + QIH  ++  G  Q  YIL KL+      G  ++  
Sbjct:    42 SNQKELLVSSLISKLDDCINLNQIKQIHGHVLRKGLDQSCYILTKLIRTLTKLGVPMDPY 101

Query:    71 AHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCAR 130
             A +V E  +  +  +W  +IRG+A     ++++ +Y  M  +E  P  +T+S LL  C  
Sbjct:   102 ARRVIEPVQFRNPFLWTAVIRGYAIEGKFDEAIAMYGCMRKEEITPVSFTFSALLKACGT 161

Query:   131 CGLFREGEQVHGRVLA-SGYCSNVFIRTNLMNLYLMSGGEC-GVGCARLLFDDMPARSVV 188
                   G Q H +     G+C  V++   ++++Y+    +C  + CAR +FD+MP R V+
Sbjct:   162 MKDLNLGRQFHAQTFRLRGFCF-VYVGNTMIDMYV----KCESIDCARKVFDEMPERDVI 216

Query:   189 SWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR 248
             SW  L+  Y + G+++ A ++F+ +P +++V+WT M++G AQN K ++AL  F+ M ++ 
Sbjct:   217 SWTELIAAYARVGNMECAAELFESLPTKDMVAWTAMVTGFAQNAKPQEALEYFDRMEKSG 276

Query:   249 VGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEI 308
             +  D+V +   +SACA++G  K         +++     + V++   +ALI MY+ CG +
Sbjct:   277 IRADEVTVAGYISACAQLGASKYADRAVQIAQKSGYSPSDHVVIG--SALIDMYSKCGNV 334

Query:   309 EEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL----------------LTFLGVLSA 352
             EEA  VF  M  +N  +++SMI G A  G AQEAL                +TF+G L A
Sbjct:   335 EEAVNVFMSMNNKNVFTYSSMILGLATHGRAQEALHLFHYMVTQTEIKPNTVTFVGALMA 394

Query:   353 CSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDA 412
             CSH G VD+GRQ F+ M Q +G++P  +HY CMVDL  R G + EA  L++ M ++P+  
Sbjct:   395 CSHSGLVDQGRQVFDSMYQTFGVQPTRDHYTCMVDLLGRTGRLQEALELIKTMSVEPHGG 454

Query:   413 VLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQXXXXXXXXXXXXXXXKRWQDVAAVRQK 472
             V G+LL  CRIHNN E+A   A+ L  E++P+                  W  V  VR+ 
Sbjct:   455 VWGALLGACRIHNNPEIAEIAAEHLF-ELEPDIIGNYILLSNVYASAGD-WGGVLRVRKL 512

Query:   473 MIKMGVRKPPGQSWV-QINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISE 531
             + + G++K P  SWV   NG +H F  G+  +  ++ I   L E+  +    GY+PD+S 
Sbjct:   513 IKEKGLKKTPAVSWVVDKNGQMHKFFPGNLNHPMSNKIQDKLEELVERLTVLGYQPDLSS 572

Query:   532 L 532
             +
Sbjct:   573 V 573

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2060640 OTP81 "ORGANELLE TRANSCRIPT PROCESSING 81" [Arabidopsis thaliana (taxid:3702)]

 Score = 787 (282.1 bits), Expect = 3.0e-78, P = 3.0e-78
 Identities = 164/517 (31%), Positives = 287/517 (55%)

Query:    39 IHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSET 98
             +H   + +      ++   L+  Y + G L +A KVF   +      WN MI G  +  +
Sbjct:   153 LHGMAVKSAVGSDVFVANSLIHCYFSCGDLDSACKVFTTIKEKDVVSWNSMINGFVQKGS 212

Query:    99 PEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTN 158
             P+K++ L+K+M  ++ +    T   +LS CA+      G QV   +  +    N+ +   
Sbjct:   213 PDKALELFKKMESEDVKASHVTMVGVLSACAKIRNLEFGRQVCSYIEENRVNVNLTLANA 272

Query:   159 LMNLYLMSGGECG-VGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRN 217
             ++++Y     +CG +  A+ LFD M  +  V+W ++L GY    D + A ++ + MP ++
Sbjct:   273 MLDMYT----KCGSIEDAKRLFDAMEEKDNVTWTTMLDGYAISEDYEAAREVLNSMPQKD 328

Query:   218 VVSWTTMISGCAQNGKSRQALSLFNEMR-RARVGLDQVALVAALSACAEIGDLKLGKWIH 276
             +V+W  +IS   QNGK  +AL +F+E++ +  + L+Q+ LV+ LSACA++G L+LG+WIH
Sbjct:   329 IVAWNALISAYEQNGKPNEALIVFHELQLQKNMKLNQITLVSTLSACAQVGALELGRWIH 388

Query:   277 SYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQ 336
             SY++++   G   +   + +ALIHMY+ CG++E++  VF  +++R+   W++MI G A  
Sbjct:   389 SYIKKH---GIR-MNFHVTSALIHMYSKCGDLEKSREVFNSVEKRDVFVWSAMIGGLAMH 444

Query:   337 GYAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEH 381
             G   EA+               +TF  V  ACSH G VDE    F  M  N+GI P  +H
Sbjct:   445 GCGNEAVDMFYKMQEANVKPNGVTFTNVFCACSHTGLVDEAESLFHQMESNYGIVPEEKH 504

Query:   382 YGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEI 441
             Y C+VD+  R+G +++A   ++ MP+ P+ +V G+LL  C+IH N  LA     +L+ E+
Sbjct:   505 YACIVDVLGRSGYLEKAVKFIEAMPIPPSTSVWGALLGACKIHANLNLAEMACTRLL-EL 563

Query:   442 DPEQXXXXXXXXXXXXXXXKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDS 501
             +P                 K W++V+ +R+ M   G++K PG S ++I+G++H+F++GD+
Sbjct:   564 EPRNDGAHVLLSNIYAKLGK-WENVSELRKHMRVTGLKKEPGCSSIEIDGMIHEFLSGDN 622

Query:   502 TYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE 538
              +  +  +Y  L E+  +    GY+P+IS++   IEE
Sbjct:   623 AHPMSEKVYGKLHEVMEKLKSNGYEPEISQVLQIIEE 659

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0031425 "chloroplast RNA processing" evidence=IMP

TAIR|locus:2041198 SLO1 "SLOW GROWTH 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 784 (281.0 bits), Expect = 6.2e-78, P = 6.2e-78
 Identities = 162/468 (34%), Positives = 269/468 (57%)

Query:    62 YVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTY 121
             + + G + NA KVF+++       WN +I G+ +    EK++Y+YK M  +  +PD+ T 
Sbjct:   201 FASCGDMENARKVFDESPVRDLVSWNCLINGYKKIGEAEKAIYVYKLMESEGVKPDDVTM 260

Query:   122 SFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECG-VGCARLLFD 180
               L+S C+  G    G++ +  V  +G    + +   LM+++     +CG +  AR +FD
Sbjct:   261 IGLVSSCSMLGDLNRGKEFYEYVKENGLRMTIPLVNALMDMF----SKCGDIHEARRIFD 316

Query:   181 DMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSL 240
             ++  R++VSW +++ GY + G +D + K+FD+M  ++VV W  MI G  Q  + + AL+L
Sbjct:   317 NLEKRTIVSWTTMISGYARCGLLDVSRKLFDDMEEKDVVLWNAMIGGSVQAKRGQDALAL 376

Query:   241 FNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIH 300
             F EM+ +    D++ ++  LSAC+++G L +G WIH Y+E+ +S+      V+L  +L+ 
Sbjct:   377 FQEMQTSNTKPDEITMIHCLSACSQLGALDVGIWIHRYIEK-YSLSLN---VALGTSLVD 432

Query:   301 MYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL---------------LT 345
             MYA CG I EA  VF  +Q RN++++T++I G A  G A  A+               +T
Sbjct:   433 MYAKCGNISEALSVFHGIQTRNSLTYTAIIGGLALHGDASTAISYFNEMIDAGIAPDEIT 492

Query:   346 FLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNM 405
             F+G+LSAC HGG +  GR +F  M   + + P+++HY  MVDL  RAGL++EA  L+++M
Sbjct:   493 FIGLLSACCHGGMIQTGRDYFSQMKSRFNLNPQLKHYSIMVDLLGRAGLLEEADRLMESM 552

Query:   406 PMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQXXXXXXXXXXXXXXXKRWQD 465
             PM+ + AV G+LL GCR+H N EL  + A+KL+ E+DP                   W+D
Sbjct:   553 PMEADAAVWGALLFGCRMHGNVELGEKAAKKLL-ELDPSDSGIYVLLDGMYGEA-NMWED 610

Query:   466 VAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTL 513
                 R+ M + GV K PG S +++NG++ +F+  D +  ++  IY  L
Sbjct:   611 AKRARRMMNERGVEKIPGCSSIEVNGIVCEFIVRDKSRPESEKIYDRL 658

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2130354 AT4G14820 "AT4G14820" [Arabidopsis thaliana (taxid:3702)]

 Score = 780 (279.6 bits), Expect = 1.6e-77, P = 1.6e-77
 Identities = 171/501 (34%), Positives = 267/501 (53%)

Query:    53 YILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDK 112
             ++    +  Y + G +  A  VF++  +     WN MI  + R    +++  L+++M D 
Sbjct:   147 FVETGFMDMYASCGRINYARNVFDEMSHRDVVTWNTMIERYCRFGLVDEAFKLFEEMKDS 206

Query:   113 ETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGV 172
                PDE     ++S C R G  R    ++  ++ +    +  + T L+ +Y  +G  C +
Sbjct:   207 NVMPDEMILCNIVSACGRTGNMRYNRAIYEFLIENDVRMDTHLLTALVTMY--AGAGC-M 263

Query:   173 GCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNG 232
               AR  F  M  R++    +++ GY K G +D A  IFD+   +++V WTTMIS   ++ 
Sbjct:   264 DMAREFFRKMSVRNLFVSTAMVSGYSKCGRLDDAQVIFDQTEKKDLVCWTTMISAYVESD 323

Query:   233 KSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLV 292
               ++AL +F EM  + +  D V++ + +SACA +G L   KW+HS +  N   G E  L 
Sbjct:   324 YPQEALRVFEEMCCSGIKPDVVSMFSVISACANLGILDKAKWVHSCIHVN---GLESEL- 379

Query:   293 SLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL--------- 343
             S+NNALI+MYA CG ++    VF KM RRN VSW+SMI   +  G A +AL         
Sbjct:   380 SINNALINMYAKCGGLDATRDVFEKMPRRNVVSWSSMINALSMHGEASDALSLFARMKQE 439

Query:   344 ------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDE 397
                   +TF+GVL  CSH G V+EG++ F  M   + I P++EHYGCMVDLF RA L+ E
Sbjct:   440 NVEPNEVTFVGVLYGCSHSGLVEEGKKIFASMTDEYNITPKLEHYGCMVDLFGRANLLRE 499

Query:   398 AFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQXXXXXXXXXXXX 457
             A  ++++MP+  N  + GSL+  CRIH   EL  + A K + E++P+             
Sbjct:   500 ALEVIESMPVASNVVIWGSLMSACRIHGELELG-KFAAKRILELEPDHDGALVLMSNIYA 558

Query:   458 XXXKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEIT 517
                +RW+DV  +R+ M +  V K  G S +  NG  H+F+ GD  +KQ++ IY  L E+ 
Sbjct:   559 RE-QRWEDVRNIRRVMEEKNVFKEKGLSRIDQNGKSHEFLIGDKRHKQSNEIYAKLDEVV 617

Query:   518 MQAMQEGYKPDISELFLGIEE 538
              +    GY PD   + + +EE
Sbjct:   618 SKLKLAGYVPDCGSVLVDVEE 638

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2144143 AT5G06540 [Arabidopsis thaliana (taxid:3702)]

 Score = 768 (275.4 bits), Expect = 3.1e-76, P = 3.1e-76
 Identities = 172/538 (31%), Positives = 293/538 (54%)

Query:    25 SLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVT-------SGYLINAHKVFEK 77
             +LLQ  ++   L  IH  ++        ++ ++LLA  V        +  L  A+ +F +
Sbjct:    17 ALLQSCSSFSDLKIIHGFLLRTHLISDVFVASRLLALCVDDSTFNKPTNLLGYAYGIFSQ 76

Query:    78 TENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREG 137
              +NP+  ++N +IR  +    P K+   Y QM+     PD  T+ FL+   +       G
Sbjct:    77 IQNPNLFVFNLLIRCFSTGAEPSKAFGFYTQMLKSRIWPDNITFPFLIKASSEMECVLVG 136

Query:   138 EQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECG-VGCARLLFDDMPARSVVSWNSLLKG 196
             EQ H +++  G+ ++V++  +L+++Y      CG +  A  +F  M  R VVSW S++ G
Sbjct:   137 EQTHSQIVRFGFQNDVYVENSLVHMY----ANCGFIAAAGRIFGQMGFRDVVSWTSMVAG 192

Query:   197 YVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVAL 256
             Y K G ++ A ++FDEMPHRN+ +W+ MI+G A+N    +A+ LF  M+R  V  ++  +
Sbjct:   193 YCKCGMVENAREMFDEMPHRNLFTWSIMINGYAKNNCFEKAIDLFEFMKREGVVANETVM 252

Query:   257 VAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFR 316
             V+ +S+CA +G L+ G+  + YV ++       V + L  AL+ M+  CG+IE+A  VF 
Sbjct:   253 VSVISSCAHLGALEFGERAYEYVVKSHMT----VNLILGTALVDMFWRCGDIEKAIHVFE 308

Query:   317 KMQRRNTVSWTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDE 361
              +   +++SW+S+I G A  G+A +A+               +TF  VLSACSHGG V++
Sbjct:   309 GLPETDSLSWSSIIKGLAVHGHAHKAMHYFSQMISLGFIPRDVTFTAVLSACSHGGLVEK 368

Query:   362 GRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGC 421
             G + +E M ++ GI+PR+EHYGC+VD+  RAG + EA + +  M +KPN  +LG+LL  C
Sbjct:   369 GLEIYENMKKDHGIEPRLEHYGCIVDMLGRAGKLAEAENFILKMHVKPNAPILGALLGAC 428

Query:   422 RIHNNAELASQVAQKLVAEIDPEQXXXXXXXXXXXXXXXKRWQDVAAVRQKMIKMGVRKP 481
             +I+ N E+A +V   L+ ++ PE                + W  + ++R  M +  V+KP
Sbjct:   429 KIYKNTEVAERVGNMLI-KVKPEHSGYYVLLSNIYACAGQ-WDKIESLRDMMKEKLVKKP 486

Query:   482 PGQSWVQINGVLHDFVAGDST-YKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE 538
             PG S ++I+G ++ F  GD   + +   I +   EI  +    GYK +  + F  ++E
Sbjct:   487 PGWSLIEIDGKINKFTMGDDQKHPEMGKIRRKWEEILGKIRLIGYKGNTGDAFFDVDE 544

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9FJY7	PP449_ARATH	No assigned EC number	0.3883	0.9405	0.8161	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00016303001 SubName- Full=Chromosome chr17 scaffold_12, whole genome shotgun sequence; (609 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	538
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	8e-95
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-92
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-48
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-42
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-31
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-29
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	4e-29
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-12
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-12
pfam13041	50	pfam13041, PPR_2, PPR repeat family	4e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	9e-08
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-07
pfam01535	31	pfam01535, PPR, PPR repeat	9e-07
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	3e-06
pfam01535	31	pfam01535, PPR, PPR repeat	6e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-05
pfam12854	34	pfam12854, PPR_1, PPR repeat	4e-05
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	9e-05
pfam12854	34	pfam12854, PPR_1, PPR repeat	1e-04
pfam01535	31	pfam01535, PPR, PPR repeat	7e-04

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score =  302 bits (776), Expect = 8e-95
 Identities = 151/512 (29%), Positives = 260/512 (50%), Gaps = 57/512 (11%)

Query: 43  IIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKS 102
           +  +GF    Y++ ++L  +V  G LI+A ++F++    + A W  +I G   +    ++
Sbjct: 149 VESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREA 208

Query: 103 VYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNL 162
             L+++M +  ++ +  T+  +L   A  G  R G+Q+H  VL +G   + F        
Sbjct: 209 FALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTF-------- 260

Query: 163 YLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWT 222
                    V CA +   DM              Y K GDI+ A  +FD MP +  V+W 
Sbjct: 261 ---------VSCALI---DM--------------YSKCGDIEDARCVFDGMPEKTTVAWN 294

Query: 223 TMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIH-SYVEE 281
           +M++G A +G S +AL L+ EMR + V +DQ      +   + +  L+  K  H   +  
Sbjct: 295 SMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRT 354

Query: 282 NFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQE 341
            F     P+ +  N AL+ +Y+  G +E+A  VF +M R+N +SW ++I G+   G   +
Sbjct: 355 GF-----PLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTK 409

Query: 342 AL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMV 386
           A+               +TFL VLSAC + G  ++G + F+ M++N  IKPR  HY CM+
Sbjct: 410 AVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMI 469

Query: 387 DLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQA 446
           +L  R GL+DEA+++++  P KP   +  +LL  CRIH N EL    A+KL   + PE+ 
Sbjct: 470 ELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYG-MGPEKL 528

Query: 447 AGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQA 506
             Y+ L+ N+Y ++ R  + A V + + + G+   P  +W+++    H F +GD  + Q+
Sbjct: 529 NNYVVLL-NLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQS 587

Query: 507 SLIYKTLGEITMQAMQEGYKPDISELFLGIEE 538
             IY+ L E+  +  + GY  + +EL   ++E
Sbjct: 588 REIYQKLDELMKEISEYGYVAEENELLPDVDE 619

Length = 697

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score =  301 bits (772), Expect = 1e-92
 Identities = 154/483 (31%), Positives = 246/483 (50%), Gaps = 57/483 (11%)

Query: 38  QIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSE 97
           ++H  ++  GF+    +   L+  Y++ G    A KVF + E      W  MI G+ ++ 
Sbjct: 309 EMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNG 368

Query: 98  TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRT 157
            P+K++  Y  M      PDE T + +LS CA  G    G ++H           +  R 
Sbjct: 369 LPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLH----------ELAERK 418

Query: 158 NLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRN 217
            L+                          VV  N+L++ Y K   ID A ++F  +P ++
Sbjct: 419 GLI------------------------SYVVVANALIEMYSKCKCIDKALEVFHNIPEKD 454

Query: 218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHS 277
           V+SWT++I+G   N +  +AL  F +M    +  + V L+AALSACA IG L  GK IH+
Sbjct: 455 VISWTSIIAGLRLNNRCFEALIFFRQML-LTLKPNSVTLIAALSACARIGALMCGKEIHA 513

Query: 278 YVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQG 337
           +V     +G +  L    NAL+ +Y  CG +  A+  F     ++ VSW  ++TG+   G
Sbjct: 514 HVLRT-GIGFDGFL---PNALLDLYVRCGRMNYAWNQF-NSHEKDVVSWNILLTGYVAHG 568

Query: 338 YAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHY 382
               A+               +TF+ +L ACS  G V +G ++F  M + + I P ++HY
Sbjct: 569 KGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHY 628

Query: 383 GCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEID 442
            C+VDL  RAG + EA++ +  MP+ P+ AV G+LL  CRIH + EL  ++A + + E+D
Sbjct: 629 ACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELG-ELAAQHIFELD 687

Query: 443 PEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDST 502
           P  + GY  L+ N+YA A +W +VA VR+ M + G+   PG SWV++ G +H F+  D +
Sbjct: 688 PN-SVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDES 746

Query: 503 YKQ 505
           + Q
Sbjct: 747 HPQ 749

Length = 857

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score =  180 bits (458), Expect = 1e-48
 Identities = 120/413 (29%), Positives = 199/413 (48%), Gaps = 57/413 (13%)

Query: 58  LLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPD 117
           +L+ +V  G L++A  VF K        WN ++ G+A++   ++++ LY +M+     PD
Sbjct: 127 MLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPD 186

Query: 118 EYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARL 177
            YT+  +L  C        G +VH  V+  G+  +V                        
Sbjct: 187 VYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDV------------------------ 222

Query: 178 LFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQA 237
                    VV  N+L+  YVK GD+  A  +FD MP R+ +SW  MISG  +NG+  + 
Sbjct: 223 --------DVV--NALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENGECLEG 272

Query: 238 LSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSY-VEENFSVGREPVLVSLNN 296
           L LF  MR   V  D + + + +SAC  +GD +LG+ +H Y V+  F+V      VS+ N
Sbjct: 273 LELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVD-----VSVCN 327

Query: 297 ALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL------------- 343
           +LI MY S G   EA  VF +M+ ++ VSWT+MI+G+ K G   +AL             
Sbjct: 328 SLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSP 387

Query: 344 --LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSL 401
             +T   VLSAC+  G +D G +  E + +  G+   +     +++++S+   +D+A  +
Sbjct: 388 DEITIASVLSACACLGDLDVGVKLHE-LAERKGLISYVVVANALIEMYSKCKCIDKALEV 446

Query: 402 VQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVA 454
             N+P K +     S++ G R++N    A    ++++  + P       AL A
Sbjct: 447 FHNIPEK-DVISWTSIIAGLRLNNRCFEALIFFRQMLLTLKPNSVTLIAALSA 498

Length = 857

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score =  161 bits (409), Expect = 3e-42
 Identities = 109/427 (25%), Positives = 189/427 (44%), Gaps = 64/427 (14%)

Query: 38  QIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSE 97
           ++H+ ++  GF     ++  L+  YV  G +++A  VF++        WN MI G+  + 
Sbjct: 208 EVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFENG 267

Query: 98  TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRT 157
              + + L+  M +   +PD  T + ++S C   G  R G ++HG V+ +G+  +V +  
Sbjct: 268 ECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSV-- 325

Query: 158 NLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRN 217
                                            NSL++ Y+  G    A K+F  M  ++
Sbjct: 326 --------------------------------CNSLIQMYLSLGSWGEAEKVFSRMETKD 353

Query: 218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHS 277
            VSWT MISG  +NG   +AL  +  M +  V  D++ + + LSACA +GDL +G  +H 
Sbjct: 354 AVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHE 413

Query: 278 YVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQG 337
             E           V + NALI MY+ C  I++A  VF  +  ++ +SWTS+I G     
Sbjct: 414 LAERK----GLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNN 469

Query: 338 YAQEAL--------------LTFLGVLSACSHGGFVDEGRQF----FECMNQNWGIKPRI 379
              EAL              +T +  LSAC+  G +  G++             G  P  
Sbjct: 470 RCFEALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLP-- 527

Query: 380 EHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLV- 438
                ++DL+ R G M+ A++  Q    + +      LL G   H    +A ++  ++V 
Sbjct: 528 ---NALLDLYVRCGRMNYAWN--QFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVE 582

Query: 439 AEIDPEQ 445
           + ++P++
Sbjct: 583 SGVNPDE 589

Length = 857

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score =  129 bits (325), Expect = 1e-31
 Identities = 93/336 (27%), Positives = 148/336 (44%), Gaps = 55/336 (16%)

Query: 120 TYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLF 179
           TY  L+  C      R  + V+  V +SG+           + Y+               
Sbjct: 125 TYDALVEACIALKSIRCVKAVYWHVESSGF---------EPDQYM--------------- 160

Query: 180 DDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALS 239
                      N +L  +VK G +  A ++FDEMP RN+ SW T+I G    G  R+A +
Sbjct: 161 ----------MNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFA 210

Query: 240 LFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALI 299
           LF EM       +    V  L A A +G  + G+ +H  V +   VG       ++ ALI
Sbjct: 211 LFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGD----TFVSCALI 266

Query: 300 HMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL---------------L 344
            MY+ CG+IE+A  VF  M  + TV+W SM+ G+A  GY++EAL                
Sbjct: 267 DMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQF 326

Query: 345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQN 404
           TF  ++   S    ++  +Q    + +  G    I     +VDL+S+ G M++A ++   
Sbjct: 327 TFSIMIRIFSRLALLEHAKQAHAGLIRT-GFPLDIVANTALVDLYSKWGRMEDARNVFDR 385

Query: 405 MPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAE 440
           MP K N     +L+ G   H     A ++ ++++AE
Sbjct: 386 MPRK-NLISWNALIAGYGNHGRGTKAVEMFERMIAE 420

Length = 697

>gnl|CDD|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score =  122 bits (308), Expect = 3e-29
 Identities = 91/347 (26%), Positives = 143/347 (41%), Gaps = 56/347 (16%)

Query: 82  STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVH 141
           ST   N  +R        E+++ L + M +     DE  Y  L  +C       EG +V 
Sbjct: 50  STHDSNSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVC 109

Query: 142 GRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRG 201
            R L+S                                   P+  V   N++L  +V+ G
Sbjct: 110 SRALSS----------------------------------HPSLGVRLGNAMLSMFVRFG 135

Query: 202 DIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALS 261
           ++  AW +F +MP R++ SW  ++ G A+ G   +AL L++ M  A V  D       L 
Sbjct: 136 ELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLR 195

Query: 262 ACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR 321
            C  I DL  G+ +H++V   F    +   V + NALI MY  CG++  A  VF +M RR
Sbjct: 196 TCGGIPDLARGREVHAHVVR-FGFELD---VDVVNALITMYVKCGDVVSARLVFDRMPRR 251

Query: 322 NTVSWTSMITGFAKQGYAQEA---------------LLTFLGVLSACSHGGFVDEGRQFF 366
           + +SW +MI+G+ + G   E                L+T   V+SAC   G    GR+  
Sbjct: 252 DCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMH 311

Query: 367 ECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAV 413
             + +  G    +     ++ ++   G   EA  +   M  K  DAV
Sbjct: 312 GYVVKT-GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETK--DAV 355

Length = 857

>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing protein; Provisional

 Score =  121 bits (305), Expect = 4e-29
 Identities = 83/373 (22%), Positives = 163/373 (43%), Gaps = 62/373 (16%)

Query: 38  QIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSE 97
           Q+H  ++  G     ++   L+  Y   G + +A  VF+     +T  WN M+ G+A   
Sbjct: 245 QLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHG 304

Query: 98  TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRT 157
             E+++ LY +M D     D++T+S ++ + +R  L    +Q H  ++ +G+  ++   T
Sbjct: 305 YSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANT 364

Query: 158 NLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRN 217
            L++L                                  Y K G ++ A  +FD MP +N
Sbjct: 365 ALVDL----------------------------------YSKWGRMEDARNVFDRMPRKN 390

Query: 218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHS 277
           ++SW  +I+G   +G+  +A+ +F  M    V  + V  +A LSAC   G  + G  I  
Sbjct: 391 LISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQ 450

Query: 278 YVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVS-WTSMITGFAKQ 336
            + EN  +    +  +    +I +    G ++EAY + R+   + TV+ W +++T     
Sbjct: 451 SMSENHRIKPRAMHYA---CMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIH 507

Query: 337 GYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLM 395
              +      LG L+A                  + +G+ P ++ +Y  +++L++ +G  
Sbjct: 508 KNLE------LGRLAA-----------------EKLYGMGPEKLNNYVVLLNLYNSSGRQ 544

Query: 396 DEAFSLVQNMPMK 408
            EA  +V+ +  K
Sbjct: 545 AEAAKVVETLKRK 557

Length = 697

>gnl|CDD|215636 PLN03218, PLN03218, maturation of RBCL 1; Provisional

 Score = 70.3 bits (172), Expect = 1e-12
 Identities = 61/264 (23%), Positives = 116/264 (43%), Gaps = 44/264 (16%)

Query: 190 WNSLLKGYVKRGDIDGAWKIFDEMPHR----NVVSWTTMISGCAQNGKSRQALSLFNEMR 245
           + +L+    K G +D  +++F EM +     NV ++  +I GCA+ G+  +A   +  MR
Sbjct: 475 YTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMR 534

Query: 246 RARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGRE------PVL---VSLNN 296
              V  D+V   A +SAC + G           V+  F V  E      P+    +++  
Sbjct: 535 SKNVKPDRVVFNALISACGQSGA----------VDRAFDVLAEMKAETHPIDPDHITV-G 583

Query: 297 ALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHG 356
           AL+   A+ G+++ A  V++ +   N       I G  +          +   +++CS  
Sbjct: 584 ALMKACANAGQVDRAKEVYQMIHEYN-------IKGTPE---------VYTIAVNSCSQK 627

Query: 357 GFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP---MKPNDAV 413
           G  D     ++ M +  G+KP    +  +VD+   AG +D+AF ++Q+     +K     
Sbjct: 628 GDWDFALSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVS 686

Query: 414 LGSLLLGCRIHNNAELASQVAQKL 437
             SL+  C    N + A ++ + +
Sbjct: 687 YSSLMGACSNAKNWKKALELYEDI 710

Length = 1060

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 61.3 bits (150), Expect = 2e-12
 Identities = 18/49 (36%), Positives = 32/49 (65%), Gaps = 4/49 (8%)

Query: 186 SVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR----NVVSWTTMISGCAQ 230
            VV++N+L+ GY K+G ++ A K+F+EM  R    NV +++ +I G  +
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 49.3 bits (119), Expect = 4e-08
 Identities = 14/33 (42%), Positives = 23/33 (69%)

Query: 217 NVVSWTTMISGCAQNGKSRQALSLFNEMRRARV 249
           +VV++ T+I G  + GK  +AL LFNEM++  +
Sbjct: 2   DVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGI 34

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 48.2 bits (116), Expect = 9e-08
 Identities = 13/50 (26%), Positives = 27/50 (54%)

Query: 81  PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCAR 130
           P    +N +I G+ +    E+++ L+ +M  +  +P+ YTYS L+    +
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|205222 pfam13041, PPR_2, PPR repeat family

 Score = 48.2 bits (116), Expect = 1e-07
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 4/44 (9%)

Query: 296 NALIHMYASCGEIEEAYGVFRKMQRR----NTVSWTSMITGFAK 335
           N LI  Y   G++EEA  +F +M++R    N  +++ +I G  K
Sbjct: 7   NTLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 50

This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. Length = 50

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 44.8 bits (107), Expect = 9e-07
 Identities = 13/31 (41%), Positives = 20/31 (64%)

Query: 219 VSWTTMISGCAQNGKSRQALSLFNEMRRARV 249
           V++ ++ISG  + GK  +AL LF EM+   V
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 43.6 bits (104), Expect = 3e-06
 Identities = 11/32 (34%), Positives = 20/32 (62%)

Query: 188 VSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVV 219
           V++N+L+ G  K G ++ A ++F EM  R + 
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIE 32

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 42.8 bits (102), Expect = 6e-06
 Identities = 13/31 (41%), Positives = 21/31 (67%)

Query: 188 VSWNSLLKGYVKRGDIDGAWKIFDEMPHRNV 218
           V++NSL+ GY K G ++ A ++F EM  + V
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

>gnl|CDD|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 41.3 bits (98), Expect = 2e-05
 Identities = 12/34 (35%), Positives = 20/34 (58%)

Query: 219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD 252
           V++ T+I G  + G+  +AL LF EM+   +  D
Sbjct: 1   VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34

This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam model pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. Length = 35

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 40.0 bits (95), Expect = 4e-05
 Identities = 11/28 (39%), Positives = 19/28 (67%)

Query: 187 VVSWNSLLKGYVKRGDIDGAWKIFDEMP 214
           VV++N+L+ G  + G +D A ++ DEM 
Sbjct: 7   VVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 39.5 bits (93), Expect = 9e-05
 Identities = 10/33 (30%), Positives = 17/33 (51%)

Query: 187 VVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVV 219
           + ++N+LL    K GD D A  + +EM    + 
Sbjct: 1   LETYNALLLALAKAGDPDLALAVLEEMKASGLK 33

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|205109 pfam12854, PPR_1, PPR repeat

 Score = 39.3 bits (93), Expect = 1e-04
 Identities = 10/29 (34%), Positives = 19/29 (65%)

Query: 217 NVVSWTTMISGCAQNGKSRQALSLFNEMR 245
           +VV++ T+I G  + G+  +A+ L +EM 
Sbjct: 6   DVVTYNTLIDGLCRAGRVDEAVELLDEME 34

This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. Length = 34

>gnl|CDD|144943 pfam01535, PPR, PPR repeat

 Score = 36.7 bits (86), Expect = 7e-04
 Identities = 10/27 (37%), Positives = 18/27 (66%)

Query: 296 NALIHMYASCGEIEEAYGVFRKMQRRN 322
           N+LI  Y   G++EEA  +F++M+ + 
Sbjct: 4   NSLISGYCKAGKLEEALELFKEMKEKG 30

This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309, which may be involved in RNA stabilisation. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein that has a domain organisation similar to the human BRCA1 protein. The repeat has been called PPR. Length = 31

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	538
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.98
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.97
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.93
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.92
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.9
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.88
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.87
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.87
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.85
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.85
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.84
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.84
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.84
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.83
PRK14574	822	hmsH outer membrane protein; Provisional	99.82
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.8
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.8
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.78
PRK14574	822	hmsH outer membrane protein; Provisional	99.77
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.68
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.67
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.67
KOG2003	840	consensus TPR repeat-containing protein [General f	99.65
KOG2076	895	consensus RNA polymerase III transcription factor	99.62
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.61
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.61
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.59
KOG2076	895	consensus RNA polymerase III transcription factor	99.58
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.55
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.55
KOG2003	840	consensus TPR repeat-containing protein [General f	99.54
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.54
KOG1126	638	consensus DNA-binding cell division cycle control	99.53
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.52
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.52
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.51
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.5
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.49
KOG1126	638	consensus DNA-binding cell division cycle control	99.48
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.47
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.46
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.41
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.4
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.39
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.37
PF13041	50	PPR_2: PPR repeat family	99.37
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.36
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.36
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.35
PF13041	50	PPR_2: PPR repeat family	99.33
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.29
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.27
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.25
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.24
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.23
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.22
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.22
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.21
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.17
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.15
PRK12370	553	invasion protein regulator; Provisional	99.15
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.15
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.15
KOG1129	478	consensus TPR repeat-containing protein [General f	99.15
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.13
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.12
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.1
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.06
KOG1129	478	consensus TPR repeat-containing protein [General f	99.05
PRK12370	553	invasion protein regulator; Provisional	99.05
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.04
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.0
PRK11189	296	lipoprotein NlpI; Provisional	98.98
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.95
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.94
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.91
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.9
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.9
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.89
KOG2376	652	consensus Signal recognition particle, subunit Srp	98.88
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.87
PRK11189	296	lipoprotein NlpI; Provisional	98.86
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.86
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.81
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.79
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.77
PRK04841	903	transcriptional regulator MalT; Provisional	98.75
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.75
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.74
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.74
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.73
KOG1125	579	consensus TPR repeat-containing protein [General f	98.69
PF12854	34	PPR_1: PPR repeat	98.69
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.66
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.62
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.58
PF12854	34	PPR_1: PPR repeat	98.56
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	98.52
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.51
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.5
PRK04841	903	transcriptional regulator MalT; Provisional	98.48
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.44
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.44
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.43
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	98.42
KOG1125	579	consensus TPR repeat-containing protein [General f	98.42
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.4
PRK15359	144	type III secretion system chaperone protein SscB;	98.4
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.37
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.33
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.28
PLN02789	320	farnesyltranstransferase	98.28
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.25
PRK15359	144	type III secretion system chaperone protein SscB;	98.25
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.23
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.22
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.2
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.2
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.19
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.18
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.18
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.17
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.17
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.16
PLN02789	320	farnesyltranstransferase	98.15
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	98.14
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.14
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.13
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.11
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.1
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.1
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.09
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.08
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.04
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.98
PRK10370	198	formate-dependent nitrite reductase complex subuni	97.94
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.9
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.86
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.84
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.83
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.8
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	97.79
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.75
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.74
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.72
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.7
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.69
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.66
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.63
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.63
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.61
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.61
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.61
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.61
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	97.59
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.59
KOG2041	1189	consensus WD40 repeat protein [General function pr	97.58
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.53
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.51
KOG0553	304	consensus TPR repeat-containing protein [General f	97.47
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.47
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	97.46
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.44
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.44
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.42
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.41
PF12688	120	TPR_5: Tetratrico peptide repeat	97.38
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.38
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.37
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.32
PF13371	73	TPR_9: Tetratricopeptide repeat	97.29
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.28
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.25
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.24
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.23
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.23
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.22
COG3898	531	Uncharacterized membrane-bound protein [Function u	97.22
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.22
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.22
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.22
KOG0553	304	consensus TPR repeat-containing protein [General f	97.21
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	97.18
PRK15331	165	chaperone protein SicA; Provisional	97.16
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.04
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.04
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.03
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	96.98
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.96
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	96.91
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	96.9
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	96.83
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.8
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	96.76
PF12688	120	TPR_5: Tetratrico peptide repeat	96.7
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.7
PRK10803	263	tol-pal system protein YbgF; Provisional	96.65
PRK10803	263	tol-pal system protein YbgF; Provisional	96.62
PRK15331	165	chaperone protein SicA; Provisional	96.59
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.52
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.46
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.42
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.38
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.37
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.35
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	96.34
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	96.33
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.32
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	96.28
PF13371	73	TPR_9: Tetratricopeptide repeat	96.23
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.09
KOG1585	308	consensus Protein required for fusion of vesicles	96.03
PF13428	44	TPR_14: Tetratricopeptide repeat	96.01
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	95.97
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.93
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	95.92
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	95.91
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.89
PF13431	34	TPR_17: Tetratricopeptide repeat	95.87
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	95.87
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	95.86
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	95.84
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	95.83
PF03704	146	BTAD: Bacterial transcriptional activator domain;	95.7
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	95.55
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	95.41
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.37
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.22
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	95.21
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.2
KOG1941	518	consensus Acetylcholine receptor-associated protei	95.15
COG3898	531	Uncharacterized membrane-bound protein [Function u	95.13
PRK11906	458	transcriptional regulator; Provisional	95.07
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.06
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	95.04
KOG3941	406	consensus Intermediate in Toll signal transduction	94.88
PF14432	116	DYW_deaminase: DYW family of nucleic acid deaminas	94.83
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	94.69
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	94.6
COG3118	304	Thioredoxin domain-containing protein [Posttransla	94.53
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	94.49
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.31
KOG3941	406	consensus Intermediate in Toll signal transduction	94.3
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	94.29
KOG1941	518	consensus Acetylcholine receptor-associated protei	94.18
PF13512	142	TPR_18: Tetratricopeptide repeat	94.17
COG3118	304	Thioredoxin domain-containing protein [Posttransla	93.93
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	93.85
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	93.84
KOG4555	175	consensus TPR repeat-containing protein [Function	93.8
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	93.75
KOG1258	577	consensus mRNA processing protein [RNA processing	93.63
KOG4555	175	consensus TPR repeat-containing protein [Function	93.55
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	93.46
PRK11906	458	transcriptional regulator; Provisional	93.26
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	93.25
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	93.2
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	92.88
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	92.69
COG3629	280	DnrI DNA-binding transcriptional activator of the	92.47
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	92.21
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	92.17
KOG4570	418	consensus Uncharacterized conserved protein [Funct	92.14
KOG2610	491	consensus Uncharacterized conserved protein [Funct	91.82
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	91.78
PF13428	44	TPR_14: Tetratricopeptide repeat	91.71
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	91.7
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	91.62
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	91.49
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	91.43
PRK11619	644	lytic murein transglycosylase; Provisional	91.32
PF13431	34	TPR_17: Tetratricopeptide repeat	91.16
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	90.84
KOG1258	577	consensus mRNA processing protein [RNA processing	90.66
COG4105	254	ComL DNA uptake lipoprotein [General function pred	90.37
KOG1585	308	consensus Protein required for fusion of vesicles	89.74
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	89.65
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	89.63
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	89.59
COG3629	280	DnrI DNA-binding transcriptional activator of the	89.4
KOG2041	1189	consensus WD40 repeat protein [General function pr	89.16
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	88.82
PRK09687	280	putative lyase; Provisional	88.8
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	88.57
KOG4234	271	consensus TPR repeat-containing protein [General f	88.51
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	88.47
KOG1586	288	consensus Protein required for fusion of vesicles	88.17
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	87.97
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	87.79
PF13512	142	TPR_18: Tetratricopeptide repeat	87.74
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	87.67
PF14853	53	Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repe	87.56
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	87.5
KOG3364	149	consensus Membrane protein involved in organellar	87.34
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	87.2
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	87.02
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	86.77
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	86.62
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	86.52
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	86.52
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	86.23
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	86.0
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	85.97
KOG1586	288	consensus Protein required for fusion of vesicles	85.76
COG0457	291	NrfG FOG: TPR repeat [General function prediction	85.7
PF13762	145	MNE1: Mitochondrial splicing apparatus component	84.86
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	84.53
COG0457	291	NrfG FOG: TPR repeat [General function prediction	84.51
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	84.24
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	83.76
KOG2610	491	consensus Uncharacterized conserved protein [Funct	83.55
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	83.26
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	83.14
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	82.97
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	82.91
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	82.9
COG1747	711	Uncharacterized N-terminal domain of the transcrip	82.75
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	82.68
KOG4570	418	consensus Uncharacterized conserved protein [Funct	82.59
PRK09687	280	putative lyase; Provisional	82.46
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	82.37
COG5159	421	RPN6 26S proteasome regulatory complex component [	82.17
PF04190	260	DUF410: Protein of unknown function (DUF410) ; Int	81.92
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	81.43
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	81.38

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=7.3e-78  Score=633.35  Aligned_cols=515  Identities=32%  Similarity=0.590  Sum_probs=473.5

Q ss_pred             CCCCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHH
Q 044988           12 ATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIR   91 (538)
Q Consensus        12 ~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~   91 (538)
                      +..|+..+|+.++.+|+..++...+.+++..+.+.|+.|++.+++.|+.+|++.|++++|.++|++|++||..+||.+|.
T Consensus       182 g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~lf~~m~~~d~~s~n~li~  261 (857)
T PLN03077        182 GVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMIS  261 (857)
T ss_pred             CCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHHHHHHhcCCCCCcchhHHHHH
Confidence            45566666677777666666666667777777777777777888999999999999999999999999999999999999


Q ss_pred             HHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCC
Q 044988           92 GHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECG  171 (538)
Q Consensus        92 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  171 (538)
                      +|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|+++.|.+++..|.+.|+.||..+|+.|+.+|++.|+   
T Consensus       262 ~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~---  338 (857)
T PLN03077        262 GYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGS---  338 (857)
T ss_pred             HHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCC---
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999   


Q ss_pred             hhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHH----------------------------------------------
Q 044988          172 VGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDG----------------------------------------------  205 (538)
Q Consensus       172 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~----------------------------------------------  205 (538)
                      +++|.++|++|.+||..+||++|.+|++.|++++                                              
T Consensus       339 ~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~  418 (857)
T PLN03077        339 WGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERK  418 (857)
T ss_pred             HHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHh
Confidence            9999999999999888888888888755555554                                              


Q ss_pred             ------------------------HHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 044988          206 ------------------------AWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALS  261 (538)
Q Consensus       206 ------------------------A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  261 (538)
                                              |.++|++|.++|..+|+.+|.+|++.|+.++|+.+|++|.. +++||..||+.++.
T Consensus       419 g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~  497 (857)
T PLN03077        419 GLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALS  497 (857)
T ss_pred             CCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHH
Confidence                                    44555555556667777777777777778888888888865 58999999999999


Q ss_pred             HHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccH
Q 044988          262 ACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQE  341 (538)
Q Consensus       262 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~  341 (538)
                      +|++.|+++.+.+++..+.+.    +..++..++++|+++|+++|++++|.++|+.+ .+|..+|+++|.+|++.|+.++
T Consensus       498 a~~~~g~l~~~~~i~~~~~~~----g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~-~~d~~s~n~lI~~~~~~G~~~~  572 (857)
T PLN03077        498 ACARIGALMCGKEIHAHVLRT----GIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGSM  572 (857)
T ss_pred             HHhhhchHHHhHHHHHHHHHh----CCCccceechHHHHHHHHcCCHHHHHHHHHhc-CCChhhHHHHHHHHHHcCCHHH
Confidence            999999999999999999998    99999999999999999999999999999999 9999999999999999999999


Q ss_pred             HH---------------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          342 AL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       342 a~---------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      |+               .+|..++.+|++.|.+++|.++|+.|.+.+|+.|+..+|+.++++|++.|++++|.+++++|+
T Consensus       573 A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~  652 (857)
T PLN03077        573 AVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMP  652 (857)
T ss_pred             HHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHCC
Confidence            98               789999999999999999999999999777999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeE
Q 044988          407 MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSW  486 (538)
Q Consensus       407 ~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~  486 (538)
                      .+||..+|++|+.+|..+|+.+.+....+++ .++.|++...|. +|+++|++.|+|++|.++.+.|+++|+++.||++|
T Consensus       653 ~~pd~~~~~aLl~ac~~~~~~e~~e~~a~~l-~~l~p~~~~~y~-ll~n~ya~~g~~~~a~~vr~~M~~~g~~k~~g~s~  730 (857)
T PLN03077        653 ITPDPAVWGALLNACRIHRHVELGELAAQHI-FELDPNSVGYYI-LLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSW  730 (857)
T ss_pred             CCCCHHHHHHHHHHHHHcCChHHHHHHHHHH-HhhCCCCcchHH-HHHHHHHHCCChHHHHHHHHHHHHcCCCCCCCccE
Confidence            9999999999999999999999999999999 999999999888 99999999999999999999999999999999999


Q ss_pred             EEECCEEEEEEeCCCCCcchHHHHHHHHHHHHHHHHcCcccCCcccccCCC
Q 044988          487 VQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIE  537 (538)
Q Consensus       487 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~m~~~~~~p~~~~~~~~~~  537 (538)
                      |+++++++.|+.++..||+.++|+..|+++..+|++.||.||++.++++.|
T Consensus       731 ie~~~~~~~f~~~d~~h~~~~~i~~~l~~l~~~~~~~g~~~~~~~~~~~~~  781 (857)
T PLN03077        731 VEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKASGLAGSESSSMDEIE  781 (857)
T ss_pred             EEECCEEEEEecCCCCCcchHHHHHHHHHHHHHHHhCCcCCCcchhccccH
Confidence            999999999999999999999999999999999999999999999886543

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=100.00  E-value=6.4e-77  Score=611.72  Aligned_cols=513  Identities=26%  Similarity=0.471  Sum_probs=490.9

Q ss_pred             CCCccccHHHHHHHHhccCChHHHHHHHHHHHHhC-CCCChhHHHHHHHHHHccCChhHHHHHHhcCC----CCCcchHH
Q 044988           13 TSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIING-FSQKNYILAKLLAFYVTSGYLINAHKVFEKTE----NPSTAIWN   87 (538)
Q Consensus        13 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~----~~~~~~~~   87 (538)
                      ...+..+++.++..+.+.|++..|.++|+.|...+ +.|+..+|+.++.+|++.++++.|.+++..|.    .||..+||
T Consensus        83 ~~~~~~~~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n  162 (697)
T PLN03081         83 IRKSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMN  162 (697)
T ss_pred             CCCCceeHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHH
Confidence            33455689999999999999999999999998865 78999999999999999999999999998886    58999999


Q ss_pred             HHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcC
Q 044988           88 QMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSG  167 (538)
Q Consensus        88 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  167 (538)
                      .++.+|++.|+++.|.++|++|.    .||..+|++++.+|++.|++++|.++|++|.+.|+.|+..+|+.++.++++.|
T Consensus       163 ~Li~~y~k~g~~~~A~~lf~~m~----~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~  238 (697)
T PLN03081        163 RVLLMHVKCGMLIDARRLFDEMP----ERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLG  238 (697)
T ss_pred             HHHHHHhcCCCHHHHHHHHhcCC----CCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCC
Confidence            99999999999999999999997    48999999999999999999999999999999999999999999999999999


Q ss_pred             CCCChhHHHHHhhcCC----CCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHH
Q 044988          168 GECGVGCARLLFDDMP----ARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNE  243 (538)
Q Consensus       168 ~~~~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  243 (538)
                      .   .+.+.+++..+.    .+|..+|++++.+|++.|++++|.++|++|.++|+.+||.+|.+|++.|++++|+++|++
T Consensus       239 ~---~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~  315 (697)
T PLN03081        239 S---ARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYE  315 (697)
T ss_pred             c---HHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            9   999998877665    468999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCc
Q 044988          244 MRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNT  323 (538)
Q Consensus       244 m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~  323 (538)
                      |.+.|+.||..||+.++.+|++.|+++.|.+++..+.+.    +.+++..++++|+++|+++|++++|.++|++|.+||.
T Consensus       316 M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~----g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~~~d~  391 (697)
T PLN03081        316 MRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRT----GFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNL  391 (697)
T ss_pred             HHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHh----CCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCCCCCe
Confidence            999999999999999999999999999999999999999    9999999999999999999999999999999999999


Q ss_pred             chHHHHHHHHHhcCCccHHH---------------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHH
Q 044988          324 VSWTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDL  388 (538)
Q Consensus       324 ~~~~~li~~~~~~~~~~~a~---------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~  388 (538)
                      .+||+||.+|++.|+.++|+               .+|..++.+|++.|.+++|.++|+.|.+.+|+.|+..+|+.++++
T Consensus       392 ~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~  471 (697)
T PLN03081        392 ISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIEL  471 (697)
T ss_pred             eeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHH
Confidence            99999999999999999998               789999999999999999999999999878999999999999999


Q ss_pred             hhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHH
Q 044988          389 FSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAA  468 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~  468 (538)
                      |++.|++++|.+++++|..+|+..+|++|+.+|...|+++.|..+++++ .+..|++...|. .|+++|++.|+|++|.+
T Consensus       472 l~r~G~~~eA~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l-~~~~p~~~~~y~-~L~~~y~~~G~~~~A~~  549 (697)
T PLN03081        472 LGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKL-YGMGPEKLNNYV-VLLNLYNSSGRQAEAAK  549 (697)
T ss_pred             HHhcCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHH-hCCCCCCCcchH-HHHHHHHhCCCHHHHHH
Confidence            9999999999999999999999999999999999999999999999999 999999988899 99999999999999999


Q ss_pred             HHHHHHhCCCCCCCceeEEEECCEEEEEEeCCCCCcchHHHHHHHHHHHHHHHHcCcccCCcccccCCCC
Q 044988          469 VRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE  538 (538)
Q Consensus       469 ~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~m~~~~~~p~~~~~~~~~~~  538 (538)
                      +++.|+++|+.+.|+++|+.+++.++.|+.++..||+.++++..+.++..+|++.||.||+++++||+||
T Consensus       550 v~~~m~~~g~~k~~g~s~i~~~~~~~~f~~~d~~h~~~~~i~~~l~~l~~~~~~~gy~~~~~~~~~~~~~  619 (697)
T PLN03081        550 VVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDE  619 (697)
T ss_pred             HHHHHHHcCCccCCCeeEEEECCeEEEEccCCCCCccHHHHHHHHHHHHHHHHHcCCCCCcchhhccccH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999975

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=6.9e-66  Score=542.62  Aligned_cols=492  Identities=26%  Similarity=0.431  Sum_probs=445.6

Q ss_pred             CCCCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHH
Q 044988           12 ATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIR   91 (538)
Q Consensus        12 ~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~   91 (538)
                      +.+|+..+|..++.+|.+.+....+.+++..+.+.|..++..+++.++..|++.|+++.|.++|++|++||..+||.+|.
T Consensus        81 g~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~n~li~~~~~~g~~~~A~~~f~~m~~~d~~~~n~li~  160 (857)
T PLN03077         81 RVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVG  160 (857)
T ss_pred             CCCCChhHHHHHHHHHhhCCCHHHHHHHHHHHHHcCCCCCchHHHHHHHHHHhCCChHHHHHHHhcCCCCCeeEHHHHHH
Confidence            45667778888888888888888888888888888888888889999999999999999999999999999999999999


Q ss_pred             HHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCC
Q 044988           92 GHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECG  171 (538)
Q Consensus        92 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  171 (538)
                      +|++.|++++|+++|++|...|+.||..||+.++++|+..+++..+.+++..+.+.|+.||..+++.|+.+|++.|+   
T Consensus       161 ~~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~---  237 (857)
T PLN03077        161 GYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGD---  237 (857)
T ss_pred             HHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCC---
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999   


Q ss_pred             hhHHHHHhhcCCCCCchhHHHHHHHH------------------------------------------------------
Q 044988          172 VGCARLLFDDMPARSVVSWNSLLKGY------------------------------------------------------  197 (538)
Q Consensus       172 ~~~a~~~~~~~~~~~~~~~~~li~~~------------------------------------------------------  197 (538)
                      ++.|.++|++|.++|..+||++|.+|                                                      
T Consensus       238 ~~~A~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~  317 (857)
T PLN03077        238 VVSARLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKT  317 (857)
T ss_pred             HHHHHHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHh
Confidence            99999999999887777777776666                                                      


Q ss_pred             ----------------HhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 044988          198 ----------------VKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALS  261 (538)
Q Consensus       198 ----------------~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  261 (538)
                                      ++.|++++|.++|++|..||..+||++|.+|++.|++++|+++|++|.+.|+.||..||+.++.
T Consensus       318 g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~  397 (857)
T PLN03077        318 GFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLS  397 (857)
T ss_pred             CCccchHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHH
Confidence                            4556666777777777778889999999999999999999999999999999999999999999


Q ss_pred             HHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccH
Q 044988          262 ACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQE  341 (538)
Q Consensus       262 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~  341 (538)
                      +|++.|+++.|.++++.+.+.    +..++..++++|+++|+++|++++|.++|++|.++|.++|+++|.+|.+.|+.++
T Consensus       398 a~~~~g~~~~a~~l~~~~~~~----g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~e  473 (857)
T PLN03077        398 ACACLGDLDVGVKLHELAERK----GLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFE  473 (857)
T ss_pred             HHhccchHHHHHHHHHHHHHh----CCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHH
Confidence            999999999999999999999    9999999999999999999999999999999999999999999999999999999


Q ss_pred             HH--------------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCC
Q 044988          342 AL--------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPM  407 (538)
Q Consensus       342 a~--------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  407 (538)
                      |+              .+|..++.+|++.|+++.+.+++..+.+. |+.+|..++++|+++|+++|++++|.++|+.+  
T Consensus       474 A~~lf~~m~~~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~-g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~--  550 (857)
T PLN03077        474 ALIFFRQMLLTLKPNSVTLIAALSACARIGALMCGKEIHAHVLRT-GIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH--  550 (857)
T ss_pred             HHHHHHHHHhCCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHh-CCCccceechHHHHHHHHcCCHHHHHHHHHhc--
Confidence            98              67888999999999999999999999988 99999999999999999999999999999998  


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHch-hccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH-hCCCCCCCcee
Q 044988          408 KPNDAVLGSLLLGCRIHNNAELASQVAQKLV-AEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI-KMGVRKPPGQS  485 (538)
Q Consensus       408 ~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~-~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~-~~~~~~~~~~~  485 (538)
                      .||..+|+++|.+|++.|+.++|.++|++|. .+..|+..+ |. .++.+|.+.|++++|.++|+.|. +.|+.|+..++
T Consensus       551 ~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T-~~-~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y  628 (857)
T PLN03077        551 EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVT-FI-SLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHY  628 (857)
T ss_pred             CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCccc-HH-HHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHH
Confidence            7999999999999999999999999999997 678888888 99 88899999999999999999999 78888876443


Q ss_pred             EEEECCEEEEEEeCCCCCcchHHHHHHHHHHHHHHHHcCcccCCc
Q 044988          486 WVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDIS  530 (538)
Q Consensus       486 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~m~~~~~~p~~~  530 (538)
                      .        .++......+..+++++.++    +|   .++||..
T Consensus       629 ~--------~lv~~l~r~G~~~eA~~~~~----~m---~~~pd~~  658 (857)
T PLN03077        629 A--------CVVDLLGRAGKLTEAYNFIN----KM---PITPDPA  658 (857)
T ss_pred             H--------HHHHHHHhCCCHHHHHHHHH----HC---CCCCCHH
Confidence            3        23344455666677766654    33   4667654

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1e-62  Score=508.64  Aligned_cols=493  Identities=17%  Similarity=0.225  Sum_probs=443.9

Q ss_pred             CCccccHHHHHHHHhccCChHHHHHHHHHHHHhCC-CCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHH
Q 044988           14 SSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGF-SQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRG   92 (538)
Q Consensus        14 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~   92 (538)
                      +++...|..++..|.+.|++..|.++|+.|.+.|+ +++...++.++..|.+.|.+++|..+|+.|..||..+|+.+|.+
T Consensus       367 ~~~~~~~~~~y~~l~r~G~l~eAl~Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~pd~~Tyn~LL~a  446 (1060)
T PLN03218        367 KRKSPEYIDAYNRLLRDGRIKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRNPTLSTFNMLMSV  446 (1060)
T ss_pred             CCCchHHHHHHHHHHHCcCHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence            34456788888999999999999999999999995 56778888999999999999999999999999999999999999


Q ss_pred             HhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCCh
Q 044988           93 HARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGV  172 (538)
Q Consensus        93 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~  172 (538)
                      |++.|+++.|.++|++|.+.|+.||..+|+.+|.+|++.|+++.|.++|++|.+.|+.||..+|+.+|.+|++.|+   +
T Consensus       447 ~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~---~  523 (1060)
T PLN03218        447 CASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQ---V  523 (1060)
T ss_pred             HHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcC---H
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999   9


Q ss_pred             hHHHHHhhcCCC----CCchhHHHHHHHHHhcCCHHHHHHHHccCC------CCChHHHHHHHHHHHHcCCHHHHHHHHH
Q 044988          173 GCARLLFDDMPA----RSVVSWNSLLKGYVKRGDIDGAWKIFDEMP------HRNVVSWTTMISGCAQNGKSRQALSLFN  242 (538)
Q Consensus       173 ~~a~~~~~~~~~----~~~~~~~~li~~~~~~g~~~~A~~~~~~m~------~~~~~~~~~li~~~~~~~~~~~a~~~~~  242 (538)
                      ++|.++|++|.+    ||..+|+.+|.+|++.|++++|.++|++|.      .||..+|+++|.+|++.|++++|.++|+
T Consensus       524 eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~  603 (1060)
T PLN03218        524 AKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQ  603 (1060)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            999999999964    799999999999999999999999999994      4899999999999999999999999999


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--
Q 044988          243 EMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--  320 (538)
Q Consensus       243 ~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--  320 (538)
                      +|.+.|+.|+..+|+.+|.+|++.|++++|..+|+.|.+.    +..++..+|+.++.+|++.|++++|.++|++|.+  
T Consensus       604 ~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~----Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G  679 (1060)
T PLN03218        604 MIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKK----GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQG  679 (1060)
T ss_pred             HHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc----CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcC
Confidence            9999999999999999999999999999999999999998    9999999999999999999999999999999985  


Q ss_pred             --CCcchHHHHHHHHHhcCCccHHH---------------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHH
Q 044988          321 --RNTVSWTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYG  383 (538)
Q Consensus       321 --~~~~~~~~li~~~~~~~~~~~a~---------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~  383 (538)
                        ||..+|+++|.+|++.|+.++|.               .+|+.++.+|++.|++++|.++|++|.+. |+.||..+|+
T Consensus       680 ~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~-Gi~Pd~~Ty~  758 (1060)
T PLN03218        680 IKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRL-GLCPNTITYS  758 (1060)
T ss_pred             CCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc-CCCCCHHHHH
Confidence              78999999999999999999997               67889999999999999999999999887 9999999999


Q ss_pred             HHHHHhhhcCChHHHHHHHHhCC---CCCCHHHHHHHHHHHHh----c-------------------CCHHHHHHHHHHc
Q 044988          384 CMVDLFSRAGLMDEAFSLVQNMP---MKPNDAVLGSLLLGCRI----H-------------------NNAELASQVAQKL  437 (538)
Q Consensus       384 ~l~~~~~~~g~~~~A~~~~~~~~---~~p~~~~~~~l~~~~~~----~-------------------~~~~~A~~~~~~~  437 (538)
                      .++.+|++.|++++|.+++++|.   ..||..+|+.++..|.+    .                   +..+.|..+|++|
T Consensus       759 sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~Al~lf~eM  838 (1060)
T PLN03218        759 ILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRET  838 (1060)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHHHHHHHHH
Confidence            99999999999999999999984   77999999999876542    1                   2246799999999


Q ss_pred             h-hccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeEEEECCEEEEEEeCCCCCcchHHHHHHHHHH
Q 044988          438 V-AEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEI  516 (538)
Q Consensus       438 ~-~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  516 (538)
                      . .++.|+..+ |. .++.++.+.+..+.+..+++.|...+..+....+..        .+.+.+.+  ..+++..+   
T Consensus       839 ~~~Gi~Pd~~T-~~-~vL~cl~~~~~~~~~~~m~~~m~~~~~~~~~~~y~~--------Li~g~~~~--~~~A~~l~---  903 (1060)
T PLN03218        839 ISAGTLPTMEV-LS-QVLGCLQLPHDATLRNRLIENLGISADSQKQSNLST--------LVDGFGEY--DPRAFSLL---  903 (1060)
T ss_pred             HHCCCCCCHHH-HH-HHHHHhcccccHHHHHHHHHHhccCCCCcchhhhHH--------HHHhhccC--hHHHHHHH---
Confidence            8 777787777 88 555788888899999999988887776555433332        22222222  24565555   


Q ss_pred             HHHHHHcCcccCCc
Q 044988          517 TMQAMQEGYKPDIS  530 (538)
Q Consensus       517 ~~~m~~~~~~p~~~  530 (538)
                       ++|++.|+.|+.+
T Consensus       904 -~em~~~Gi~p~~~  916 (1060)
T PLN03218        904 -EEAASLGVVPSVS  916 (1060)
T ss_pred             -HHHHHcCCCCCcc
Confidence             5999999999986

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=6.6e-61  Score=495.13  Aligned_cols=506  Identities=17%  Similarity=0.238  Sum_probs=438.8

Q ss_pred             ccCCCCCCCCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC----CC
Q 044988            6 IIPANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE----NP   81 (538)
Q Consensus         6 ~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~----~~   81 (538)
                      .+....-.+++..++..++..|.+.+....|..++..|..    |+..+|+.++.+|++.|++++|.++|+.|.    .|
T Consensus       395 ~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~----pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~p  470 (1060)
T PLN03218        395 DMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRN----PTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKA  470 (1060)
T ss_pred             HHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCC----CCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCC
Confidence            3444444566778888999999999999999999988864    899999999999999999999999999987    48


Q ss_pred             CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHH
Q 044988           82 STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMN  161 (538)
Q Consensus        82 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  161 (538)
                      |..+|+.||.+|++.|++++|.++|++|.+.|+.||..||+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.++.
T Consensus       471 D~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~  550 (1060)
T PLN03218        471 DCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALIS  550 (1060)
T ss_pred             CHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCCCChhHHHHHhhcCC------CCCchhHHHHHHHHHhcCCHHHHHHHHccCCC----CChHHHHHHHHHHHHc
Q 044988          162 LYLMSGGECGVGCARLLFDDMP------ARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH----RNVVSWTTMISGCAQN  231 (538)
Q Consensus       162 ~~~~~g~~~~~~~a~~~~~~~~------~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----~~~~~~~~li~~~~~~  231 (538)
                      +|++.|+   +++|.++|++|.      .||..+|+++|.+|++.|++++|.++|++|.+    |+..+|+.+|.+|++.
T Consensus       551 a~~k~G~---~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~  627 (1060)
T PLN03218        551 ACGQSGA---VDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQK  627 (1060)
T ss_pred             HHHHCCC---HHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhc
Confidence            9999999   999999999995      47899999999999999999999999999975    6789999999999999


Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHH
Q 044988          232 GKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEA  311 (538)
Q Consensus       232 ~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  311 (538)
                      |++++|.++|++|.+.|+.||..||+.++.+|++.|+++.|.++++.|.+.    +.+++..+|++|+.+|+++|++++|
T Consensus       628 G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~----G~~pd~~tynsLI~ay~k~G~~eeA  703 (1060)
T PLN03218        628 GDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQ----GIKLGTVSYSSLMGACSNAKNWKKA  703 (1060)
T ss_pred             CCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHc----CCCCCHHHHHHHHHHHHhCCCHHHH
Confidence            999999999999999999999999999999999999999999999999998    9999999999999999999999999


Q ss_pred             HHHHHhcC----CCCcchHHHHHHHHHhcCCccHHH---------------HHHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          312 YGVFRKMQ----RRNTVSWTSMITGFAKQGYAQEAL---------------LTFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       312 ~~~~~~m~----~~~~~~~~~li~~~~~~~~~~~a~---------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                      .++|++|.    .||..+|+.||.+|++.|+.++|.               .+|..++.+|++.|+++.|.++|.+|.+.
T Consensus       704 ~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~  783 (1060)
T PLN03218        704 LELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKED  783 (1060)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence            99999995    589999999999999999999998               78999999999999999999999999988


Q ss_pred             cCCCccHHHHHHHHHHhhh----c-------------------CChHHHHHHHHhCC---CCCCHHHHHHHHHHHHhcCC
Q 044988          373 WGIKPRIEHYGCMVDLFSR----A-------------------GLMDEAFSLVQNMP---MKPNDAVLGSLLLGCRIHNN  426 (538)
Q Consensus       373 ~~~~p~~~~~~~l~~~~~~----~-------------------g~~~~A~~~~~~~~---~~p~~~~~~~l~~~~~~~~~  426 (538)
                       |+.||..+|+.++..|.+    +                   +..++|..+|++|.   +.||..||+.++.+++..+.
T Consensus       784 -Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~Al~lf~eM~~~Gi~Pd~~T~~~vL~cl~~~~~  862 (1060)
T PLN03218        784 -GIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRETISAGTLPTMEVLSQVLGCLQLPHD  862 (1060)
T ss_pred             -CCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhccccc
Confidence             999999999999876432    2                   12467999999995   78999999999988888899


Q ss_pred             HHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCce---eEEEECCEEEEEEeCCC-C
Q 044988          427 AELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQ---SWVQINGVLHDFVAGDS-T  502 (538)
Q Consensus       427 ~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~---~~~~~~~~~~~~~~~~~-~  502 (538)
                      .+.+..+++.+.....+.+..+|. .|++++.+.  .++|..++++|...|+.|+...   .|.         +.... .
T Consensus       863 ~~~~~~m~~~m~~~~~~~~~~~y~-~Li~g~~~~--~~~A~~l~~em~~~Gi~p~~~~~~~~~~---------~d~~~~~  930 (1060)
T PLN03218        863 ATLRNRLIENLGISADSQKQSNLS-TLVDGFGEY--DPRAFSLLEEAASLGVVPSVSFKKSPIV---------IDAEELP  930 (1060)
T ss_pred             HHHHHHHHHHhccCCCCcchhhhH-HHHHhhccC--hHHHHHHHHHHHHcCCCCCcccccCceE---------EEcccCc
Confidence            999999999885333344444488 888887432  3689999999999999887531   242         11111 1


Q ss_pred             CcchHHHHHHHHHHHHHHHHcC-cccCCcccccC
Q 044988          503 YKQASLIYKTLGEITMQAMQEG-YKPDISELFLG  535 (538)
Q Consensus       503 ~~~~~~~~~~l~~~~~~m~~~~-~~p~~~~~~~~  535 (538)
                      -+.+.-.+..|-+-.++..+.| --|+...++|+
T Consensus       931 ~~aa~~~l~~wl~~~~~~~~~g~~lp~~~~~~~~  964 (1060)
T PLN03218        931 VFAAEVYLLTILKGLKHRLAAGAKLPNVTILLPT  964 (1060)
T ss_pred             chhHHHHHHHHHHHHHHHHhccCcCCcceeeecc
Confidence            2233444444444334444555 56776665544

>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional

Probab=100.00  E-value=6.8e-53  Score=433.84  Aligned_cols=453  Identities=14%  Similarity=0.177  Sum_probs=411.2

Q ss_pred             CCCChhHHHHHHHHHHccCChhHHHHHHhcCC-----CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHH
Q 044988           48 FSQKNYILAKLLAFYVTSGYLINAHKVFEKTE-----NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYS  122 (538)
Q Consensus        48 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~  122 (538)
                      ...+...|+.++..|.+.|++++|.++|+.|.     .||..+|+.++.+|++.++++.+.+++..|.+.|+.||..+|+
T Consensus        83 ~~~~~~~~~~~i~~l~~~g~~~~Al~~f~~m~~~~~~~~~~~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~~n  162 (697)
T PLN03081         83 IRKSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYMMN  162 (697)
T ss_pred             CCCCceeHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHHHH
Confidence            44567789999999999999999999999886     4788999999999999999999999999999999999999999


Q ss_pred             HHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC----CCchhHHHHHHHHH
Q 044988          123 FLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA----RSVVSWNSLLKGYV  198 (538)
Q Consensus       123 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~----~~~~~~~~li~~~~  198 (538)
                      .++.+|++.|+++.|.++|++|.    .||..+|+.++.+|++.|+   +++|.++|++|.+    |+..+|+.++.+|+
T Consensus       163 ~Li~~y~k~g~~~~A~~lf~~m~----~~~~~t~n~li~~~~~~g~---~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~  235 (697)
T PLN03081        163 RVLLMHVKCGMLIDARRLFDEMP----ERNLASWGTIIGGLVDAGN---YREAFALFREMWEDGSDAEPRTFVVMLRASA  235 (697)
T ss_pred             HHHHHHhcCCCHHHHHHHHhcCC----CCCeeeHHHHHHHHHHCcC---HHHHHHHHHHHHHhCCCCChhhHHHHHHHHh
Confidence            99999999999999999999995    5899999999999999999   9999999999964    68899999999999


Q ss_pred             hcCCHHHHHHHHccCC----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHH
Q 044988          199 KRGDIDGAWKIFDEMP----HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKW  274 (538)
Q Consensus       199 ~~g~~~~A~~~~~~m~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~  274 (538)
                      +.|..+.+.+++..+.    .+|..+|+.||.+|++.|++++|.++|++|.    .+|..+|+.++.+|++.|++++|..
T Consensus       236 ~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~----~~~~vt~n~li~~y~~~g~~~eA~~  311 (697)
T PLN03081        236 GLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMP----EKTTVAWNSMLAGYALHGYSEEALC  311 (697)
T ss_pred             cCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCC----CCChhHHHHHHHHHHhCCCHHHHHH
Confidence            9999999999988765    4899999999999999999999999999995    5799999999999999999999999


Q ss_pred             HHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC----CCcchHHHHHHHHHhcCCccHHH-------
Q 044988          275 IHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR----RNTVSWTSMITGFAKQGYAQEAL-------  343 (538)
Q Consensus       275 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~-------  343 (538)
                      +|+.|.+.    +..++..+|+.++.+|++.|++++|.+++..|.+    +|..+|++++.+|++.|+.++|.       
T Consensus       312 lf~~M~~~----g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~  387 (697)
T PLN03081        312 LYYEMRDS----GVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP  387 (697)
T ss_pred             HHHHHHHc----CCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC
Confidence            99999998    9999999999999999999999999999999875    78999999999999999999998       


Q ss_pred             ----HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC----CCCCHHHHH
Q 044988          344 ----LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP----MKPNDAVLG  415 (538)
Q Consensus       344 ----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~p~~~~~~  415 (538)
                          .+|+.++.+|++.|+.++|.++|++|.+. |+.||..||+.++.+|.+.|.+++|.++|+.|.    ..|+..+|+
T Consensus       388 ~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~-g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~  466 (697)
T PLN03081        388 RKNLISWNALIAGYGNHGRGTKAVEMFERMIAE-GVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYA  466 (697)
T ss_pred             CCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHh-CCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchH
Confidence                67899999999999999999999999988 999999999999999999999999999999994    679999999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeEEEECCEEEE
Q 044988          416 SLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHD  495 (538)
Q Consensus       416 ~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~~~~~~~~~~  495 (538)
                      .++.++.+.|++++|.++++++  ...|+..+ |. .|+.+|...|+++.|..+++++.+  +.|.....++       .
T Consensus       467 ~li~~l~r~G~~~eA~~~~~~~--~~~p~~~~-~~-~Ll~a~~~~g~~~~a~~~~~~l~~--~~p~~~~~y~-------~  533 (697)
T PLN03081        467 CMIELLGREGLLDEAYAMIRRA--PFKPTVNM-WA-ALLTACRIHKNLELGRLAAEKLYG--MGPEKLNNYV-------V  533 (697)
T ss_pred             hHHHHHHhcCCHHHHHHHHHHC--CCCCCHHH-HH-HHHHHHHHcCCcHHHHHHHHHHhC--CCCCCCcchH-------H
Confidence            9999999999999999999987  46676665 88 888999999999999999999975  3343222221       2


Q ss_pred             EEeCCCCCcchHHHHHHHHHHHHHHHHcCc--ccCCcccc
Q 044988          496 FVAGDSTYKQASLIYKTLGEITMQAMQEGY--KPDISELF  533 (538)
Q Consensus       496 ~~~~~~~~~~~~~~~~~l~~~~~~m~~~~~--~p~~~~~~  533 (538)
                      .+..+...+..+++.+.++    .|++.|+  .|..+|+.
T Consensus       534 L~~~y~~~G~~~~A~~v~~----~m~~~g~~k~~g~s~i~  569 (697)
T PLN03081        534 LLNLYNSSGRQAEAAKVVE----TLKRKGLSMHPACTWIE  569 (697)
T ss_pred             HHHHHHhCCCHHHHHHHHH----HHHHcCCccCCCeeEEE
Confidence            2334566777777766664    8999997  47777764

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=99.98  E-value=6.2e-28  Score=260.59  Aligned_cols=443  Identities=14%  Similarity=0.078  Sum_probs=245.2

Q ss_pred             ccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHh
Q 044988           18 LTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHA   94 (538)
Q Consensus        18 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~   94 (538)
                      ..+..+...+...++++.|...++...+.... .......++..+.+.|++++|..+++.+.   +++..+|..+...+.
T Consensus       398 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~  476 (899)
T TIGR02917       398 AARTQLGISKLSQGDPSEAIADLETAAQLDPE-LGRADLLLILSYLRSGQFDKALAAAKKLEKKQPDNASLHNLLGAIYL  476 (899)
T ss_pred             HHHHHHHHHHHhCCChHHHHHHHHHHHhhCCc-chhhHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCCcHHHHHHHHHHH
Confidence            34555555666666666666666666655422 22334445556666666666666666554   234445666666666


Q ss_pred             cCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhH
Q 044988           95 RSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGC  174 (538)
Q Consensus        95 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~  174 (538)
                      ..|++++|...|+++.+.. +.+...+..+...+...|++++|.+.++++.+.+ +.+..++..+...+.+.|+   .++
T Consensus       477 ~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~---~~~  551 (899)
T TIGR02917       477 GKGDLAKAREAFEKALSIE-PDFFPAAANLARIDIQEGNPDDAIQRFEKVLTID-PKNLRAILALAGLYLRTGN---EEE  551 (899)
T ss_pred             hCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHHHHcCC---HHH
Confidence            6666666666666665532 2233445555556666666666666666666543 3445556666666666666   666


Q ss_pred             HHHHhhcCCC---CCchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 044988          175 ARLLFDDMPA---RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR  248 (538)
Q Consensus       175 a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  248 (538)
                      |...++++.+   .+...+..+...+.+.|++++|..+++.+.+   .+..+|..+...|...|++++|...|+++.+..
T Consensus       552 A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  631 (899)
T TIGR02917       552 AVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ  631 (899)
T ss_pred             HHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            6666655533   1334455555666666666666666665542   334456666666666666666666666665432


Q ss_pred             CCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcch
Q 044988          249 VGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVS  325 (538)
Q Consensus       249 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~  325 (538)
                       +.+...+..+..++.+.|+++.|...++.+.+.     .|.+...+..++..+...|++++|.++++.+.+   ++...
T Consensus       632 -~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  705 (899)
T TIGR02917       632 -PDSALALLLLADAYAVMKNYAKAITSLKRALEL-----KPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPKAALG  705 (899)
T ss_pred             -CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCChHH
Confidence             223444555555556666666666666665554     444455555566666666666666666655543   23344


Q ss_pred             HHHHHHHHHhcCCccHHHHH-------------HHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhc
Q 044988          326 WTSMITGFAKQGYAQEALLT-------------FLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRA  392 (538)
Q Consensus       326 ~~~li~~~~~~~~~~~a~~~-------------~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  392 (538)
                      +..+...+...|++++|...             +..+..++...|++++|.+.++.+.+.  .+.+...+..+...|...
T Consensus       706 ~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~--~~~~~~~~~~la~~~~~~  783 (899)
T TIGR02917       706 FELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNTAEAVKTLEAWLKT--HPNDAVLRTALAELYLAQ  783 (899)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHC
Confidence            55555555556666555522             223344455555566666555555543  122455555555555555


Q ss_pred             CChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHH
Q 044988          393 GLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVR  470 (538)
Q Consensus       393 g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~  470 (538)
                      |++++|.+.|+++.  .+++...++.+...+...|+ ++|+..++++ ....|+++..+. .++.++...|++++|.+++
T Consensus       784 g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~g~~~~A~~~~  860 (899)
T TIGR02917       784 KDYDKAIKHYRTVVKKAPDNAVVLNNLAWLYLELKD-PRALEYAEKA-LKLAPNIPAILD-TLGWLLVEKGEADRALPLL  860 (899)
T ss_pred             cCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCc-HHHHHHHHHH-HhhCCCCcHHHH-HHHHHHHHcCCHHHHHHHH
Confidence            66666665555542  22334455555555555555 4555555555 555555555444 5555555555555555555


Q ss_pred             HHHHhCC
Q 044988          471 QKMIKMG  477 (538)
Q Consensus       471 ~~m~~~~  477 (538)
                      +++.+.+
T Consensus       861 ~~a~~~~  867 (899)
T TIGR02917       861 RKAVNIA  867 (899)
T ss_pred             HHHHhhC
Confidence            5555543

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.

>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein

Probab=99.97  E-value=5.3e-28  Score=261.13  Aligned_cols=443  Identities=13%  Similarity=0.042  Sum_probs=357.6

Q ss_pred             ccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHHH
Q 044988           16 KALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIRG   92 (538)
Q Consensus        16 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~   92 (538)
                      +...+..+...+...|+++.|..+++.+.+... .+...+..+...+...|++++|.+.|+...+   .+...+..++..
T Consensus       362 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~  440 (899)
T TIGR02917       362 DPAALSLLGEAYLALGDFEKAAEYLAKATELDP-ENAAARTQLGISKLSQGDPSEAIADLETAAQLDPELGRADLLLILS  440 (899)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHHhCCChHHHHHHHHHHHhhCCcchhhHHHHHHH
Confidence            455677788888888999999999988877643 3566777888888889999999998887663   233456667788


Q ss_pred             HhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCCh
Q 044988           93 HARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGV  172 (538)
Q Consensus        93 ~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~  172 (538)
                      +.+.|++++|..+++.+.... +++..++..+...+...|++++|...|+++.+.. +.+...+..+...+...|+   +
T Consensus       441 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~---~  515 (899)
T TIGR02917       441 YLRSGQFDKALAAAKKLEKKQ-PDNASLHNLLGAIYLGKGDLAKAREAFEKALSIE-PDFFPAAANLARIDIQEGN---P  515 (899)
T ss_pred             HHhcCCHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHCCC---H
Confidence            888999999999999887653 5567788888888999999999999999888764 4556677888888899999   9


Q ss_pred             hHHHHHhhcCCC---CCchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 044988          173 GCARLLFDDMPA---RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRR  246 (538)
Q Consensus       173 ~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  246 (538)
                      ++|...|+++.+   .+..++..+...+.+.|+.++|..+|+++..   .+...+..++..|...|++++|..+++.+.+
T Consensus       516 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  595 (899)
T TIGR02917       516 DDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAAD  595 (899)
T ss_pred             HHHHHHHHHHHHhCcCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999998888764   3567788888888889999999999888753   3455677888888999999999999998876


Q ss_pred             CCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCc
Q 044988          247 ARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNT  323 (538)
Q Consensus       247 ~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~  323 (538)
                      . .+.+...+..+..++...|+++.|...++.+.+.     .|.+...+..+...|.+.|++++|...|+++.+   .+.
T Consensus       596 ~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~  669 (899)
T TIGR02917       596 A-APDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLAL-----QPDSALALLLLADAYAVMKNYAKAITSLKRALELKPDNT  669 (899)
T ss_pred             c-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCH
Confidence            4 3456778888888888999999999999888876     566677777888889999999999999988765   346


Q ss_pred             chHHHHHHHHHhcCCccHHH--------------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHh
Q 044988          324 VSWTSMITGFAKQGYAQEAL--------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLF  389 (538)
Q Consensus       324 ~~~~~li~~~~~~~~~~~a~--------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~  389 (538)
                      .++..++..+...|++++|.              ..+..+...+...|++++|...|+.+...   .|+..++..++.++
T Consensus       670 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~~l~~~~  746 (899)
T TIGR02917       670 EAQIGLAQLLLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKR---APSSQNAIKLHRAL  746 (899)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhh---CCCchHHHHHHHHH
Confidence            68888888888999998887              33444566777889999999999988865   56667777888889


Q ss_pred             hhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHH
Q 044988          390 SRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVA  467 (538)
Q Consensus       390 ~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~  467 (538)
                      .+.|++++|.+.++++.  .+.+...+..+...+...|++++|.++|+++ .+..|+++..+. .++.++.+.|+ ++|+
T Consensus       747 ~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~-~~~~p~~~~~~~-~l~~~~~~~~~-~~A~  823 (899)
T TIGR02917       747 LASGNTAEAVKTLEAWLKTHPNDAVLRTALAELYLAQKDYDKAIKHYRTV-VKKAPDNAVVLN-NLAWLYLELKD-PRAL  823 (899)
T ss_pred             HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHHhcCc-HHHH
Confidence            99999999998888873  3345777888888888899999999999998 888888888777 88888999888 8899


Q ss_pred             HHHHHHHhC
Q 044988          468 AVRQKMIKM  476 (538)
Q Consensus       468 ~~~~~m~~~  476 (538)
                      .+++++...
T Consensus       824 ~~~~~~~~~  832 (899)
T TIGR02917       824 EYAEKALKL  832 (899)
T ss_pred             HHHHHHHhh
Confidence            999888764

This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.93  E-value=4.9e-23  Score=189.98  Aligned_cols=419  Identities=16%  Similarity=0.120  Sum_probs=333.6

Q ss_pred             cHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHHHHhc
Q 044988           19 TTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIRGHAR   95 (538)
Q Consensus        19 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~   95 (538)
                      ....|..-.-+.|++.+|.+-....-+.... +....-.+-..+....+.+.....-....+   .-..+|+.+.+.+-.
T Consensus        50 ~~l~lah~~yq~gd~~~a~~h~nmv~~~d~t-~~~~llll~ai~~q~~r~d~s~a~~~~a~r~~~q~ae~ysn~aN~~ke  128 (966)
T KOG4626|consen   50 DRLELAHRLYQGGDYKQAEKHCNMVGQEDPT-NTERLLLLSAIFFQGSRLDKSSAGSLLAIRKNPQGAEAYSNLANILKE  128 (966)
T ss_pred             hHHHHHHHHHhccCHHHHHHHHhHhhccCCC-cccceeeehhhhhcccchhhhhhhhhhhhhccchHHHHHHHHHHHHHH
Confidence            3445555566667777776655554444322 122222222334444444443322211111   233578899999999


Q ss_pred             CCCchHHHHHHHHhHhCCCCC-CcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCc-hhHHhHHHHHHHhcCCCCChh
Q 044988           96 SETPEKSVYLYKQMIDKETEP-DEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSN-VFIRTNLMNLYLMSGGECGVG  173 (538)
Q Consensus        96 ~~~~~~a~~~~~~m~~~~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~~~  173 (538)
                      .|++++|+.+++.+.+.  +| ....|..+..++...|+.+.|.+.|...++.+  |+ ....+.+.+.+...|+   ++
T Consensus       129 rg~~~~al~~y~~aiel--~p~fida~inla~al~~~~~~~~a~~~~~~alqln--P~l~ca~s~lgnLlka~Gr---l~  201 (966)
T KOG4626|consen  129 RGQLQDALALYRAAIEL--KPKFIDAYINLAAALVTQGDLELAVQCFFEALQLN--PDLYCARSDLGNLLKAEGR---LE  201 (966)
T ss_pred             hchHHHHHHHHHHHHhc--CchhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcC--cchhhhhcchhHHHHhhcc---cc
Confidence            99999999999999985  45 56799999999999999999999999998864  54 4466677777888898   99


Q ss_pred             HHHHHhhcCCC--C-CchhHHHHHHHHHhcCCHHHHHHHHccCCC--CC-hHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 044988          174 CARLLFDDMPA--R-SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--RN-VVSWTTMISGCAQNGKSRQALSLFNEMRRA  247 (538)
Q Consensus       174 ~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  247 (538)
                      +|...+.+..+  | =...|+.|...+-.+|++..|+..|++..+  |+ ...|-.|...|...+.+++|+..|.+... 
T Consensus       202 ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkldP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~-  280 (966)
T KOG4626|consen  202 EAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLDPNFLDAYINLGNVYKEARIFDRAVSCYLRALN-  280 (966)
T ss_pred             hhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcCCCcchHHHhhHHHHHHHHhcchHHHHHHHHHHh-
Confidence            99888877664  3 347899999999999999999999999876  43 24788899999999999999999998876 


Q ss_pred             CCCCC-HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCc
Q 044988          248 RVGLD-QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNT  323 (538)
Q Consensus       248 g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~  323 (538)
                       ..|+ ...+..+...|...|.++.|.+.|++..+.     .|.....|+.|..++-..|++.+|.+.+++...   ...
T Consensus       281 -lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~-----~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p~ha  354 (966)
T KOG4626|consen  281 -LRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALEL-----QPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLCPNHA  354 (966)
T ss_pred             -cCCcchhhccceEEEEeccccHHHHHHHHHHHHhc-----CCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhCCccH
Confidence             4565 566778888888999999999999999986     888899999999999999999999999998876   345


Q ss_pred             chHHHHHHHHHhcCCccHHH--------------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHH
Q 044988          324 VSWTSMITGFAKQGYAQEAL--------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDL  388 (538)
Q Consensus       324 ~~~~~li~~~~~~~~~~~a~--------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~  388 (538)
                      .+.+.|...|...|..++|.              ..++.+...|.+.|++++|...+++..   .+.|+ ...|+.+...
T Consensus       355 dam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykeal---rI~P~fAda~~NmGnt  431 (966)
T KOG4626|consen  355 DAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEAL---RIKPTFADALSNMGNT  431 (966)
T ss_pred             HHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHH---hcCchHHHHHHhcchH
Confidence            68889999999999999998              445667778888999999999999998   56898 6799999999


Q ss_pred             hhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHH
Q 044988          389 FSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVY  457 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~  457 (538)
                      |-..|+.+.|.+.+.+.. +.|. ...++.|...+...|+..+|+.-++++ ..++||.+.+|. .++.++
T Consensus       432 ~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI~sY~~a-LklkPDfpdA~c-Nllh~l  500 (966)
T KOG4626|consen  432 YKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAIQSYRTA-LKLKPDFPDAYC-NLLHCL  500 (966)
T ss_pred             HHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHHHHHHHH-HccCCCCchhhh-HHHHHH
Confidence            999999999999998874 6676 678899999999999999999999999 999999999898 554444

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.92  E-value=7.2e-21  Score=206.32  Aligned_cols=437  Identities=13%  Similarity=0.054  Sum_probs=312.9

Q ss_pred             HHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC--C-CcchHHHHHHHHhcCCC
Q 044988           22 QIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN--P-STAIWNQMIRGHARSET   98 (538)
Q Consensus        22 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~   98 (538)
                      .+...+...|++++|...++.+.+...+........+.......|+.++|++.++++..  | +...+..+...+...|+
T Consensus       117 ~~A~ll~~~g~~~eA~~~~~~~l~~~p~~~~la~~y~~~~~~~~g~~~~A~~~L~~ll~~~P~~~~~~~~LA~ll~~~g~  196 (1157)
T PRK11447        117 QQARLLATTGRTEEALASYDKLFNGAPPELDLAVEYWRLVAKLPAQRPEAINQLQRLNADYPGNTGLRNTLALLLFSSGR  196 (1157)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHccCCCCChHHHHHHHHHHhhCCccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHccCC
Confidence            33456778899999999999988764332221222222223346889999999988773  3 44567788888888999


Q ss_pred             chHHHHHHHHhHhCCC------------------C--------------CCcchH---------------------HHHH
Q 044988           99 PEKSVYLYKQMIDKET------------------E--------------PDEYTY---------------------SFLL  125 (538)
Q Consensus        99 ~~~a~~~~~~m~~~~~------------------~--------------p~~~~~---------------------~~li  125 (538)
                      .++|+..|+++.+...                  .              |+....                     ....
T Consensus       197 ~~eAl~~l~~~~~~~~~~~~aa~~~~~~l~~~~~~~~~~~~l~~~l~~~p~~~~~~~A~~~L~~~~~~~~dp~~~~~~~G  276 (1157)
T PRK11447        197 RDEGFAVLEQMAKSPAGRDAAAQLWYGQIKDMPVSDASVAALQKYLQVFSDGDSVAAARSQLAEQQKQLADPAFRARAQG  276 (1157)
T ss_pred             HHHHHHHHHHHhhCCCchHHHHHHHHHHHhccCCChhhHHHHHHHHHHCCCchHHHHHHHHHHHHHHhccCcchHHHHHH
Confidence            9999999888754210                  0              111000                     0113


Q ss_pred             HHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC--CCc---hhHHH--------
Q 044988          126 SVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA--RSV---VSWNS--------  192 (538)
Q Consensus       126 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~--~~~---~~~~~--------  192 (538)
                      ..+...|++++|...|++.++.. +.+..++..+..+|.+.|+   .++|...|++..+  |+.   ..|..        
T Consensus       277 ~~~~~~g~~~~A~~~l~~aL~~~-P~~~~a~~~Lg~~~~~~g~---~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~  352 (1157)
T PRK11447        277 LAAVDSGQGGKAIPELQQAVRAN-PKDSEALGALGQAYSQQGD---RARAVAQFEKALALDPHSSNRDKWESLLKVNRYW  352 (1157)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCC---HHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHH
Confidence            34567789999999999998874 4577888999999999999   9999999988765  221   12222        


Q ss_pred             ----HHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC-HHHHHH------
Q 044988          193 ----LLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD-QVALVA------  258 (538)
Q Consensus       193 ----li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~------  258 (538)
                          ....+.+.|++++|+..|++...   .+...+..+...+...|++++|++.|++..+.  .|+ ...+..      
T Consensus       353 ~~~~~g~~~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~--~p~~~~a~~~L~~l~~  430 (1157)
T PRK11447        353 LLIQQGDAALKANNLAQAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALRM--DPGNTNAVRGLANLYR  430 (1157)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHH
Confidence                23456788999999999998764   34557777888999999999999999998874  233 222222      


Q ss_pred             ------------------------------------HHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHH
Q 044988          259 ------------------------------------ALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMY  302 (538)
Q Consensus       259 ------------------------------------li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~  302 (538)
                                                          +...+...|++++|...++...+.     .|.+...+..+...|
T Consensus       431 ~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~-----~P~~~~~~~~LA~~~  505 (1157)
T PRK11447        431 QQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLAL-----DPGSVWLTYRLAQDL  505 (1157)
T ss_pred             hcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHH
Confidence                                                223344678889999999988886     677777777899999


Q ss_pred             HhCCCHHHHHHHHHhcCC--C-CcchHHHHHHHHHhcCCccHHHHHHH------------------------HHHHHhcc
Q 044988          303 ASCGEIEEAYGVFRKMQR--R-NTVSWTSMITGFAKQGYAQEALLTFL------------------------GVLSACSH  355 (538)
Q Consensus       303 ~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~------------------------~ll~~~~~  355 (538)
                      .+.|++++|...++++.+  | +...+..+...+...++.++|+..+.                        .....+..
T Consensus       506 ~~~G~~~~A~~~l~~al~~~P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~  585 (1157)
T PRK11447        506 RQAGQRSQADALMRRLAQQKPNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRD  585 (1157)
T ss_pred             HHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHH
Confidence            999999999999998754  3 34444444555566777777763332                        23455677


Q ss_pred             cCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHH
Q 044988          356 GGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQV  433 (538)
Q Consensus       356 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~  433 (538)
                      .|+.++|..+++.   .   +++...+..+...+.+.|++++|++.|++.. ..| +...+..++..+...|++++|++.
T Consensus       586 ~G~~~eA~~~l~~---~---p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~  659 (1157)
T PRK11447        586 SGKEAEAEALLRQ---Q---PPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQ  659 (1157)
T ss_pred             CCCHHHHHHHHHh---C---CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            7888888888761   1   3355667778888888899999988888774 344 467788888888888999999998


Q ss_pred             HHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 044988          434 AQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       434 ~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                      ++.+ ....|++...+. .++.++...|++++|.++++++....
T Consensus       660 l~~l-l~~~p~~~~~~~-~la~~~~~~g~~~eA~~~~~~al~~~  701 (1157)
T PRK11447        660 LAKL-PATANDSLNTQR-RVALAWAALGDTAAAQRTFNRLIPQA  701 (1157)
T ss_pred             HHHH-hccCCCChHHHH-HHHHHHHhCCCHHHHHHHHHHHhhhC
Confidence            8888 778888887666 78888888899999999888887643

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.90  E-value=2.7e-19  Score=194.15  Aligned_cols=426  Identities=10%  Similarity=0.031  Sum_probs=324.9

Q ss_pred             HHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC--C-CcchHHHHHHHHhcCCCchHHHHHHHHhH
Q 044988           34 KTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN--P-STAIWNQMIRGHARSETPEKSVYLYKQMI  110 (538)
Q Consensus        34 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~  110 (538)
                      ..+...+....+....|... .......+...|++++|+..|++..+  | +...+..+..++.+.|++++|+..|++..
T Consensus       252 ~~A~~~L~~~~~~~~dp~~~-~~~~G~~~~~~g~~~~A~~~l~~aL~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al  330 (1157)
T PRK11447        252 AAARSQLAEQQKQLADPAFR-ARAQGLAAVDSGQGGKAIPELQQAVRANPKDSEALGALGQAYSQQGDRARAVAQFEKAL  330 (1157)
T ss_pred             HHHHHHHHHHHHhccCcchH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34444444443332233222 12335567789999999999988763  3 66788899999999999999999999998


Q ss_pred             hCCCCCCcc---hHH------------HHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHH
Q 044988          111 DKETEPDEY---TYS------------FLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCA  175 (538)
Q Consensus       111 ~~~~~p~~~---~~~------------~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a  175 (538)
                      +..  |+..   .|.            .....+.+.|++++|...++++++.. +.+...+..+..++...|+   +++|
T Consensus       331 ~~~--p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~~-P~~~~a~~~Lg~~~~~~g~---~~eA  404 (1157)
T PRK11447        331 ALD--PHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQVD-NTDSYAVLGLGDVAMARKD---YAAA  404 (1157)
T ss_pred             HhC--CCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCC---HHHH
Confidence            753  4321   121            22345678999999999999999875 5567788889999999999   9999


Q ss_pred             HHHhhcCCC--C-CchhHHHHHHHHHhcCCHHHHHHHHccCCCCC------------hHHHHHHHHHHHHcCCHHHHHHH
Q 044988          176 RLLFDDMPA--R-SVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRN------------VVSWTTMISGCAQNGKSRQALSL  240 (538)
Q Consensus       176 ~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~------------~~~~~~li~~~~~~~~~~~a~~~  240 (538)
                      ++.|++..+  | +...+..+...+. .++.++|..+++.+....            ...+..+...+...|++++|++.
T Consensus       405 ~~~y~~aL~~~p~~~~a~~~L~~l~~-~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~  483 (1157)
T PRK11447        405 ERYYQQALRMDPGNTNAVRGLANLYR-QQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAEL  483 (1157)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHH-hcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHH
Confidence            999999875  3 4456666666664 567899999998876421            12345567788899999999999


Q ss_pred             HHHHHHCCCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 044988          241 FNEMRRARVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       241 ~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  319 (538)
                      |++..+.  .| +...+..+...+.+.|++++|...++.+.+.     .|.+...+..+...+...|+.++|...++++.
T Consensus       484 ~~~Al~~--~P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~-----~P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~  556 (1157)
T PRK11447        484 QRQRLAL--DPGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQ-----KPNDPEQVYAYGLYLSGSDRDRAALAHLNTLP  556 (1157)
T ss_pred             HHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-----CCCCHHHHHHHHHHHHhCCCHHHHHHHHHhCC
Confidence            9999884  45 4556777888899999999999999999875     56666666667777788999999999999886


Q ss_pred             CCC----c---------chHHHHHHHHHhcCCccHHH----------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCC
Q 044988          320 RRN----T---------VSWTSMITGFAKQGYAQEAL----------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIK  376 (538)
Q Consensus       320 ~~~----~---------~~~~~li~~~~~~~~~~~a~----------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  376 (538)
                      ...    .         ..+..+...+...|+.++|.          ..+..+...+.+.|++++|+..|+.+.+.   .
T Consensus       557 ~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~---~  633 (1157)
T PRK11447        557 RAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTR---E  633 (1157)
T ss_pred             chhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHh---C
Confidence            421    1         11223456788889999888          34556778888999999999999999975   5


Q ss_pred             c-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc------
Q 044988          377 P-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA------  447 (538)
Q Consensus       377 p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~------  447 (538)
                      | +...+..++..|...|++++|++.++... ..|+ ...+..+..++...|++++|.++++++ ....|+++.      
T Consensus       634 P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~~eA~~~~~~a-l~~~~~~~~~~~~a~  712 (1157)
T PRK11447        634 PGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQRRVALAWAALGDTAAAQRTFNRL-IPQAKSQPPSMESAL  712 (1157)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCHHHHHHHHHHH-hhhCccCCcchhhHH
Confidence            5 58889999999999999999999999875 3444 556677788899999999999999999 666555432      


Q ss_pred             cHHHHHHHHHHhcCChHHHHHHHHHHHh-CCCC
Q 044988          448 GYLALVANVYAAAKRWQDVAAVRQKMIK-MGVR  479 (538)
Q Consensus       448 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~-~~~~  479 (538)
                      .+. .++.++...|++++|++.|++... .|+.
T Consensus       713 ~~~-~~a~~~~~~G~~~~A~~~y~~Al~~~~~~  744 (1157)
T PRK11447        713 VLR-DAARFEAQTGQPQQALETYKDAMVASGIT  744 (1157)
T ss_pred             HHH-HHHHHHHHcCCHHHHHHHHHHHHhhcCCC
Confidence            344 568899999999999999988863 3443

>KOG4626 consensus O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.88  E-value=8.6e-20  Score=168.83  Aligned_cols=405  Identities=13%  Similarity=0.132  Sum_probs=331.2

Q ss_pred             HHHHHHHHHccCChhHHHHHHhcCCC--CC-cchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHcc
Q 044988           55 LAKLLAFYVTSGYLINAHKVFEKTEN--PS-TAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARC  131 (538)
Q Consensus        55 ~~~l~~~~~~~g~~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  131 (538)
                      ...|..-..+.|++.+|++.....-.  |+ ....-.+-..+.+..+.+....--....+. .+--..+|..+...+-..
T Consensus        51 ~l~lah~~yq~gd~~~a~~h~nmv~~~d~t~~~~llll~ai~~q~~r~d~s~a~~~~a~r~-~~q~ae~ysn~aN~~ker  129 (966)
T KOG4626|consen   51 RLELAHRLYQGGDYKQAEKHCNMVGQEDPTNTERLLLLSAIFFQGSRLDKSSAGSLLAIRK-NPQGAEAYSNLANILKER  129 (966)
T ss_pred             HHHHHHHHHhccCHHHHHHHHhHhhccCCCcccceeeehhhhhcccchhhhhhhhhhhhhc-cchHHHHHHHHHHHHHHh
Confidence            44556666778999999887655442  22 222222334556666666655543333332 234567999999999999


Q ss_pred             CCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhH---HHHHHHHHhcCCHHHHHH
Q 044988          132 GLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSW---NSLLKGYVKRGDIDGAWK  208 (538)
Q Consensus       132 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~---~~li~~~~~~g~~~~A~~  208 (538)
                      |+++.|...++.+++.. +.....|..+..++...|+   .+.|...|.+..+-|+..|   +.+...+...|++.+|..
T Consensus       130 g~~~~al~~y~~aiel~-p~fida~inla~al~~~~~---~~~a~~~~~~alqlnP~l~ca~s~lgnLlka~Grl~ea~~  205 (966)
T KOG4626|consen  130 GQLQDALALYRAAIELK-PKFIDAYINLAAALVTQGD---LELAVQCFFEALQLNPDLYCARSDLGNLLKAEGRLEEAKA  205 (966)
T ss_pred             chHHHHHHHHHHHHhcC-chhhHHHhhHHHHHHhcCC---CcccHHHHHHHHhcCcchhhhhcchhHHHHhhcccchhHH
Confidence            99999999999999975 4567899999999999999   9999999998887544332   234455566899999999


Q ss_pred             HHccCCC--CC-hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCChHHHHHHHHHHHHhcc
Q 044988          209 IFDEMPH--RN-VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD-QVALVAALSACAEIGDLKLGKWIHSYVEENFS  284 (538)
Q Consensus       209 ~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~  284 (538)
                      .+.+..+  |. .+.|+.|...+-..|+...|+..|++..+  +.|+ ...|..|-..|...+.++.|...|......  
T Consensus       206 cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvk--ldP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~l--  281 (966)
T KOG4626|consen  206 CYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVK--LDPNFLDAYINLGNVYKEARIFDRAVSCYLRALNL--  281 (966)
T ss_pred             HHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhc--CCCcchHHHhhHHHHHHHHhcchHHHHHHHHHHhc--
Confidence            8887553  44 35799999999999999999999999987  5665 567889999999999999999999999886  


Q ss_pred             CCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CC-cchHHHHHHHHHhcCCccHHHHHHH--------------
Q 044988          285 VGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RN-TVSWTSMITGFAKQGYAQEALLTFL--------------  347 (538)
Q Consensus       285 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~--------------  347 (538)
                         .|....++..+.-.|-..|..+.|+..+++..+  |+ +..|+.|..++...|+..+|...|+              
T Consensus       282 ---rpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l~p~hadam~  358 (966)
T KOG4626|consen  282 ---RPNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRLCPNHADAMN  358 (966)
T ss_pred             ---CCcchhhccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHhCCccHHHHH
Confidence               788888888999999999999999999999876  43 5689999999999999999995554              


Q ss_pred             HHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhc
Q 044988          348 GVLSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNM-PMKPN-DAVLGSLLLGCRIH  424 (538)
Q Consensus       348 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~  424 (538)
                      .+..++...|.++.|..+|....+   +.|. ....+.|...|-.+|++++|+..|++. +++|+ ...++.+...|...
T Consensus       359 NLgni~~E~~~~e~A~~ly~~al~---v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke~  435 (966)
T KOG4626|consen  359 NLGNIYREQGKIEEATRLYLKALE---VFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKEM  435 (966)
T ss_pred             HHHHHHHHhccchHHHHHHHHHHh---hChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHHh
Confidence            455667778999999999998884   4676 668899999999999999999999887 57888 57899999999999


Q ss_pred             CCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          425 NNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       425 ~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      |+.+.|.+.+.++ ..+.|....++. .|+.+|...|...+|++-++...+-
T Consensus       436 g~v~~A~q~y~rA-I~~nPt~AeAhs-NLasi~kDsGni~~AI~sY~~aLkl  485 (966)
T KOG4626|consen  436 GDVSAAIQCYTRA-IQINPTFAEAHS-NLASIYKDSGNIPEAIQSYRTALKL  485 (966)
T ss_pred             hhHHHHHHHHHHH-HhcCcHHHHHHh-hHHHHhhccCCcHHHHHHHHHHHcc
Confidence            9999999999999 999999998888 9999999999999999999998864

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=99.87  E-value=2.3e-18  Score=175.48  Aligned_cols=385  Identities=12%  Similarity=0.037  Sum_probs=253.5

Q ss_pred             HHHHHHHHHccCChhHHHHHHhcCC--CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccC
Q 044988           55 LAKLLAFYVTSGYLINAHKVFEKTE--NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCG  132 (538)
Q Consensus        55 ~~~l~~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~  132 (538)
                      +....+.+.+.|++++|+..|++..  .|+...|..+..+|.+.|++++|++.++...+.. +.+...|..+..++...|
T Consensus       130 ~k~~G~~~~~~~~~~~Ai~~y~~al~~~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~a~a~~~lg  208 (615)
T TIGR00990       130 LKEKGNKAYRNKDFNKAIKLYSKAIECKPDPVYYSNRAACHNALGDWEKVVEDTTAALELD-PDYSKALNRRANAYDGLG  208 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHcC
Confidence            4455666777788888888877655  4666677777777777888888888887777642 223456777777777888


Q ss_pred             CcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC----------------------------
Q 044988          133 LFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA----------------------------  184 (538)
Q Consensus       133 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~----------------------------  184 (538)
                      ++++|...+......+-..+.. ...++..+.....   ...+...++.-+.                            
T Consensus       209 ~~~eA~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~a---~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (615)
T TIGR00990       209 KYADALLDLTASCIIDGFRNEQ-SAQAVERLLKKFA---ESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSN  284 (615)
T ss_pred             CHHHHHHHHHHHHHhCCCccHH-HHHHHHHHHHHHH---HHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhccc
Confidence            8887777666554432111111 1111111111101   1222222211111                            


Q ss_pred             -CCc---hhHHHHHHH---HHhcCCHHHHHHHHccCCC-----C-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC
Q 044988          185 -RSV---VSWNSLLKG---YVKRGDIDGAWKIFDEMPH-----R-NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGL  251 (538)
Q Consensus       185 -~~~---~~~~~li~~---~~~~g~~~~A~~~~~~m~~-----~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  251 (538)
                       .+.   ..+..+...   ....+++++|.+.|++..+     | ....|+.+...+...|++++|+..|++..+.  .|
T Consensus       285 ~~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l--~P  362 (615)
T TIGR00990       285 ELDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIEL--DP  362 (615)
T ss_pred             ccccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CC
Confidence             000   011111111   0223577788888877553     2 3346777777778888888888888887764  44


Q ss_pred             C-HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC---CcchHH
Q 044988          252 D-QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR---NTVSWT  327 (538)
Q Consensus       252 ~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~  327 (538)
                      + ...|..+...+...|+++.|...++.+.+.     .|.+..++..+...+...|++++|...|++..+.   +...+.
T Consensus       363 ~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~-----~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~  437 (615)
T TIGR00990       363 RVTQSYIKRASMNLELGDPDKAEEDFDKALKL-----NSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHI  437 (615)
T ss_pred             CcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHH
Confidence            4 456677777777888888888888888775     5666777777888888888888888888877652   223333


Q ss_pred             HHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          328 SMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       328 ~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      .                    +..++.+.|++++|...|+...+.   .| +...++.+..++...|++++|++.|++..
T Consensus       438 ~--------------------la~~~~~~g~~~eA~~~~~~al~~---~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al  494 (615)
T TIGR00990       438 Q--------------------LGVTQYKEGSIASSMATFRRCKKN---FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAI  494 (615)
T ss_pred             H--------------------HHHHHHHCCCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence            3                    334445556888888999988864   45 47789999999999999999999998863


Q ss_pred             -CCCCH-H-------HHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          407 -MKPND-A-------VLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       407 -~~p~~-~-------~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                       ..|+. .       .++..+..+...|++++|.++++++ ..+.|++...+. .++.++.+.|++++|++.|++..+.
T Consensus       495 ~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kA-l~l~p~~~~a~~-~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       495 ELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKA-LIIDPECDIAVA-TMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             hcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHH-HhcCCCcHHHHH-HHHHHHHHccCHHHHHHHHHHHHHH
Confidence             33431 1       1122222344579999999999999 888999988777 9999999999999999999998753

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.87  E-value=2.4e-19  Score=173.68  Aligned_cols=163  Identities=12%  Similarity=0.121  Sum_probs=113.8

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHhcCC--CC-cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhh
Q 044988          295 NNALIHMYASCGEIEEAYGVFRKMQR--RN-TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQ  371 (538)
Q Consensus       295 ~~~l~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  371 (538)
                      +..+...+.+.|++++|...|+++.+  |+ ...+..+...+                    ...|++++|.++|+++.+
T Consensus       183 ~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~--------------------~~~g~~~~A~~~~~~~~~  242 (389)
T PRK11788        183 YCELAQQALARGDLDAARALLKKALAADPQCVRASILLGDLA--------------------LAQGDYAAAIEALERVEE  242 (389)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHhHCcCCHHHHHHHHHHH--------------------HHCCCHHHHHHHHHHHHH
Confidence            34455566666666666666666543  11 22222333333                    333466666667776664


Q ss_pred             hcCCCcc--HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCccc
Q 044988          372 NWGIKPR--IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAG  448 (538)
Q Consensus       372 ~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~  448 (538)
                      .   .|+  ..+++.++.+|...|++++|.+.++++. ..|+...+..++..+.+.|++++|..+++++ .+..|++.. 
T Consensus       243 ~---~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~-l~~~P~~~~-  317 (389)
T PRK11788        243 Q---DPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQ-LRRHPSLRG-  317 (389)
T ss_pred             H---ChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHH-HHhCcCHHH-
Confidence            4   333  4567888889999999999999998874 5677777788888899999999999999998 778898876 


Q ss_pred             HHHHHHHHHHh---cCChHHHHHHHHHHHhCCCCCCCc
Q 044988          449 YLALVANVYAA---AKRWQDVAAVRQKMIKMGVRKPPG  483 (538)
Q Consensus       449 ~~~~l~~~~~~---~g~~~~A~~~~~~m~~~~~~~~~~  483 (538)
                      +. .+...+..   .|+.+++..++++|.++++.++|.
T Consensus       318 ~~-~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~~p~  354 (389)
T PRK11788        318 FH-RLLDYHLAEAEEGRAKESLLLLRDLVGEQLKRKPR  354 (389)
T ss_pred             HH-HHHHHhhhccCCccchhHHHHHHHHHHHHHhCCCC
Confidence            55 44445443   558999999999999988888874

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.85  E-value=3.1e-17  Score=170.26  Aligned_cols=166  Identities=10%  Similarity=0.011  Sum_probs=101.8

Q ss_pred             CCCCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHH
Q 044988           12 ATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQ   88 (538)
Q Consensus        12 ~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~   88 (538)
                      ..+.++....-.+......|+..+|..++....... +.+...+..+...+...|++++|..+|++..   +.+...+..
T Consensus        10 ~~~~~~~~~~d~~~ia~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~   88 (765)
T PRK10049         10 KSALSNNQIADWLQIALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLEPQNDDYQRG   88 (765)
T ss_pred             ccCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            334444455556666666777777777776665522 2334456666677777777777777777643   234445566


Q ss_pred             HHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCC
Q 044988           89 MIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGG  168 (538)
Q Consensus        89 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  168 (538)
                      +...+...|++++|+..+++..+.. +.+.. +..+..++...|+.++|...++++.+.. +.+...+..+..++...|.
T Consensus        89 la~~l~~~g~~~eA~~~l~~~l~~~-P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~-P~~~~~~~~la~~l~~~~~  165 (765)
T PRK10049         89 LILTLADAGQYDEALVKAKQLVSGA-PDKAN-LLALAYVYKRAGRHWDELRAMTQALPRA-PQTQQYPTEYVQALRNNRL  165 (765)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCC
Confidence            6666677777777777777776542 22333 6666666667777777777777777653 3344455556666666666


Q ss_pred             CCChhHHHHHhhcCCC
Q 044988          169 ECGVGCARLLFDDMPA  184 (538)
Q Consensus       169 ~~~~~~a~~~~~~~~~  184 (538)
                         .+.|.+.++....
T Consensus       166 ---~e~Al~~l~~~~~  178 (765)
T PRK10049        166 ---SAPALGAIDDANL  178 (765)
T ss_pred             ---hHHHHHHHHhCCC
Confidence               6666666665554

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.85  E-value=2.2e-16  Score=164.12  Aligned_cols=213  Identities=10%  Similarity=0.009  Sum_probs=165.2

Q ss_pred             CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CCcchHHHH
Q 044988          252 DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RNTVSWTSM  329 (538)
Q Consensus       252 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~l  329 (538)
                      +...+..+..++.. ++.++|...+......     .|.+. ....+...+...|++++|...|+++..  ++...+..+
T Consensus       476 ~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~-----~Pd~~-~~L~lA~al~~~Gr~eeAi~~~rka~~~~p~~~a~~~l  548 (987)
T PRK09782        476 DAAAWNRLAKCYRD-TLPGVALYAWLQAEQR-----QPDAW-QHRAVAYQAYQVEDYATALAAWQKISLHDMSNEDLLAA  548 (987)
T ss_pred             CHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh-----CCchH-HHHHHHHHHHHCCCHHHHHHHHHHHhccCCCcHHHHHH
Confidence            34444555555544 6777777777776665     33322 233445555689999999999987765  444556677


Q ss_pred             HHHHHhcCCccHHHHHHHHHHH--------------HhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCCh
Q 044988          330 ITGFAKQGYAQEALLTFLGVLS--------------ACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLM  395 (538)
Q Consensus       330 i~~~~~~~~~~~a~~~~~~ll~--------------~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  395 (538)
                      ...+.+.|+.++|...|..++.              .+...|++++|...+++..+.   .|+...|..+..++.+.|++
T Consensus       549 a~all~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l---~P~~~a~~~LA~~l~~lG~~  625 (987)
T PRK09782        549 ANTAQAAGNGAARDRWLQQAEQRGLGDNALYWWLHAQRYIPGQPELALNDLTRSLNI---APSANAYVARATIYRQRHNV  625 (987)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh---CCCHHHHHHHHHHHHHCCCH
Confidence            7888899999998855433322              233449999999999999855   67888899999999999999


Q ss_pred             HHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHH
Q 044988          396 DEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKM  473 (538)
Q Consensus       396 ~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m  473 (538)
                      ++|+..+++.. ..|+ ...++.+..++...|++++|+..++++ ....|+++..+. .++.++...|++++|...+++.
T Consensus       626 deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~A-L~l~P~~~~a~~-nLA~al~~lGd~~eA~~~l~~A  703 (987)
T PRK09782        626 PAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERA-HKGLPDDPALIR-QLAYVNQRLDDMAATQHYARLV  703 (987)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHHHCCCHHHHHHHHHHH
Confidence            99999999874 4565 567777888899999999999999999 999999999778 9999999999999999999999


Q ss_pred             HhC
Q 044988          474 IKM  476 (538)
Q Consensus       474 ~~~  476 (538)
                      .+.
T Consensus       704 l~l  706 (987)
T PRK09782        704 IDD  706 (987)
T ss_pred             Hhc
Confidence            864

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.84  E-value=1.9e-17  Score=168.17  Aligned_cols=348  Identities=10%  Similarity=-0.044  Sum_probs=252.2

Q ss_pred             ccCChhHHHHHHhcCCC------CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHH
Q 044988           64 TSGYLINAHKVFEKTEN------PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREG  137 (538)
Q Consensus        64 ~~g~~~~a~~~~~~~~~------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a  137 (538)
                      +..+++.-.-+|...++      .+......++..+.+.|++++|..+++...... +-+...+..++.+....|+++.|
T Consensus        17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~-p~~~~~l~~l~~~~l~~g~~~~A   95 (656)
T PRK15174         17 KQEDWEGLCLYFSQHPEKVRDSAGNEQNIILFAIACLRKDETDVGLTLLSDRVLTA-KNGRDLLRRWVISPLASSQPDAV   95 (656)
T ss_pred             hhhchhhHhHHhhcccHhhhhhcccccCHHHHHHHHHhcCCcchhHHHhHHHHHhC-CCchhHHHHHhhhHhhcCCHHHH
Confidence            44455555555554442      123334556677778888888888888887653 22344556666667778888888


Q ss_pred             HHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC--C-CchhHHHHHHHHHhcCCHHHHHHHHccCC
Q 044988          138 EQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA--R-SVVSWNSLLKGYVKRGDIDGAWKIFDEMP  214 (538)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~  214 (538)
                      ...++++.... +.+...+..+...+...|+   .++|...+++..+  | +...+..+...+...|++++|...++.+.
T Consensus        96 ~~~l~~~l~~~-P~~~~a~~~la~~l~~~g~---~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~  171 (656)
T PRK15174         96 LQVVNKLLAVN-VCQPEDVLLVASVLLKSKQ---YATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQA  171 (656)
T ss_pred             HHHHHHHHHhC-CCChHHHHHHHHHHHHcCC---HHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHH
Confidence            88888888764 4556677888888888888   8888888888765  3 45677788888888899998888887654


Q ss_pred             C--CCh-HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc
Q 044988          215 H--RNV-VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL  291 (538)
Q Consensus       215 ~--~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  291 (538)
                      .  |+. ..+..+ ..+...|++++|...++.+.+....++...+..+...+...|++++|...++.+.+.     .|.+
T Consensus       172 ~~~P~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~-----~p~~  245 (656)
T PRK15174        172 QEVPPRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALAR-----GLDG  245 (656)
T ss_pred             HhCCCCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhc-----CCCC
Confidence            2  333 333333 347788999999999998877644445555556667788899999999999998876     5677


Q ss_pred             hhHHHHHHHHHHhCCCHHH----HHHHHHhcCC--C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHH
Q 044988          292 VSLNNALIHMYASCGEIEE----AYGVFRKMQR--R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQ  364 (538)
Q Consensus       292 ~~~~~~l~~~~~~~g~~~~----a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~  364 (538)
                      ...+..+...|...|++++    |...|++..+  | +...+..+...+...|                    ++++|..
T Consensus       246 ~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g--------------------~~~eA~~  305 (656)
T PRK15174        246 AALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFNSDNVRIVTLYADALIRTG--------------------QNEKAIP  305 (656)
T ss_pred             HHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCC--------------------CHHHHHH
Confidence            7888889999999999885    7888888765  3 3345555555555555                    6777778


Q ss_pred             HHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHH-HHHHHHHHHhcCCHHHHHHHHHHchhcc
Q 044988          365 FFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAV-LGSLLLGCRIHNNAELASQVAQKLVAEI  441 (538)
Q Consensus       365 ~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~-~~~l~~~~~~~~~~~~A~~~~~~~~~~~  441 (538)
                      .+++..+.   .|+ ...+..+..+|.+.|++++|.+.|+++. ..|+... +..+..++...|+.++|...|+++ ...
T Consensus       306 ~l~~al~l---~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~~~~~~~~a~al~~~G~~deA~~~l~~a-l~~  381 (656)
T PRK15174        306 LLQQSLAT---HPDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVTSKWNRYAAAALLQAGKTSEAESVFEHY-IQA  381 (656)
T ss_pred             HHHHHHHh---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHCCCHHHHHHHHHHH-HHh
Confidence            88887754   454 6677788899999999999999998874 4566544 334566788999999999999999 777


Q ss_pred             CCCCc
Q 044988          442 DPEQA  446 (538)
Q Consensus       442 ~p~~~  446 (538)
                      .|++.
T Consensus       382 ~P~~~  386 (656)
T PRK15174        382 RASHL  386 (656)
T ss_pred             Chhhc
Confidence            77754

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.84  E-value=3.5e-18  Score=165.51  Aligned_cols=287  Identities=14%  Similarity=0.149  Sum_probs=194.4

Q ss_pred             HHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCC
Q 044988           92 GHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECG  171 (538)
Q Consensus        92 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  171 (538)
                      .+...|++++|+..|+++.+.+ +.+..++..+...+...|++++|..+++.+...+..++..                 
T Consensus        44 ~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~-----------------  105 (389)
T PRK11788         44 NFLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQ-----------------  105 (389)
T ss_pred             HHHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHH-----------------
Confidence            3456677777777777777643 2234466667777777777777777777666542111100                 


Q ss_pred             hhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 044988          172 VGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR  248 (538)
Q Consensus       172 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  248 (538)
                                    ....+..+...|.+.|++++|..+|+++.+   .+..+++.++..+.+.|++++|.+.++.+.+.+
T Consensus       106 --------------~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~  171 (389)
T PRK11788        106 --------------RLLALQELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLG  171 (389)
T ss_pred             --------------HHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhc
Confidence                          011234444555555555566666655543   345567777777777788888888887777654


Q ss_pred             CCCCH----HHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CC
Q 044988          249 VGLDQ----VALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RN  322 (538)
Q Consensus       249 ~~p~~----~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~  322 (538)
                      ..++.    ..+..+...+.+.|+++.|...++.+.+.     .|.+...+..+...|.+.|++++|.+.|+++.+  |+
T Consensus       172 ~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~-----~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~  246 (389)
T PRK11788        172 GDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAA-----DPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPE  246 (389)
T ss_pred             CCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhH-----CcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChh
Confidence            33321    23445666677778888888888877775     455566667778888888888888888888774  32


Q ss_pred             --cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHH
Q 044988          323 --TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFS  400 (538)
Q Consensus       323 --~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~  400 (538)
                        ..+++.++.+|...|                    ++++|...++.+.+.   .|+...+..++..+.+.|++++|.+
T Consensus       247 ~~~~~~~~l~~~~~~~g--------------------~~~~A~~~l~~~~~~---~p~~~~~~~la~~~~~~g~~~~A~~  303 (389)
T PRK11788        247 YLSEVLPKLMECYQALG--------------------DEAEGLEFLRRALEE---YPGADLLLALAQLLEEQEGPEAAQA  303 (389)
T ss_pred             hHHHHHHHHHHHHHHcC--------------------CHHHHHHHHHHHHHh---CCCchHHHHHHHHHHHhCCHHHHHH
Confidence              235667777777776                    566666777777654   5776667888999999999999999


Q ss_pred             HHHhC-CCCCCHHHHHHHHHHHHh---cCCHHHHHHHHHHch
Q 044988          401 LVQNM-PMKPNDAVLGSLLLGCRI---HNNAELASQVAQKLV  438 (538)
Q Consensus       401 ~~~~~-~~~p~~~~~~~l~~~~~~---~~~~~~A~~~~~~~~  438 (538)
                      +++++ ...|+..+++.++..+..   .|+.+++..+++++.
T Consensus       304 ~l~~~l~~~P~~~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~  345 (389)
T PRK11788        304 LLREQLRRHPSLRGFHRLLDYHLAEAEEGRAKESLLLLRDLV  345 (389)
T ss_pred             HHHHHHHhCcCHHHHHHHHHHhhhccCCccchhHHHHHHHHH
Confidence            99876 456898888888887664   458889999999886

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.84  E-value=1.3e-16  Score=165.72  Aligned_cols=404  Identities=9%  Similarity=0.043  Sum_probs=291.7

Q ss_pred             CCChhHHHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHH
Q 044988           49 SQKNYILAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLL  125 (538)
Q Consensus        49 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li  125 (538)
                      +.++....-.+.+....|+.++|+++|.+..+   .+...+..+...+.+.|++++|..+|++..+.. +.+...+..+.
T Consensus        12 ~~~~~~~~d~~~ia~~~g~~~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la   90 (765)
T PRK10049         12 ALSNNQIADWLQIALWAGQDAEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSLE-PQNDDYQRGLI   90 (765)
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            44667777788888999999999999988764   333458899999999999999999999998752 33456777888


Q ss_pred             HHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC--C-CchhHHHHHHHHHhcCC
Q 044988          126 SVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA--R-SVVSWNSLLKGYVKRGD  202 (538)
Q Consensus       126 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~  202 (538)
                      ..+...|++++|...+++..+.. +.+.. +..+..++...|+   .++|...+++..+  | +...+..+...+...|.
T Consensus        91 ~~l~~~g~~~eA~~~l~~~l~~~-P~~~~-~~~la~~l~~~g~---~~~Al~~l~~al~~~P~~~~~~~~la~~l~~~~~  165 (765)
T PRK10049         91 LTLADAGQYDEALVKAKQLVSGA-PDKAN-LLALAYVYKRAGR---HWDELRAMTQALPRAPQTQQYPTEYVQALRNNRL  165 (765)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhC-CCCHH-HHHHHHHHHHCCC---HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCC
Confidence            88999999999999999999874 55566 8889999999999   9999999999876  3 45566778888889999


Q ss_pred             HHHHHHHHccCCC-CCh------HHHHHHHHHHH-----HcCCH---HHHHHHHHHHHHC-CCCCCHH-HHH----HHHH
Q 044988          203 IDGAWKIFDEMPH-RNV------VSWTTMISGCA-----QNGKS---RQALSLFNEMRRA-RVGLDQV-ALV----AALS  261 (538)
Q Consensus       203 ~~~A~~~~~~m~~-~~~------~~~~~li~~~~-----~~~~~---~~a~~~~~~m~~~-g~~p~~~-~~~----~li~  261 (538)
                      .+.|++.++.... |+.      .....++....     ..+++   ++|+..++.+.+. ...|+.. .+.    ..+.
T Consensus       166 ~e~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~  245 (765)
T PRK10049        166 SAPALGAIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLG  245 (765)
T ss_pred             hHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHH
Confidence            9999999998775 221      01222222222     12234   7788899988854 2233321 111    1134


Q ss_pred             HHHccCChHHHHHHHHHHHHhccCCCC--CcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCC-------cchHHHHHHH
Q 044988          262 ACAEIGDLKLGKWIHSYVEENFSVGRE--PVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRN-------TVSWTSMITG  332 (538)
Q Consensus       262 ~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~-------~~~~~~li~~  332 (538)
                      ++...|+.++|...|+.+.+.    +.  |.....  .+...|...|++++|...|+++.+.+       ......+..+
T Consensus       246 ~Ll~~g~~~eA~~~~~~ll~~----~~~~P~~a~~--~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a  319 (765)
T PRK10049        246 ALLARDRYKDVISEYQRLKAE----GQIIPPWAQR--WVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYS  319 (765)
T ss_pred             HHHHhhhHHHHHHHHHHhhcc----CCCCCHHHHH--HHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHH
Confidence            456779999999999998876    42  333333  36788999999999999999886532       1245556678


Q ss_pred             HHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc---HHHHHHHHHHhhhcCChHHHHHHHHhCC-CC
Q 044988          333 FAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR---IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MK  408 (538)
Q Consensus       333 ~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~  408 (538)
                      +...|++++|...+..+...-...      ..++. ..   .-.|+   ...+..+...+...|++++|+++++++. ..
T Consensus       320 ~~~~g~~~eA~~~l~~~~~~~P~~------~~~~~-~~---~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~  389 (765)
T PRK10049        320 LLESENYPGALTVTAHTINNSPPF------LRLYG-SP---TSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNA  389 (765)
T ss_pred             HHhcccHHHHHHHHHHHhhcCCce------EeecC-CC---CCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            899999999987777666542111      01111 11   11344   2345566777778888888888888763 23


Q ss_pred             C-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          409 P-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       409 p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      | +...+..+...+...|++++|++.++++ ....|++...+. .++..+.+.|++++|..+++++.+.
T Consensus       390 P~n~~l~~~lA~l~~~~g~~~~A~~~l~~a-l~l~Pd~~~l~~-~~a~~al~~~~~~~A~~~~~~ll~~  456 (765)
T PRK10049        390 PGNQGLRIDYASVLQARGWPRAAENELKKA-EVLEPRNINLEV-EQAWTALDLQEWRQMDVLTDDVVAR  456 (765)
T ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHH-HhhCCCChHHHH-HHHHHHHHhCCHHHHHHHHHHHHHh
Confidence            3 3566777777788888888888888888 778888877666 7777788888888888888887653

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.83  E-value=5.1e-17  Score=165.12  Aligned_cols=354  Identities=12%  Similarity=0.027  Sum_probs=275.8

Q ss_pred             HhcCCCchHHHHHHHHhHhC--CCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCC
Q 044988           93 HARSETPEKSVYLYKQMIDK--ETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGEC  170 (538)
Q Consensus        93 ~~~~~~~~~a~~~~~~m~~~--~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  170 (538)
                      +.++.+|+.-.-.|..-.++  .-.-+..-...++..+.+.|+++.|..+++..+... +-+......++.+....|+  
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~-p~~~~~l~~l~~~~l~~g~--   91 (656)
T PRK15174         15 LLKQEDWEGLCLYFSQHPEKVRDSAGNEQNIILFAIACLRKDETDVGLTLLSDRVLTA-KNGRDLLRRWVISPLASSQ--   91 (656)
T ss_pred             hhhhhchhhHhHHhhcccHhhhhhcccccCHHHHHHHHHhcCCcchhHHHhHHHHHhC-CCchhHHHHHhhhHhhcCC--
Confidence            35666777766666655432  112344456677888899999999999999999875 4445566777788888999  


Q ss_pred             ChhHHHHHhhcCCC--C-CchhHHHHHHHHHhcCCHHHHHHHHccCCC--C-ChHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 044988          171 GVGCARLLFDDMPA--R-SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--R-NVVSWTTMISGCAQNGKSRQALSLFNEM  244 (538)
Q Consensus       171 ~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m  244 (538)
                       .+.|...|+++.+  | +...+..+...+...|++++|...|++...  | +...+..+...+...|++++|...++.+
T Consensus        92 -~~~A~~~l~~~l~~~P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~  170 (656)
T PRK15174         92 -PDAVLQVVNKLLAVNVCQPEDVLLVASVLLKSKQYATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQ  170 (656)
T ss_pred             -HHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHH
Confidence             9999999999875  3 567788888999999999999999999764  4 4567888999999999999999999988


Q ss_pred             HHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---C
Q 044988          245 RRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---R  321 (538)
Q Consensus       245 ~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~  321 (538)
                      ......+. ..+..+ ..+...|++++|...++.+.+.    ..+.+......+...+.+.|++++|...+++..+   .
T Consensus       171 ~~~~P~~~-~a~~~~-~~l~~~g~~~eA~~~~~~~l~~----~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~  244 (656)
T PRK15174        171 AQEVPPRG-DMIATC-LSFLNKSRLPEDHDLARALLPF----FALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLD  244 (656)
T ss_pred             HHhCCCCH-HHHHHH-HHHHHcCCHHHHHHHHHHHHhc----CCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC
Confidence            76543332 233233 3478899999999999998776    3333344445567888999999999999998875   2


Q ss_pred             CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHH
Q 044988          322 NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFS  400 (538)
Q Consensus       322 ~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~  400 (538)
                      +...+..+...+...|++++|.                ..|...|++..+.   .| +...+..+...+.+.|++++|..
T Consensus       245 ~~~~~~~Lg~~l~~~G~~~eA~----------------~~A~~~~~~Al~l---~P~~~~a~~~lg~~l~~~g~~~eA~~  305 (656)
T PRK15174        245 GAALRRSLGLAYYQSGRSREAK----------------LQAAEHWRHALQF---NSDNVRIVTLYADALIRTGQNEKAIP  305 (656)
T ss_pred             CHHHHHHHHHHHHHcCCchhhH----------------HHHHHHHHHHHhh---CCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence            4556666777777777655431                3578888888854   56 47789999999999999999999


Q ss_pred             HHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 044988          401 LVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       401 ~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                      .+++.. ..|+ ...+..+..++...|++++|...++++ ....|++...+. .++.++...|++++|.+.|++..+..
T Consensus       306 ~l~~al~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~a-l~~~P~~~~~~~-~~a~al~~~G~~deA~~~l~~al~~~  382 (656)
T PRK15174        306 LLQQSLATHPDLPYVRAMYARALRQVGQYTAASDEFVQL-AREKGVTSKWNR-YAAAALLQAGKTSEAESVFEHYIQAR  382 (656)
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH-HHhCccchHHHH-HHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            999874 4455 566777888899999999999999999 888998876455 67888999999999999999987643

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.82  E-value=1e-15  Score=155.98  Aligned_cols=442  Identities=12%  Similarity=0.020  Sum_probs=309.7

Q ss_pred             CCCCCCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHH-H
Q 044988           10 NPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWN-Q   88 (538)
Q Consensus        10 ~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~   88 (538)
                      .+..|..+.+...-+-...+.|++..|...+++..+....-.+.++ .++..+...|+.++|+..+++...|+...+. .
T Consensus        27 ~~~~p~~~~~~y~~aii~~r~Gd~~~Al~~L~qaL~~~P~~~~av~-dll~l~~~~G~~~~A~~~~eka~~p~n~~~~~l  105 (822)
T PRK14574         27 FVVNPAMADTQYDSLIIRARAGDTAPVLDYLQEESKAGPLQSGQVD-DWLQIAGWAGRDQEVIDVYERYQSSMNISSRGL  105 (822)
T ss_pred             cccCccchhHHHHHHHHHHhCCCHHHHHHHHHHHHhhCccchhhHH-HHHHHHHHcCCcHHHHHHHHHhccCCCCCHHHH
Confidence            3333434444445555667899999999999999987644223444 8888899999999999999998876544443 3


Q ss_pred             H--HHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhc
Q 044988           89 M--IRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMS  166 (538)
Q Consensus        89 l--i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  166 (538)
                      +  ...+...|++++|+++|+++.+.. +-|...+..++..+...++.++|.+.++++...  .|+...+..++..+...
T Consensus       106 lalA~ly~~~gdyd~Aiely~kaL~~d-P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~  182 (822)
T PRK14574        106 ASAARAYRNEKRWDQALALWQSSLKKD-PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRAT  182 (822)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhc
Confidence            3  457778899999999999999864 334567777888899999999999999999876  45555554444444444


Q ss_pred             CCCCChhHHHHHhhcCCC--C-CchhHHHHHHHHHhcCCHHHHHHHHccCCC-CChHHHHHH----HHHHHH--------
Q 044988          167 GGECGVGCARLLFDDMPA--R-SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH-RNVVSWTTM----ISGCAQ--------  230 (538)
Q Consensus       167 g~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~~~~~~~~l----i~~~~~--------  230 (538)
                      ++   ..+|+..++++.+  | +...+..+..++.+.|-...|.++..+-+. -+...+..+    +.-.++        
T Consensus       183 ~~---~~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~  259 (822)
T PRK14574        183 DR---NYDALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRS  259 (822)
T ss_pred             ch---HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhccccccc
Confidence            44   6569999998875  3 566778888999999999999999988663 111111110    111111        


Q ss_pred             -cCC---HHHHHHHHHHHHH-CCCCCCHH-----HHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHH
Q 044988          231 -NGK---SRQALSLFNEMRR-ARVGLDQV-----ALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIH  300 (538)
Q Consensus       231 -~~~---~~~a~~~~~~m~~-~g~~p~~~-----~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~  300 (538)
                       ..+   .+.|+.-++.+.. .+-.|...     ...-.+-++...++..++.+.++.+...    +.+....+-..+.+
T Consensus       260 ~~~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~----~~~~P~y~~~a~ad  335 (822)
T PRK14574        260 ETERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAE----GYKMPDYARRWAAS  335 (822)
T ss_pred             chhhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhc----CCCCCHHHHHHHHH
Confidence             122   3456666666554 23334322     2223455677889999999999999887    66655566678999


Q ss_pred             HHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcC------
Q 044988          301 MYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWG------  374 (538)
Q Consensus       301 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~------  374 (538)
                      +|...+.+++|..+|..+..++..+.           .....+.....|.-++...+++++|..+++.+.+...      
T Consensus       336 ayl~~~~P~kA~~l~~~~~~~~~~~~-----------~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~  404 (822)
T PRK14574        336 AYIDRRLPEKAAPILSSLYYSDGKTF-----------RNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVY  404 (822)
T ss_pred             HHHhcCCcHHHHHHHHHHhhcccccc-----------CCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEecc
Confidence            99999999999999999865332110           0000001123344455555677777888888776311      


Q ss_pred             ------CCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC
Q 044988          375 ------IKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ  445 (538)
Q Consensus       375 ------~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~  445 (538)
                            ..|| ...+..++..+...|++.+|++.++++.  .+-|......+...+...|.+.+|++.++.+ ..+.|++
T Consensus       405 ~~~~~~pn~d~~~~~~l~a~~~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a-~~l~P~~  483 (822)
T PRK14574        405 GLPGKEPNDDWIEGQTLLVQSLVALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKAEQELKAV-ESLAPRS  483 (822)
T ss_pred             CCCCCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHH-hhhCCcc
Confidence                  1223 3345566778888999999999998884  3445777788888899999999999999888 8889998


Q ss_pred             cccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          446 AAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       446 ~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ..+.. ..+.++...|+|++|..+.+.+.+
T Consensus       484 ~~~~~-~~~~~al~l~e~~~A~~~~~~l~~  512 (822)
T PRK14574        484 LILER-AQAETAMALQEWHQMELLTDDVIS  512 (822)
T ss_pred             HHHHH-HHHHHHHhhhhHHHHHHHHHHHHh
Confidence            88777 888888899999999888877754

>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70)

Probab=99.80  E-value=5.9e-16  Score=157.96  Aligned_cols=397  Identities=10%  Similarity=-0.035  Sum_probs=271.3

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHHHHhcC
Q 044988           20 TRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIRGHARS   96 (538)
Q Consensus        20 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~   96 (538)
                      +......+...++++.|...|+..++.  .|++..|..+..+|.+.|++++|++.++...+   .+...|..+..+|...
T Consensus       130 ~k~~G~~~~~~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~a~a~~~l  207 (615)
T TIGR00990       130 LKEKGNKAYRNKDFNKAIKLYSKAIEC--KPDPVYYSNRAACHNALGDWEKVVEDTTAALELDPDYSKALNRRANAYDGL  207 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHc
Confidence            335556778889999999999998875  46778899999999999999999999988763   3455788899999999


Q ss_pred             CCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHH-------------HHH------------h--CC
Q 044988           97 ETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGR-------------VLA------------S--GY  149 (538)
Q Consensus        97 ~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~-------------~~~------------~--~~  149 (538)
                      |++++|+.-|......+ ..+......++..+........+...++.             ...            .  ..
T Consensus       208 g~~~eA~~~~~~~~~~~-~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  286 (615)
T TIGR00990       208 GKYADALLDLTASCIID-GFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNEL  286 (615)
T ss_pred             CCHHHHHHHHHHHHHhC-CCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhccccc
Confidence            99999998887665432 11111111111111100000111111000             000            0  00


Q ss_pred             CCc-hhHHhHHHHHH---HhcCCCCChhHHHHHhhcCCCC------CchhHHHHHHHHHhcCCHHHHHHHHccCCC--CC
Q 044988          150 CSN-VFIRTNLMNLY---LMSGGECGVGCARLLFDDMPAR------SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--RN  217 (538)
Q Consensus       150 ~~~-~~~~~~l~~~~---~~~g~~~~~~~a~~~~~~~~~~------~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~  217 (538)
                      .+. ...+..+...+   ...++   +++|.+.|+...+.      ....|+.+...+...|++++|+..|++..+  |+
T Consensus       287 ~~~~~~~~~~l~~~~~e~~~~~~---y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~P~  363 (615)
T TIGR00990       287 DEETGNGQLQLGLKSPESKADES---YEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELDPR  363 (615)
T ss_pred             ccccccchHHHHHHHHHhhhhhh---HHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC
Confidence            000 00011111111   12245   88888888877642      345677888888889999999999988654  43


Q ss_pred             -hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          218 -VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       218 -~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                       ...|..+...+...|++++|...|++..+.. +-+...+..+...+...|+++.|...++...+.     .|.+...+.
T Consensus       364 ~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l-----~P~~~~~~~  437 (615)
T TIGR00990       364 VTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL-----DPDFIFSHI  437 (615)
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-----CccCHHHHH
Confidence             4578888888889999999999999887753 334677888888888999999999999998886     677777788


Q ss_pred             HHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc
Q 044988          297 ALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       297 ~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  373 (538)
                      .+..++.+.|++++|...|++..+   .+...|+.+...+...|++++|+..|...+...-..             .   
T Consensus       438 ~la~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~-------------~---  501 (615)
T TIGR00990       438 QLGVTQYKEGSIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKET-------------K---  501 (615)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCcc-------------c---
Confidence            888999999999999999988765   356788888899999999999986665554321110             0   


Q ss_pred             CCCccH-HHHHHHHHHhhhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC
Q 044988          374 GIKPRI-EHYGCMVDLFSRAGLMDEAFSLVQNM-PMKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ  445 (538)
Q Consensus       374 ~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~  445 (538)
                      +..++. ..++.....+...|++++|.+++++. ...|+ ...+..+...+.+.|++++|++.|+++ .++.+..
T Consensus       502 ~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A-~~l~~~~  575 (615)
T TIGR00990       502 PMYMNVLPLINKALALFQWKQDFIEAENLCEKALIIDPECDIAVATMAQLLLQQGDVDEALKLFERA-AELARTE  575 (615)
T ss_pred             cccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHH-HHHhccH
Confidence            111221 12233333444568999999999875 34455 456788888899999999999999998 6666553

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=99.80  E-value=1.6e-16  Score=154.95  Aligned_cols=433  Identities=13%  Similarity=0.070  Sum_probs=304.6

Q ss_pred             hHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCC------cchHHHHHHHHhcCCCchHHHHHH
Q 044988           33 TKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPS------TAIWNQMIRGHARSETPEKSVYLY  106 (538)
Q Consensus        33 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~------~~~~~~li~~~~~~~~~~~a~~~~  106 (538)
                      +..+.+.+....... +.+|.+.+.|.+.|...|+++.+..+...+...+      ..+|-.+.++|-..|++++|...|
T Consensus       252 ~~~~~~ll~~ay~~n-~~nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY  330 (1018)
T KOG2002|consen  252 YKKGVQLLQRAYKEN-NENPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYY  330 (1018)
T ss_pred             HHHHHHHHHHHHhhc-CCCcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHH
Confidence            344444444444333 3367778888888888888888888877665322      234667888888889999998888


Q ss_pred             HHhHhCCCCCCcch--HHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcC-CCCChhHHHHHhhcCC
Q 044988          107 KQMIDKETEPDEYT--YSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSG-GECGVGCARLLFDDMP  183 (538)
Q Consensus       107 ~~m~~~~~~p~~~~--~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~~~~a~~~~~~~~  183 (538)
                      .+..+.  .|+..+  +--|...+...|+++.+...|+...+.. +.+..+...|...|...+ ..-..+.|..++.+..
T Consensus       331 ~~s~k~--~~d~~~l~~~GlgQm~i~~~dle~s~~~fEkv~k~~-p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~  407 (1018)
T KOG2002|consen  331 MESLKA--DNDNFVLPLVGLGQMYIKRGDLEESKFCFEKVLKQL-PNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVL  407 (1018)
T ss_pred             HHHHcc--CCCCccccccchhHHHHHhchHHHHHHHHHHHHHhC-cchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHH
Confidence            777654  455543  4456777888889999988888888874 556677777777787774 1112677777777776


Q ss_pred             CC---CchhHHHHHHHHHhcCC------HHHHHHHHcc-CCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHC---CCC
Q 044988          184 AR---SVVSWNSLLKGYVKRGD------IDGAWKIFDE-MPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRA---RVG  250 (538)
Q Consensus       184 ~~---~~~~~~~li~~~~~~g~------~~~A~~~~~~-m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~---g~~  250 (538)
                      ++   |...|-.+...+....-      +..|..++.. +....+...|.+...+...|++.+|...|......   -..
T Consensus       408 ~~~~~d~~a~l~laql~e~~d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n  487 (1018)
T KOG2002|consen  408 EQTPVDSEAWLELAQLLEQTDPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVAN  487 (1018)
T ss_pred             hcccccHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcC
Confidence            54   55566665555544332      3334433333 22366778888988899999999999999988764   223


Q ss_pred             CCH------HHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---C
Q 044988          251 LDQ------VALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---R  321 (538)
Q Consensus       251 p~~------~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~  321 (538)
                      +|.      .+--.+....-..++.+.|...|..+.+.     .|.-+..|-.++-.....+...+|...++....   .
T Consensus       488 ~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilke-----hp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~  562 (1018)
T KOG2002|consen  488 KDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKE-----HPGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSS  562 (1018)
T ss_pred             ccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHH-----CchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccC
Confidence            333      23334555566778999999999999886     777777765555444455788889998888765   4


Q ss_pred             CcchHHHHHHHHHhcCCccHHHHH--------------HH--HHHHHhc------------ccCcHHHHHHHHHHhhhhc
Q 044988          322 NTVSWTSMITGFAKQGYAQEALLT--------------FL--GVLSACS------------HGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       322 ~~~~~~~li~~~~~~~~~~~a~~~--------------~~--~ll~~~~------------~~~~~~~a~~~~~~~~~~~  373 (538)
                      ++..++.+...+.+...+..|...              |.  .|.+.|.            ..+..++|.++|.++.+. 
T Consensus       563 np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~-  641 (1018)
T KOG2002|consen  563 NPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRN-  641 (1018)
T ss_pred             CcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhc-
Confidence            666777777777777666666522              22  2222222            124578899999998864 


Q ss_pred             CCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHH
Q 044988          374 GIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLA  451 (538)
Q Consensus       374 ~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~  451 (538)
                       -+.|...-|-+.-.++..|++.+|..+|..+.  ...+..+|-.+..+|...|++..|++.|+.......+.+......
T Consensus       642 -dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~  720 (1018)
T KOG2002|consen  642 -DPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLH  720 (1018)
T ss_pred             -CcchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHH
Confidence             24478888999999999999999999999885  223456788999999999999999999999874444444332334


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          452 LVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       452 ~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      .|+.++.+.|++.+|.+.+......
T Consensus       721 ~Lara~y~~~~~~eak~~ll~a~~~  745 (1018)
T KOG2002|consen  721 YLARAWYEAGKLQEAKEALLKARHL  745 (1018)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            8999999999999999998877654

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.78  E-value=4.6e-14  Score=147.08  Aligned_cols=438  Identities=8%  Similarity=-0.038  Sum_probs=313.4

Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHc-cCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCc
Q 044988           21 RQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVT-SGYLINAHKVFEKTENPSTAIWNQMIRGHARSETP   99 (538)
Q Consensus        21 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~   99 (538)
                      ..+...+...++.+.+..++..+.+.+.. +......|..+|.. .++ +++..+++...+.++..+..+...|.+.|+.
T Consensus       186 L~~~rlY~~l~dw~~Ai~lL~~L~k~~pl-~~~~~~~L~~ay~q~l~~-~~a~al~~~~lk~d~~l~~ala~~yi~~G~~  263 (987)
T PRK09782        186 TDLLQRAIYLKQWSQADTLYNEARQQNTL-SAAERRQWFDVLLAGQLD-DRLLALQSQGIFTDPQSRITYATALAYRGEK  263 (987)
T ss_pred             HHHHHHHHHHhCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHHhhCH-HHHHHHhchhcccCHHHHHHHHHHHHHCCCH
Confidence            33488899999999999999999999744 45667777778887 466 8888887765566888899999999999999


Q ss_pred             hHHHHHHHHhHhCCCC-CCcchHHHH------------------------------HHHHHccCCcHHHHHHH-------
Q 044988          100 EKSVYLYKQMIDKETE-PDEYTYSFL------------------------------LSVCARCGLFREGEQVH-------  141 (538)
Q Consensus       100 ~~a~~~~~~m~~~~~~-p~~~~~~~l------------------------------i~~~~~~~~~~~a~~~~-------  141 (538)
                      ++|..+++++...... |...+|.-+                              +..+.+.++++.++++.       
T Consensus       264 ~~A~~~L~~~~~~~~~~~~~~~~~~~l~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  343 (987)
T PRK09782        264 ARLQHYLIENKPLFTTDAQEKSWLYLLSKYSANPVQALANYTVQFADNRQYVVGATLPVLLKEGQYDAAQKLLATLPANE  343 (987)
T ss_pred             HHHHHHHHhCcccccCCCccHHHHHHHHhccCchhhhccchhhhhHHHHHHHHHHHHHHHHhccHHHHHHHHhcCCCcch
Confidence            9999999998653211 333333222                              22333444444443331       


Q ss_pred             ----------------------HHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC-C-----CchhHHHH
Q 044988          142 ----------------------GRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA-R-----SVVSWNSL  193 (538)
Q Consensus       142 ----------------------~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~-~-----~~~~~~~l  193 (538)
                                            ..|.+. .+-+....-.+.......|+   .++|.++|+.... +     +....+-+
T Consensus       344 ~~~~r~~~~~~~~~~~~~~~~~~~~y~~-~~~~~~~l~q~~~~~~~~~~---~~~a~~~~~~~~~~~~~~~~~~~l~~~l  419 (987)
T PRK09782        344 MLEERYAVSVATRNKAEALRLARLLYQQ-EPANLTRLDQLTWQLMQNGQ---SREAADLLLQRYPFQGDARLSQTLMARL  419 (987)
T ss_pred             HHHHHHhhccccCchhHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHccc---HHHHHHHHHHhcCCCcccccCHHHHHHH
Confidence                                  111111 02233344444445566777   8888888887765 2     22234456


Q ss_pred             HHHHHhcCC---HHHHHHHHc-------------------------cCCC---C--ChHHHHHHHHHHHHcCCHHHHHHH
Q 044988          194 LKGYVKRGD---IDGAWKIFD-------------------------EMPH---R--NVVSWTTMISGCAQNGKSRQALSL  240 (538)
Q Consensus       194 i~~~~~~g~---~~~A~~~~~-------------------------~m~~---~--~~~~~~~li~~~~~~~~~~~a~~~  240 (538)
                      +..|.+.+.   ..++..+-.                         ....   +  +...|..+..++.. +++++|+..
T Consensus       420 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a  498 (987)
T PRK09782        420 ASLLESHPYLATPAKVAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYA  498 (987)
T ss_pred             HHHHHhCCcccchHHHHHhccccccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHH
Confidence            667766655   333333311                         1111   2  45677777777776 788899998


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          241 FNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       241 ~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      |.+....  .|+......+...+...|+++.|...++.+...      ++....+..+...+.+.|+.++|...+++..+
T Consensus       499 ~~~Al~~--~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~------~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~  570 (987)
T PRK09782        499 WLQAEQR--QPDAWQHRAVAYQAYQVEDYATALAAWQKISLH------DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQ  570 (987)
T ss_pred             HHHHHHh--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc------CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            8887764  466655444555556899999999999987553      33333455778888999999999999998876


Q ss_pred             CCcchHHHH---HHHHHhcCCccHHH-------------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHH
Q 044988          321 RNTVSWTSM---ITGFAKQGYAQEAL-------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYG  383 (538)
Q Consensus       321 ~~~~~~~~l---i~~~~~~~~~~~a~-------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~  383 (538)
                      .++......   ...+...|++++|.             ..+..+..++.+.|++++|...+++..+.   .| +...++
T Consensus       571 l~P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l---~Pd~~~a~~  647 (987)
T PRK09782        571 RGLGDNALYWWLHAQRYIPGQPELALNDLTRSLNIAPSANAYVARATIYRQRHNVPAAVSDLRAALEL---EPNNSNYQA  647 (987)
T ss_pred             cCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHH
Confidence            443333333   23344459999998             34555567888999999999999999865   66 477888


Q ss_pred             HHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcC
Q 044988          384 CMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAK  461 (538)
Q Consensus       384 ~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g  461 (538)
                      .+..++...|+.++|++.+++.. ..|+ ...+..+..++...|++++|+..++++ ..+.|+...... ..++...+..
T Consensus       648 nLG~aL~~~G~~eeAi~~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~A-l~l~P~~a~i~~-~~g~~~~~~~  725 (987)
T PRK09782        648 ALGYALWDSGDIAQSREMLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLV-IDDIDNQALITP-LTPEQNQQRF  725 (987)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH-HhcCCCCchhhh-hhhHHHHHHH
Confidence            99999999999999999999874 4454 678889999999999999999999999 999999988677 8889999999


Q ss_pred             ChHHHHHHHHHHHhCCC
Q 044988          462 RWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       462 ~~~~A~~~~~~m~~~~~  478 (538)
                      +++.|.+-+++....+.
T Consensus       726 ~~~~a~~~~~r~~~~~~  742 (987)
T PRK09782        726 NFRRLHEEVGRRWTFSF  742 (987)
T ss_pred             HHHHHHHHHHHHhhcCc
Confidence            99999999888776544

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.77  E-value=9.6e-15  Score=148.99  Aligned_cols=428  Identities=10%  Similarity=0.018  Sum_probs=307.8

Q ss_pred             cccccCCCCCCCCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC--
Q 044988            3 VEEIIPANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN--   80 (538)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--   80 (538)
                      +.++++.+|..++...   .++..+...|+.++|...++..... .+........+...|...|++++|+++|+++.+  
T Consensus        57 L~qaL~~~P~~~~av~---dll~l~~~~G~~~~A~~~~eka~~p-~n~~~~~llalA~ly~~~gdyd~Aiely~kaL~~d  132 (822)
T PRK14574         57 LQEESKAGPLQSGQVD---DWLQIAGWAGRDQEVIDVYERYQSS-MNISSRGLASAARAYRNEKRWDQALALWQSSLKKD  132 (822)
T ss_pred             HHHHHhhCccchhhHH---HHHHHHHHcCCcHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            4556667776654323   7788888889999999999998821 122333444446688889999999999999873  


Q ss_pred             -CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHH
Q 044988           81 -PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNL  159 (538)
Q Consensus        81 -~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  159 (538)
                       .++..+..++..+...++.++|++.++++...  .|+...+..++..+...++..+|.+.++++.+.. +.+...+..+
T Consensus       133 P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~~-P~n~e~~~~~  209 (822)
T PRK14574        133 PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRNYDALQASSEAVRLA-PTSEEVLKNH  209 (822)
T ss_pred             CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchHHHHHHHHHHHHHhC-CCCHHHHHHH
Confidence             34556777788899999999999999999875  5666666555444544566666999999999985 6678888999


Q ss_pred             HHHHHhcCCCCChhHHHHHhhcCCCC-Cchh--H------HHHHHHH-----HhcCC---HHHHHHHHccCCC-----CC
Q 044988          160 MNLYLMSGGECGVGCARLLFDDMPAR-SVVS--W------NSLLKGY-----VKRGD---IDGAWKIFDEMPH-----RN  217 (538)
Q Consensus       160 ~~~~~~~g~~~~~~~a~~~~~~~~~~-~~~~--~------~~li~~~-----~~~g~---~~~A~~~~~~m~~-----~~  217 (538)
                      +.+..+.|-   ...|.++..+-+.- +...  +      ..+++.-     ....+   .+.|+.-++.+..     |.
T Consensus       210 ~~~l~~~~~---~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~ala~~~~l~~~~~~~p~  286 (822)
T PRK14574        210 LEILQRNRI---VEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIADKALADYQNLLTRWGKDPE  286 (822)
T ss_pred             HHHHHHcCC---cHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHHHHHHhhccCCCc
Confidence            999999999   88999888876631 1111  1      1111110     01122   3344444444332     32


Q ss_pred             hH-----HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCC-CCCcc
Q 044988          218 VV-----SWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVG-REPVL  291 (538)
Q Consensus       218 ~~-----~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~-~~~~~  291 (538)
                      ..     ..--.+-++...|++.+|++.|+.+...|.+....+-..+..+|...+++++|..++..+....... ..+.+
T Consensus       287 ~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~  366 (822)
T PRK14574        287 AQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDD  366 (822)
T ss_pred             cchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcc
Confidence            21     1223456778899999999999999999877667788899999999999999999999997752110 12334


Q ss_pred             hhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHH-HHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhh
Q 044988          292 VSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMI-TGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMN  370 (538)
Q Consensus       292 ~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li-~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~  370 (538)
                      ......|.-+|...+++++|..+++++.+..+.-+.... ..-.-+.++.   ..+..++..+...|++.+|++.++++.
T Consensus       367 ~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~---~~~~l~a~~~~~~gdl~~Ae~~le~l~  443 (822)
T PRK14574        367 LLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWI---EGQTLLVQSLVALNDLPTAQKKLEDLS  443 (822)
T ss_pred             hHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHH---HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            444567889999999999999999999863221000000 0000111222   334455666777889999999999998


Q ss_pred             hhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          371 QNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       371 ~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      ..   .| |......+.+.+...|.+.+|.+.++... ..|+ ..+....+.++...+++++|..+.+.+ .+..|++..
T Consensus       444 ~~---aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~~~A~~~~~~l-~~~~Pe~~~  519 (822)
T PRK14574        444 ST---APANQNLRIALASIYLARDLPRKAEQELKAVESLAPRSLILERAQAETAMALQEWHQMELLTDDV-ISRSPEDIP  519 (822)
T ss_pred             Hh---CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhhHHHHHHHHHHH-HhhCCCchh
Confidence            65   55 79999999999999999999999998764 4555 556667778889999999999999999 999999987

>KOG0495 consensus HAT repeat protein [RNA processing and modification]

Probab=99.68  E-value=5.4e-12  Score=118.59  Aligned_cols=447  Identities=12%  Similarity=0.094  Sum_probs=281.4

Q ss_pred             HHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC--------CCCcchHHHHHHHH
Q 044988           22 QIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE--------NPSTAIWNQMIRGH   93 (538)
Q Consensus        22 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~--------~~~~~~~~~li~~~   93 (538)
                      -|..++++...++.|..+++...+. ++.++.+|..-...--.+|+.+....+.++-.        +.+...|-.=...|
T Consensus       411 dLwlAlarLetYenAkkvLNkaRe~-iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~  489 (913)
T KOG0495|consen  411 DLWLALARLETYENAKKVLNKAREI-IPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEAC  489 (913)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhh-CCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHH
Confidence            3455566666666667676666554 44466666666665666666666666665432        13444455555555


Q ss_pred             hcCCCchHHHHHHHHhHhCCCCCC--cchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCC
Q 044988           94 ARSETPEKSVYLYKQMIDKETEPD--EYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECG  171 (538)
Q Consensus        94 ~~~~~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  171 (538)
                      -..|..--+..+......-|+.-.  ..||..-...|.+.+.++-|..+|...++- ++.+...|......--..|.   
T Consensus       490 e~agsv~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqv-fp~k~slWlra~~~ek~hgt---  565 (913)
T KOG0495|consen  490 EDAGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQV-FPCKKSLWLRAAMFEKSHGT---  565 (913)
T ss_pred             hhcCChhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhh-ccchhHHHHHHHHHHHhcCc---
Confidence            555666666666666655554321  236666666677777777777777766665 34555666666666666666   


Q ss_pred             hhHHHHHhhcCCC---CCchhHHHHHHHHHhcCCHHHHHHHHccCCC--C-ChHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 044988          172 VGCARLLFDDMPA---RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--R-NVVSWTTMISGCAQNGKSRQALSLFNEMR  245 (538)
Q Consensus       172 ~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~  245 (538)
                      .++...+|.+...   .....|-...+.+-..|+...|..++...-+  | +...|-.-+.....+.+++.|..+|.+..
T Consensus       566 ~Esl~Allqkav~~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar  645 (913)
T KOG0495|consen  566 RESLEALLQKAVEQCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKAR  645 (913)
T ss_pred             HHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHh
Confidence            7777777666654   2345566666666777777777777766543  2 33456666666677777777877777665


Q ss_pred             HCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CCc
Q 044988          246 RARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RNT  323 (538)
Q Consensus       246 ~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~~  323 (538)
                      .  ..|+...|..-+..---.+..++|.++++...+.     +|.....|..+.+.+-+.++++.|.+.|..=.+  |+.
T Consensus       646 ~--~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~-----fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~  718 (913)
T KOG0495|consen  646 S--ISGTERVWMKSANLERYLDNVEEALRLLEEALKS-----FPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNS  718 (913)
T ss_pred             c--cCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHh-----CCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCC
Confidence            5  4566666655555555567777777777777775     677777777777777777777777777765544  433


Q ss_pred             -chHHHHHHHHHhcCCccHHH--------------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHH
Q 044988          324 -VSWTSMITGFAKQGYAQEAL--------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDL  388 (538)
Q Consensus       324 -~~~~~li~~~~~~~~~~~a~--------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~  388 (538)
                       ..|-.+...--+.|....|.              ..|...+..-.+.|..+.|..+..+..+.+  +.+...|..-|..
T Consensus       719 ipLWllLakleEk~~~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQec--p~sg~LWaEaI~l  796 (913)
T KOG0495|consen  719 IPLWLLLAKLEEKDGQLVRARSILDRARLKNPKNALLWLESIRMELRAGNKEQAELLMAKALQEC--PSSGLLWAEAIWL  796 (913)
T ss_pred             chHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CccchhHHHHHHh
Confidence             33444444334444333333              334444444455555555555555555431  2234445555555


Q ss_pred             hhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHH
Q 044988          389 FSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAA  468 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~  468 (538)
                      ..+.++-......+++..  -|+...-.+...+....++++|.+.|++. ....|+...+|. .+...+.+.|.-++-.+
T Consensus       797 e~~~~rkTks~DALkkce--~dphVllaia~lfw~e~k~~kar~Wf~Ra-vk~d~d~GD~wa-~fykfel~hG~eed~ke  872 (913)
T KOG0495|consen  797 EPRPQRKTKSIDALKKCE--HDPHVLLAIAKLFWSEKKIEKAREWFERA-VKKDPDNGDAWA-WFYKFELRHGTEEDQKE  872 (913)
T ss_pred             ccCcccchHHHHHHHhcc--CCchhHHHHHHHHHHHHHHHHHHHHHHHH-HccCCccchHHH-HHHHHHHHhCCHHHHHH
Confidence            555555444444444442  35555556666777888999999999999 999999999888 88888999999888888


Q ss_pred             HHHHHHhCCCCCCCceeEEE
Q 044988          469 VRQKMIKMGVRKPPGQSWVQ  488 (538)
Q Consensus       469 ~~~~m~~~~~~~~~~~~~~~  488 (538)
                      ++++...  -.|.-|..|+.
T Consensus       873 v~~~c~~--~EP~hG~~W~a  890 (913)
T KOG0495|consen  873 VLKKCET--AEPTHGELWQA  890 (913)
T ss_pred             HHHHHhc--cCCCCCcHHHH
Confidence            9888776  34666778853

>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]

Probab=99.67  E-value=3.6e-13  Score=132.03  Aligned_cols=385  Identities=11%  Similarity=0.086  Sum_probs=169.8

Q ss_pred             CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCC--CCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHH
Q 044988           82 STAIWNQMIRGHARSETPEKSVYLYKQMIDKETE--PDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNL  159 (538)
Q Consensus        82 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~--p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  159 (538)
                      |+...+.|.+-|.-.|+++.++.+.+.+......  .-...|-.+.++|-..|++++|...|.+..+..-..-...+..+
T Consensus       269 nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d~~~l~~~Gl  348 (1018)
T KOG2002|consen  269 NPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVGL  348 (1018)
T ss_pred             CcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCCccccccch
Confidence            4444444444444455555555555544432100  11223444445555555555555555444443211112233344


Q ss_pred             HHHHHhcCCCCChhHHHHHhhcCCCC---CchhHHHHHHHHHhcC----CHHHHHHHHccCCCC---ChHHHHHHHHHHH
Q 044988          160 MNLYLMSGGECGVGCARLLFDDMPAR---SVVSWNSLLKGYVKRG----DIDGAWKIFDEMPHR---NVVSWTTMISGCA  229 (538)
Q Consensus       160 ~~~~~~~g~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g----~~~~A~~~~~~m~~~---~~~~~~~li~~~~  229 (538)
                      ...|.+.|+   ++.+...|+.+...   +..+...+...|...+    ..+.|..++.+..++   |...|-.+...+.
T Consensus       349 gQm~i~~~d---le~s~~~fEkv~k~~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~~~d~~a~l~laql~e  425 (1018)
T KOG2002|consen  349 GQMYIKRGD---LEESKFCFEKVLKQLPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQTPVDSEAWLELAQLLE  425 (1018)
T ss_pred             hHHHHHhch---HHHHHHHHHHHHHhCcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcccccHHHHHHHHHHHH
Confidence            445555555   55555555544431   2333333333333332    334444444443332   2334444444333


Q ss_pred             HcCCHHHHHHHHHHHH----HCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhcc----CCC-CCcchhHHHHHHH
Q 044988          230 QNGKSRQALSLFNEMR----RARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFS----VGR-EPVLVSLNNALIH  300 (538)
Q Consensus       230 ~~~~~~~a~~~~~~m~----~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~----~~~-~~~~~~~~~~l~~  300 (538)
                      .. +...++.+|....    ..+-.+.....+.+...+...|+++.|...|........    ... ...++++--.+..
T Consensus       426 ~~-d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlar  504 (1018)
T KOG2002|consen  426 QT-DPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLAR  504 (1018)
T ss_pred             hc-ChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHH
Confidence            32 2222244443332    233334445555555555555555555555555444311    000 0111212223444


Q ss_pred             HHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhc-------CCccHHH--------------HHHHHHHHHhcccCcH
Q 044988          301 MYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQ-------GYAQEAL--------------LTFLGVLSACSHGGFV  359 (538)
Q Consensus       301 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~-------~~~~~a~--------------~~~~~ll~~~~~~~~~  359 (538)
                      .+-..++++.|.+.|..+.+..+.    .|.+|.+.       +...+|.              ..+..+...+.....+
T Consensus       505 l~E~l~~~~~A~e~Yk~Ilkehp~----YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~  580 (1018)
T KOG2002|consen  505 LLEELHDTEVAEEMYKSILKEHPG----YIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEW  580 (1018)
T ss_pred             HHHhhhhhhHHHHHHHHHHHHCch----hHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhh
Confidence            444555555555555555442211    11122221       2222332              1222222233333333


Q ss_pred             HHHHHHHHHhhhhcCCCccHHHHHHHHHHhhh------------cCChHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcC
Q 044988          360 DEGRQFFECMNQNWGIKPRIEHYGCMVDLFSR------------AGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGCRIHN  425 (538)
Q Consensus       360 ~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~------------~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~~~~~  425 (538)
                      ..|..-|..+.+.....+|..+.-+|...|..            .+..++|+++|.++. . +-|...-|.+.-.++..|
T Consensus       581 ~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~dpkN~yAANGIgiVLA~kg  660 (1018)
T KOG2002|consen  581 KPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRNDPKNMYAANGIGIVLAEKG  660 (1018)
T ss_pred             cccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcCcchhhhccchhhhhhhcc
Confidence            44444333333322223444444444443331            223556666665542 2 233455555555666777


Q ss_pred             CHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          426 NAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       426 ~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      ++..|..+|.+. .+-..+...+|. .++.+|..+|+|-.|+++|+....+
T Consensus       661 ~~~~A~dIFsqV-rEa~~~~~dv~l-Nlah~~~e~~qy~~AIqmYe~~lkk  709 (1018)
T KOG2002|consen  661 RFSEARDIFSQV-REATSDFEDVWL-NLAHCYVEQGQYRLAIQMYENCLKK  709 (1018)
T ss_pred             CchHHHHHHHHH-HHHHhhCCceee-eHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777777777776 333334445566 6667777777777777777665543

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.67  E-value=8.4e-12  Score=111.61  Aligned_cols=427  Identities=12%  Similarity=0.113  Sum_probs=264.3

Q ss_pred             CCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHc--cCChhHH-HH-----------------
Q 044988           14 SSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVT--SGYLINA-HK-----------------   73 (538)
Q Consensus        14 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~g~~~~a-~~-----------------   73 (538)
                      +.+..+-+.|+... ..+....+.-+++.|.+.|++.++.+--.|+..-+-  +.++.-| .+                 
T Consensus       113 ~~~V~~E~nL~kmI-S~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK  191 (625)
T KOG4422|consen  113 PLQVETENNLLKMI-SSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWK  191 (625)
T ss_pred             chhhcchhHHHHHH-hhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccc
Confidence            33444566676665 456678888999999999999888877777654332  2221111 11                 


Q ss_pred             ------HHhcCCCCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHh
Q 044988           74 ------VFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLAS  147 (538)
Q Consensus        74 ------~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  147 (538)
                            ++-+..+.+..+|.+||.++|+-...+.|.+++++-.....+.+..+||.+|.+-.-    ...++++.+|...
T Consensus       192 ~G~vAdL~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~----~~~K~Lv~EMisq  267 (625)
T KOG4422|consen  192 SGAVADLLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSY----SVGKKLVAEMISQ  267 (625)
T ss_pred             cccHHHHHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHh----hccHHHHHHHHHh
Confidence                  222222345567777777777777777777777777766667777777777766432    2226677777777


Q ss_pred             CCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCC----CCChHHHHH
Q 044988          148 GYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMP----HRNVVSWTT  223 (538)
Q Consensus       148 ~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~----~~~~~~~~~  223 (538)
                      .+.||..|+|+++.+..+.|+   ++.|.+                           .|.+++.+|.    +|...+|..
T Consensus       268 km~Pnl~TfNalL~c~akfg~---F~~ar~---------------------------aalqil~EmKeiGVePsLsSyh~  317 (625)
T KOG4422|consen  268 KMTPNLFTFNALLSCAAKFGK---FEDARK---------------------------AALQILGEMKEIGVEPSLSSYHL  317 (625)
T ss_pred             hcCCchHhHHHHHHHHHHhcc---hHHHHH---------------------------HHHHHHHHHHHhCCCcchhhHHH
Confidence            777777777777777777776   655543                           2344555554    488888888


Q ss_pred             HHHHHHHcCCHHH-HHHHHHHHHHC--C--C---CC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc---
Q 044988          224 MISGCAQNGKSRQ-ALSLFNEMRRA--R--V---GL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL---  291 (538)
Q Consensus       224 li~~~~~~~~~~~-a~~~~~~m~~~--g--~---~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~---  291 (538)
                      +|..+++.++..+ |..++.+.+..  |  +   .| |...|...+..|.+..+.+.|.++.............+++   
T Consensus       318 iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~  397 (625)
T KOG4422|consen  318 IIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHR  397 (625)
T ss_pred             HHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHH
Confidence            8888888877644 55555665542  2  2   23 5566788888899999999999988877654322223333   


Q ss_pred             hhHHHHHHHHHHhCCCHHHHHHHHHhcCC----CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHH
Q 044988          292 VSLNNALIHMYASCGEIEEAYGVFRKMQR----RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFE  367 (538)
Q Consensus       292 ~~~~~~l~~~~~~~g~~~~a~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~  367 (538)
                      ...|..+....|.....+.-...|+.|..    |+..+...++.+....|+++-....|...+ .+.+.-+-+..++++.
T Consensus       398 ~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~-~~ght~r~~l~eeil~  476 (625)
T KOG4422|consen  398 NFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIHLLRALDVANRLEVIPRIWKDSK-EYGHTFRSDLREEILM  476 (625)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHHHHHHHhhcCcchhHHHHHHHHH-HhhhhhhHHHHHHHHH
Confidence            34566778888888889999999998875    566666666777666666655444443332 2232333344455555


Q ss_pred             HhhhhcCCCccHHHHHHHHHHhhhcC-ChHHH-HHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHch--hccC
Q 044988          368 CMNQNWGIKPRIEHYGCMVDLFSRAG-LMDEA-FSLVQNMP-MKPNDAVLGSLLLGCRIHNNAELASQVAQKLV--AEID  442 (538)
Q Consensus       368 ~~~~~~~~~p~~~~~~~l~~~~~~~g-~~~~A-~~~~~~~~-~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~--~~~~  442 (538)
                      .+... ...|+...-..+-.+.+++- ++.++ ...-.+++ .+-.....+.....+.+.|..++|.+++..+.  ..-.
T Consensus       477 ~L~~~-k~hp~tp~r~Ql~~~~ak~aad~~e~~e~~~~R~r~~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~i  555 (625)
T KOG4422|consen  477 LLARD-KLHPLTPEREQLQVAFAKCAADIKEAYESQPIRQRAQDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKI  555 (625)
T ss_pred             HHhcC-CCCCCChHHHHHHHHHHHHHHHHHHHHHhhHHHHHhccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcC
Confidence            55544 33443332222222222211 11111 11112222 23445666777777889999999999998873  2233


Q ss_pred             CCCcccHH--HHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          443 PEQAAGYL--ALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       443 p~~~~~~~--~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      |..+. ..  .-+.+.-.+.++...|+.+++-|...+.
T Consensus       556 p~~p~-lnAm~El~d~a~~~~spsqA~~~lQ~a~~~n~  592 (625)
T KOG4422|consen  556 PRSPL-LNAMAELMDSAKVSNSPSQAIEVLQLASAFNL  592 (625)
T ss_pred             CCCcc-hhhHHHHHHHHHhcCCHHHHHHHHHHHHHcCc
Confidence            44443 22  0234555667788889999998877665

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.65  E-value=4.1e-14  Score=126.95  Aligned_cols=427  Identities=12%  Similarity=0.097  Sum_probs=274.1

Q ss_pred             HHHHHhccCChHHHHHHHHHHHHhCCCCChhHHH-HHHHHHHccCChhHHHHHHhcCCC--CC------cchHHHHHHHH
Q 044988           23 IFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILA-KLLAFYVTSGYLINAHKVFEKTEN--PS------TAIWNQMIRGH   93 (538)
Q Consensus        23 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~~a~~~~~~~~~--~~------~~~~~~li~~~   93 (538)
                      |...|.......+|...++.+++...-|+...+. .+-+.+.+...+.+|+++++-...  |+      ....+.+.-.+
T Consensus       207 laqqy~~ndm~~ealntyeiivknkmf~nag~lkmnigni~~kkr~fskaikfyrmaldqvpsink~~rikil~nigvtf  286 (840)
T KOG2003|consen  207 LAQQYEANDMTAEALNTYEIIVKNKMFPNAGILKMNIGNIHFKKREFSKAIKFYRMALDQVPSINKDMRIKILNNIGVTF  286 (840)
T ss_pred             HHHHhhhhHHHHHHhhhhhhhhcccccCCCceeeeeecceeeehhhHHHHHHHHHHHHhhccccchhhHHHHHhhcCeeE
Confidence            3444555667788889999999888777765443 355778888899999998864331  22      22455566678


Q ss_pred             hcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCc------------hhHHhH---
Q 044988           94 ARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSN------------VFIRTN---  158 (538)
Q Consensus        94 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~------------~~~~~~---  158 (538)
                      .+.|+++.|+..|+...+.  .||-.+--.|+-++...|+.++..+.|.+|+.....||            ....+.   
T Consensus       287 iq~gqy~dainsfdh~m~~--~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddkyi~~~ddp~~~ll~eai~  364 (840)
T KOG2003|consen  287 IQAGQYDDAINSFDHCMEE--APNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDKYIKEKDDPDDNLLNEAIK  364 (840)
T ss_pred             EecccchhhHhhHHHHHHh--CccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCcccccCCcCCcchHHHHHHHh
Confidence            8999999999999998875  58877666666666677999999999999987533332            222221   


Q ss_pred             --HHHHHHhcCCCCChhH----HHHHhhcCCCCCch-------------hHHH--------HHHHHHhcCCHHHHHHHHc
Q 044988          159 --LMNLYLMSGGECGVGC----ARLLFDDMPARSVV-------------SWNS--------LLKGYVKRGDIDGAWKIFD  211 (538)
Q Consensus       159 --l~~~~~~~g~~~~~~~----a~~~~~~~~~~~~~-------------~~~~--------li~~~~~~g~~~~A~~~~~  211 (538)
                        .+.-+-+... ...++    +.++..-...|+..             .+.-        -..-+.+.|+++.|.++++
T Consensus       365 nd~lk~~ek~~k-a~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk~~d~~~aieilk  443 (840)
T KOG2003|consen  365 NDHLKNMEKENK-ADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAIDLEINKAGELLKNGDIEGAIEILK  443 (840)
T ss_pred             hHHHHHHHHhhh-hhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhccCHHHHHHHHH
Confidence              1122222221 00122    22222222233211             0000        1123588999999999888


Q ss_pred             cCCCCChHHHHH------HHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccC
Q 044988          212 EMPHRNVVSWTT------MISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSV  285 (538)
Q Consensus       212 ~m~~~~~~~~~~------li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~  285 (538)
                      -..+.|..+-..      ++..+...+++..|..+-+...... .-+....+.--......|++++|...|.+....   
T Consensus       444 v~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~d-ryn~~a~~nkgn~~f~ngd~dka~~~ykeal~n---  519 (840)
T KOG2003|consen  444 VFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNID-RYNAAALTNKGNIAFANGDLDKAAEFYKEALNN---  519 (840)
T ss_pred             HHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhccc-ccCHHHhhcCCceeeecCcHHHHHHHHHHHHcC---
Confidence            777644433221      1222222335666666655554321 112222222222233467777777777777665   


Q ss_pred             CCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHH--------------HHHHH
Q 044988          286 GREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEAL--------------LTFLG  348 (538)
Q Consensus       286 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~--------------~~~~~  348 (538)
                       ........| .+.-.+...|++++|.+.|-++..   .+......+.+.|-...+...|+              .+...
T Consensus       520 -dasc~ealf-niglt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~~q~~slip~dp~ilsk  597 (840)
T KOG2003|consen  520 -DASCTEALF-NIGLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELLMQANSLIPNDPAILSK  597 (840)
T ss_pred             -chHHHHHHH-HhcccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhcccCCCCHHHHHH
Confidence             333333344 344556667777777777766543   45555556666666666666665              45566


Q ss_pred             HHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHHHHHHH-HhcCC
Q 044988          349 VLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGSLLLGC-RIHNN  426 (538)
Q Consensus       349 ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l~~~~-~~~~~  426 (538)
                      +...|.+.|+-..|.+++-.--+  -++.|..+..-|..-|....-+++++.+|++.. ++|+..-|..++..| .+.|+
T Consensus       598 l~dlydqegdksqafq~~ydsyr--yfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwqlmiasc~rrsgn  675 (840)
T KOG2003|consen  598 LADLYDQEGDKSQAFQCHYDSYR--YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQLMIASCFRRSGN  675 (840)
T ss_pred             HHHHhhcccchhhhhhhhhhccc--ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHHHHHHHHHhccc
Confidence            67777788888888888765443  234478888888888999999999999999885 789999999888765 67899


Q ss_pred             HHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCC
Q 044988          427 AELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKR  462 (538)
Q Consensus       427 ~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~  462 (538)
                      +++|+.+++.. ..-.|.+..... .|+.++...|-
T Consensus       676 yqka~d~yk~~-hrkfpedldclk-flvri~~dlgl  709 (840)
T KOG2003|consen  676 YQKAFDLYKDI-HRKFPEDLDCLK-FLVRIAGDLGL  709 (840)
T ss_pred             HHHHHHHHHHH-HHhCccchHHHH-HHHHHhccccc
Confidence            99999999999 888899988666 78888777663

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=99.62  E-value=5.4e-11  Score=116.31  Aligned_cols=438  Identities=12%  Similarity=0.071  Sum_probs=278.6

Q ss_pred             HHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHh---cCCCCCcchHHHHHHHHhcCCCchH
Q 044988           25 SLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFE---KTENPSTAIWNQMIRGHARSETPEK  101 (538)
Q Consensus        25 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~---~~~~~~~~~~~~li~~~~~~~~~~~  101 (538)
                      ..+-..|+.+.|..++..+.+..+ .....|..|..+|-..|+.+++...+-   .+.+.|...|..+.....+.|+++.
T Consensus       147 N~lfarg~~eeA~~i~~EvIkqdp-~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~~i~q  225 (895)
T KOG2076|consen  147 NNLFARGDLEEAEEILMEVIKQDP-RNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLGNINQ  225 (895)
T ss_pred             HHHHHhCCHHHHHHHHHHHHHhCc-cchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhcccHHH
Confidence            334445889999999988888753 367788888899999999888888764   3345566778888888888888999


Q ss_pred             HHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhH----HhHHHHHHHhcCCCCChhHHHH
Q 044988          102 SVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFI----RTNLMNLYLMSGGECGVGCARL  177 (538)
Q Consensus       102 a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~----~~~l~~~~~~~g~~~~~~~a~~  177 (538)
                      |.-+|.+..+.. +++...+---...|-+.|+...|...|.++.....+.|..-    --..+..+...++   -+.|.+
T Consensus       226 A~~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~---~e~a~~  301 (895)
T KOG2076|consen  226 ARYCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNE---RERAAK  301 (895)
T ss_pred             HHHHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhH---HHHHHH
Confidence            988888888764 44544555556677888888888888888887643222222    2233445666666   677777


Q ss_pred             HhhcCCC-----CCchhHHHHHHHHHhcCCHHHHHHHHccCCC-------------------------------------
Q 044988          178 LFDDMPA-----RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH-------------------------------------  215 (538)
Q Consensus       178 ~~~~~~~-----~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-------------------------------------  215 (538)
                      .++....     -+...++.++..+.+...++.|......+..                                     
T Consensus       302 ~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~  381 (895)
T KOG2076|consen  302 ALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVI  381 (895)
T ss_pred             HHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhH
Confidence            7666554     1344566666666665555555544322210                                     


Q ss_pred             ------------------------------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 044988          216 ------------------------------RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAE  265 (538)
Q Consensus       216 ------------------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  265 (538)
                                                    .++..|.-+..+|.+.|++.+|+.+|..+...-..-+...|-.+..++..
T Consensus       382 rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~  461 (895)
T KOG2076|consen  382 RLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYME  461 (895)
T ss_pred             hHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHH
Confidence                                          12234666778889999999999999999876555567788889999999


Q ss_pred             cCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcc------------hHHHHHHHH
Q 044988          266 IGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTV------------SWTSMITGF  333 (538)
Q Consensus       266 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~------------~~~~li~~~  333 (538)
                      .|..+.|...|..+...     .|.+..+-..|...+.+.|+.++|.+.+..+..||..            ..-.....+
T Consensus       462 l~e~e~A~e~y~kvl~~-----~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~r~d~l  536 (895)
T KOG2076|consen  462 LGEYEEAIEFYEKVLIL-----APDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAHRCDIL  536 (895)
T ss_pred             HhhHHHHHHHHHHHHhc-----CCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHHHHHHH
Confidence            99999999999999986     7777777788999999999999999999998765521            122233455


Q ss_pred             HhcCCccHHHHHHHHHHHHhc-------------------------------------ccCcHHHHHHHHHH-----hhh
Q 044988          334 AKQGYAQEALLTFLGVLSACS-------------------------------------HGGFVDEGRQFFEC-----MNQ  371 (538)
Q Consensus       334 ~~~~~~~~a~~~~~~ll~~~~-------------------------------------~~~~~~~a~~~~~~-----~~~  371 (538)
                      .+.|+.++=+.+-..|+.-+.                                     +.++.....+-...     ...
T Consensus       537 ~~~gk~E~fi~t~~~Lv~~~~~~~~~f~~~~k~r~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~l~d~~~~~~~e  616 (895)
T KOG2076|consen  537 FQVGKREEFINTASTLVDDFLKKRYIFPRNKKKRRRAIAGTTSKRYSELLKQIIRAREKATDDNVMEKALSDGTEFRAVE  616 (895)
T ss_pred             HHhhhHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHhhccccccccchhHHHHHHHHhccCchHHhhhcccchhhhhhhh
Confidence            666666664422222222111                                     11111100000000     000


Q ss_pred             hcCCCcc--HHHHHHHHHHhhhcCChHHHHHHHHhCC-----CCCCH-H-HH-HHHHHHHHhcCCHHHHHHHHHHchhcc
Q 044988          372 NWGIKPR--IEHYGCMVDLFSRAGLMDEAFSLVQNMP-----MKPND-A-VL-GSLLLGCRIHNNAELASQVAQKLVAEI  441 (538)
Q Consensus       372 ~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~p~~-~-~~-~~l~~~~~~~~~~~~A~~~~~~~~~~~  441 (538)
                      ..++..+  -..+.-++..+++.+++++|+.+...+.     ..++. . .+ ...+.++...+++..|...++.+. ..
T Consensus       617 ~~~Lsiddwfel~~e~i~~L~k~~r~qeAl~vv~~a~~~~~f~~~~~~~k~l~~~~l~~s~~~~d~~~a~~~lR~~i-~~  695 (895)
T KOG2076|consen  617 LRGLSIDDWFELFRELILSLAKLQRVQEALSVVFTALEAYIFFQDSEIRKELQFLGLKASLYARDPGDAFSYLRSVI-TQ  695 (895)
T ss_pred             hccCcHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhhhccHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH-HH
Confidence            0022222  1244566777888888888888887664     12222 1 22 233445677788888888888774 32


Q ss_pred             -----CCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          442 -----DPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       442 -----~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                           .|.....|. +..+...+.|+-.--.+++....
T Consensus       696 ~~~~~~~~q~~l~n-~~~s~~~~~~q~v~~~R~~~~~~  732 (895)
T KOG2076|consen  696 FQFYLDVYQLNLWN-LDFSYFSKYGQRVCYLRLIMRLL  732 (895)
T ss_pred             HhhhhhhHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHh
Confidence                 444444444 34445555554444444444433

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.61  E-value=3.3e-12  Score=114.12  Aligned_cols=350  Identities=14%  Similarity=0.160  Sum_probs=245.9

Q ss_pred             CCCChhHHHHHHHHHHccCChhHHHHHHhcCC----CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHH
Q 044988           48 FSQKNYILAKLLAFYVTSGYLINAHKVFEKTE----NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSF  123 (538)
Q Consensus        48 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~  123 (538)
                      .+.++.++..+|...++....+.|.+++++..    +.+..+||.+|.+-.    +..-.++..+|....+.||..|+|+
T Consensus       203 ~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S----~~~~K~Lv~EMisqkm~Pnl~TfNa  278 (625)
T KOG4422|consen  203 LPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASS----YSVGKKLVAEMISQKMTPNLFTFNA  278 (625)
T ss_pred             cCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHH----hhccHHHHHHHHHhhcCCchHhHHH
Confidence            44578899999999999999999999998876    356778888887643    3333889999999999999999999


Q ss_pred             HHHHHHccCCcHH----HHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhc----CC----CC----Cc
Q 044988          124 LLSVCARCGLFRE----GEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDD----MP----AR----SV  187 (538)
Q Consensus       124 li~~~~~~~~~~~----a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~----~~----~~----~~  187 (538)
                      ++++..+.|+++.    |.+++.+|++.|+.|...+|..++..+++.+++.+  .|...+.+    +.    +|    |.
T Consensus       279 lL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k--~as~~i~dI~N~ltGK~fkp~~p~d~  356 (625)
T KOG4422|consen  279 LLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQK--VASSWINDIQNSLTGKTFKPITPTDN  356 (625)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchh--hhHHHHHHHHHhhccCcccCCCCchh
Confidence            9999999998765    56788999999999999999999999999998322  23333332    22    11    45


Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHccCCC--------CC---hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHH
Q 044988          188 VSWNSLLKGYVKRGDIDGAWKIFDEMPH--------RN---VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVAL  256 (538)
Q Consensus       188 ~~~~~li~~~~~~g~~~~A~~~~~~m~~--------~~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~  256 (538)
                      ..+..-+..|....+.+-|.++-.-...        ++   ..-|..+....|+....+.-+.+|+.|.-.-+-|+..+.
T Consensus       357 ~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m  436 (625)
T KOG4422|consen  357 KFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTM  436 (625)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhH
Confidence            5667777788888888888877655432        22   234667888889999999999999999988889999999


Q ss_pred             HHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhc
Q 044988          257 VAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQ  336 (538)
Q Consensus       257 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~  336 (538)
                      ..++++..-.+.++-..++|..++..    |.........-++..+++..            ..|+...-..+-.+.++.
T Consensus       437 ~~~lrA~~v~~~~e~ipRiw~D~~~~----ght~r~~l~eeil~~L~~~k------------~hp~tp~r~Ql~~~~ak~  500 (625)
T KOG4422|consen  437 IHLLRALDVANRLEVIPRIWKDSKEY----GHTFRSDLREEILMLLARDK------------LHPLTPEREQLQVAFAKC  500 (625)
T ss_pred             HHHHHHHhhcCcchhHHHHHHHHHHh----hhhhhHHHHHHHHHHHhcCC------------CCCCChHHHHHHHHHHHH
Confidence            99999999999999999999988887    54444333322333332221            012211000110011000


Q ss_pred             CCccHHHHHHHHHHHHhcccCcHHHH-HHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-------CC
Q 044988          337 GYAQEALLTFLGVLSACSHGGFVDEG-RQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-------MK  408 (538)
Q Consensus       337 ~~~~~a~~~~~~ll~~~~~~~~~~~a-~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-------~~  408 (538)
                      -                   -++.++ +..-.++.+   ........+...-.+.+.|+.++|.++|.-+.       ..
T Consensus       501 a-------------------ad~~e~~e~~~~R~r~---~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~  558 (625)
T KOG4422|consen  501 A-------------------ADIKEAYESQPIRQRA---QDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRS  558 (625)
T ss_pred             H-------------------HHHHHHHHhhHHHHHh---ccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCC
Confidence            0                   011111 112223332   24455566777778889999999999987662       33


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccC
Q 044988          409 PNDAVLGSLLLGCRIHNNAELASQVAQKLVAEID  442 (538)
Q Consensus       409 p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~  442 (538)
                      |......-+++...+.++...|...++-| ....
T Consensus       559 p~lnAm~El~d~a~~~~spsqA~~~lQ~a-~~~n  591 (625)
T KOG4422|consen  559 PLLNAMAELMDSAKVSNSPSQAIEVLQLA-SAFN  591 (625)
T ss_pred             cchhhHHHHHHHHHhcCCHHHHHHHHHHH-HHcC
Confidence            44444556777788889999999999988 4433

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.61  E-value=3.4e-12  Score=116.03  Aligned_cols=383  Identities=14%  Similarity=0.086  Sum_probs=237.7

Q ss_pred             HHHHHHHHccCChhHHHHHHhcCC--CCC-cchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCc-chHHHHHHHHHcc
Q 044988           56 AKLLAFYVTSGYLINAHKVFEKTE--NPS-TAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDE-YTYSFLLSVCARC  131 (538)
Q Consensus        56 ~~l~~~~~~~g~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~  131 (538)
                      ...-+-|.+.|++++|++.+.+..  .|+ +..|.....+|...|+|+++.+--...++  +.|+- ..+..-.+++-..
T Consensus       119 K~~GN~~f~~kkY~eAIkyY~~AI~l~p~epiFYsNraAcY~~lgd~~~Vied~TkALE--l~P~Y~KAl~RRA~A~E~l  196 (606)
T KOG0547|consen  119 KTKGNKFFRNKKYDEAIKYYTQAIELCPDEPIFYSNRAACYESLGDWEKVIEDCTKALE--LNPDYVKALLRRASAHEQL  196 (606)
T ss_pred             HhhhhhhhhcccHHHHHHHHHHHHhcCCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhh--cCcHHHHHHHHHHHHHHhh
Confidence            334456777788888888887765  466 66777777888888888877776666665  34542 2455555566666


Q ss_pred             CCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC---Cch--------------------
Q 044988          132 GLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPAR---SVV--------------------  188 (538)
Q Consensus       132 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~---~~~--------------------  188 (538)
                      |++++|+.=+.-..-.|--.|..+--.+=+.+-+.|    ..++.+.+.+-..|   +..                    
T Consensus       197 g~~~eal~D~tv~ci~~~F~n~s~~~~~eR~Lkk~a----~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~~~~~~~  272 (606)
T KOG0547|consen  197 GKFDEALFDVTVLCILEGFQNASIEPMAERVLKKQA----MKKAKEKLKENRPPVLPSATFIASYFGSFHADPKPLFDNK  272 (606)
T ss_pred             ccHHHHHHhhhHHHHhhhcccchhHHHHHHHHHHHH----HHHHHHhhcccCCCCCCcHHHHHHHHhhccccccccccCC
Confidence            777666532222211111111111111111111111    22233333311111   111                    


Q ss_pred             ---hHHHHHHHHHh--cC---CHHHHHHHHccCC-------CCC---------hHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 044988          189 ---SWNSLLKGYVK--RG---DIDGAWKIFDEMP-------HRN---------VVSWTTMISGCAQNGKSRQALSLFNEM  244 (538)
Q Consensus       189 ---~~~~li~~~~~--~g---~~~~A~~~~~~m~-------~~~---------~~~~~~li~~~~~~~~~~~a~~~~~~m  244 (538)
                         +...+..++..  .+   .+..|...+.+-.       ..+         ..+...-...+.-.|+.-.|..-|+..
T Consensus       273 ~~ksDa~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~~~a~~d~~~~  352 (606)
T KOG0547|consen  273 SDKSDAALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDSLGAQEDFDAA  352 (606)
T ss_pred             CccchhhHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCchhhhhhHHHH
Confidence               11111111100  11   2233333322210       111         112222223344567888888888888


Q ss_pred             HHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCC--
Q 044988          245 RRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRN--  322 (538)
Q Consensus       245 ~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~--  322 (538)
                      .+....++.. |..+...|....+.++....|+...+.     .|.++.+|..-.+.+.-.+++++|..-|++...-+  
T Consensus       353 I~l~~~~~~l-yI~~a~~y~d~~~~~~~~~~F~~A~~l-----dp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~pe  426 (606)
T KOG0547|consen  353 IKLDPAFNSL-YIKRAAAYADENQSEKMWKDFNKAEDL-----DPENPDVYYHRGQMRFLLQQYEEAIADFQKAISLDPE  426 (606)
T ss_pred             HhcCcccchH-HHHHHHHHhhhhccHHHHHHHHHHHhc-----CCCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcChh
Confidence            8754444332 666677788888888888888888886     67777777777888888888999999998877633  


Q ss_pred             -cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHH
Q 044988          323 -TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSL  401 (538)
Q Consensus       323 -~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~  401 (538)
                       +.+|-.+.-+..+.                    +.++++...|++.++++  +--+.+|+.....+...+++++|.+.
T Consensus       427 ~~~~~iQl~~a~Yr~--------------------~k~~~~m~~Fee~kkkF--P~~~Evy~~fAeiLtDqqqFd~A~k~  484 (606)
T KOG0547|consen  427 NAYAYIQLCCALYRQ--------------------HKIAESMKTFEEAKKKF--PNCPEVYNLFAEILTDQQQFDKAVKQ  484 (606)
T ss_pred             hhHHHHHHHHHHHHH--------------------HHHHHHHHHHHHHHHhC--CCCchHHHHHHHHHhhHHhHHHHHHH
Confidence             33443333333333                    47888899999999873  33478999999999999999999999


Q ss_pred             HHhCC-CCCC---------HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHH
Q 044988          402 VQNMP-MKPN---------DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQ  471 (538)
Q Consensus       402 ~~~~~-~~p~---------~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~  471 (538)
                      |+... ..|.         ..+.-.++. +.-.+++..|..+++++ .+++|....+|. .|+..-.+.|+.++|+++|+
T Consensus       485 YD~ai~LE~~~~~~~v~~~plV~Ka~l~-~qwk~d~~~a~~Ll~KA-~e~Dpkce~A~~-tlaq~~lQ~~~i~eAielFE  561 (606)
T KOG0547|consen  485 YDKAIELEPREHLIIVNAAPLVHKALLV-LQWKEDINQAENLLRKA-IELDPKCEQAYE-TLAQFELQRGKIDEAIELFE  561 (606)
T ss_pred             HHHHHhhccccccccccchhhhhhhHhh-hchhhhHHHHHHHHHHH-HccCchHHHHHH-HHHHHHHHHhhHHHHHHHHH
Confidence            98763 3333         222223332 23448999999999999 999999999899 99999999999999999999


Q ss_pred             HHHh
Q 044988          472 KMIK  475 (538)
Q Consensus       472 ~m~~  475 (538)
                      +-..
T Consensus       562 ksa~  565 (606)
T KOG0547|consen  562 KSAQ  565 (606)
T ss_pred             HHHH
Confidence            8653

>KOG1915 consensus Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning]

Probab=99.59  E-value=6.7e-11  Score=107.30  Aligned_cols=407  Identities=11%  Similarity=0.112  Sum_probs=290.1

Q ss_pred             ChhHHHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcc-hHHHHHH
Q 044988           51 KNYILAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEY-TYSFLLS  126 (538)
Q Consensus        51 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-~~~~li~  126 (538)
                      +...|....+.-...+++..|..+|++...   .+...|-.-+..=.+++.+..|..++++....  -|-+. .|--.+.
T Consensus        72 ~~~~WikYaqwEesq~e~~RARSv~ERALdvd~r~itLWlkYae~Emknk~vNhARNv~dRAvt~--lPRVdqlWyKY~y  149 (677)
T KOG1915|consen   72 NMQVWIKYAQWEESQKEIQRARSVFERALDVDYRNITLWLKYAEFEMKNKQVNHARNVWDRAVTI--LPRVDQLWYKYIY  149 (677)
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHhhhhHhHHHHHHHHHHHh--cchHHHHHHHHHH
Confidence            344555555555567788899999998774   56667777888888999999999999999863  45433 4555555


Q ss_pred             HHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCC--CCCchhHHHHHHHHHhcCCHH
Q 044988          127 VCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMP--ARSVVSWNSLLKGYVKRGDID  204 (538)
Q Consensus       127 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~g~~~  204 (538)
                      .=-..|++..|.++|++-.+  ..|+...|++.++.-.+...   ++.|..++++.+  .|++.+|--..+.=.++|...
T Consensus       150 mEE~LgNi~gaRqiferW~~--w~P~eqaW~sfI~fElRyke---ieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~  224 (677)
T KOG1915|consen  150 MEEMLGNIAGARQIFERWME--WEPDEQAWLSFIKFELRYKE---IERARSIYERFVLVHPKVSNWIKYARFEEKHGNVA  224 (677)
T ss_pred             HHHHhcccHHHHHHHHHHHc--CCCcHHHHHHHHHHHHHhhH---HHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHH
Confidence            56678999999999999987  47999999999999999999   999999999866  589999999999999999999


Q ss_pred             HHHHHHccCCC------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHccCChHHHHHH-
Q 044988          205 GAWKIFDEMPH------RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD--QVALVAALSACAEIGDLKLGKWI-  275 (538)
Q Consensus       205 ~A~~~~~~m~~------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~~~~~~a~~~-  275 (538)
                      .|..+|+...+      -+...++++...-.+...++.|.-+|+-.... ++.+  ...|.....---+-|+.....+. 
T Consensus       225 ~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~-~pk~raeeL~k~~~~fEKqfGd~~gIEd~I  303 (677)
T KOG1915|consen  225 LARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDH-IPKGRAEELYKKYTAFEKQFGDKEGIEDAI  303 (677)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCcccHHHHHHHHHHHHHHhcchhhhHHHH
Confidence            99999988654      12335666666666778899999999888764 2222  23344433333345655443332 


Q ss_pred             -------HHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CCc---chHHHHHHHHHhcCCccHHH
Q 044988          276 -------HSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RNT---VSWTSMITGFAKQGYAQEAL  343 (538)
Q Consensus       276 -------~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~~---~~~~~li~~~~~~~~~~~a~  343 (538)
                             ++..++     ..|.+..+|--.+..-...|+.+...++|++...  |..   ..|...|-....--      
T Consensus       304 v~KRk~qYE~~v~-----~np~nYDsWfdylrL~e~~g~~~~Ire~yErAIanvpp~~ekr~W~RYIYLWinYa------  372 (677)
T KOG1915|consen  304 VGKRKFQYEKEVS-----KNPYNYDSWFDYLRLEESVGDKDRIRETYERAIANVPPASEKRYWRRYIYLWINYA------  372 (677)
T ss_pred             hhhhhhHHHHHHH-----hCCCCchHHHHHHHHHHhcCCHHHHHHHHHHHHccCCchhHHHHHHHHHHHHHHHH------
Confidence                   333444     3788888888999999999999999999998765  211   12222222111100      


Q ss_pred             HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHh----hhcCChHHHHHHHHhC-CCCCCHHHHHHHH
Q 044988          344 LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLF----SRAGLMDEAFSLVQNM-PMKPNDAVLGSLL  418 (538)
Q Consensus       344 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~----~~~g~~~~A~~~~~~~-~~~p~~~~~~~l~  418 (538)
                            +-.-....+.+.+.++++...+.  ++....|+.-+--+|    .++.++..|.+++-.. ..-|-..+|...|
T Consensus       373 ------lyeEle~ed~ertr~vyq~~l~l--IPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YI  444 (677)
T KOG1915|consen  373 ------LYEELEAEDVERTRQVYQACLDL--IPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAIGKCPKDKLFKGYI  444 (677)
T ss_pred             ------HHHHHHhhhHHHHHHHHHHHHhh--cCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHhccCCchhHHHHHH
Confidence                  00112345778888888887752  233445554443333    4677888888888665 4568888888888


Q ss_pred             HHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeE
Q 044988          419 LGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSW  486 (538)
Q Consensus       419 ~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~  486 (538)
                      ..-.+.+++|....++++. .+..|.+..+|. -.+..-...|+++.|..+|.-..+......|..-|
T Consensus       445 elElqL~efDRcRkLYEkf-le~~Pe~c~~W~-kyaElE~~LgdtdRaRaifelAi~qp~ldmpellw  510 (677)
T KOG1915|consen  445 ELELQLREFDRCRKLYEKF-LEFSPENCYAWS-KYAELETSLGDTDRARAIFELAISQPALDMPELLW  510 (677)
T ss_pred             HHHHHHhhHHHHHHHHHHH-HhcChHhhHHHH-HHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHH
Confidence            8888888888888888888 888888887777 77777777888888888888877665555565666

>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]

Probab=99.58  E-value=2.3e-11  Score=118.84  Aligned_cols=412  Identities=13%  Similarity=0.105  Sum_probs=294.2

Q ss_pred             HHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHcc
Q 044988           55 LAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARC  131 (538)
Q Consensus        55 ~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  131 (538)
                      .-...+...-.|+.++|.+++.++.+   .+...|..|...|-+.|+.+++...+-..-... +-|...|..+.....++
T Consensus       142 ll~eAN~lfarg~~eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~-p~d~e~W~~ladls~~~  220 (895)
T KOG2076|consen  142 LLGEANNLFARGDLEEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN-PKDYELWKRLADLSEQL  220 (895)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHhc
Confidence            33344444455999999999998874   466789999999999999999998875554322 34667899999999999


Q ss_pred             CCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCc----h----hHHHHHHHHHhcCCH
Q 044988          132 GLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSV----V----SWNSLLKGYVKRGDI  203 (538)
Q Consensus       132 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~----~----~~~~li~~~~~~g~~  203 (538)
                      |+++.|.-+|.+.++.. +++....-.-...|-+.|+   ...|..-|.++.+.++    .    .--..++.+...++-
T Consensus       221 ~~i~qA~~cy~rAI~~~-p~n~~~~~ers~L~~~~G~---~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~  296 (895)
T KOG2076|consen  221 GNINQARYCYSRAIQAN-PSNWELIYERSSLYQKTGD---LKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNER  296 (895)
T ss_pred             ccHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHhCh---HHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHH
Confidence            99999999999999986 6777777778899999999   9999988888776332    2    222345667777777


Q ss_pred             HHHHHHHccCCC-----CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC---------------------------CCC
Q 044988          204 DGAWKIFDEMPH-----RNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR---------------------------VGL  251 (538)
Q Consensus       204 ~~A~~~~~~m~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g---------------------------~~p  251 (538)
                      +.|.+.++....     .+...++.++..|.+...++.|......+....                           +.+
T Consensus       297 e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~  376 (895)
T KOG2076|consen  297 ERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSY  376 (895)
T ss_pred             HHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCc
Confidence            889888887653     344578899999999999999999998887722                           222


Q ss_pred             CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCC--CCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC----CCcch
Q 044988          252 DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGR--EPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR----RNTVS  325 (538)
Q Consensus       252 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~----~~~~~  325 (538)
                      +...+ .+.-++.+....+....+.....+.    .  ....+..+.-+..+|...|++.+|..+|..+..    .+...
T Consensus       377 ~l~v~-rl~icL~~L~~~e~~e~ll~~l~~~----n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~v  451 (895)
T KOG2076|consen  377 DLRVI-RLMICLVHLKERELLEALLHFLVED----NVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFV  451 (895)
T ss_pred             cchhH-hHhhhhhcccccchHHHHHHHHHHh----cCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhh
Confidence            33331 2233445555556665566666555    3  455677888899999999999999999999876    35678


Q ss_pred             HHHHHHHHHhcCCccHHHHHHHHH--------------HHHhcccCcHHHHHHHHHHhhh-------hcCCCccHHHHHH
Q 044988          326 WTSMITGFAKQGYAQEALLTFLGV--------------LSACSHGGFVDEGRQFFECMNQ-------NWGIKPRIEHYGC  384 (538)
Q Consensus       326 ~~~li~~~~~~~~~~~a~~~~~~l--------------l~~~~~~~~~~~a~~~~~~~~~-------~~~~~p~~~~~~~  384 (538)
                      |-.+...|...|..+.|+..|..+              -..+...|+.++|.+++..+.-       ..+..|+......
T Consensus       452 w~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~~e~ri~~~  531 (895)
T KOG2076|consen  452 WYKLARCYMELGEYEEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWEPERRILAH  531 (895)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhccccHHHHHHHH
Confidence            999999999999999999666554              3466778999999999988531       1134455555555


Q ss_pred             HHHHhhhcCChHHHHHHHHhCC-----------------------------------------------------CCC--
Q 044988          385 MVDLFSRAGLMDEAFSLVQNMP-----------------------------------------------------MKP--  409 (538)
Q Consensus       385 l~~~~~~~g~~~~A~~~~~~~~-----------------------------------------------------~~p--  409 (538)
                      ..+.+...|+.++-+.....|.                                                     ..+  
T Consensus       532 r~d~l~~~gk~E~fi~t~~~Lv~~~~~~~~~f~~~~k~r~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~l~d~~~  611 (895)
T KOG2076|consen  532 RCDILFQVGKREEFINTASTLVDDFLKKRYIFPRNKKKRRRAIAGTTSKRYSELLKQIIRAREKATDDNVMEKALSDGTE  611 (895)
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHhhccccccccchhHHHHHHHHhccCchHHhhhcccchhh
Confidence            5666667776665333322210                                                     000  


Q ss_pred             ---------CH----HHHHHHHHHHHhcCCHHHHHHHHHHch--hccCCCCc--ccHHHHHHHHHHhcCChHHHHHHHHH
Q 044988          410 ---------ND----AVLGSLLLGCRIHNNAELASQVAQKLV--AEIDPEQA--AGYLALVANVYAAAKRWQDVAAVRQK  472 (538)
Q Consensus       410 ---------~~----~~~~~l~~~~~~~~~~~~A~~~~~~~~--~~~~p~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~  472 (538)
                               ..    ..+.-++...++.+++++|+.+...+.  ..+.-+..  ..+......+....+++..|...++.
T Consensus       612 ~~~~e~~~Lsiddwfel~~e~i~~L~k~~r~qeAl~vv~~a~~~~~f~~~~~~~k~l~~~~l~~s~~~~d~~~a~~~lR~  691 (895)
T KOG2076|consen  612 FRAVELRGLSIDDWFELFRELILSLAKLQRVQEALSVVFTALEAYIFFQDSEIRKELQFLGLKASLYARDPGDAFSYLRS  691 (895)
T ss_pred             hhhhhhccCcHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhhhhhhccHHHHHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence                     01    233445667889999999999998886  11122221  11222455677889999999999999


Q ss_pred             HHhC
Q 044988          473 MIKM  476 (538)
Q Consensus       473 m~~~  476 (538)
                      |...
T Consensus       692 ~i~~  695 (895)
T KOG2076|consen  692 VITQ  695 (895)
T ss_pred             HHHH
Confidence            9854

>KOG4318 consensus Bicoid mRNA stability factor [RNA processing and modification]

Probab=99.55  E-value=1.1e-11  Score=120.44  Aligned_cols=420  Identities=15%  Similarity=0.127  Sum_probs=241.3

Q ss_pred             HHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC----CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCC
Q 044988           38 QIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE----NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKE  113 (538)
Q Consensus        38 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~  113 (538)
                      .++..+...|+.|+..+|.++|..|+..|+.+.|- +|.-|.    ..+...++.++.+..+.++.+.+.          
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk----------   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK----------   79 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC----------
Confidence            56777788888888888888888888888888887 777666    235556788887777777776665          


Q ss_pred             CCCCcchHHHHHHHHHccCCcHHHHHHHHHHHH-------hCCCC--------------chhHHhHHHHHHHhcCCCCCh
Q 044988          114 TEPDEYTYSFLLSVCARCGLFREGEQVHGRVLA-------SGYCS--------------NVFIRTNLMNLYLMSGGECGV  172 (538)
Q Consensus       114 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-------~~~~~--------------~~~~~~~l~~~~~~~g~~~~~  172 (538)
                       .|.+.||..|..+|...||+..-..+-+.+..       .|+..              ....-.+.+......|-   +
T Consensus        80 -ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~egl---w  155 (1088)
T KOG4318|consen   80 -EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGL---W  155 (1088)
T ss_pred             -CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHH---H
Confidence             57777888888888888876542222221211       12110              00111122333333344   5


Q ss_pred             hHHHHHhhcCCCCC-chhHHHHHHHHHhc-CCHHHHHHHHccCCC-CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC
Q 044988          173 GCARLLFDDMPARS-VVSWNSLLKGYVKR-GDIDGAWKIFDEMPH-RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARV  249 (538)
Q Consensus       173 ~~a~~~~~~~~~~~-~~~~~~li~~~~~~-g~~~~A~~~~~~m~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  249 (538)
                      +.+.+++..++... ......+++-+... ..+++-........+ ++..+|..++.+-..+|+.+.|..++.+|.+.|+
T Consensus       156 aqllkll~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gf  235 (1088)
T KOG4318|consen  156 AQLLKLLAKVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGF  235 (1088)
T ss_pred             HHHHHHHhhCCcccccchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCC
Confidence            55555555554310 00111112222222 223333344444443 7777777777777777788888888888877777


Q ss_pred             CCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHH-------------------
Q 044988          250 GLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEE-------------------  310 (538)
Q Consensus       250 ~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~-------------------  310 (538)
                      +.+.+-|-.++-+   .++...++.++..|.+.    |+.++..++...+-.+.+.|....                   
T Consensus       236 pir~HyFwpLl~g---~~~~q~~e~vlrgmqe~----gv~p~seT~adyvip~l~N~~t~~~~e~sq~~hg~tAavrsaa  308 (1088)
T KOG4318|consen  236 PIRAHYFWPLLLG---INAAQVFEFVLRGMQEK----GVQPGSETQADYVIPQLSNGQTKYGEEGSQLAHGFTAAVRSAA  308 (1088)
T ss_pred             Ccccccchhhhhc---CccchHHHHHHHHHHHh----cCCCCcchhHHHHHhhhcchhhhhcccccchhhhhhHHHHHHH
Confidence            7777777666655   66666666666666666    666665555444333333221110                   


Q ss_pred             -----HHHHHHh---------cCC-------CCcchHHHHHHHHHhcCCccHHH--------------------------
Q 044988          311 -----AYGVFRK---------MQR-------RNTVSWTSMITGFAKQGYAQEAL--------------------------  343 (538)
Q Consensus       311 -----a~~~~~~---------m~~-------~~~~~~~~li~~~~~~~~~~~a~--------------------------  343 (538)
                           |.+.++.         .++       .....|.. +.-....|+.++..                          
T Consensus       309 ~rg~~a~k~l~~nl~~~v~~s~k~~fLlg~d~~~aiws~-c~~l~hQgk~e~veqlvg~l~npt~r~s~~~V~a~~~~lr  387 (1088)
T KOG4318|consen  309 CRGLLANKRLRQNLRKSVIGSTKKLFLLGTDILEAIWSM-CEKLRHQGKGEEVEQLVGQLLNPTLRDSGQNVDAFGALLR  387 (1088)
T ss_pred             hcccHhHHHHHHHHHHHHHHHhhHHHHhccccchHHHHH-HHHHHHcCCCchHHHHHhhhcCCccccCcchHHHHHHHHH
Confidence                 1111110         000       00111211 11122234333332                          


Q ss_pred             ------------------------------------------------------------------------HHHHHHHH
Q 044988          344 ------------------------------------------------------------------------LTFLGVLS  351 (538)
Q Consensus       344 ------------------------------------------------------------------------~~~~~ll~  351 (538)
                                                                                              ..-+.++.
T Consensus       388 qyFrr~e~~~~~~i~~~~qgls~~l~se~tp~vsell~~lrkns~lr~lv~Lss~Eler~he~~~~~~h~irdi~~ql~l  467 (1088)
T KOG4318|consen  388 QYFRRIERHICSRIYYAGQGLSLNLNSEDTPRVSELLENLRKNSFLRQLVGLSSTELERSHEPWPLIAHLIRDIANQLHL  467 (1088)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHhhhchhhhHHHHHHHHHhCcchHHHHHhhhhHHHHhcccccchhhhhHHHHHHHHHHH
Confidence                                                                                    11222222


Q ss_pred             HhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-----CCCCHHHHHHHHHHHHhcCC
Q 044988          352 ACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-----MKPNDAVLGSLLLGCRIHNN  426 (538)
Q Consensus       352 ~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~p~~~~~~~l~~~~~~~~~  426 (538)
                      .|+..-+..+++..-+..... - -  ...|..||+.+....+.+.|..+.++..     ..-|..-+..+.+...+.+.
T Consensus       468 ~l~se~n~lK~l~~~ekye~~-l-f--~g~ya~Li~l~~~hdkle~Al~~~~e~d~~d~s~~Ld~~~m~~l~dLL~r~~~  543 (1088)
T KOG4318|consen  468 TLNSEYNKLKILCDEEKYEDL-L-F--AGLYALLIKLMDLHDKLEYALSFVDEIDTRDESIHLDLPLMTSLQDLLQRLAI  543 (1088)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-H-h--hhHHHHHhhhHHHHHHHHHHHhchhhhcccchhhhcccHhHHHHHHHHHHhHH
Confidence            333333333333322222211 1 1  1467888888888999999999998885     22445566778888899999


Q ss_pred             HHHHHHHHHHch--hccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeE
Q 044988          427 AELASQVAQKLV--AEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSW  486 (538)
Q Consensus       427 ~~~A~~~~~~~~--~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~  486 (538)
                      ...+..+++.+.  ....|.....+. -+.+..+..|+.+...++.+-+...|+.. .+--|
T Consensus       544 l~dl~tiL~e~ks~a~n~~~~a~~~f-~~lns~a~agqqe~Lkkl~d~lvslgl~e-tgPl~  603 (1088)
T KOG4318|consen  544 LYDLSTILYEDKSSAENEPLVAIILF-PLLNSGAPAGQQEKLKKLADILVSLGLSE-TGPLW  603 (1088)
T ss_pred             HHHHHHHHhhhhHHhhCCchHHHHHH-HHHhhhhhccCHHHHHHHHHHHHHhhhhh-cccce
Confidence            999999999996  444454444344 45567788999999999999998888865 34445

>KOG1915 consensus Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning]

Probab=99.55  E-value=8.9e-11  Score=106.51  Aligned_cols=414  Identities=10%  Similarity=0.088  Sum_probs=301.0

Q ss_pred             CChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC--CCc-chHHHHHHHHhcCCCchHHHHHHH
Q 044988           31 NTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN--PST-AIWNQMIRGHARSETPEKSVYLYK  107 (538)
Q Consensus        31 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~~~-~~~~~li~~~~~~~~~~~a~~~~~  107 (538)
                      +++..|+.+|+..+... ..+...|-..+.+-.++..+..|..+|++...  |-+ ..|--.+..=-..|++..|.++|+
T Consensus        87 ~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~lPRVdqlWyKY~ymEE~LgNi~gaRqife  165 (677)
T KOG1915|consen   87 KEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVDQLWYKYIYMEEMLGNIAGARQIFE  165 (677)
T ss_pred             HHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcccHHHHHHHH
Confidence            46678999999988776 44778888899999999999999999998663  332 234444444456799999999999


Q ss_pred             HhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC--
Q 044988          108 QMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPAR--  185 (538)
Q Consensus       108 ~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~--  185 (538)
                      +-.+  ..|+...|.+.|+.=.+...++.|..++++.+-.  .|++..|--....--++|.   +..|.++|+...+.  
T Consensus       166 rW~~--w~P~eqaW~sfI~fElRykeieraR~IYerfV~~--HP~v~~wikyarFE~k~g~---~~~aR~VyerAie~~~  238 (677)
T KOG1915|consen  166 RWME--WEPDEQAWLSFIKFELRYKEIERARSIYERFVLV--HPKVSNWIKYARFEEKHGN---VALARSVYERAIEFLG  238 (677)
T ss_pred             HHHc--CCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhee--cccHHHHHHHHHHHHhcCc---HHHHHHHHHHHHHHhh
Confidence            9887  5899999999999999999999999999999864  6999999999999999999   99999999887652  


Q ss_pred             ----CchhHHHHHHHHHhcCCHHHHHHHHccC----CCC-ChHHHHHHHHHHHHcCCHHHHHHH--------HHHHHHCC
Q 044988          186 ----SVVSWNSLLKGYVKRGDIDGAWKIFDEM----PHR-NVVSWTTMISGCAQNGKSRQALSL--------FNEMRRAR  248 (538)
Q Consensus       186 ----~~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~-~~~~~~~li~~~~~~~~~~~a~~~--------~~~m~~~g  248 (538)
                          +...+++....=..+..++.|.-+|+-.    ++. ....|..+...--+-|+.....+.        |+.+++. 
T Consensus       239 ~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~-  317 (677)
T KOG1915|consen  239 DDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSK-  317 (677)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHh-
Confidence                2334555555556677788888887553    332 233555555555556765544433        3344433 


Q ss_pred             CCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcch--hHHHHHHH--------HHHhCCCHHHHHHHHHhc
Q 044988          249 VGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLV--SLNNALIH--------MYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       249 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~--~~~~~l~~--------~~~~~g~~~~a~~~~~~m  318 (538)
                      -+-|-.++--.+..-...|+.+...++|+.+...     +||..  ..|...|-        .-....+++.+.++|+..
T Consensus       318 np~nYDsWfdylrL~e~~g~~~~Ire~yErAIan-----vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~  392 (677)
T KOG1915|consen  318 NPYNYDSWFDYLRLEESVGDKDRIRETYERAIAN-----VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQAC  392 (677)
T ss_pred             CCCCchHHHHHHHHHHhcCCHHHHHHHHHHHHcc-----CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            2457778878888888889999999999999886     44421  12222211        112467888899988876


Q ss_pred             CC--C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCCh
Q 044988          319 QR--R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLM  395 (538)
Q Consensus       319 ~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  395 (538)
                      .+  | ...|+..+=-.|+                .--.+..++..|.+++...+   |..|-..++...|..-.+.+++
T Consensus       393 l~lIPHkkFtFaKiWlmyA----------------~feIRq~~l~~ARkiLG~AI---G~cPK~KlFk~YIelElqL~ef  453 (677)
T KOG1915|consen  393 LDLIPHKKFTFAKIWLMYA----------------QFEIRQLNLTGARKILGNAI---GKCPKDKLFKGYIELELQLREF  453 (677)
T ss_pred             HhhcCcccchHHHHHHHHH----------------HHHHHHcccHHHHHHHHHHh---ccCCchhHHHHHHHHHHHHhhH
Confidence            65  3 3344443322222                22234458889999999888   7799999999999999999999


Q ss_pred             HHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCccc-HHHHHHHHHHhcCChHHHHHHHHH
Q 044988          396 DEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAG-YLALVANVYAAAKRWQDVAAVRQK  472 (538)
Q Consensus       396 ~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~-~~~~l~~~~~~~g~~~~A~~~~~~  472 (538)
                      +.+..++++.. ..| |-.+|......-...|+.+.|..+|+-+..+-.-+-+.. +. ..++.-...|.++.|..++++
T Consensus       454 DRcRkLYEkfle~~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwk-aYIdFEi~~~E~ekaR~LYer  532 (677)
T KOG1915|consen  454 DRCRKLYEKFLEFSPENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWK-AYIDFEIEEGEFEKARALYER  532 (677)
T ss_pred             HHHHHHHHHHHhcChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHH-HhhhhhhhcchHHHHHHHHHH
Confidence            99999999874 444 468888888888899999999999998842222222221 22 333444578999999999999


Q ss_pred             HHhCCC
Q 044988          473 MIKMGV  478 (538)
Q Consensus       473 m~~~~~  478 (538)
                      +.+..-
T Consensus       533 lL~rt~  538 (677)
T KOG1915|consen  533 LLDRTQ  538 (677)
T ss_pred             HHHhcc
Confidence            987533

>KOG2003 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.54  E-value=1.7e-11  Score=110.50  Aligned_cols=410  Identities=13%  Similarity=0.121  Sum_probs=275.8

Q ss_pred             hhHHHHHHHHHHccCChhHHHHHHhcCCC----CCcchH-HHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcch----HH
Q 044988           52 NYILAKLLAFYVTSGYLINAHKVFEKTEN----PSTAIW-NQMIRGHARSETPEKSVYLYKQMIDKETEPDEYT----YS  122 (538)
Q Consensus        52 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~----~~~~~~-~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~----~~  122 (538)
                      -.++..|.+-|.......+|+..++-+.+    ||.... -.+.+.+.+...+.+|+..|+..+..-...+..+    .+
T Consensus       201 fsvl~nlaqqy~~ndm~~ealntyeiivknkmf~nag~lkmnigni~~kkr~fskaikfyrmaldqvpsink~~rikil~  280 (840)
T KOG2003|consen  201 FSVLFNLAQQYEANDMTAEALNTYEIIVKNKMFPNAGILKMNIGNIHFKKREFSKAIKFYRMALDQVPSINKDMRIKILN  280 (840)
T ss_pred             HHHHHHHHHHhhhhHHHHHHhhhhhhhhcccccCCCceeeeeecceeeehhhHHHHHHHHHHHHhhccccchhhHHHHHh
Confidence            34555666777778888999999987764    443322 2345677888999999999988876421122223    33


Q ss_pred             HHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC----------------CC
Q 044988          123 FLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA----------------RS  186 (538)
Q Consensus       123 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~----------------~~  186 (538)
                      .+.-.+.+.|.++.|..-|+...+.  .|+-.+-..|+-++...|+   .++..+.|.+|..                |+
T Consensus       281 nigvtfiq~gqy~dainsfdh~m~~--~pn~~a~~nl~i~~f~i~d---~ekmkeaf~kli~ip~~~dddkyi~~~ddp~  355 (840)
T KOG2003|consen  281 NIGVTFIQAGQYDDAINSFDHCMEE--APNFIAALNLIICAFAIGD---AEKMKEAFQKLIDIPGEIDDDKYIKEKDDPD  355 (840)
T ss_pred             hcCeeEEecccchhhHhhHHHHHHh--CccHHhhhhhhhhheecCc---HHHHHHHHHHHhcCCCCCCcccccCCcCCcc
Confidence            3344578899999999999998886  5887777778888888888   8888888887753                12


Q ss_pred             chhHHH-----HHHHHHhcC--CHHHHHHHHccCC----CCChH---HH----------HH--------HHHHHHHcCCH
Q 044988          187 VVSWNS-----LLKGYVKRG--DIDGAWKIFDEMP----HRNVV---SW----------TT--------MISGCAQNGKS  234 (538)
Q Consensus       187 ~~~~~~-----li~~~~~~g--~~~~A~~~~~~m~----~~~~~---~~----------~~--------li~~~~~~~~~  234 (538)
                      ....|-     .++-.-+..  +.++++-.--++.    .|+-.   -|          .-        -...|.++|++
T Consensus       356 ~~ll~eai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk~~d~  435 (840)
T KOG2003|consen  356 DNLLNEAIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAIDLEINKAGELLKNGDI  435 (840)
T ss_pred             hHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHhccCH
Confidence            222222     222222221  2222222222222    23221   01          11        12346789999


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHH--HccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHH
Q 044988          235 RQALSLFNEMRRARVGLDQVALVAALSAC--AEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAY  312 (538)
Q Consensus       235 ~~a~~~~~~m~~~g~~p~~~~~~~li~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  312 (538)
                      +.|+++++-..+..-+.-...-+.|-..+  -.-.++..|.++-+.....     ...+......-.+.-...|+++.|.
T Consensus       436 ~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~-----dryn~~a~~nkgn~~f~ngd~dka~  510 (840)
T KOG2003|consen  436 EGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNI-----DRYNAAALTNKGNIAFANGDLDKAA  510 (840)
T ss_pred             HHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhcc-----cccCHHHhhcCCceeeecCcHHHHH
Confidence            99999999887654333333333322222  2345677777777666654     3333333333344445679999999


Q ss_pred             HHHHhcCCCCcchHHHH---HHHHHhcCCccHHHH--------------HHHHHHHHhcccCcHHHHHHHHHHhhhhcCC
Q 044988          313 GVFRKMQRRNTVSWTSM---ITGFAKQGYAQEALL--------------TFLGVLSACSHGGFVDEGRQFFECMNQNWGI  375 (538)
Q Consensus       313 ~~~~~m~~~~~~~~~~l---i~~~~~~~~~~~a~~--------------~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  375 (538)
                      +.+++....|...-.+|   .-.+-..|+.++|+.              +...+.+.|.-..+...|.+++.+..   .+
T Consensus       511 ~~ykeal~ndasc~ealfniglt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~~q~~---sl  587 (840)
T KOG2003|consen  511 EFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELLMQAN---SL  587 (840)
T ss_pred             HHHHHHHcCchHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhc---cc
Confidence            99999988765543333   345677899999983              34445566666778888888887766   44


Q ss_pred             Cc-cHHHHHHHHHHhhhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHH
Q 044988          376 KP-RIEHYGCMVDLFSRAGLMDEAFSLVQNM-P-MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLAL  452 (538)
Q Consensus       376 ~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~  452 (538)
                      .| |+.+..-|.+.|-+.|+-..|.+.+-+- + ++-|..+..=|..-|....-.++|+.+|+++ .-+.|+... |.-.
T Consensus       588 ip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~eka-aliqp~~~k-wqlm  665 (840)
T KOG2003|consen  588 IPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKA-ALIQPNQSK-WQLM  665 (840)
T ss_pred             CCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHH-HhcCccHHH-HHHH
Confidence            55 6889999999999999999998876543 4 4456777777777788888999999999999 888999888 6636


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhC
Q 044988          453 VANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       453 l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      ++.++.+.|.+++|.++++.+..+
T Consensus       666 iasc~rrsgnyqka~d~yk~~hrk  689 (840)
T KOG2003|consen  666 IASCFRRSGNYQKAFDLYKDIHRK  689 (840)
T ss_pred             HHHHHHhcccHHHHHHHHHHHHHh
Confidence            777888999999999999998864

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.54  E-value=3.2e-11  Score=109.10  Aligned_cols=212  Identities=14%  Similarity=0.140  Sum_probs=145.8

Q ss_pred             HHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHH
Q 044988          255 ALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMIT  331 (538)
Q Consensus       255 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~  331 (538)
                      |.-.+.+-|+-.++-++|...|+...+.     .|....+|+.+..-|....+...|.+.+++..+   .|-..|-.+.+
T Consensus       332 TCCiIaNYYSlr~eHEKAv~YFkRALkL-----Np~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQ  406 (559)
T KOG1155|consen  332 TCCIIANYYSLRSEHEKAVMYFKRALKL-----NPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLGQ  406 (559)
T ss_pred             ceeeehhHHHHHHhHHHHHHHHHHHHhc-----CcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhhH
Confidence            4455555556666666666677666665     666677777777777777777777777777665   34555555655


Q ss_pred             HHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCCC--C
Q 044988          332 GFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMPM--K  408 (538)
Q Consensus       332 ~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~  408 (538)
                      +|.-.+                    .+.-|+-.|++..+   ++| |...|.+|.++|.+.++.++|++.|.+...  .
T Consensus       407 aYeim~--------------------Mh~YaLyYfqkA~~---~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~d  463 (559)
T KOG1155|consen  407 AYEIMK--------------------MHFYALYYFQKALE---LKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGD  463 (559)
T ss_pred             HHHHhc--------------------chHHHHHHHHHHHh---cCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccc
Confidence            555544                    45556677777664   366 688899999999999999999999888752  2


Q ss_pred             CCHHHHHHHHHHHHhcCCHHHHHHHHHHch----hc--cCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCC
Q 044988          409 PNDAVLGSLLLGCRIHNNAELASQVAQKLV----AE--IDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPP  482 (538)
Q Consensus       409 p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~----~~--~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~  482 (538)
                      .+...+..|...+-+.++.++|...+++..    .+  ..|....+.. .|+.-+.+.+++++|..........      
T Consensus       464 te~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~~~t~ka~~-fLA~~f~k~~~~~~As~Ya~~~~~~------  536 (559)
T KOG1155|consen  464 TEGSALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEIDDETIKARL-FLAEYFKKMKDFDEASYYATLVLKG------  536 (559)
T ss_pred             cchHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccchHHHHHHH-HHHHHHHhhcchHHHHHHHHHHhcC------
Confidence            345788888888988999999988888874    11  3333333334 5777788889999888876654431      


Q ss_pred             ceeEEEECCEEEEEEeCCCCCcchHHHHHHHHHHHHHHH
Q 044988          483 GQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAM  521 (538)
Q Consensus       483 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~m~  521 (538)
                                          .++.+++-..++++++.|.
T Consensus       537 --------------------~~e~eeak~LlReir~~~~  555 (559)
T KOG1155|consen  537 --------------------ETECEEAKALLREIRKIQA  555 (559)
T ss_pred             --------------------CchHHHHHHHHHHHHHhcC
Confidence                                3355777777777776663

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=99.53  E-value=1e-12  Score=124.19  Aligned_cols=275  Identities=12%  Similarity=0.038  Sum_probs=155.8

Q ss_pred             cHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC------CchhHHHHHHHHHhcCCHH-HH
Q 044988          134 FREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPAR------SVVSWNSLLKGYVKRGDID-GA  206 (538)
Q Consensus       134 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~------~~~~~~~li~~~~~~g~~~-~A  206 (538)
                      ..+|...|..+... +.....+...+..+|...++   +++|+++|+.+.+.      +...|.+.+--+-+.-... -|
T Consensus       335 ~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~---Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~La  410 (638)
T KOG1126|consen  335 CREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIE---YDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLA  410 (638)
T ss_pred             HHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHH---HHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHH
Confidence            45566666663322 23334566666666666666   66666666665542      4455555554332221111 12


Q ss_pred             HHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccC
Q 044988          207 WKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSV  285 (538)
Q Consensus       207 ~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~  285 (538)
                      ..+.+. ....+.+|..+.++|.-+++++.|++.|++..+  +.| ..++|+.+-+-+.....+|.|...|+..+..   
T Consensus       411 q~Li~~-~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQ--ldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~---  484 (638)
T KOG1126|consen  411 QDLIDT-DPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQ--LDPRFAYAYTLLGHESIATEEFDKAMKSFRKALGV---  484 (638)
T ss_pred             HHHHhh-CCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhc--cCCccchhhhhcCChhhhhHHHHhHHHHHHhhhcC---
Confidence            222222 123455677777777777777777777766655  334 4455555555555555555555555555443   


Q ss_pred             CCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHH
Q 044988          286 GREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQF  365 (538)
Q Consensus       286 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~  365 (538)
                        .|.+..+|..|.-.|.+.++++.|+-                                                   .
T Consensus       485 --~~rhYnAwYGlG~vy~Kqek~e~Ae~---------------------------------------------------~  511 (638)
T KOG1126|consen  485 --DPRHYNAWYGLGTVYLKQEKLEFAEF---------------------------------------------------H  511 (638)
T ss_pred             --CchhhHHHHhhhhheeccchhhHHHH---------------------------------------------------H
Confidence              34444444444444444444444444                                                   4


Q ss_pred             HHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccC
Q 044988          366 FECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MK-PNDAVLGSLLLGCRIHNNAELASQVAQKLVAEID  442 (538)
Q Consensus       366 ~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~-p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~  442 (538)
                      |++..   .+.| +.+....+...+.+.|+.++|+.+++++. .. -|...--.-+..+...+++++|+..++++ .++.
T Consensus       512 fqkA~---~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~~~~~eal~~LEeL-k~~v  587 (638)
T KOG1126|consen  512 FQKAV---EINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRASILFSLGRYVEALQELEEL-KELV  587 (638)
T ss_pred             HHhhh---cCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhhcchHHHHHHHHHH-HHhC
Confidence            44444   3345 35555566666777777777777777763 22 23333333444555667777777777777 7777


Q ss_pred             CCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          443 PEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       443 p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      |++...|. +++.+|.+.|+.+.|+.-|--+.+-
T Consensus       588 P~es~v~~-llgki~k~~~~~~~Al~~f~~A~~l  620 (638)
T KOG1126|consen  588 PQESSVFA-LLGKIYKRLGNTDLALLHFSWALDL  620 (638)
T ss_pred             cchHHHHH-HHHHHHHHHccchHHHHhhHHHhcC
Confidence            77777777 7777888888777777777666653

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=99.52  E-value=3e-14  Score=130.63  Aligned_cols=249  Identities=14%  Similarity=0.172  Sum_probs=97.2

Q ss_pred             HHHHHhcCCHHHHHHHHccC-CC----CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 044988          194 LKGYVKRGDIDGAWKIFDEM-PH----RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGD  268 (538)
Q Consensus       194 i~~~~~~g~~~~A~~~~~~m-~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~  268 (538)
                      ...+.+.|++++|++++++. ..    .+...|..+...+...++++.|...|+++...+.. +...+..++.. ...++
T Consensus        15 A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~~~   92 (280)
T PF13429_consen   15 ARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQDGD   92 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccc-ccccc
Confidence            33444555566666666332 11    23334444444555566677777777776654322 33445455544 56666


Q ss_pred             hHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC-----CCcchHHHHHHHHHhcCCccHHH
Q 044988          269 LKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR-----RNTVSWTSMITGFAKQGYAQEAL  343 (538)
Q Consensus       269 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~li~~~~~~~~~~~a~  343 (538)
                      +++|..++....+.      ..+...+..++..+.+.++++++.++++.+..     ++...|..+...+.+        
T Consensus        93 ~~~A~~~~~~~~~~------~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~--------  158 (280)
T PF13429_consen   93 PEEALKLAEKAYER------DGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQ--------  158 (280)
T ss_dssp             -------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHH--------
T ss_pred             cccccccccccccc------ccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHH--------
Confidence            77766666554433      12334445566677777777777777776432     233333333344444        


Q ss_pred             HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHH
Q 044988          344 LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLG  420 (538)
Q Consensus       344 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~  420 (538)
                                  .|+.++|+.++++..+.   .| |....+.++..+...|+.+++.++++...  ...|...+..+..+
T Consensus       159 ------------~G~~~~A~~~~~~al~~---~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~  223 (280)
T PF13429_consen  159 ------------LGDPDKALRDYRKALEL---DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAA  223 (280)
T ss_dssp             ------------CCHHHHHHHHHHHHHHH----TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHH
T ss_pred             ------------cCCHHHHHHHHHHHHHc---CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence                        44777778888888765   56 47788899999999999999887777663  23556678889999


Q ss_pred             HHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          421 CRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       421 ~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +...|+.++|+..+++. ....|+++.... .+++++...|+.++|.++.++...
T Consensus       224 ~~~lg~~~~Al~~~~~~-~~~~p~d~~~~~-~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  224 YLQLGRYEEALEYLEKA-LKLNPDDPLWLL-AYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             HHHHT-HHHHHHHHHHH-HHHSTT-HHHHH-HHHHHHT-----------------
T ss_pred             hcccccccccccccccc-cccccccccccc-cccccccccccccccccccccccc
Confidence            99999999999999999 999999999777 999999999999999999887653

>KOG0495 consensus HAT repeat protein [RNA processing and modification]

Probab=99.52  E-value=6.5e-10  Score=104.96  Aligned_cols=401  Identities=11%  Similarity=0.092  Sum_probs=215.4

Q ss_pred             cCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHHHHHHHh----HhCCCCCCcchHHHHHHHHHccCCcHHH
Q 044988           65 SGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSVYLYKQM----IDKETEPDEYTYSFLLSVCARCGLFREG  137 (538)
Q Consensus        65 ~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m----~~~~~~p~~~~~~~li~~~~~~~~~~~a  137 (538)
                      ...++.|..++....   +.+...|-+-...--.+|+.+....++.+-    ...|+..+...|..=...|-..|..-.+
T Consensus       419 LetYenAkkvLNkaRe~iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~e~agsv~Tc  498 (913)
T KOG0495|consen  419 LETYENAKKVLNKAREIIPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEACEDAGSVITC  498 (913)
T ss_pred             HHHHHHHHHHHHHHHhhCCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHHhhcCChhhH
Confidence            334444444443332   334445544444444555555555554443    2345555555565555556556666666


Q ss_pred             HHHHHHHHHhCCCCc--hhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC---CCchhHHHHHHHHHhcCCHHHHHHHHcc
Q 044988          138 EQVHGRVLASGYCSN--VFIRTNLMNLYLMSGGECGVGCARLLFDDMPA---RSVVSWNSLLKGYVKRGDIDGAWKIFDE  212 (538)
Q Consensus       138 ~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~  212 (538)
                      ..+....+..|+...  ..+|..-...|.+.+.   ++-|..+|....+   .+...|......--..|..+.-..+|++
T Consensus       499 QAIi~avigigvEeed~~~tw~~da~~~~k~~~---~~carAVya~alqvfp~k~slWlra~~~ek~hgt~Esl~Allqk  575 (913)
T KOG0495|consen  499 QAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPA---IECARAVYAHALQVFPCKKSLWLRAAMFEKSHGTRESLEALLQK  575 (913)
T ss_pred             HHHHHHHHhhccccchhHhHHhhhHHHHHhcch---HHHHHHHHHHHHhhccchhHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            666665555554322  2355555555555555   6666666555543   2445555555555555666666666655


Q ss_pred             CCC--C-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCC
Q 044988          213 MPH--R-NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREP  289 (538)
Q Consensus       213 m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  289 (538)
                      ...  | ....|-.....+-..|+...|..++....+.... +...+...+..-.....++.|..+|......      .
T Consensus       576 av~~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pn-seeiwlaavKle~en~e~eraR~llakar~~------s  648 (913)
T KOG0495|consen  576 AVEQCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPN-SEEIWLAAVKLEFENDELERARDLLAKARSI------S  648 (913)
T ss_pred             HHHhCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCC-cHHHHHHHHHHhhccccHHHHHHHHHHHhcc------C
Confidence            442  2 2233444445555566666666666666554322 4455555555556666666666666655442      3


Q ss_pred             cchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CCc-chHHHHHHHHHhcCCccHHHHHHHH--------------HHHH
Q 044988          290 VLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RNT-VSWTSMITGFAKQGYAQEALLTFLG--------------VLSA  352 (538)
Q Consensus       290 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~~-~~~~~li~~~~~~~~~~~a~~~~~~--------------ll~~  352 (538)
                      ++..+|.--+....-.++.++|.+++++..+  |+. ..|-.+.+.+-+.++.+.|..+|..              +...
T Consensus       649 gTeRv~mKs~~~er~ld~~eeA~rllEe~lk~fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakl  728 (913)
T KOG0495|consen  649 GTERVWMKSANLERYLDNVEEALRLLEEALKSFPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKL  728 (913)
T ss_pred             CcchhhHHHhHHHHHhhhHHHHHHHHHHHHHhCCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHH
Confidence            3444444444444555666666666665554  332 2344444555555555555533332              2222


Q ss_pred             hcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHH
Q 044988          353 CSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAEL  429 (538)
Q Consensus       353 ~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~  429 (538)
                      --+.|.+-+|+.+++...-+   .| |...|-..|++-.+.|+.+.|..+..+..  .+.+...|..-|...-+.++-.+
T Consensus       729 eEk~~~~~rAR~ildrarlk---NPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQecp~sg~LWaEaI~le~~~~rkTk  805 (913)
T KOG0495|consen  729 EEKDGQLVRARSILDRARLK---NPKNALLWLESIRMELRAGNKEQAELLMAKALQECPSSGLLWAEAIWLEPRPQRKTK  805 (913)
T ss_pred             HHHhcchhhHHHHHHHHHhc---CCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccchhHHHHHHhccCcccchH
Confidence            22335555666666655443   23 45555666666666666666655554432  22334555555555555555445


Q ss_pred             HHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeE
Q 044988          430 ASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSW  486 (538)
Q Consensus       430 A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~  486 (538)
                      ....+++.     -.++.... .++..+....++++|.+.|.+..+.+  |+.|-.|
T Consensus       806 s~DALkkc-----e~dphVll-aia~lfw~e~k~~kar~Wf~Ravk~d--~d~GD~w  854 (913)
T KOG0495|consen  806 SIDALKKC-----EHDPHVLL-AIAKLFWSEKKIEKAREWFERAVKKD--PDNGDAW  854 (913)
T ss_pred             HHHHHHhc-----cCCchhHH-HHHHHHHHHHHHHHHHHHHHHHHccC--CccchHH
Confidence            55555544     22333355 67778888999999999999988744  4556666

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.51  E-value=2.5e-11  Score=116.62  Aligned_cols=274  Identities=11%  Similarity=-0.018  Sum_probs=166.1

Q ss_pred             cCCCCChhHHHHHhhcCCCC--Cch-hHHHHHHHHHhcCCHHHHHHHHccCCC--CChHHHH--HHHHHHHHcCCHHHHH
Q 044988          166 SGGECGVGCARLLFDDMPAR--SVV-SWNSLLKGYVKRGDIDGAWKIFDEMPH--RNVVSWT--TMISGCAQNGKSRQAL  238 (538)
Q Consensus       166 ~g~~~~~~~a~~~~~~~~~~--~~~-~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~--~li~~~~~~~~~~~a~  238 (538)
                      .|+   ++.|++.+....+.  ++. .|........+.|+++.|...|.++.+  |+...+.  .....+...|+++.|.
T Consensus        97 eGd---~~~A~k~l~~~~~~~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al  173 (398)
T PRK10747         97 EGD---YQQVEKLMTRNADHAEQPVVNYLLAAEAAQQRGDEARANQHLERAAELADNDQLPVEITRVRIQLARNENHAAR  173 (398)
T ss_pred             CCC---HHHHHHHHHHHHhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHH
Confidence            456   66666666554432  112 222223333556666666666666543  2322221  2234555566666666


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcch-------hHHHHHHHHHHhCCCHHHH
Q 044988          239 SLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLV-------SLNNALIHMYASCGEIEEA  311 (538)
Q Consensus       239 ~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~g~~~~a  311 (538)
                      ..++++.+.. +-+......+...+.+.|+++.|..++..+.+.    ...+..       ..|..++.......+.+..
T Consensus       174 ~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~----~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l  248 (398)
T PRK10747        174 HGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKA----HVGDEEHRAMLEQQAWIGLMDQAMADQGSEGL  248 (398)
T ss_pred             HHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHc----CCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHH
Confidence            6666665533 223444555555666666666666666666655    221111       1112222222333344445


Q ss_pred             HHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHH
Q 044988          312 YGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDL  388 (538)
Q Consensus       312 ~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~  388 (538)
                      .++++.+.+   .++...                    ..+..++...|+.+.|..++++..+.   .|+....  ++.+
T Consensus       249 ~~~w~~lp~~~~~~~~~~--------------------~~~A~~l~~~g~~~~A~~~L~~~l~~---~~~~~l~--~l~~  303 (398)
T PRK10747        249 KRWWKNQSRKTRHQVALQ--------------------VAMAEHLIECDDHDTAQQIILDGLKR---QYDERLV--LLIP  303 (398)
T ss_pred             HHHHHhCCHHHhCCHHHH--------------------HHHHHHHHHCCCHHHHHHHHHHHHhc---CCCHHHH--HHHh
Confidence            555555433   233333                    33445555566888888999888754   5555322  3334


Q ss_pred             hhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHH
Q 044988          389 FSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDV  466 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A  466 (538)
                      ....++.+++.+..+... ..|+ ...+..+...|.+.+++++|.+.|+.+ ....|++.. +. .++.++.+.|+.++|
T Consensus       304 ~l~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~a-l~~~P~~~~-~~-~La~~~~~~g~~~~A  380 (398)
T PRK10747        304 RLKTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAA-LKQRPDAYD-YA-WLADALDRLHKPEEA  380 (398)
T ss_pred             hccCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH-HhcCCCHHH-HH-HHHHHHHHcCCHHHH
Confidence            445699999999998874 4465 556778888899999999999999999 999999888 88 999999999999999


Q ss_pred             HHHHHHHHh
Q 044988          467 AAVRQKMIK  475 (538)
Q Consensus       467 ~~~~~~m~~  475 (538)
                      .+++++-..
T Consensus       381 ~~~~~~~l~  389 (398)
T PRK10747        381 AAMRRDGLM  389 (398)
T ss_pred             HHHHHHHHh
Confidence            999987653

>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B

Probab=99.50  E-value=2.8e-13  Score=124.29  Aligned_cols=180  Identities=17%  Similarity=0.201  Sum_probs=93.1

Q ss_pred             HhcCCHHHHHHHHccCC--CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHccCChHHHHH
Q 044988          198 VKRGDIDGAWKIFDEMP--HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR-VGLDQVALVAALSACAEIGDLKLGKW  274 (538)
Q Consensus       198 ~~~g~~~~A~~~~~~m~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p~~~~~~~li~~~~~~~~~~~a~~  274 (538)
                      ...+++++|..++...-  .++...+..++..+.+.++++++..+++.+.... .+++...|..+...+.+.|+.+.|..
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~  167 (280)
T PF13429_consen   88 LQDGDPEEALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALR  167 (280)
T ss_dssp             ------------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHH
T ss_pred             cccccccccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            34555566665555432  2455566677777888888888888888876532 34566667777777788888888888


Q ss_pred             HHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHH
Q 044988          275 IHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLS  351 (538)
Q Consensus       275 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~  351 (538)
                      .++...+.     .|.+..+.+.++..+...|+.+++.++++...+   .|+..|..+..++...|              
T Consensus       168 ~~~~al~~-----~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg--------------  228 (280)
T PF13429_consen  168 DYRKALEL-----DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLG--------------  228 (280)
T ss_dssp             HHHHHHHH------TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT--------------
T ss_pred             HHHHHHHc-----CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccc--------------
Confidence            88888886     677777777888888888888876666665543   45556666666666655              


Q ss_pred             HhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhC
Q 044988          352 ACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNM  405 (538)
Q Consensus       352 ~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~  405 (538)
                            +.++|..+|++..+.   .| |......+.+++...|+.++|.++.++.
T Consensus       229 ------~~~~Al~~~~~~~~~---~p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~  274 (280)
T PF13429_consen  229 ------RYEEALEYLEKALKL---NPDDPLWLLAYADALEQAGRKDEALRLRRQA  274 (280)
T ss_dssp             -------HHHHHHHHHHHHHH---STT-HHHHHHHHHHHT---------------
T ss_pred             ------ccccccccccccccc---ccccccccccccccccccccccccccccccc
Confidence                  566666777776654   34 6777778888888888888888877654

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.49  E-value=4.6e-11  Score=114.77  Aligned_cols=216  Identities=12%  Similarity=0.061  Sum_probs=161.6

Q ss_pred             HHHHHhcCCHHHHHHHHccCCC--C-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCH-------HHHHHHHHHH
Q 044988          194 LKGYVKRGDIDGAWKIFDEMPH--R-NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQ-------VALVAALSAC  263 (538)
Q Consensus       194 i~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~-------~~~~~li~~~  263 (538)
                      ...+...|+++.|...+++..+  | +......+...|.+.|++++|.+++..+.+.+..++.       .+|..++...
T Consensus       160 a~l~l~~g~~~~Al~~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~  239 (398)
T PRK10747        160 VRIQLARNENHAARHGVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQA  239 (398)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH
Confidence            3455667777777777777654  3 4567788889999999999999999999987655332       1333344444


Q ss_pred             HccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHH
Q 044988          264 AEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL  343 (538)
Q Consensus       264 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~  343 (538)
                      ....+.+...++++.+.+.     .+.++.....+...+...|+.++|.+++++..+.....  .++..|.         
T Consensus       240 ~~~~~~~~l~~~w~~lp~~-----~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~~~~~--~l~~l~~---------  303 (398)
T PRK10747        240 MADQGSEGLKRWWKNQSRK-----TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKRQYDE--RLVLLIP---------  303 (398)
T ss_pred             HHhcCHHHHHHHHHhCCHH-----HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCH--HHHHHHh---------
Confidence            4445566666666666554     56677788899999999999999999998876632222  2222221         


Q ss_pred             HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHHHHHHH
Q 044988          344 LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGSLLLGC  421 (538)
Q Consensus       344 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l~~~~  421 (538)
                               ....++.+++.+..+...+.   .| |...+..+...+.+.|++++|.+.|+... ..|+..++..+...+
T Consensus       304 ---------~l~~~~~~~al~~~e~~lk~---~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~  371 (398)
T PRK10747        304 ---------RLKTNNPEQLEKVLRQQIKQ---HGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADAL  371 (398)
T ss_pred             ---------hccCCChHHHHHHHHHHHhh---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence                     12235778888999888876   45 56778899999999999999999999884 679999999999999


Q ss_pred             HhcCCHHHHHHHHHHc
Q 044988          422 RIHNNAELASQVAQKL  437 (538)
Q Consensus       422 ~~~~~~~~A~~~~~~~  437 (538)
                      .+.|+.++|.+++++.
T Consensus       372 ~~~g~~~~A~~~~~~~  387 (398)
T PRK10747        372 DRLHKPEEAAAMRRDG  387 (398)
T ss_pred             HHcCCHHHHHHHHHHH
Confidence            9999999999999988

>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]

Probab=99.48  E-value=6.2e-12  Score=118.96  Aligned_cols=240  Identities=13%  Similarity=0.113  Sum_probs=184.0

Q ss_pred             CHHHHHHHHccCCC--CCh-HHHHHHHHHHHHcCCHHHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHccCChHHHHHHH
Q 044988          202 DIDGAWKIFDEMPH--RNV-VSWTTMISGCAQNGKSRQALSLFNEMRRAR--VGLDQVALVAALSACAEIGDLKLGKWIH  276 (538)
Q Consensus       202 ~~~~A~~~~~~m~~--~~~-~~~~~li~~~~~~~~~~~a~~~~~~m~~~g--~~p~~~~~~~li~~~~~~~~~~~a~~~~  276 (538)
                      +..+|...|.+.++  +|. .+...+..+|...+++++|.++|+...+..  .--+..+|.+.+-.+-+.    -+..++
T Consensus       334 ~~~~A~~~~~klp~h~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~----v~Ls~L  409 (638)
T KOG1126|consen  334 NCREALNLFEKLPSHHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDE----VALSYL  409 (638)
T ss_pred             HHHHHHHHHHhhHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhh----HHHHHH
Confidence            46788888888653  333 345567889999999999999999998742  112566777776554321    222222


Q ss_pred             -HHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCC---cchHHHHHHHHHhcCCccHHHHHHHHHHHH
Q 044988          277 -SYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRN---TVSWTSMITGFAKQGYAQEALLTFLGVLSA  352 (538)
Q Consensus       277 -~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~ll~~  352 (538)
                       +.+.+     ..|..+.+|.++.++|.-.++.+.|++.|++..+-|   ..+|+.+..-+....               
T Consensus       410 aq~Li~-----~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~e---------------  469 (638)
T KOG1126|consen  410 AQDLID-----TDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATE---------------  469 (638)
T ss_pred             HHHHHh-----hCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhH---------------
Confidence             23333     378889999999999999999999999999998744   455555554444444               


Q ss_pred             hcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHH
Q 044988          353 CSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAEL  429 (538)
Q Consensus       353 ~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~  429 (538)
                           .+|.|...|+...   ++.|+ -..|.-|.-.|.+.++++.|+-.|+++. +.|. .+....+...+.+.|+.++
T Consensus       470 -----e~d~a~~~fr~Al---~~~~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~  541 (638)
T KOG1126|consen  470 -----EFDKAMKSFRKAL---GVDPRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDK  541 (638)
T ss_pred             -----HHHhHHHHHHhhh---cCCchhhHHHHhhhhheeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhH
Confidence                 6788889998877   44553 4466667889999999999999999885 5555 5566667777899999999


Q ss_pred             HHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          430 ASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       430 A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      |+++++++ ..++|.++..-. ..+.++...+++++|+..++++++
T Consensus       542 AL~~~~~A-~~ld~kn~l~~~-~~~~il~~~~~~~eal~~LEeLk~  585 (638)
T KOG1126|consen  542 ALQLYEKA-IHLDPKNPLCKY-HRASILFSLGRYVEALQELEELKE  585 (638)
T ss_pred             HHHHHHHH-HhcCCCCchhHH-HHHHHHHhhcchHHHHHHHHHHHH
Confidence            99999999 999999998777 788999999999999999999987

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.47  E-value=2.4e-10  Score=106.19  Aligned_cols=437  Identities=12%  Similarity=0.037  Sum_probs=289.7

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhc--CCCCCcchHHHHHHHHhcCC
Q 044988           20 TRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEK--TENPSTAIWNQMIRGHARSE   97 (538)
Q Consensus        20 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~--~~~~~~~~~~~li~~~~~~~   97 (538)
                      +..+.+-+....++..|.-+-+.....+..  +...--+.+++.-.|..+.|..+...  +.+.|..+.......+.+..
T Consensus        19 ~~~~~r~~l~q~~y~~a~f~adkV~~l~~d--p~d~~~~aq~l~~~~~y~ra~~lit~~~le~~d~~cryL~~~~l~~lk   96 (611)
T KOG1173|consen   19 YRRLVRDALMQHRYKTALFWADKVAGLTND--PADIYWLAQVLYLGRQYERAAHLITTYKLEKRDIACRYLAAKCLVKLK   96 (611)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHhccCC--hHHHHHHHHHHHhhhHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHH
Confidence            444555555555666666666666665544  44444477888888888888777754  44678888888889999999


Q ss_pred             CchHHHHHHH----HhHhC---------CCCCCcch----HHHHH-------HHHHccCCcHHHHHHHHHHHHhCCCCch
Q 044988           98 TPEKSVYLYK----QMIDK---------ETEPDEYT----YSFLL-------SVCARCGLFREGEQVHGRVLASGYCSNV  153 (538)
Q Consensus        98 ~~~~a~~~~~----~m~~~---------~~~p~~~~----~~~li-------~~~~~~~~~~~a~~~~~~~~~~~~~~~~  153 (538)
                      +++.|..++.    .+...         -+.+|..-    -+.-.       ..|....+++.|...|.+.....+ -.-
T Consensus        97 ~~~~al~vl~~~~~~~~~f~yy~~~~~~~l~~n~~~~~~~~~~essic~lRgk~y~al~n~~~ar~~Y~~Al~~D~-~c~  175 (611)
T KOG1173|consen   97 EWDQALLVLGRGHVETNPFSYYEKDAANTLELNSAGEDLMINLESSICYLRGKVYVALDNREEARDKYKEALLADA-KCF  175 (611)
T ss_pred             HHHHHHHHhcccchhhcchhhcchhhhceeccCcccccccccchhceeeeeeehhhhhccHHHHHHHHHHHHhcch-hhH
Confidence            9999999988    32110         01111111    11111       234445567777777777655431 111


Q ss_pred             hHHhHHHHHHHhcCCCCChhHHHHHhhcCCC-----CCchhHHHHHHHHHhcCCHHHHHHHH--ccCC--CCChHHHHHH
Q 044988          154 FIRTNLMNLYLMSGGECGVGCARLLFDDMPA-----RSVVSWNSLLKGYVKRGDIDGAWKIF--DEMP--HRNVVSWTTM  224 (538)
Q Consensus       154 ~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~-----~~~~~~~~li~~~~~~g~~~~A~~~~--~~m~--~~~~~~~~~l  224 (538)
                      ..+-.++....-.     ..+-..+|+...-     .+......+.....-...-+.....-  ..+.  +.++.....-
T Consensus       176 Ea~~~lvs~~mlt-----~~Ee~~ll~~l~~a~~~~ed~e~l~~lyel~~~k~~n~~~~~r~~~~sl~~l~~~~dll~~~  250 (611)
T KOG1173|consen  176 EAFEKLVSAHMLT-----AQEEFELLESLDLAMLTKEDVERLEILYELKLCKNRNEESLTRNEDESLIGLAENLDLLAEK  250 (611)
T ss_pred             HHHHHHHHHHhcc-----hhHHHHHHhcccHHhhhhhHHHHHHHHHHhhhhhhccccccccCchhhhhhhhhcHHHHHHH
Confidence            2222222222111     1222333332211     01111111111110000000000000  0000  1234444455


Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHh
Q 044988          225 ISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYAS  304 (538)
Q Consensus       225 i~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  304 (538)
                      ..-+...+++.+..++.+...+. .++....+..-|.++...|+...-..+=..+++.     .|....+|-++.-.|..
T Consensus       251 ad~~y~~c~f~~c~kit~~lle~-dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~-----yP~~a~sW~aVg~YYl~  324 (611)
T KOG1173|consen  251 ADRLYYGCRFKECLKITEELLEK-DPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL-----YPSKALSWFAVGCYYLM  324 (611)
T ss_pred             HHHHHHcChHHHHHHHhHHHHhh-CCCCcchHHHHHHHHHHhcccchHHHHHHHHHHh-----CCCCCcchhhHHHHHHH
Confidence            56677789999999999998775 2455556666667888888887776666667765     88888889899999999


Q ss_pred             CCCHHHHHHHHHhcCCC---CcchHHHHHHHHHhcCCccHHHHHHHHHH--------------HHhcccCcHHHHHHHHH
Q 044988          305 CGEIEEAYGVFRKMQRR---NTVSWTSMITGFAKQGYAQEALLTFLGVL--------------SACSHGGFVDEGRQFFE  367 (538)
Q Consensus       305 ~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~ll--------------~~~~~~~~~~~a~~~~~  367 (538)
                      .|+..+|++.|.+...-   =...|-.....|.-.|..+.|+..|...-              --|.+.++.+.|.+.|.
T Consensus       325 i~k~seARry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LYlgmey~~t~n~kLAe~Ff~  404 (611)
T KOG1173|consen  325 IGKYSEARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLYLGMEYMRTNNLKLAEKFFK  404 (611)
T ss_pred             hcCcHHHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHHHHHHHHHhccHHHHHHHHH
Confidence            99999999999886652   24588899999999999999985554432              24456789999999999


Q ss_pred             HhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--------CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHc
Q 044988          368 CMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--------MKP-NDAVLGSLLLGCRIHNNAELASQVAQKL  437 (538)
Q Consensus       368 ~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--------~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~  437 (538)
                      +..   ++.| |+..++.+.-..-..+.+.+|..+|+...        .++ ...+++.|..+|.+.+.+++|+..+++.
T Consensus       405 ~A~---ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~a  481 (611)
T KOG1173|consen  405 QAL---AIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKA  481 (611)
T ss_pred             HHH---hcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHH
Confidence            887   6677 68888999888888999999999998763        112 4567888999999999999999999999


Q ss_pred             hhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          438 VAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       438 ~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                       ....|.+..++. .++-+|...|.++.|++.|.+..-
T Consensus       482 -L~l~~k~~~~~a-sig~iy~llgnld~Aid~fhKaL~  517 (611)
T KOG1173|consen  482 -LLLSPKDASTHA-SIGYIYHLLGNLDKAIDHFHKALA  517 (611)
T ss_pred             -HHcCCCchhHHH-HHHHHHHHhcChHHHHHHHHHHHh
Confidence             999999999888 999999999999999999988764

>TIGR00540 hemY_coli hemY protein

Probab=99.46  E-value=1.4e-10  Score=112.08  Aligned_cols=222  Identities=11%  Similarity=-0.001  Sum_probs=130.3

Q ss_pred             HHHHHhcCCHHHHHHHHccCCC--C-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH---HccC
Q 044988          194 LKGYVKRGDIDGAWKIFDEMPH--R-NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSAC---AEIG  267 (538)
Q Consensus       194 i~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~---~~~~  267 (538)
                      ...+...|+++.|...++.+.+  | +...+..+...+...|++++|.+++..+.+.++.+.......-..++   ...+
T Consensus       160 a~l~l~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~  239 (409)
T TIGR00540       160 TRILLAQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEA  239 (409)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH
Confidence            4455556667777777776653  3 45567788888888999999999999888876543332211111111   2222


Q ss_pred             ChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CCcchHH-HHHHHHHhcCCccHHHH
Q 044988          268 DLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RNTVSWT-SMITGFAKQGYAQEALL  344 (538)
Q Consensus       268 ~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~-~li~~~~~~~~~~~a~~  344 (538)
                      ..+.+...+..+.+.. +...+.+...+..++..+...|+.++|.+++++..+  ||..... .++..+..         
T Consensus       240 ~~~~~~~~L~~~~~~~-p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~---------  309 (409)
T TIGR00540       240 MADEGIDGLLNWWKNQ-PRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPR---------  309 (409)
T ss_pred             HHhcCHHHHHHHHHHC-CHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhh---------
Confidence            2222223344343330 001224677777888888888888888888888765  3322100 01111111         


Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-H--HHHHHHHHHhhhcCChHHHHHHHHh--C-CCCCCHHHHHHHH
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-I--EHYGCMVDLFSRAGLMDEAFSLVQN--M-PMKPNDAVLGSLL  418 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~--~~~~~l~~~~~~~g~~~~A~~~~~~--~-~~~p~~~~~~~l~  418 (538)
                               ...++.+.+.+.++...+.   .|+ .  ....++...+.+.|++++|.+.|+.  . ...|+...+..+.
T Consensus       310 ---------l~~~~~~~~~~~~e~~lk~---~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La  377 (409)
T TIGR00540       310 ---------LKPEDNEKLEKLIEKQAKN---VDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAA  377 (409)
T ss_pred             ---------cCCCChHHHHHHHHHHHHh---CCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHH
Confidence                     1123455666666666554   332 3  4555677777777777777777773  2 3467776676777


Q ss_pred             HHHHhcCCHHHHHHHHHHc
Q 044988          419 LGCRIHNNAELASQVAQKL  437 (538)
Q Consensus       419 ~~~~~~~~~~~A~~~~~~~  437 (538)
                      ..+.+.|+.++|.+++++.
T Consensus       378 ~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       378 DAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             HHHHHcCCHHHHHHHHHHH
Confidence            7777777777777777765

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=99.41  E-value=7e-10  Score=96.04  Aligned_cols=286  Identities=13%  Similarity=0.138  Sum_probs=165.3

Q ss_pred             CCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHH
Q 044988           96 SETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCA  175 (538)
Q Consensus        96 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a  175 (538)
                      ++++++|.++|-+|.+.. +-+..+--+|.+.|.+.|..+.|..+++.+.++   ||...-.                +.
T Consensus        48 s~Q~dKAvdlF~e~l~~d-~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~s---pdlT~~q----------------r~  107 (389)
T COG2956          48 SNQPDKAVDLFLEMLQED-PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLES---PDLTFEQ----------------RL  107 (389)
T ss_pred             hcCcchHHHHHHHHHhcC-chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcC---CCCchHH----------------HH
Confidence            456777777777777632 223334556666677777777777777776653   3321111                01


Q ss_pred             HHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCCh---HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC
Q 044988          176 RLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNV---VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD  252 (538)
Q Consensus       176 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~---~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  252 (538)
                                  ...-.|.+-|...|-+|.|+.+|..+.+.+.   .....|+..|-...+|++|++.-+++.+.|-.+.
T Consensus       108 ------------lAl~qL~~Dym~aGl~DRAE~~f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~  175 (389)
T COG2956         108 ------------LALQQLGRDYMAAGLLDRAEDIFNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTY  175 (389)
T ss_pred             ------------HHHHHHHHHHHHhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccc
Confidence                        1122345567778888888888888776222   3566788889999999999999998888665554


Q ss_pred             HH----HHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHH
Q 044988          253 QV----ALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTS  328 (538)
Q Consensus       253 ~~----~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~  328 (538)
                      ..    .|--+...+....+++.|...+....+.     .|..+..--.+.+.+...|+++.|.+.++.+.+.|+.... 
T Consensus       176 ~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa-----~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~-  249 (389)
T COG2956         176 RVEIAQFYCELAQQALASSDVDRARELLKKALQA-----DKKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLS-  249 (389)
T ss_pred             hhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhh-----CccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHH-
Confidence            32    2334444444556777777777777765     4555555556677777777777777777777665543222 


Q ss_pred             HHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHH-HhCCC
Q 044988          329 MITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLV-QNMPM  407 (538)
Q Consensus       329 li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~-~~~~~  407 (538)
                                     .+...+..+|.+.|+.+++...+..+.+.   .++...-..+.+.-......+.|...+ +.+..
T Consensus       250 ---------------evl~~L~~~Y~~lg~~~~~~~fL~~~~~~---~~g~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~r  311 (389)
T COG2956         250 ---------------EVLEMLYECYAQLGKPAEGLNFLRRAMET---NTGADAELMLADLIELQEGIDAAQAYLTRQLRR  311 (389)
T ss_pred             ---------------HHHHHHHHHHHHhCCHHHHHHHHHHHHHc---cCCccHHHHHHHHHHHhhChHHHHHHHHHHHhh
Confidence                           12233344444455666666666666544   233333333333333333344443333 44455


Q ss_pred             CCCHHHHHHHHHHHHh---cCCHHHHHHHHHHc
Q 044988          408 KPNDAVLGSLLLGCRI---HNNAELASQVAQKL  437 (538)
Q Consensus       408 ~p~~~~~~~l~~~~~~---~~~~~~A~~~~~~~  437 (538)
                      +|+...+..|+.....   .|...+-+..++.|
T Consensus       312 ~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~m  344 (389)
T COG2956         312 KPTMRGFHRLMDYHLADAEEGRAKESLDLLRDM  344 (389)
T ss_pred             CCcHHHHHHHHHhhhccccccchhhhHHHHHHH
Confidence            6666666666665322   22234444444444

>TIGR00540 hemY_coli hemY protein

Probab=99.40  E-value=6.5e-10  Score=107.48  Aligned_cols=280  Identities=13%  Similarity=0.081  Sum_probs=202.0

Q ss_pred             HHHHHHHHH--ccCChhHHHHHHhcCCC--CCcch-HHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcc--hHHHHHHH
Q 044988           55 LAKLLAFYV--TSGYLINAHKVFEKTEN--PSTAI-WNQMIRGHARSETPEKSVYLYKQMIDKETEPDEY--TYSFLLSV  127 (538)
Q Consensus        55 ~~~l~~~~~--~~g~~~~a~~~~~~~~~--~~~~~-~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~--~~~~li~~  127 (538)
                      ...+..+..  ..|+++.|.+.+.+..+  |+... +-....+..+.|+++.|.+.|++..+.  .|+..  ........
T Consensus        85 ~~~~~~glla~~~g~~~~A~~~l~~~~~~~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~--~p~~~l~~~~~~a~l  162 (409)
T TIGR00540        85 QKQTEEALLKLAEGDYAKAEKLIAKNADHAAEPVLNLIKAAEAAQQRGDEARANQHLEEAAEL--AGNDNILVEIARTRI  162 (409)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCcCchHHHHHHHHH
Confidence            333444433  47999999999987664  43332 334456677889999999999998764  36554  33445777


Q ss_pred             HHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC---CchhHH--------HHHHH
Q 044988          128 CARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPAR---SVVSWN--------SLLKG  196 (538)
Q Consensus       128 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~---~~~~~~--------~li~~  196 (538)
                      +...|+++.|...++.+.+.. +-+..+...+..++...|+   ++.|.+.+....+.   +...+.        .++..
T Consensus       163 ~l~~~~~~~Al~~l~~l~~~~-P~~~~~l~ll~~~~~~~~d---~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~  238 (409)
T TIGR00540       163 LLAQNELHAARHGVDKLLEMA-PRHKEVLKLAEEAYIRSGA---WQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDE  238 (409)
T ss_pred             HHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHhh---HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence            888999999999999999986 5567788999999999999   99999998888753   222221        11221


Q ss_pred             HHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHH--H-HHHHHHHHccCChH
Q 044988          197 YVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVA--L-VAALSACAEIGDLK  270 (538)
Q Consensus       197 ~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~--~-~~li~~~~~~~~~~  270 (538)
                      -......+...+.++..++   .+...+..+...+...|+.++|.+.+++..+.  .||...  + ..........++.+
T Consensus       239 ~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~~~~~~~l~~~~~l~~~~~~  316 (409)
T TIGR00540       239 AMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDRAISLPLCLPIPRLKPEDNE  316 (409)
T ss_pred             HHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcccchhHHHHHhhhcCCCChH
Confidence            1223334555666666664   47788899999999999999999999999885  344332  1 11222234457888


Q ss_pred             HHHHHHHHHHHhccCCCCCcch--hHHHHHHHHHHhCCCHHHHHHHHH--hcC--CCCcchHHHHHHHHHhcCCccHHHH
Q 044988          271 LGKWIHSYVEENFSVGREPVLV--SLNNALIHMYASCGEIEEAYGVFR--KMQ--RRNTVSWTSMITGFAKQGYAQEALL  344 (538)
Q Consensus       271 ~a~~~~~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~g~~~~a~~~~~--~m~--~~~~~~~~~li~~~~~~~~~~~a~~  344 (538)
                      .+...++...+.     .|.+.  ....++...+.+.|++++|.+.|+  ...  .|+...+..+...+.+.|+.++|..
T Consensus       317 ~~~~~~e~~lk~-----~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~  391 (409)
T TIGR00540       317 KLEKLIEKQAKN-----VDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAA  391 (409)
T ss_pred             HHHHHHHHHHHh-----CCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            888888888875     67777  777799999999999999999999  352  4788778888888888886665554


Q ss_pred             HHH
Q 044988          345 TFL  347 (538)
Q Consensus       345 ~~~  347 (538)
                      +|.
T Consensus       392 ~~~  394 (409)
T TIGR00540       392 MRQ  394 (409)
T ss_pred             HHH
Confidence            443

This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.

>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.39  E-value=1.9e-09  Score=97.86  Aligned_cols=296  Identities=14%  Similarity=0.082  Sum_probs=180.3

Q ss_pred             CCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHH-HHHHHH
Q 044988          150 CSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWT-TMISGC  228 (538)
Q Consensus       150 ~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~-~li~~~  228 (538)
                      ..|...+-...-.+.+.|.   ...|+..|......-+..|.+.+....-..+.+.+..+....+..+...-. -+..++
T Consensus       161 ~~D~fllYL~Gvv~k~~~~---~s~A~~sfv~~v~~~P~~W~AWleL~~lit~~e~~~~l~~~l~~~~h~M~~~F~~~a~  237 (559)
T KOG1155|consen  161 EKDEFLLYLYGVVLKELGL---LSLAIDSFVEVVNRYPWFWSAWLELSELITDIEILSILVVGLPSDMHWMKKFFLKKAY  237 (559)
T ss_pred             cchhHHHHHHHHHHHhhch---HHHHHHHHHHHHhcCCcchHHHHHHHHhhchHHHHHHHHhcCcccchHHHHHHHHHHH
Confidence            4455555555555566666   677777766665544445555444443344444443333333322111111 122344


Q ss_pred             HHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH------------
Q 044988          229 AQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN------------  296 (538)
Q Consensus       229 ~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~------------  296 (538)
                      ....+.+++..-.+.....|++-+...-+....+.-...++++|+.+|+.+.+.. + -.-.+..+|+            
T Consensus       238 ~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knD-P-YRl~dmdlySN~LYv~~~~skL  315 (559)
T KOG1155|consen  238 QELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKND-P-YRLDDMDLYSNVLYVKNDKSKL  315 (559)
T ss_pred             HHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcC-C-CcchhHHHHhHHHHHHhhhHHH
Confidence            4444555555555555555554444444444444445556666666666665540 0 0111222332            


Q ss_pred             -------------------HHHHHHHhCCCHHHHHHHHHhcCCCC---cchHHHHHHHHHhcCCccHHHHHHHHHHHHhc
Q 044988          297 -------------------ALIHMYASCGEIEEAYGVFRKMQRRN---TVSWTSMITGFAKQGYAQEALLTFLGVLSACS  354 (538)
Q Consensus       297 -------------------~l~~~~~~~g~~~~a~~~~~~m~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~  354 (538)
                                         .+.+.|.-.++.+.|...|++..+-|   ...|+.|..-|...                  
T Consensus       316 s~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLNp~~~~aWTLmGHEyvEm------------------  377 (559)
T KOG1155|consen  316 SYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLNPKYLSAWTLMGHEYVEM------------------  377 (559)
T ss_pred             HHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcCcchhHHHHHhhHHHHHh------------------
Confidence                               33344444555566666666555422   23444444444444                  


Q ss_pred             ccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHH
Q 044988          355 HGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELAS  431 (538)
Q Consensus       355 ~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~  431 (538)
                        .+...|.+-++..++   +.| |-..|-.|.++|.-.+...-|+-.|++.. .+| |...|.+|..+|.+.++.++|+
T Consensus       378 --KNt~AAi~sYRrAvd---i~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAi  452 (559)
T KOG1155|consen  378 --KNTHAAIESYRRAVD---INPRDYRAWYGLGQAYEIMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAI  452 (559)
T ss_pred             --cccHHHHHHHHHHHh---cCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHH
Confidence              466667777777774   355 78899999999999999999999999884 444 5789999999999999999999


Q ss_pred             HHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          432 QVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       432 ~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +.|... ....-.+...+. .|+++|.+.++.++|...+++-.+
T Consensus       453 KCykra-i~~~dte~~~l~-~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  453 KCYKRA-ILLGDTEGSALV-RLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             HHHHHH-HhccccchHHHH-HHHHHHHHHHhHHHHHHHHHHHHH
Confidence            999998 555555556688 999999999999999999888765

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=99.37  E-value=5.9e-10  Score=96.49  Aligned_cols=284  Identities=12%  Similarity=0.114  Sum_probs=202.2

Q ss_pred             hhHHHHHhhcCCCCCchhH---HHHHHHHHhcCCHHHHHHHHccCCC-CChH------HHHHHHHHHHHcCCHHHHHHHH
Q 044988          172 VGCARLLFDDMPARSVVSW---NSLLKGYVKRGDIDGAWKIFDEMPH-RNVV------SWTTMISGCAQNGKSRQALSLF  241 (538)
Q Consensus       172 ~~~a~~~~~~~~~~~~~~~---~~li~~~~~~g~~~~A~~~~~~m~~-~~~~------~~~~li~~~~~~~~~~~a~~~~  241 (538)
                      .++|..+|-+|.+.|+.++   -+|.+.|-+.|..|.|+++-+.+.+ ||..      ..-.|..-|...|-+|.|..+|
T Consensus        51 ~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f  130 (389)
T COG2956          51 PDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIF  130 (389)
T ss_pred             cchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHH
Confidence            6667777766666554444   3466677777777888877777654 4432      3445667788999999999999


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC
Q 044988          242 NEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR  321 (538)
Q Consensus       242 ~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  321 (538)
                      ..+.+.| ..-......|+..|-...+|++|.++-..+.+.........-..+|.-|...+....+++.|..++.+..+.
T Consensus       131 ~~L~de~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa  209 (389)
T COG2956         131 NQLVDEG-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQA  209 (389)
T ss_pred             HHHhcch-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhh
Confidence            9998754 233456778899999999999999999988887221112222456667777777788999999999988763


Q ss_pred             Cc---chHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc--HHHHHHHHHHhhhcCChH
Q 044988          322 NT---VSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR--IEHYGCMVDLFSRAGLMD  396 (538)
Q Consensus       322 ~~---~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~  396 (538)
                      |+   ..--.+.......                    |+++.|.+.++.+.+.   .|+  ..+...|..+|...|+.+
T Consensus       210 ~~~cvRAsi~lG~v~~~~--------------------g~y~~AV~~~e~v~eQ---n~~yl~evl~~L~~~Y~~lg~~~  266 (389)
T COG2956         210 DKKCVRASIILGRVELAK--------------------GDYQKAVEALERVLEQ---NPEYLSEVLEMLYECYAQLGKPA  266 (389)
T ss_pred             CccceehhhhhhHHHHhc--------------------cchHHHHHHHHHHHHh---ChHHHHHHHHHHHHHHHHhCCHH
Confidence            32   2323333344444                    5788888999988876   454  678899999999999999


Q ss_pred             HHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHH---hcCChHHHHHHHHH
Q 044988          397 EAFSLVQNMP-MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYA---AAKRWQDVAAVRQK  472 (538)
Q Consensus       397 ~A~~~~~~~~-~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~---~~g~~~~A~~~~~~  472 (538)
                      +....+.++. ..++...-..+...-....-.+.|..++.+- ..-+|+-.. +. .|++...   ..|++.+...++++
T Consensus       267 ~~~~fL~~~~~~~~g~~~~l~l~~lie~~~G~~~Aq~~l~~Q-l~r~Pt~~g-f~-rl~~~~l~daeeg~~k~sL~~lr~  343 (389)
T COG2956         267 EGLNFLRRAMETNTGADAELMLADLIELQEGIDAAQAYLTRQ-LRRKPTMRG-FH-RLMDYHLADAEEGRAKESLDLLRD  343 (389)
T ss_pred             HHHHHHHHHHHccCCccHHHHHHHHHHHhhChHHHHHHHHHH-HhhCCcHHH-HH-HHHHhhhccccccchhhhHHHHHH
Confidence            9999998774 5566666666666666666667777777776 777888777 55 4545443   45678899999999


Q ss_pred             HHhCCCCCCC
Q 044988          473 MIKMGVRKPP  482 (538)
Q Consensus       473 m~~~~~~~~~  482 (538)
                      |....++..|
T Consensus       344 mvge~l~~~~  353 (389)
T COG2956         344 MVGEQLRRKP  353 (389)
T ss_pred             HHHHHHhhcC
Confidence            9866565554

>PF13041 PPR_2: PPR repeat family

Probab=99.37  E-value=2.3e-12  Score=82.73  Aligned_cols=50  Identities=30%  Similarity=0.513  Sum_probs=48.4

Q ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 044988          216 RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAE  265 (538)
Q Consensus       216 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  265 (538)
                      ||+.+||++|.+|++.|++++|.++|++|.+.|++||..||+.+|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            78999999999999999999999999999999999999999999999875

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.36  E-value=2e-08  Score=94.95  Aligned_cols=284  Identities=14%  Similarity=0.136  Sum_probs=168.6

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHccCChHHHHHHHHHHHHhccC-------CCCC
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRARVGLD---QVALVAALSACAEIGDLKLGKWIHSYVEENFSV-------GREP  289 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~---~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-------~~~~  289 (538)
                      .|..+...|-++|+.+.|..+|++..+...+--   ..+|-.-...=.+..+++.|..+.+........       ++.|
T Consensus       389 Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~p  468 (835)
T KOG2047|consen  389 LWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEP  468 (835)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCc
Confidence            577788888888888888888888866432221   122222223333556677777766665443111       1112


Q ss_pred             c------chhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHH---HHHhcCCccHHH----------------H
Q 044988          290 V------LVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMIT---GFAKQGYAQEAL----------------L  344 (538)
Q Consensus       290 ~------~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~---~~~~~~~~~~a~----------------~  344 (538)
                      .      +..+|..+++..-..|-++....+++++.+--+.|-..+++   -+-.+..++++.                .
T Consensus       469 vQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLriaTPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~v~d  548 (835)
T KOG2047|consen  469 VQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRIATPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPNVYD  548 (835)
T ss_pred             HHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCccHHH
Confidence            1      23455566677777888888888888887632222222221   223344444444                3


Q ss_pred             HHHHHHHHhc---ccCcHHHHHHHHHHhhhhcCCCcc-HH-HHHHHHHHhhhcCChHHHHHHHHhCC--CCCC--HHHHH
Q 044988          345 TFLGVLSACS---HGGFVDEGRQFFECMNQNWGIKPR-IE-HYGCMVDLFSRAGLMDEAFSLVQNMP--MKPN--DAVLG  415 (538)
Q Consensus       345 ~~~~ll~~~~---~~~~~~~a~~~~~~~~~~~~~~p~-~~-~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~--~~~~~  415 (538)
                      .|+.-+.-+.   ..-.++.|+.+|++..+  |.+|. .. .|-.....--+.|-...|+.++++..  +++.  ...||
T Consensus       549 iW~tYLtkfi~rygg~klEraRdLFEqaL~--~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyerat~~v~~a~~l~myn  626 (835)
T KOG2047|consen  549 IWNTYLTKFIKRYGGTKLERARDLFEQALD--GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERATSAVKEAQRLDMYN  626 (835)
T ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence            4444333332   23478999999999987  55664 22 23333333345688889999999985  3333  35788


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH-HHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeEEEECCEEE
Q 044988          416 SLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL-ALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLH  494 (538)
Q Consensus       416 ~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~-~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~~~~~~~~~  494 (538)
                      ..|.-.+..=.+.....+++++ .+.-|++...-. --.++.=.+.|..+.|..++..-.+---+....-+|.    ..+
T Consensus       627 i~I~kaae~yGv~~TR~iYeka-Ie~Lp~~~~r~mclrFAdlEtklGEidRARaIya~~sq~~dPr~~~~fW~----twk  701 (835)
T KOG2047|consen  627 IYIKKAAEIYGVPRTREIYEKA-IESLPDSKAREMCLRFADLETKLGEIDRARAIYAHGSQICDPRVTTEFWD----TWK  701 (835)
T ss_pred             HHHHHHHHHhCCcccHHHHHHH-HHhCChHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhhcCCCcCChHHHH----HHH
Confidence            8888766666667788899999 666777654222 1345666789999999999987665433233334451    113


Q ss_pred             EEEeCCCCCcchHHHHHHH
Q 044988          495 DFVAGDSTYKQASLIYKTL  513 (538)
Q Consensus       495 ~~~~~~~~~~~~~~~~~~l  513 (538)
                      .|-..   ||..+..-++|
T Consensus       702 ~FEvr---HGnedT~keML  717 (835)
T KOG2047|consen  702 EFEVR---HGNEDTYKEML  717 (835)
T ss_pred             HHHHh---cCCHHHHHHHH
Confidence            34444   66644444444

>KOG4318 consensus Bicoid mRNA stability factor [RNA processing and modification]

Probab=99.36  E-value=2.3e-11  Score=118.28  Aligned_cols=262  Identities=15%  Similarity=0.170  Sum_probs=188.2

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          239 SLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       239 ~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                      .++-.+...|+.|+.+||..+|.-||..|+++.|- +|..|.-.    ..|.+...++.++.+....++.+.+.      
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~k----sLpv~e~vf~~lv~sh~~And~Enpk------   79 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIK----SLPVREGVFRGLVASHKEANDAENPK------   79 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcc----cccccchhHHHHHhcccccccccCCC------
Confidence            45667888999999999999999999999999998 89888877    78888889999999999988887776      


Q ss_pred             CCCCcchHHHHHHHHHhcCCccHHH---HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCCh
Q 044988          319 QRRNTVSWTSMITGFAKQGYAQEAL---LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLM  395 (538)
Q Consensus       319 ~~~~~~~~~~li~~~~~~~~~~~a~---~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  395 (538)
                       +|...+|+.+..+|..+|+...-.   .....+...++..|.-..-..++..+.-..+.-||..+   .+......|-+
T Consensus        80 -ep~aDtyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n---~illlv~eglw  155 (1088)
T KOG4318|consen   80 -EPLADTYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAEN---AILLLVLEGLW  155 (1088)
T ss_pred             -CCchhHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHH---HHHHHHHHHHH
Confidence             788889999999999999876422   22444455566666665556666554433345566543   44445567888


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHhcC-CHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          396 DEAFSLVQNMPMKPNDAVLGSLLLGCRIHN-NAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       396 ~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      +.+++++..++......++..+++-+.... .+++-..+.... .+ .|+..+ |. .+..+-..+|+.+-|..++.+|+
T Consensus       156 aqllkll~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl-~e-~~~s~~-l~-a~l~~alaag~~d~Ak~ll~emk  231 (1088)
T KOG4318|consen  156 AQLLKLLAKVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSL-VE-APTSET-LH-AVLKRALAAGDVDGAKNLLYEMK  231 (1088)
T ss_pred             HHHHHHHhhCCcccccchHHHHHHHhccCCchHHHHHHHHHHh-hc-CCChHH-HH-HHHHHHHhcCchhhHHHHHHHHH
Confidence            999999988862211112222344444333 344444444444 44 455544 88 77788889999999999999999


Q ss_pred             hCCCCCCCceeEEEECCEEEEEEeCCCCCcchHHHHHHHHHHHHHHHHcCcccCCccccc
Q 044988          475 KMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFL  534 (538)
Q Consensus       475 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~m~~~~~~p~~~~~~~  534 (538)
                      ++|+...+..+|        ..+.+   -+...    .+..+++.|++.|+.||.++.++
T Consensus       232 e~gfpir~HyFw--------pLl~g---~~~~q----~~e~vlrgmqe~gv~p~seT~ad  276 (1088)
T KOG4318|consen  232 EKGFPIRAHYFW--------PLLLG---INAAQ----VFEFVLRGMQEKGVQPGSETQAD  276 (1088)
T ss_pred             HcCCCcccccch--------hhhhc---Cccch----HHHHHHHHHHHhcCCCCcchhHH
Confidence            999999999999        34444   12222    33344569999999999988765

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=99.35  E-value=5.5e-09  Score=93.44  Aligned_cols=279  Identities=13%  Similarity=0.049  Sum_probs=171.8

Q ss_pred             CCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHH
Q 044988           96 SETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCA  175 (538)
Q Consensus        96 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a  175 (538)
                      .|+|.+|..+..+-.+.+ .-....|..-..+.-+.||.+.+-.++.+..+..-.++....-+..               
T Consensus        97 eG~~~qAEkl~~rnae~~-e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltra---------------  160 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHG-EQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRA---------------  160 (400)
T ss_pred             cCcHHHHHHHHHHhhhcC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHH---------------
Confidence            466666666666655443 1222344444455555566666666666655542223333333333               


Q ss_pred             HHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCC---CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC
Q 044988          176 RLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMP---HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD  252 (538)
Q Consensus       176 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  252 (538)
                                         ......|+++.|..-.++..   ..++........+|.+.|++..+..++..|.+.|+--|
T Consensus       161 -------------------rlll~~~d~~aA~~~v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~  221 (400)
T COG3071         161 -------------------RLLLNRRDYPAARENVDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSD  221 (400)
T ss_pred             -------------------HHHHhCCCchhHHHHHHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCCh
Confidence                               44444555555555554433   35667788888999999999999999999998886555


Q ss_pred             HH-------HHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC--Cc
Q 044988          253 QV-------ALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR--NT  323 (538)
Q Consensus       253 ~~-------~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~--~~  323 (538)
                      ..       +|..++.-+...+..+.-...|+...+.     ...++..-.+++.-+.++|+.++|.++..+..+.  |.
T Consensus       222 ~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~-----lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~  296 (400)
T COG3071         222 EEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRK-----LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDP  296 (400)
T ss_pred             HHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHH-----hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccCh
Confidence            43       4556666666666666656666665554     4444555567788888888888888887776552  22


Q ss_pred             chHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHH
Q 044988          324 VSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQ  403 (538)
Q Consensus       324 ~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~  403 (538)
                      .    +..-                  -.+.+.++...-.+..++-.+.++..|  ..+.+|...|.+.+.+.+|.+.|+
T Consensus       297 ~----L~~~------------------~~~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tLG~L~~k~~~w~kA~~~le  352 (400)
T COG3071         297 R----LCRL------------------IPRLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTLGRLALKNKLWGKASEALE  352 (400)
T ss_pred             h----HHHH------------------HhhcCCCCchHHHHHHHHHHHhCCCCh--hHHHHHHHHHHHhhHHHHHHHHHH
Confidence            2    1111                  112233344444555555544433333  566777777778888888877777


Q ss_pred             hC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHch
Q 044988          404 NM-PMKPNDAVLGSLLLGCRIHNNAELASQVAQKLV  438 (538)
Q Consensus       404 ~~-~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  438 (538)
                      .. ...|+..+|+-+..++.+.|+..+|.+..++..
T Consensus       353 aAl~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L  388 (400)
T COG3071         353 AALKLRPSASDYAELADALDQLGEPEEAEQVRREAL  388 (400)
T ss_pred             HHHhcCCChhhHHHHHHHHHHcCChHHHHHHHHHHH
Confidence            55 366777788888888888888887777777764

>PF13041 PPR_2: PPR repeat family

Probab=99.33  E-value=2e-12  Score=82.98  Aligned_cols=50  Identities=28%  Similarity=0.598  Sum_probs=41.9

Q ss_pred             CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHc
Q 044988           81 PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCAR  130 (538)
Q Consensus        81 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  130 (538)
                      ||..+||++|++|++.|++++|.++|++|.+.|+.||..||+++|++|++
T Consensus         1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            67888888888888888888888888888888888888888888888764

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=99.29  E-value=8.2e-09  Score=92.36  Aligned_cols=274  Identities=9%  Similarity=0.044  Sum_probs=215.0

Q ss_pred             HHHHHHHc--cCChhHHHHHHhcCCCC---CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHcc
Q 044988           57 KLLAFYVT--SGYLINAHKVFEKTENP---STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARC  131 (538)
Q Consensus        57 ~l~~~~~~--~g~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~  131 (538)
                      .+..+..+  .|++..|+++..+-.+.   ....|-.-..+--+.|+.+.+-.++.+.-+.--.++...+.+..+.....
T Consensus        87 ~~~egl~~l~eG~~~qAEkl~~rnae~~e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~  166 (400)
T COG3071          87 ALNEGLLKLFEGDFQQAEKLLRRNAEHGEQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNR  166 (400)
T ss_pred             HHHHHHHHHhcCcHHHHHHHHHHhhhcCcchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhC
Confidence            34444433  69999999998776532   22234444556678899999999999998742244455566667778899


Q ss_pred             CCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC-----------CchhHHHHHHHHHhc
Q 044988          132 GLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPAR-----------SVVSWNSLLKGYVKR  200 (538)
Q Consensus       132 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~-----------~~~~~~~li~~~~~~  200 (538)
                      |+.+.|..-+.++.+.+ +-+..+......+|.+.|+   +..+..++..+.+.           ...+|+.+++-....
T Consensus       167 ~d~~aA~~~v~~ll~~~-pr~~~vlrLa~r~y~~~g~---~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~  242 (400)
T COG3071         167 RDYPAARENVDQLLEMT-PRHPEVLRLALRAYIRLGA---WQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDD  242 (400)
T ss_pred             CCchhHHHHHHHHHHhC-cCChHHHHHHHHHHHHhcc---HHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999886 5667788899999999999   99999999888764           224788888888888


Q ss_pred             CCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHH
Q 044988          201 GDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHS  277 (538)
Q Consensus       201 g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~  277 (538)
                      +..+.-...++..+.   .++..-..++.-+.+.|+.++|.++..+..+.+..|+..    ..-.+.+.++.+.-.+..+
T Consensus       243 ~~~~gL~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~----~~~~~l~~~d~~~l~k~~e  318 (400)
T COG3071         243 NGSEGLKTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLC----RLIPRLRPGDPEPLIKAAE  318 (400)
T ss_pred             ccchHHHHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHH----HHHhhcCCCCchHHHHHHH
Confidence            888888888888874   567777888899999999999999999999988777722    2234567788888777777


Q ss_pred             HHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CCcchHHHHHHHHHhcCCccHHH
Q 044988          278 YVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RNTVSWTSMITGFAKQGYAQEAL  343 (538)
Q Consensus       278 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~  343 (538)
                      ...+.     .|.++..+.+|...|.+.+.|.+|...|+...+  |+..+|+-+..++.+.|+..+|.
T Consensus       319 ~~l~~-----h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~  381 (400)
T COG3071         319 KWLKQ-----HPEDPLLLSTLGRLALKNKLWGKASEALEAALKLRPSASDYAELADALDQLGEPEEAE  381 (400)
T ss_pred             HHHHh-----CCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHH
Confidence            77765     677778888999999999999999999997765  78888888888888888555544

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.27  E-value=1.7e-09  Score=96.57  Aligned_cols=198  Identities=13%  Similarity=0.032  Sum_probs=115.3

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHH
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNAL  298 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l  298 (538)
                      ..+..+...+...|++++|...+++..+.. +.+...+..+...+...|+++.|...++...+.     .|.+...+..+
T Consensus        32 ~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~-----~~~~~~~~~~~  105 (234)
T TIGR02521        32 KIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTL-----NPNNGDVLNNY  105 (234)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh-----CCCCHHHHHHH
Confidence            455556666666666666666666665532 222344444555555555555555555555544     23333344444


Q ss_pred             HHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc
Q 044988          299 IHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR  378 (538)
Q Consensus       299 ~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~  378 (538)
                      ...+...|++++|.+.+++                                                   ..........
T Consensus       106 ~~~~~~~g~~~~A~~~~~~---------------------------------------------------~~~~~~~~~~  134 (234)
T TIGR02521       106 GTFLCQQGKYEQAMQQFEQ---------------------------------------------------AIEDPLYPQP  134 (234)
T ss_pred             HHHHHHcccHHHHHHHHHH---------------------------------------------------HHhccccccc
Confidence            4445555555555444444                                                   3322111112


Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ...+..+...+...|++++|.+.+++.. ..| +...+..+...+...|++++|...++++ ....|+++..+. .++.+
T Consensus       135 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~-~~~~~~~~~~~~-~~~~~  212 (234)
T TIGR02521       135 ARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDARAYLERY-QQTYNQTAESLW-LGIRI  212 (234)
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHH
Confidence            3445556666777777777777776653 223 3456666777777778888888888877 555666666455 66777


Q ss_pred             HHhcCChHHHHHHHHHHHh
Q 044988          457 YAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       457 ~~~~g~~~~A~~~~~~m~~  475 (538)
                      +...|+.++|..+.+.+..
T Consensus       213 ~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       213 ARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHhhHHHHHHHHHHHHh
Confidence            7778888888877776654

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.25  E-value=1.1e-08  Score=98.15  Aligned_cols=244  Identities=19%  Similarity=0.189  Sum_probs=151.6

Q ss_pred             chHHHHHHHHHccCCcHHHHHHHHHHHHh-----C-CCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHH
Q 044988          119 YTYSFLLSVCARCGLFREGEQVHGRVLAS-----G-YCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNS  192 (538)
Q Consensus       119 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~-----~-~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~  192 (538)
                      .+...+...|...|+++.|..+++..++.     | ..|...+                                 ..+.
T Consensus       200 ~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~---------------------------------~l~~  246 (508)
T KOG1840|consen  200 RTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVAS---------------------------------MLNI  246 (508)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHH---------------------------------HHHH
Confidence            35556777777778888777777766654     1 0111111                                 1112


Q ss_pred             HHHHHHhcCCHHHHHHHHccCC----------CCC-hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 044988          193 LLKGYVKRGDIDGAWKIFDEMP----------HRN-VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALS  261 (538)
Q Consensus       193 li~~~~~~g~~~~A~~~~~~m~----------~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  261 (538)
                      +...|...+++++|..+|+++.          .|. ..+++.|...|.+.|++++|..++++..+               
T Consensus       247 ~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~---------------  311 (508)
T KOG1840|consen  247 LALVYRSLGKYDEAVNLYEEALTIREEVFGEDHPAVAATLNNLAVLYYKQGKFAEAEEYCERALE---------------  311 (508)
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhccCChHHHHHHHHHHHH---------------
Confidence            3444555555555555555443          122 23677788889999999999888887754               


Q ss_pred             HHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccH
Q 044988          262 ACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQE  341 (538)
Q Consensus       262 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~  341 (538)
                                   ++......    ..+.-...++.+...++..+++++|..++.+.                       
T Consensus       312 -------------I~~~~~~~----~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~a-----------------------  351 (508)
T KOG1840|consen  312 -------------IYEKLLGA----SHPEVAAQLSELAAILQSMNEYEEAKKLLQKA-----------------------  351 (508)
T ss_pred             -------------HHHHhhcc----ChHHHHHHHHHHHHHHHHhcchhHHHHHHHHH-----------------------
Confidence                         11110000    12223334456677777788888888777642                       


Q ss_pred             HHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC---------CCCC-
Q 044988          342 ALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP---------MKPN-  410 (538)
Q Consensus       342 a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~---------~~p~-  410 (538)
                                           .+++......  ..|+ ..+++.|...|...|++++|.++++++.         ..+. 
T Consensus       352 ---------------------l~i~~~~~g~--~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~  408 (508)
T KOG1840|consen  352 ---------------------LKIYLDAPGE--DNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGV  408 (508)
T ss_pred             ---------------------HHHHHhhccc--cchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhh
Confidence                                 2222211110  1222 4578888888888888888888887763         1122 


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHch---hccCCCC---cccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          411 DAVLGSLLLGCRIHNNAELASQVAQKLV---AEIDPEQ---AAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       411 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~---~~~~p~~---~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      ...++.+...|.+.+++++|.++|.+..   ....|+.   ..+|. .|+..|.+.|++++|.++.+...
T Consensus       409 ~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~-nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  409 GKPLNQLAEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYL-NLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             hHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHH-HHHHHHHHcccHHHHHHHHHHHH
Confidence            4566777788888888888888888775   3344444   34566 78889999999999999988876

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.24  E-value=3.7e-07  Score=85.97  Aligned_cols=424  Identities=11%  Similarity=0.101  Sum_probs=252.1

Q ss_pred             HHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHH--hcCCCc
Q 044988           22 QIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGH--ARSETP   99 (538)
Q Consensus        22 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~--~~~~~~   99 (538)
                      +=+.-....+++++|.+..+.++..+ +-+..++..-+-+..+.+++++|+.+.+.-........-.+=.+|  .+.+..
T Consensus        17 t~ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~~~~~~~~fEKAYc~Yrlnk~   95 (652)
T KOG2376|consen   17 TDLNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGALLVINSFFFEKAYCEYRLNKL   95 (652)
T ss_pred             HHHHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchhhhcchhhHHHHHHHHHcccH
Confidence            33445566788999999999999887 446677888888899999999999777654421111111133444  478999


Q ss_pred             hHHHHHHHHhHhCCCCCCcc-hHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCc-hhHHhHHHHHHHhcCCCCChhHHHH
Q 044988          100 EKSVYLYKQMIDKETEPDEY-TYSFLLSVCARCGLFREGEQVHGRVLASGYCSN-VFIRTNLMNLYLMSGGECGVGCARL  177 (538)
Q Consensus       100 ~~a~~~~~~m~~~~~~p~~~-~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~~~~a~~  177 (538)
                      ++|+..++     |..++.. +...-...+-+.|++++|..+|+.+.+++.... ...-..++.+-.       .-.+. 
T Consensus        96 Dealk~~~-----~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a-------~l~~~-  162 (652)
T KOG2376|consen   96 DEALKTLK-----GLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAA-------ALQVQ-  162 (652)
T ss_pred             HHHHHHHh-----cccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHH-------hhhHH-
Confidence            99999988     3444443 667777788999999999999999988763221 222222222111       11111 


Q ss_pred             HhhcCCCCCchhHHHH---HHHHHhcCCHHHHHHHHccCC--------CC--C---hH-----HHHHHHHHHHHcCCHHH
Q 044988          178 LFDDMPARSVVSWNSL---LKGYVKRGDIDGAWKIFDEMP--------HR--N---VV-----SWTTMISGCAQNGKSRQ  236 (538)
Q Consensus       178 ~~~~~~~~~~~~~~~l---i~~~~~~g~~~~A~~~~~~m~--------~~--~---~~-----~~~~li~~~~~~~~~~~  236 (538)
                      +.+..+.....+|..+   ...+...|++.+|+++++...        +.  +   ..     .-..+...+...|+..+
T Consensus       163 ~~q~v~~v~e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~e  242 (652)
T KOG2376|consen  163 LLQSVPEVPEDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAE  242 (652)
T ss_pred             HHHhccCCCcchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHH
Confidence            3444444334444444   345677999999999998861        11  1   11     12334556778899999


Q ss_pred             HHHHHHHHHHCCCCCCHHH---H-HHHHHHHHccCCh-HH-HH------------HHHHHHHHhccCCCCCcchhHHHHH
Q 044988          237 ALSLFNEMRRARVGLDQVA---L-VAALSACAEIGDL-KL-GK------------WIHSYVEENFSVGREPVLVSLNNAL  298 (538)
Q Consensus       237 a~~~~~~m~~~g~~p~~~~---~-~~li~~~~~~~~~-~~-a~------------~~~~~~~~~~~~~~~~~~~~~~~~l  298 (538)
                      |..+|....+.. .+|...   + |.++ +.....++ +. +.            .....+...     ........+.+
T Consensus       243 a~~iy~~~i~~~-~~D~~~~Av~~NNLv-a~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~-----qk~~i~~N~~l  315 (652)
T KOG2376|consen  243 ASSIYVDIIKRN-PADEPSLAVAVNNLV-ALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKK-----QKQAIYRNNAL  315 (652)
T ss_pred             HHHHHHHHHHhc-CCCchHHHHHhcchh-hhccccccCchHHHHHHHHHHHHhHHHHHHHHHHH-----HHHHHHHHHHH
Confidence            999999998865 334322   2 2222 22222211 20 11            111111111     11122222344


Q ss_pred             HHHHHhCCCHHHHHHHHHhcCCCC-cchHHHHHHHHH-----------------hcCCccHHHHHHHHHHHHhcccCcHH
Q 044988          299 IHMYASCGEIEEAYGVFRKMQRRN-TVSWTSMITGFA-----------------KQGYAQEALLTFLGVLSACSHGGFVD  360 (538)
Q Consensus       299 ~~~~~~~g~~~~a~~~~~~m~~~~-~~~~~~li~~~~-----------------~~~~~~~a~~~~~~ll~~~~~~~~~~  360 (538)
                      +..|.  +..+.+.++........ ...+.+++....                 ..+..+.+..+....+......|+++
T Consensus       316 L~l~t--nk~~q~r~~~a~lp~~~p~~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~~p~~s~~v~L~~aQl~is~gn~~  393 (652)
T KOG2376|consen  316 LALFT--NKMDQVRELSASLPGMSPESLFPILLQEATKVREKKHKKAIELLLQFADGHPEKSKVVLLLRAQLKISQGNPE  393 (652)
T ss_pred             HHHHh--hhHHHHHHHHHhCCccCchHHHHHHHHHHHHHHHHHHhhhHHHHHHHhccCCchhHHHHHHHHHHHHhcCCHH
Confidence            44443  44566666666665422 122222222221                 12222222245555566667789999


Q ss_pred             HHHHHHH--------HhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-----CCCC----HHHHHHHHHHHHh
Q 044988          361 EGRQFFE--------CMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-----MKPN----DAVLGSLLLGCRI  423 (538)
Q Consensus       361 ~a~~~~~--------~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~p~----~~~~~~l~~~~~~  423 (538)
                      .|.+++.        .+.+. +..|  .+...+...|.+.++.+.|..++.+..     ..+.    ..++.-+...-.+
T Consensus       394 ~A~~il~~~~~~~~ss~~~~-~~~P--~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr  470 (652)
T KOG2376|consen  394 VALEILSLFLESWKSSILEA-KHLP--GTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLR  470 (652)
T ss_pred             HHHHHHHHHhhhhhhhhhhh-ccCh--hHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHh
Confidence            9999988        44433 3344  445566777777777666666665542     1122    2344444445567


Q ss_pred             cCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          424 HNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       424 ~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      .|+.++|..+++++ .+..|++..+.. .++.+|++. +.+.|..+-+.+.
T Consensus       471 ~G~~~ea~s~leel-~k~n~~d~~~l~-~lV~a~~~~-d~eka~~l~k~L~  518 (652)
T KOG2376|consen  471 HGNEEEASSLLEEL-VKFNPNDTDLLV-QLVTAYARL-DPEKAESLSKKLP  518 (652)
T ss_pred             cCchHHHHHHHHHH-HHhCCchHHHHH-HHHHHHHhc-CHHHHHHHhhcCC
Confidence            89999999999999 999999998777 777788775 5677777766553

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.23  E-value=1.5e-07  Score=84.58  Aligned_cols=255  Identities=14%  Similarity=0.038  Sum_probs=170.3

Q ss_pred             CchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHH---HHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 044988          186 SVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWT---TMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSA  262 (538)
Q Consensus       186 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~---~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  262 (538)
                      |+.....+.+.+...|+.++|...|++...-|+.+..   ...-.+.+.|+.+....+...+.... .-....+..-...
T Consensus       231 NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~wfV~~~~  309 (564)
T KOG1174|consen  231 NEHLMMALGKCLYYNGDYFQAEDIFSSTLCANPDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV-KYTASHWFVHAQL  309 (564)
T ss_pred             cHHHHHHHhhhhhhhcCchHHHHHHHHHhhCChhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh-hcchhhhhhhhhh
Confidence            6666677777777777777777777775543332221   11222345667777666666665421 1111222222222


Q ss_pred             HHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHHHHHhcCCc
Q 044988          263 CAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTSMITGFAKQGYA  339 (538)
Q Consensus       263 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~  339 (538)
                      ....++++.|..+-+...+.     .+.+...+-.-...+...|+.++|.-.|+....  | +...|..++..|...|+.
T Consensus       310 l~~~K~~~rAL~~~eK~I~~-----~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~  384 (564)
T KOG1174|consen  310 LYDEKKFERALNFVEKCIDS-----EPRNHEALILKGRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRF  384 (564)
T ss_pred             hhhhhhHHHHHHHHHHHhcc-----CcccchHHHhccHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchH
Confidence            33456666666666665554     455555554445566677777777777776543  2 566777778888877777


Q ss_pred             cHHHHHHHHHHHHhccc----------------CcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHH
Q 044988          340 QEALLTFLGVLSACSHG----------------GFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLV  402 (538)
Q Consensus       340 ~~a~~~~~~ll~~~~~~----------------~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~  402 (538)
                      .+|..+-+..++++...                .--++|..++++-.   .+.|+ ....+.+...+...|..++++.++
T Consensus       385 kEA~~~An~~~~~~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L---~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LL  461 (564)
T KOG1174|consen  385 KEANALANWTIRLFQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSL---KINPIYTPAVNLIAELCQVEGPTKDIIKLL  461 (564)
T ss_pred             HHHHHHHHHHHHHhhcchhhhhhhcceeeccCchhHHHHHHHHHhhh---ccCCccHHHHHHHHHHHHhhCccchHHHHH
Confidence            77774444333333222                23578888888776   44776 667888999999999999999999


Q ss_pred             HhC-CCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          403 QNM-PMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       403 ~~~-~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                      ++. ...||....+.|.+.+...+.+++|...|..+ ..++|++..+..
T Consensus       462 e~~L~~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~A-Lr~dP~~~~sl~  509 (564)
T KOG1174|consen  462 EKHLIIFPDVNLHNHLGDIMRAQNEPQKAMEYYYKA-LRQDPKSKRTLR  509 (564)
T ss_pred             HHHHhhccccHHHHHHHHHHHHhhhHHHHHHHHHHH-HhcCccchHHHH
Confidence            886 46799999999999999999999999999999 999999987443

>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.22  E-value=5.7e-08  Score=89.12  Aligned_cols=351  Identities=14%  Similarity=0.051  Sum_probs=215.5

Q ss_pred             HHHHHHHHhcCCCchHHHHHHHHhHhCCCCCC-cchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCc-hhHHhHHHHHH
Q 044988           86 WNQMIRGHARSETPEKSVYLYKQMIDKETEPD-EYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSN-VFIRTNLMNLY  163 (538)
Q Consensus        86 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~  163 (538)
                      +-...+-|.++|.+++|++.|.+.++.  .|| +.-|.....+|...|++++..+--.+.++.+  |+ +..+..-..++
T Consensus       118 lK~~GN~~f~~kkY~eAIkyY~~AI~l--~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl~--P~Y~KAl~RRA~A~  193 (606)
T KOG0547|consen  118 LKTKGNKFFRNKKYDEAIKYYTQAIEL--CPDEPIFYSNRAACYESLGDWEKVIEDCTKALELN--PDYVKALLRRASAH  193 (606)
T ss_pred             HHhhhhhhhhcccHHHHHHHHHHHHhc--CCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhcC--cHHHHHHHHHHHHH
Confidence            344566788899999999999999984  688 7788888889999999999988888877753  44 45667777777


Q ss_pred             HhcCCCCChhHHHHHh------hcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHH--------
Q 044988          164 LMSGGECGVGCARLLF------DDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMIS--------  226 (538)
Q Consensus       164 ~~~g~~~~~~~a~~~~------~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~--------  226 (538)
                      -..|+   +++|+.=+      +.....   +-..++.-..+..-..++.+.+.+-..   |+.....+...        
T Consensus       194 E~lg~---~~eal~D~tv~ci~~~F~n~---s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~~  267 (606)
T KOG0547|consen  194 EQLGK---FDEALFDVTVLCILEGFQNA---SIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFHADPKP  267 (606)
T ss_pred             Hhhcc---HHHHHHhhhHHHHhhhcccc---hhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhccccccc
Confidence            78888   77764311      111110   111111111111122333333331111   22222222111        


Q ss_pred             ---------------HHHHc--C---CHHHHHHHHHHHHHC-CCCCCHH---------HHHHHHHH--HHccCChHHHHH
Q 044988          227 ---------------GCAQN--G---KSRQALSLFNEMRRA-RVGLDQV---------ALVAALSA--CAEIGDLKLGKW  274 (538)
Q Consensus       227 ---------------~~~~~--~---~~~~a~~~~~~m~~~-g~~p~~~---------~~~~li~~--~~~~~~~~~a~~  274 (538)
                                     ++...  +   .+..|...+.+-... -..++..         .-..++.+  +.-.|+.-.+..
T Consensus       268 ~~~~~~~ksDa~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~~~a~~  347 (606)
T KOG0547|consen  268 LFDNKSDKSDAALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDSLGAQE  347 (606)
T ss_pred             cccCCCccchhhHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCchhhhh
Confidence                           11110  1   223333333222110 0111111         11112222  233577777888


Q ss_pred             HHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHH
Q 044988          275 IHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLS  351 (538)
Q Consensus       275 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~  351 (538)
                      -++..++.     .|.+...|--+..+|...++.++....|++..+   .|+.+|..-...+.-.               
T Consensus       348 d~~~~I~l-----~~~~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL---------------  407 (606)
T KOG0547|consen  348 DFDAAIKL-----DPAFNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLL---------------  407 (606)
T ss_pred             hHHHHHhc-----CcccchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHH---------------
Confidence            88888776     455555566778888888888888888887765   3444554443333333               


Q ss_pred             HhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHH
Q 044988          352 ACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAE  428 (538)
Q Consensus       352 ~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~  428 (538)
                           ++++.|..=|++.+.   +.| +...|-.+.-+.-|.+++++++..|++..  ++.-+..|+.....+..+++++
T Consensus       408 -----~q~e~A~aDF~Kai~---L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDqqqFd  479 (606)
T KOG0547|consen  408 -----QQYEEAIADFQKAIS---LDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKKFPNCPEVYNLFAEILTDQQQFD  479 (606)
T ss_pred             -----HHHHHHHHHHHHHhh---cChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHhhHHhHH
Confidence                 367777788888774   467 46778888888888999999999999885  3334678888999999999999


Q ss_pred             HHHHHHHHchhccCCC------CcccHHHHHHHHHH-hcCChHHHHHHHHHHHhC
Q 044988          429 LASQVAQKLVAEIDPE------QAAGYLALVANVYA-AAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       429 ~A~~~~~~~~~~~~p~------~~~~~~~~l~~~~~-~~g~~~~A~~~~~~m~~~  476 (538)
                      +|.+.|+.+ .++.|.      +++.++ .-+-+.. =.+++..|..++++..+.
T Consensus       480 ~A~k~YD~a-i~LE~~~~~~~v~~~plV-~Ka~l~~qwk~d~~~a~~Ll~KA~e~  532 (606)
T KOG0547|consen  480 KAVKQYDKA-IELEPREHLIIVNAAPLV-HKALLVLQWKEDINQAENLLRKAIEL  532 (606)
T ss_pred             HHHHHHHHH-Hhhccccccccccchhhh-hhhHhhhchhhhHHHHHHHHHHHHcc
Confidence            999999999 888888      554443 1111111 137888899998888763

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.22  E-value=2.5e-08  Score=93.16  Aligned_cols=193  Identities=15%  Similarity=0.072  Sum_probs=145.7

Q ss_pred             CCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC--C-CchhHH
Q 044988          115 EPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA--R-SVVSWN  191 (538)
Q Consensus       115 ~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~--~-~~~~~~  191 (538)
                      .-+......-..-|-..+++.+..++.+...+.. ++....+..-|.++...|+   ..+-.-+=.++++  | ...+|-
T Consensus       241 ~~~~dll~~~ad~~y~~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~---~n~Lf~lsh~LV~~yP~~a~sW~  316 (611)
T KOG1173|consen  241 AENLDLLAEKADRLYYGCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGK---SNKLFLLSHKLVDLYPSKALSWF  316 (611)
T ss_pred             hhcHHHHHHHHHHHHHcChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcc---cchHHHHHHHHHHhCCCCCcchh
Confidence            4455555556666778889999999999998875 6666677777778888888   5555444444544  2 567899


Q ss_pred             HHHHHHHhcCCHHHHHHHHccCCCCC---hHHHHHHHHHHHHcCCHHHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHcc
Q 044988          192 SLLKGYVKRGDIDGAWKIFDEMPHRN---VVSWTTMISGCAQNGKSRQALSLFNEMRRA--RVGLDQVALVAALSACAEI  266 (538)
Q Consensus       192 ~li~~~~~~g~~~~A~~~~~~m~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--g~~p~~~~~~~li~~~~~~  266 (538)
                      ++..-|...|+.++|++.|.+...-|   ...|-.+...|+..|..+.|+..|...-+.  |..   -.+--+.--|.+.
T Consensus       317 aVg~YYl~i~k~seARry~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~h---lP~LYlgmey~~t  393 (611)
T KOG1173|consen  317 AVGCYYLMIGKYSEARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCH---LPSLYLGMEYMRT  393 (611)
T ss_pred             hHHHHHHHhcCcHHHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCc---chHHHHHHHHHHh
Confidence            99888888899999999998865422   347999999999999999999999887663  221   1122233346778


Q ss_pred             CChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 044988          267 GDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       267 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  319 (538)
                      ++++.|..+|.+....     .|.++.+.+-+.-.....+.+.+|..+|+...
T Consensus       394 ~n~kLAe~Ff~~A~ai-----~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l  441 (611)
T KOG1173|consen  394 NNLKLAEKFFKQALAI-----APSDPLVLHELGVVAYTYEEYPEALKYFQKAL  441 (611)
T ss_pred             ccHHHHHHHHHHHHhc-----CCCcchhhhhhhheeehHhhhHHHHHHHHHHH
Confidence            9999999999998886     78888888888888888888999999888764

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.21  E-value=1.4e-07  Score=91.43  Aligned_cols=395  Identities=15%  Similarity=0.094  Sum_probs=228.1

Q ss_pred             CCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCC-cchHH
Q 044988           47 GFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPD-EYTYS  122 (538)
Q Consensus        47 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~  122 (538)
                      .+.-++.+|..+.-+..+.|++..+.+.|++..+   .....|+.+-..+.-.|....|+.+++.-....-.|+ ...+-
T Consensus       318 ~~qnd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~L  397 (799)
T KOG4162|consen  318 KFQNDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLL  397 (799)
T ss_pred             hhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHH
Confidence            3555778888888888888999999998888764   3445688888888888888888888887654322243 33333


Q ss_pred             HHHHHHH-ccCCcHHHHHHHHHHHHhC--C--CCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHH
Q 044988          123 FLLSVCA-RCGLFREGEQVHGRVLASG--Y--CSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGY  197 (538)
Q Consensus       123 ~li~~~~-~~~~~~~a~~~~~~~~~~~--~--~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~  197 (538)
                      ..-+.|. +.+..+++..+-.+.....  .  ......|..+.-+|...-.....+.-                      
T Consensus       398 masklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~se----------------------  455 (799)
T KOG4162|consen  398 MASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSE----------------------  455 (799)
T ss_pred             HHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHH----------------------
Confidence            3333443 3456666666666665521  1  12233444444444332220000000                      


Q ss_pred             HhcCCHHHHHHHHccCCC-----CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHH
Q 044988          198 VKRGDIDGAWKIFDEMPH-----RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLG  272 (538)
Q Consensus       198 ~~~g~~~~A~~~~~~m~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a  272 (538)
                       +.....++.+.+++..+     |++..|-  .--|+-.++.+.|++...+..+.+-.-+...+..+.-.+...+++..|
T Consensus       456 -R~~~h~kslqale~av~~d~~dp~~if~l--alq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~A  532 (799)
T KOG4162|consen  456 -RDALHKKSLQALEEAVQFDPTDPLVIFYL--ALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEA  532 (799)
T ss_pred             -HHHHHHHHHHHHHHHHhcCCCCchHHHHH--HHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHH
Confidence             00011223333333211     2222221  122333445555555555555544344444444444444455555555


Q ss_pred             HHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHH--------------------------HHHHhcCC------
Q 044988          273 KWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAY--------------------------GVFRKMQR------  320 (538)
Q Consensus       273 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~--------------------------~~~~~m~~------  320 (538)
                      ..+.+...+.     .+.+......-+..-...|+.+++.                          +....+.-      
T Consensus       533 l~vvd~al~E-----~~~N~~l~~~~~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~  607 (799)
T KOG4162|consen  533 LDVVDAALEE-----FGDNHVLMDGKIHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPT  607 (799)
T ss_pred             HHHHHHHHHH-----hhhhhhhchhhhhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCccccc
Confidence            5555444443     1111100000011111122222222                          22222110      


Q ss_pred             CCcchHHHHHHHHHhcC---CccHHH-----------------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cH
Q 044988          321 RNTVSWTSMITGFAKQG---YAQEAL-----------------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RI  379 (538)
Q Consensus       321 ~~~~~~~~li~~~~~~~---~~~~a~-----------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~  379 (538)
                      ..+.++..+.......+   ..+..+                 ..|......+...+..+.|..++.+....   .| ..
T Consensus       608 ~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~---~~l~~  684 (799)
T KOG4162|consen  608 DAISTSRYLSSLVASQLKSAGSELKLPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKI---DPLSA  684 (799)
T ss_pred             ccchhhHHHHHHHHhhhhhcccccccCcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhc---chhhH
Confidence            11222222222211111   000001                 55667778888889999999999888743   45 57


Q ss_pred             HHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCH-HHHHHHHHHHHhcCCHHHHHH--HHHHchhccCCCCcccHHHHHHH
Q 044988          380 EHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPND-AVLGSLLLGCRIHNNAELASQ--VAQKLVAEIDPEQAAGYLALVAN  455 (538)
Q Consensus       380 ~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~-~~~~~l~~~~~~~~~~~~A~~--~~~~~~~~~~p~~~~~~~~~l~~  455 (538)
                      ..|......+...|.+++|.+.|.... ..|+. ....++...+.+.|+...|..  ++..+ .++.|.++.+|. .|+.
T Consensus       685 ~~~~~~G~~~~~~~~~~EA~~af~~Al~ldP~hv~s~~Ala~~lle~G~~~la~~~~~L~da-lr~dp~n~eaW~-~LG~  762 (799)
T KOG4162|consen  685 SVYYLRGLLLEVKGQLEEAKEAFLVALALDPDHVPSMTALAELLLELGSPRLAEKRSLLSDA-LRLDPLNHEAWY-YLGE  762 (799)
T ss_pred             HHHHHhhHHHHHHHhhHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCcchHHHHHHHHHH-HhhCCCCHHHHH-HHHH
Confidence            788888889999999999999998764 67774 567788888999998888887  99999 999999999999 9999


Q ss_pred             HHHhcCChHHHHHHHHHHHhC
Q 044988          456 VYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       456 ~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      ++-+.|+.++|.+.|....+-
T Consensus       763 v~k~~Gd~~~Aaecf~aa~qL  783 (799)
T KOG4162|consen  763 VFKKLGDSKQAAECFQAALQL  783 (799)
T ss_pred             HHHHccchHHHHHHHHHHHhh
Confidence            999999999999999988764

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.17  E-value=6.5e-09  Score=92.82  Aligned_cols=189  Identities=15%  Similarity=0.119  Sum_probs=88.6

Q ss_pred             hHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHH
Q 044988           85 IWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYL  164 (538)
Q Consensus        85 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  164 (538)
                      .+..+...+...|++++|.+.+++..+.. +.+...+..+...+...|+++.|.+.+++..+.. +.+...+..+...+.
T Consensus        33 ~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~~  110 (234)
T TIGR02521        33 IRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTFLC  110 (234)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHH
Confidence            34445555555555666655555555432 2233445555555555566666666665555543 233344444555555


Q ss_pred             hcCCCCChhHHHHHhhcCCCC-----CchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHH
Q 044988          165 MSGGECGVGCARLLFDDMPAR-----SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQ  236 (538)
Q Consensus       165 ~~g~~~~~~~a~~~~~~~~~~-----~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~  236 (538)
                      ..|+   +++|.+.+++....     ....+..+...+...|++++|...|++...   .+...+..+...+...|++++
T Consensus       111 ~~g~---~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~  187 (234)
T TIGR02521       111 QQGK---YEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKD  187 (234)
T ss_pred             Hccc---HHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHH
Confidence            5555   55555555443321     112233333344444444444444444321   123344445555555555555


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHH
Q 044988          237 ALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYV  279 (538)
Q Consensus       237 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~  279 (538)
                      |...+++..+. .+.+...+..+...+...|+.+.|..+.+.+
T Consensus       188 A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  229 (234)
T TIGR02521       188 ARAYLERYQQT-YNQTAESLWLGIRIARALGDVAAAQRYGAQL  229 (234)
T ss_pred             HHHHHHHHHHh-CCCCHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            55555555443 1223333334444444445555554444433

Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.15  E-value=1e-06  Score=83.95  Aligned_cols=441  Identities=13%  Similarity=0.097  Sum_probs=263.8

Q ss_pred             CccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHH
Q 044988           15 SKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIR   91 (538)
Q Consensus        15 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~   91 (538)
                      .....|..++..+ ..+.+.....+.+.+++. .+--..+....--.+...|+-++|.........   .+.+.|..+.-
T Consensus         6 KE~~lF~~~lk~y-E~kQYkkgLK~~~~iL~k-~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~~S~vCwHv~gl   83 (700)
T KOG1156|consen    6 KENALFRRALKCY-ETKQYKKGLKLIKQILKK-FPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDLKSHVCWHVLGL   83 (700)
T ss_pred             HHHHHHHHHHHHH-HHHHHHhHHHHHHHHHHh-CCccchhHHhccchhhcccchHHHHHHHHHHhccCcccchhHHHHHH
Confidence            3344455555554 455677777777777663 222333443333345567888899888876664   45567888888


Q ss_pred             HHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCC
Q 044988           92 GHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECG  171 (538)
Q Consensus        92 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  171 (538)
                      .+-...++++|+.+|......+ +-|...|.-+--.=++.|+++........+.+.. +.....|..+..++.-.|+   
T Consensus        84 ~~R~dK~Y~eaiKcy~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~-~~~ra~w~~~Avs~~L~g~---  158 (700)
T KOG1156|consen   84 LQRSDKKYDEAIKCYRNALKIE-KDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLR-PSQRASWIGFAVAQHLLGE---  158 (700)
T ss_pred             HHhhhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhh-hhhHHHHHHHHHHHHHHHH---
Confidence            8888889999999999988753 3345566665555577788888888877777763 4455678888888888888   


Q ss_pred             hhHHHHHhhcCCC-----CCchhHHHH------HHHHHhcCCHHHHHHHHccCCC--CChH-HHHHHHHHHHHcCCHHHH
Q 044988          172 VGCARLLFDDMPA-----RSVVSWNSL------LKGYVKRGDIDGAWKIFDEMPH--RNVV-SWTTMISGCAQNGKSRQA  237 (538)
Q Consensus       172 ~~~a~~~~~~~~~-----~~~~~~~~l------i~~~~~~g~~~~A~~~~~~m~~--~~~~-~~~~li~~~~~~~~~~~a  237 (538)
                      ...|..++++..+     ++...+...      .....+.|..+.|.+.+.....  -|-. .-.+-...+.+.++.++|
T Consensus       159 y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~Dkla~~e~ka~l~~kl~~lEeA  238 (700)
T KOG1156|consen  159 YKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQIVDKLAFEETKADLLMKLGQLEEA  238 (700)
T ss_pred             HHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHHHHHHHHhhhHHHHHHHHhhHHhH
Confidence            8888888776543     333333322      2344678888888888877553  1222 233445667888999999


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHH-cc-CChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHH
Q 044988          238 LSLFNEMRRARVGLDQVALVAALSACA-EI-GDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVF  315 (538)
Q Consensus       238 ~~~~~~m~~~g~~p~~~~~~~li~~~~-~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  315 (538)
                      ..+|..+...  .||..-|...+..+. +. +..+....+|....+.......|.....  .++..   ..-.+....++
T Consensus       239 ~~~y~~Ll~r--nPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlpl--svl~~---eel~~~vdkyL  311 (700)
T KOG1156|consen  239 VKVYRRLLER--NPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPL--SVLNG---EELKEIVDKYL  311 (700)
T ss_pred             HHHHHHHHhh--CchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccH--HHhCc---chhHHHHHHHH
Confidence            9999999874  677777666555544 23 3333333666666554221111111110  00000   01111122222


Q ss_pred             HhcCCC-------Ccc----------hHHHHHHHHHhc------------CCccHH---HHHHHHHHHHhcccCcHHHHH
Q 044988          316 RKMQRR-------NTV----------SWTSMITGFAKQ------------GYAQEA---LLTFLGVLSACSHGGFVDEGR  363 (538)
Q Consensus       316 ~~m~~~-------~~~----------~~~~li~~~~~~------------~~~~~a---~~~~~~ll~~~~~~~~~~~a~  363 (538)
                      ..+.++       |..          ....++..|...            |+.+.+   +-++.-+...+-+.|+++.|.
T Consensus       312 ~~~l~Kg~p~vf~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~  391 (700)
T KOG1156|consen  312 RPLLSKGVPSVFKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVAL  391 (700)
T ss_pred             HHHhhcCCCchhhhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHH
Confidence            222211       110          111122222211            111111   155666777788888999999


Q ss_pred             HHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhc
Q 044988          364 QFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAE  440 (538)
Q Consensus       364 ~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  440 (538)
                      ..++....   ..|+ +..|..=.+.+...|.+++|...+++..  -.||...-..-..-..++++.++|.++..... .
T Consensus       392 ~yId~AId---HTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~aDR~INsKcAKYmLrAn~i~eA~~~~skFT-r  467 (700)
T KOG1156|consen  392 EYIDLAID---HTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDTADRAINSKCAKYMLRANEIEEAEEVLSKFT-R  467 (700)
T ss_pred             HHHHHHhc---cCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccchhHHHHHHHHHHHHHccccHHHHHHHHHhh-h
Confidence            99988884   3776 4566666788888999999999988875  33555444355556677888888888888774 2


Q ss_pred             cCCCCcc-------cHH-HHHHHHHHhcCChHHHHHHHHHH
Q 044988          441 IDPEQAA-------GYL-ALVANVYAAAKRWQDVAAVRQKM  473 (538)
Q Consensus       441 ~~p~~~~-------~~~-~~l~~~~~~~g~~~~A~~~~~~m  473 (538)
                      ..-+...       .|. .-=+.+|.++|++.+|++=|..+
T Consensus       468 ~~~~~~~~L~~mqcmWf~~E~g~ay~r~~k~g~ALKkfh~i  508 (700)
T KOG1156|consen  468 EGFGAVNNLAEMQCMWFQLEDGEAYLRQNKLGLALKKFHEI  508 (700)
T ss_pred             cccchhhhHHHhhhHHHhHhhhHHHHHHHHHHHHHHHHhhH
Confidence            1111111       011 11246677887777777655444

>PRK12370 invasion protein regulator; Provisional

Probab=99.15  E-value=1.7e-08  Score=101.53  Aligned_cols=258  Identities=11%  Similarity=0.028  Sum_probs=177.9

Q ss_pred             CchhHHHHHHHHHh-----cCCHHHHHHHHccCCC--CC-hHHHHHHHHHHH---------HcCCHHHHHHHHHHHHHCC
Q 044988          186 SVVSWNSLLKGYVK-----RGDIDGAWKIFDEMPH--RN-VVSWTTMISGCA---------QNGKSRQALSLFNEMRRAR  248 (538)
Q Consensus       186 ~~~~~~~li~~~~~-----~g~~~~A~~~~~~m~~--~~-~~~~~~li~~~~---------~~~~~~~a~~~~~~m~~~g  248 (538)
                      +...|...+.+-..     .+++++|...|++..+  |+ ...|..+..++.         ..+++++|...+++..+..
T Consensus       255 ~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ldP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ld  334 (553)
T PRK12370        255 SIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMSPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELD  334 (553)
T ss_pred             ChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcC
Confidence            44555566665322     2346788899988764  43 345655555443         2245789999999988753


Q ss_pred             CCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcc---h
Q 044988          249 VGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTV---S  325 (538)
Q Consensus       249 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~---~  325 (538)
                       +-+...+..+...+...|++++|...++.+.+.     .|.+...+..+...+...|++++|...+++..+-++.   .
T Consensus       335 -P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l-----~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~  408 (553)
T PRK12370        335 -HNNPQALGLLGLINTIHSEYIVGSLLFKQANLL-----SPISADIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAA  408 (553)
T ss_pred             -CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhh
Confidence             225666777777788899999999999999987     6777888888999999999999999999988763322   2


Q ss_pred             HHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHh
Q 044988          326 WTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQN  404 (538)
Q Consensus       326 ~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~  404 (538)
                      +..++..+.                    ..|++++|...+++..+. . .| +...+..+..+|...|+.++|...+++
T Consensus       409 ~~~~~~~~~--------------------~~g~~eeA~~~~~~~l~~-~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~  466 (553)
T PRK12370        409 GITKLWITY--------------------YHTGIDDAIRLGDELRSQ-H-LQDNPILLSMQVMFLSLKGKHELARKLTKE  466 (553)
T ss_pred             HHHHHHHHH--------------------hccCHHHHHHHHHHHHHh-c-cccCHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            222222232                    235778888888887754 1 35 355677888899999999999999998


Q ss_pred             CC-CCCCHHH-HHHHHHHHHhcCCHHHHHHHHHHch--hccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          405 MP-MKPNDAV-LGSLLLGCRIHNNAELASQVAQKLV--AEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       405 ~~-~~p~~~~-~~~l~~~~~~~~~~~~A~~~~~~~~--~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      +. ..|+..+ .+.+...+...|  ++|...++.+.  ....|.++.    .+...|.-.|+-+.+..+ +++.+.|.
T Consensus       467 ~~~~~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~~~~~~~~~~----~~~~~~~~~g~~~~~~~~-~~~~~~~~  537 (553)
T PRK12370        467 ISTQEITGLIAVNLLYAEYCQNS--ERALPTIREFLESEQRIDNNPG----LLPLVLVAHGEAIAEKMW-NKFKNEDN  537 (553)
T ss_pred             hhhccchhHHHHHHHHHHHhccH--HHHHHHHHHHHHHhhHhhcCch----HHHHHHHHHhhhHHHHHH-HHhhccch
Confidence            75 3455443 344444566666  47777777765  445555555    345667778888877777 88776543

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.15  E-value=3.3e-07  Score=80.81  Aligned_cols=430  Identities=11%  Similarity=0.024  Sum_probs=233.4

Q ss_pred             HHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCch
Q 044988           24 FSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPE  100 (538)
Q Consensus        24 l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~  100 (538)
                      +.-+...++++.|..+++.-...+-.-...+--=+..++.+.|++++|...+..+.   .++...+-.|.-.+.-.|.+.
T Consensus        29 Ledfls~rDytGAislLefk~~~~~EEE~~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~~~~~el~vnLAcc~FyLg~Y~  108 (557)
T KOG3785|consen   29 LEDFLSNRDYTGAISLLEFKLNLDREEEDSLQLWIAHCYFHLGDYEEALNVYTFLMNKDDAPAELGVNLACCKFYLGQYI  108 (557)
T ss_pred             HHHHHhcccchhHHHHHHHhhccchhhhHHHHHHHHHHHHhhccHHHHHHHHHHHhccCCCCcccchhHHHHHHHHHHHH
Confidence            34445566777777777765543322211222224456667788888888776655   245555655655555566777


Q ss_pred             HHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhh
Q 044988          101 KSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFD  180 (538)
Q Consensus       101 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~  180 (538)
                      +|..+-....     .++-.-..++...-+.++-++-..+.+.+.+.     ..-..+|.......-.   +.+|..++.
T Consensus       109 eA~~~~~ka~-----k~pL~~RLlfhlahklndEk~~~~fh~~LqD~-----~EdqLSLAsvhYmR~H---YQeAIdvYk  175 (557)
T KOG3785|consen  109 EAKSIAEKAP-----KTPLCIRLLFHLAHKLNDEKRILTFHSSLQDT-----LEDQLSLASVHYMRMH---YQEAIDVYK  175 (557)
T ss_pred             HHHHHHhhCC-----CChHHHHHHHHHHHHhCcHHHHHHHHHHHhhh-----HHHHHhHHHHHHHHHH---HHHHHHHHH
Confidence            7776654432     22223334444455666666655555554332     1222334444333334   777777777


Q ss_pred             cCCCC--CchhHHHH-HHHHHhcCCHHHHHHHHccCCC--CC-hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHH
Q 044988          181 DMPAR--SVVSWNSL-LKGYVKRGDIDGAWKIFDEMPH--RN-VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQV  254 (538)
Q Consensus       181 ~~~~~--~~~~~~~l-i~~~~~~g~~~~A~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~  254 (538)
                      +....  +-...|.. .-+|.+..-++-+.++++--..  || +..-|.......+.=+-..|.+-..++...+-+.   
T Consensus       176 rvL~dn~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN~~~~---  252 (557)
T KOG3785|consen  176 RVLQDNPEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQFPDSTIAKNLKACNLFRLINGRTAEDEKKELADNIDQE---  252 (557)
T ss_pred             HHHhcChhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHhCCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhccccc---
Confidence            76653  33333333 3355666666666666654332  33 3344444443333323333444444443322111   


Q ss_pred             HHHHHHHHHHc-----cCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHH
Q 044988          255 ALVAALSACAE-----IGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSM  329 (538)
Q Consensus       255 ~~~~li~~~~~-----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~l  329 (538)
                       |- .+.-.++     -.+-+.|.+++-.+.+.     +|.   ..-.|+-.|.+.+++++|..+.+++...++.-|-.-
T Consensus       253 -~~-f~~~l~rHNLVvFrngEgALqVLP~L~~~-----IPE---ARlNL~iYyL~q~dVqeA~~L~Kdl~PttP~EyilK  322 (557)
T KOG3785|consen  253 -YP-FIEYLCRHNLVVFRNGEGALQVLPSLMKH-----IPE---ARLNLIIYYLNQNDVQEAISLCKDLDPTTPYEYILK  322 (557)
T ss_pred             -ch-hHHHHHHcCeEEEeCCccHHHhchHHHhh-----ChH---hhhhheeeecccccHHHHHHHHhhcCCCChHHHHHH
Confidence             11 1111122     13345666666555554     222   223577778899999999999988865444333322


Q ss_pred             HHHHHhcCCccHH-------HHHHH----------------HHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHH
Q 044988          330 ITGFAKQGYAQEA-------LLTFL----------------GVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMV  386 (538)
Q Consensus       330 i~~~~~~~~~~~a-------~~~~~----------------~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~  386 (538)
                      .-.++..|+--..       ...|.                ++.+++.-...+++.+-++..+..- =..-|... -.+.
T Consensus       323 gvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sY-F~NdD~Fn-~N~A  400 (557)
T KOG3785|consen  323 GVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESY-FTNDDDFN-LNLA  400 (557)
T ss_pred             HHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHH-hcCcchhh-hHHH
Confidence            2223333322211       11111                2222222333556666666665543 22223333 3478


Q ss_pred             HHhhhcCChHHHHHHHHhCC--CCCCHHHHHHH-HHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCCh
Q 044988          387 DLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSL-LLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRW  463 (538)
Q Consensus       387 ~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l-~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~  463 (538)
                      ++++..|++.+|.++|-.+.  .-.|..+|.++ .++|.+.++++.|..++-++   ..|.+......++++-|.+++.+
T Consensus       401 QAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk~---~t~~e~fsLLqlIAn~CYk~~eF  477 (557)
T KOG3785|consen  401 QAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMMLKT---NTPSERFSLLQLIANDCYKANEF  477 (557)
T ss_pred             HHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHhc---CCchhHHHHHHHHHHHHHHHHHH
Confidence            89999999999999998775  11355666554 55688999999999888776   23333332333778889999999


Q ss_pred             HHHHHHHHHHHhCCCCCCCceeEE
Q 044988          464 QDVAAVRQKMIKMGVRKPPGQSWV  487 (538)
Q Consensus       464 ~~A~~~~~~m~~~~~~~~~~~~~~  487 (538)
                      =-|.+.|+.+...+.  +| -.|-
T Consensus       478 yyaaKAFd~lE~lDP--~p-EnWe  498 (557)
T KOG3785|consen  478 YYAAKAFDELEILDP--TP-ENWE  498 (557)
T ss_pred             HHHHHhhhHHHccCC--Cc-cccC
Confidence            888888888876443  33 4463

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.15  E-value=2.2e-06  Score=81.67  Aligned_cols=412  Identities=15%  Similarity=0.180  Sum_probs=259.2

Q ss_pred             hhHHHHHHHHHHccCChhHHHHHHhcCCC-----CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHH
Q 044988           52 NYILAKLLAFYVTSGYLINAHKVFEKTEN-----PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLS  126 (538)
Q Consensus        52 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~  126 (538)
                      +..|-..++...+.|++...+..|++...     .....|...+...-..+-++-++.+|++.++    .++..-.-.|.
T Consensus       102 pRIwl~Ylq~l~~Q~~iT~tR~tfdrALraLpvtqH~rIW~lyl~Fv~~~~lPets~rvyrRYLk----~~P~~~eeyie  177 (835)
T KOG2047|consen  102 PRIWLDYLQFLIKQGLITRTRRTFDRALRALPVTQHDRIWDLYLKFVESHGLPETSIRVYRRYLK----VAPEAREEYIE  177 (835)
T ss_pred             CHHHHHHHHHHHhcchHHHHHHHHHHHHHhCchHhhccchHHHHHHHHhCCChHHHHHHHHHHHh----cCHHHHHHHHH
Confidence            45556666667777888888888876542     2445788888888888999999999999885    34445777888


Q ss_pred             HHHccCCcHHHHHHHHHHHHhC------CCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC--C--chhHHHHHHH
Q 044988          127 VCARCGLFREGEQVHGRVLASG------YCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPAR--S--VVSWNSLLKG  196 (538)
Q Consensus       127 ~~~~~~~~~~a~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~--~--~~~~~~li~~  196 (538)
                      .++..+++++|.+.+...+...      .+.+...|..+-+..++.-+...--....+++.+..+  |  ...|++|.+-
T Consensus       178 ~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdY  257 (835)
T KOG2047|consen  178 YLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADY  257 (835)
T ss_pred             HHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHH
Confidence            8899999999999888776432      2445556666666666554411122344555555543  2  3579999999


Q ss_pred             HHhcCCHHHHHHHHccCCC--CChHHHHHHHHHHHHc----------------C------CHHHHHHHHHHHHHCCC---
Q 044988          197 YVKRGDIDGAWKIFDEMPH--RNVVSWTTMISGCAQN----------------G------KSRQALSLFNEMRRARV---  249 (538)
Q Consensus       197 ~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~----------------~------~~~~a~~~~~~m~~~g~---  249 (538)
                      |.+.|.+++|..+|++...  -.+.-|+.+..+|+.-                +      +++-.+.-|+.+.+.+.   
T Consensus       258 YIr~g~~ekarDvyeeai~~v~tvrDFt~ifd~Ya~FEE~~~~~~me~a~~~~~n~ed~~dl~~~~a~~e~lm~rr~~~l  337 (835)
T KOG2047|consen  258 YIRSGLFEKARDVYEEAIQTVMTVRDFTQIFDAYAQFEESCVAAKMELADEESGNEEDDVDLELHMARFESLMNRRPLLL  337 (835)
T ss_pred             HHHhhhhHHHHHHHHHHHHhheehhhHHHHHHHHHHHHHHHHHHHHhhhhhcccChhhhhhHHHHHHHHHHHHhccchHH
Confidence            9999999999999988543  2222233333333221                1      22334444555444321   


Q ss_pred             -------CC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCC-CcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          250 -------GL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGRE-PVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       250 -------~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                             .| +..++..-+.  +..|+..+-...+..+.+..++... ...-..|..+.+.|...|+++.|+.+|++..+
T Consensus       338 NsVlLRQn~~nV~eW~kRV~--l~e~~~~~~i~tyteAv~~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~  415 (835)
T KOG2047|consen  338 NSVLLRQNPHNVEEWHKRVK--LYEGNAAEQINTYTEAVKTVDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATK  415 (835)
T ss_pred             HHHHHhcCCccHHHHHhhhh--hhcCChHHHHHHHHHHHHccCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhc
Confidence                   11 1222222221  2245566667777777776433222 22345678899999999999999999999887


Q ss_pred             CCcc-------hHHHHHHHHHhcCCccHHH--------------------------------HHHHHHHHHhcccCcHHH
Q 044988          321 RNTV-------SWTSMITGFAKQGYAQEAL--------------------------------LTFLGVLSACSHGGFVDE  361 (538)
Q Consensus       321 ~~~~-------~~~~li~~~~~~~~~~~a~--------------------------------~~~~~ll~~~~~~~~~~~  361 (538)
                      -+-.       +|......=.++.+++.|+                                .+|...++.--..|-++.
T Consensus       416 V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfes  495 (835)
T KOG2047|consen  416 VPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFES  495 (835)
T ss_pred             CCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHH
Confidence            3322       3333333334455555554                                344444555555678888


Q ss_pred             HHHHHHHhhhhcCCCccH-HHHHHHHHHhhhcCChHHHHHHHHhCC--C-CCCH-HHHHHHHHHHHh---cCCHHHHHHH
Q 044988          362 GRQFFECMNQNWGIKPRI-EHYGCMVDLFSRAGLMDEAFSLVQNMP--M-KPND-AVLGSLLLGCRI---HNNAELASQV  433 (538)
Q Consensus       362 a~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~--~-~p~~-~~~~~l~~~~~~---~~~~~~A~~~  433 (538)
                      ...+++.+.+..-..|-. ..|..+   +-...-++++.+.|++-.  + -|+. ..|+..+..+.+   ..+++.|..+
T Consensus       496 tk~vYdriidLriaTPqii~NyAmf---LEeh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEraRdL  572 (835)
T KOG2047|consen  496 TKAVYDRIIDLRIATPQIIINYAMF---LEEHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLERARDL  572 (835)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHH---HHhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHHHHHH
Confidence            888888888763334432 223333   335667899999998753  3 3554 577777665432   3378999999


Q ss_pred             HHHchhccCCCCc--ccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          434 AQKLVAEIDPEQA--AGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       434 ~~~~~~~~~p~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      |+++ .+..|+..  +.|. +.+..=.+.|--..|+.++++..
T Consensus       573 FEqa-L~~Cpp~~aKtiyL-lYA~lEEe~GLar~amsiyerat  613 (835)
T KOG2047|consen  573 FEQA-LDGCPPEHAKTIYL-LYAKLEEEHGLARHAMSIYERAT  613 (835)
T ss_pred             HHHH-HhcCCHHHHHHHHH-HHHHHHHHhhHHHHHHHHHHHHH
Confidence            9999 66666433  2233 34444446788888999998854

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.15  E-value=3.9e-09  Score=91.58  Aligned_cols=225  Identities=11%  Similarity=0.030  Sum_probs=188.0

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHH
Q 044988          222 TTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHM  301 (538)
Q Consensus       222 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  301 (538)
                      +.+..+|.+.|.+.+|.+.|+...+.  .|-..||..+-..|.+..++..|..++..-.+.     .|.++.........
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-----fP~~VT~l~g~ARi  299 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-----FPFDVTYLLGQARI  299 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-----CCchhhhhhhhHHH
Confidence            56789999999999999999988875  566778999999999999999999999998886     89999988899999


Q ss_pred             HHhCCCHHHHHHHHHhcCCC---CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc
Q 044988          302 YASCGEIEEAYGVFRKMQRR---NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR  378 (538)
Q Consensus       302 ~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~  378 (538)
                      +...++.++|.++++...+.   ++.+...+..+|.-                    .++++-|..+++++.+. |+ -+
T Consensus       300 ~eam~~~~~a~~lYk~vlk~~~~nvEaiAcia~~yfY--------------------~~~PE~AlryYRRiLqm-G~-~s  357 (478)
T KOG1129|consen  300 HEAMEQQEDALQLYKLVLKLHPINVEAIACIAVGYFY--------------------DNNPEMALRYYRRILQM-GA-QS  357 (478)
T ss_pred             HHHHHhHHHHHHHHHHHHhcCCccceeeeeeeecccc--------------------CCChHHHHHHHHHHHHh-cC-CC
Confidence            99999999999999988763   44444444334433                    44777888888888877 64 36


Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC---CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP---MKPN--DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALV  453 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~---~~p~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l  453 (538)
                      ...|+.+.-+|...+++|-++.-|++..   ..|+  ...|-.+.......||+..|.+.|+-+ ...+|++...+. .|
T Consensus       358 peLf~NigLCC~yaqQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrla-L~~d~~h~ealn-NL  435 (478)
T KOG1129|consen  358 PELFCNIGLCCLYAQQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLA-LTSDAQHGEALN-NL  435 (478)
T ss_pred             hHHHhhHHHHHHhhcchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHH-hccCcchHHHHH-hH
Confidence            7788888889999999999998888763   2344  567888888888999999999999999 889999999888 88


Q ss_pred             HHHHHhcCChHHHHHHHHHHHhCC
Q 044988          454 ANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       454 ~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                      +-.-.+.|+.++|..+++......
T Consensus       436 avL~~r~G~i~~Arsll~~A~s~~  459 (478)
T KOG1129|consen  436 AVLAARSGDILGARSLLNAAKSVM  459 (478)
T ss_pred             HHHHhhcCchHHHHHHHHHhhhhC
Confidence            888899999999999999987643

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.13  E-value=1.4e-07  Score=83.04  Aligned_cols=394  Identities=12%  Similarity=0.069  Sum_probs=208.2

Q ss_pred             HHHHHccCChhHHHHHHhcCCCC---CcchHHHH-HHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCc
Q 044988           59 LAFYVTSGYLINAHKVFEKTENP---STAIWNQM-IRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLF  134 (538)
Q Consensus        59 ~~~~~~~g~~~~a~~~~~~~~~~---~~~~~~~l-i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~  134 (538)
                      +.-+....++..|+.+++.-...   .....+.. ..++...|++++|+..+..+.+.. .|+...+..|.-.+.-.|.+
T Consensus        29 Ledfls~rDytGAislLefk~~~~~EEE~~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~-~~~~el~vnLAcc~FyLg~Y  107 (557)
T KOG3785|consen   29 LEDFLSNRDYTGAISLLEFKLNLDREEEDSLQLWIAHCYFHLGDYEEALNVYTFLMNKD-DAPAELGVNLACCKFYLGQY  107 (557)
T ss_pred             HHHHHhcccchhHHHHHHHhhccchhhhHHHHHHHHHHHHhhccHHHHHHHHHHHhccC-CCCcccchhHHHHHHHHHHH
Confidence            34455566677777766543311   11122222 234456677777777777666543 45555555555555555666


Q ss_pred             HHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCC
Q 044988          135 REGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMP  214 (538)
Q Consensus       135 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  214 (538)
                      .+|..+-.+.     +.+.-.-..|...--+.++   -++-..+-..+.. ...---++....-..-.+.+|++++.+..
T Consensus       108 ~eA~~~~~ka-----~k~pL~~RLlfhlahklnd---Ek~~~~fh~~LqD-~~EdqLSLAsvhYmR~HYQeAIdvYkrvL  178 (557)
T KOG3785|consen  108 IEAKSIAEKA-----PKTPLCIRLLFHLAHKLND---EKRILTFHSSLQD-TLEDQLSLASVHYMRMHYQEAIDVYKRVL  178 (557)
T ss_pred             HHHHHHHhhC-----CCChHHHHHHHHHHHHhCc---HHHHHHHHHHHhh-hHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            6666654432     1222223333344445555   3333333222221 12222233333334445667777777655


Q ss_pred             C--CChHHHHHH-HHHHHHcCCHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCc
Q 044988          215 H--RNVVSWTTM-ISGCAQNGKSRQALSLFNEMRRARVGLDQ-VALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPV  290 (538)
Q Consensus       215 ~--~~~~~~~~l-i~~~~~~~~~~~a~~~~~~m~~~g~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  290 (538)
                      .  |+-...|.- .-+|.+..-++-+.+++.--.+.  .||. ...+.......+.=.-..|++-...+...    +...
T Consensus       179 ~dn~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q--~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN----~~~~  252 (557)
T KOG3785|consen  179 QDNPEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ--FPDSTIAKNLKACNLFRLINGRTAEDEKKELADN----IDQE  252 (557)
T ss_pred             hcChhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh--CCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhc----cccc
Confidence            3  333444433 34555666666666665554442  2332 22222222222322222222222333222    1111


Q ss_pred             chhHHHHHHHHHHhCC-----CHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHH---------HHHHHHHHH----
Q 044988          291 LVSLNNALIHMYASCG-----EIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL---------LTFLGVLSA----  352 (538)
Q Consensus       291 ~~~~~~~l~~~~~~~g-----~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~---------~~~~~ll~~----  352 (538)
                          | ..+.-+++.+     +-+.|.+++-.+.+-=+..--.++--|.+.++..+|.         ..+.-++.+    
T Consensus       253 ----~-~f~~~l~rHNLVvFrngEgALqVLP~L~~~IPEARlNL~iYyL~q~dVqeA~~L~Kdl~PttP~EyilKgvv~a  327 (557)
T KOG3785|consen  253 ----Y-PFIEYLCRHNLVVFRNGEGALQVLPSLMKHIPEARLNLIIYYLNQNDVQEAISLCKDLDPTTPYEYILKGVVFA  327 (557)
T ss_pred             ----c-hhHHHHHHcCeEEEeCCccHHHhchHHHhhChHhhhhheeeecccccHHHHHHHHhhcCCCChHHHHHHHHHHH
Confidence                1 2333333332     2355666555444322333344555677888888887         112222222    


Q ss_pred             -----hcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhc
Q 044988          353 -----CSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIH  424 (538)
Q Consensus       353 -----~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~  424 (538)
                           ......+..|.+.|+..-+. +..-| ..--.++...+.-..++++.+-.+..++  +..|...--.+..+.+..
T Consensus       328 alGQe~gSreHlKiAqqffqlVG~S-a~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~N~AQAk~at  406 (557)
T KOG3785|consen  328 ALGQETGSREHLKIAQQFFQLVGES-ALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNLNLAQAKLAT  406 (557)
T ss_pred             HhhhhcCcHHHHHHHHHHHHHhccc-ccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhhHHHHHHHHh
Confidence                 22233466777777766444 43333 2233455666666678888888888775  333333334567888999


Q ss_pred             CCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          425 NNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       425 ~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      |++.+|+++|=++ .+.+-.+...|.+.|+.+|.+.|+.+-|.+++-++..
T Consensus       407 gny~eaEelf~~i-s~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~lk~~t  456 (557)
T KOG3785|consen  407 GNYVEAEELFIRI-SGPEIKNKILYKSMLARCYIRNKKPQLAWDMMLKTNT  456 (557)
T ss_pred             cChHHHHHHHhhh-cChhhhhhHHHHHHHHHHHHhcCCchHHHHHHHhcCC
Confidence            9999999999988 6666555556888999999999999999988776653

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=99.12  E-value=5.9e-07  Score=87.53  Aligned_cols=248  Identities=17%  Similarity=0.143  Sum_probs=133.1

Q ss_pred             HHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC--CCcc-hHHHHHHHHhcC-----
Q 044988           25 SLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN--PSTA-IWNQMIRGHARS-----   96 (538)
Q Consensus        25 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~~~~-~~~~li~~~~~~-----   96 (538)
                      ..+...|+++.|.+.++.-.+. +.............+.+.|+.++|..++..+.+  |+-. -|..+..+..-.     
T Consensus        12 ~il~e~g~~~~AL~~L~~~~~~-I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~~   90 (517)
T PF12569_consen   12 SILEEAGDYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQLSD   90 (517)
T ss_pred             HHHHHCCCHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhccccc
Confidence            4566778888888888664443 333456677777888888888888888888773  4333 344444444222     


Q ss_pred             CCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcH-HHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHH
Q 044988           97 ETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFR-EGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCA  175 (538)
Q Consensus        97 ~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~-~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a  175 (538)
                      .+.+...++|+++...  -|.......+.-.+.....+. .+...+..+...|+|+   +|+.|-..|.....   ..-.
T Consensus        91 ~~~~~~~~~y~~l~~~--yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPs---lF~~lk~Ly~d~~K---~~~i  162 (517)
T PF12569_consen   91 EDVEKLLELYDELAEK--YPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPS---LFSNLKPLYKDPEK---AAII  162 (517)
T ss_pred             ccHHHHHHHHHHHHHh--CccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCch---HHHHHHHHHcChhH---HHHH
Confidence            2456677788877664  355554444433333322332 3445566666667443   45556666654433   3333


Q ss_pred             HHHhhcCCC------------------CCch--hHHHHHHHHHhcCCHHHHHHHHccCCC--CC-hHHHHHHHHHHHHcC
Q 044988          176 RLLFDDMPA------------------RSVV--SWNSLLKGYVKRGDIDGAWKIFDEMPH--RN-VVSWTTMISGCAQNG  232 (538)
Q Consensus       176 ~~~~~~~~~------------------~~~~--~~~~li~~~~~~g~~~~A~~~~~~m~~--~~-~~~~~~li~~~~~~~  232 (538)
                      .+++.....                  |...  ++.-+...|...|++++|++.+++..+  |+ +..|..-...+-+.|
T Consensus       163 ~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G  242 (517)
T PF12569_consen  163 ESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAG  242 (517)
T ss_pred             HHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCC
Confidence            333333210                  1111  223334445555666666666555432  33 224455555555566


Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          233 KSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       233 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      ++.+|.+.++..+... .-|...=+.....+.+.|+++.|..++..+.+.
T Consensus       243 ~~~~Aa~~~~~Ar~LD-~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~  291 (517)
T PF12569_consen  243 DLKEAAEAMDEARELD-LADRYINSKCAKYLLRAGRIEEAEKTASLFTRE  291 (517)
T ss_pred             CHHHHHHHHHHHHhCC-hhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCC
Confidence            6666666655555432 223344444444455556666665555555443

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.10  E-value=4.5e-08  Score=94.01  Aligned_cols=249  Identities=17%  Similarity=0.152  Sum_probs=152.9

Q ss_pred             hHHHHHHHHhcCCCchHHHHHHHHhHhC-----CC-CCCcc-hHHHHHHHHHccCCcHHHHHHHHHHHHh-----C-CCC
Q 044988           85 IWNQMIRGHARSETPEKSVYLYKQMIDK-----ET-EPDEY-TYSFLLSVCARCGLFREGEQVHGRVLAS-----G-YCS  151 (538)
Q Consensus        85 ~~~~li~~~~~~~~~~~a~~~~~~m~~~-----~~-~p~~~-~~~~li~~~~~~~~~~~a~~~~~~~~~~-----~-~~~  151 (538)
                      +...+...|...|+++.|..+++...+.     |. .|... ..+.+...|...+++++|..+|+++...     | -.|
T Consensus       201 ~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h~  280 (508)
T KOG1840|consen  201 TLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDHP  280 (508)
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCCH
Confidence            4555888999999999999999988653     21 23333 3334666788899999999998888753     2 111


Q ss_pred             -chhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCC---CCChH-HHHHHHH
Q 044988          152 -NVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMP---HRNVV-SWTTMIS  226 (538)
Q Consensus       152 -~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~~~~-~~~~li~  226 (538)
                       -..+++.|..+|.+.|+   +++|...+                        +.|.+++++..   .+.+. .++.+..
T Consensus       281 ~va~~l~nLa~ly~~~GK---f~EA~~~~------------------------e~Al~I~~~~~~~~~~~v~~~l~~~~~  333 (508)
T KOG1840|consen  281 AVAATLNNLAVLYYKQGK---FAEAEEYC------------------------ERALEIYEKLLGASHPEVAAQLSELAA  333 (508)
T ss_pred             HHHHHHHHHHHHHhccCC---hHHHHHHH------------------------HHHHHHHHHhhccChHHHHHHHHHHHH
Confidence             13456666667777777   77776654                        34555555522   13333 3566677


Q ss_pred             HHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCC
Q 044988          227 GCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCG  306 (538)
Q Consensus       227 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  306 (538)
                      .++..+++++|..+++...+                            ++......    ..+....+++.|...|...|
T Consensus       334 ~~~~~~~~Eea~~l~q~al~----------------------------i~~~~~g~----~~~~~a~~~~nl~~l~~~~g  381 (508)
T KOG1840|consen  334 ILQSMNEYEEAKKLLQKALK----------------------------IYLDAPGE----DNVNLAKIYANLAELYLKMG  381 (508)
T ss_pred             HHHHhcchhHHHHHHHHHHH----------------------------HHHhhccc----cchHHHHHHHHHHHHHHHhc
Confidence            78888888888888886543                            11111111    23355667888999999999


Q ss_pred             CHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHH
Q 044988          307 EIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCM  385 (538)
Q Consensus       307 ~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l  385 (538)
                      ++++|.++++++...                                            .++...  +..+ ....++.|
T Consensus       382 k~~ea~~~~k~ai~~--------------------------------------------~~~~~~--~~~~~~~~~l~~l  415 (508)
T KOG1840|consen  382 KYKEAEELYKKAIQI--------------------------------------------LRELLG--KKDYGVGKPLNQL  415 (508)
T ss_pred             chhHHHHHHHHHHHH--------------------------------------------HHhccc--CcChhhhHHHHHH
Confidence            999999988876421                                            111111  1111 13344555


Q ss_pred             HHHhhhcCChHHHHHHHHhCC--------CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHch
Q 044988          386 VDLFSRAGLMDEAFSLVQNMP--------MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLV  438 (538)
Q Consensus       386 ~~~~~~~g~~~~A~~~~~~~~--------~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~  438 (538)
                      ...|.+.++..+|.++|.+..        -.|+ ..+|..|...|...|+++.|.++.+...
T Consensus       416 a~~~~~~k~~~~a~~l~~~~~~i~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  416 AEAYEELKKYEEAEQLFEEAKDIMKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHHHHhcccchHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            555555555555555554432        1233 3566666666777777777766666654

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.06  E-value=5.9e-06  Score=74.64  Aligned_cols=266  Identities=11%  Similarity=0.028  Sum_probs=170.1

Q ss_pred             HhcCCHHHHHHHHccCC-----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHH-HHHHHccCChHH
Q 044988          198 VKRGDIDGAWKIFDEMP-----HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAA-LSACAEIGDLKL  271 (538)
Q Consensus       198 ~~~g~~~~A~~~~~~m~-----~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l-i~~~~~~~~~~~  271 (538)
                      +-.++-..|...+-...     ..|+.....+...+...|+.++|...|+..+.  +.|+..+-.-+ .-.+...|+.+.
T Consensus       207 ~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~--~dpy~i~~MD~Ya~LL~~eg~~e~  284 (564)
T KOG1174|consen  207 MFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLC--ANPDNVEAMDLYAVLLGQEGGCEQ  284 (564)
T ss_pred             HHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhh--CChhhhhhHHHHHHHHHhccCHhh
Confidence            34455555555443333     25677788899999999999999999998876  34443321111 112346778887


Q ss_pred             HHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC---CcchHHHHHHHHHhcCCccHHH-----
Q 044988          272 GKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR---NTVSWTSMITGFAKQGYAQEAL-----  343 (538)
Q Consensus       272 a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~-----  343 (538)
                      ...+...+...     ...+..-|..-+.......+++.|..+-++..+-   ++..|-.-...+...++.++|.     
T Consensus       285 ~~~L~~~Lf~~-----~~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~  359 (564)
T KOG1174|consen  285 DSALMDYLFAK-----VKYTASHWFVHAQLLYDEKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRT  359 (564)
T ss_pred             HHHHHHHHHhh-----hhcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHH
Confidence            77777666654     3333344434455566778899999988887764   4444444456777888777776     


Q ss_pred             ---------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHH-HHhh-hcCChHHHHHHHHhC-CCCCC-
Q 044988          344 ---------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMV-DLFS-RAGLMDEAFSLVQNM-PMKPN-  410 (538)
Q Consensus       344 ---------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~-~~~~-~~g~~~~A~~~~~~~-~~~p~-  410 (538)
                               ..|..++.+|...|++.+|.-.-.......  .-+..+...+. ..+. ....-++|.++++.- +..|+ 
T Consensus       360 Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~~~An~~~~~~--~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~P~Y  437 (564)
T KOG1174|consen  360 AQMLAPYRLEIYRGLFHSYLAQKRFKEANALANWTIRLF--QNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKINPIY  437 (564)
T ss_pred             HHhcchhhHHHHHHHHHHHHhhchHHHHHHHHHHHHHHh--hcchhhhhhhcceeeccCchhHHHHHHHHHhhhccCCcc
Confidence                     567777777777777777776666655432  22344444442 2222 222345677777654 35566 


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          411 DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       411 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ....+.+...|...|..+.++.++++. ....||..- +. .|++.+.....+++|.+.|.....
T Consensus       438 ~~AV~~~AEL~~~Eg~~~D~i~LLe~~-L~~~~D~~L-H~-~Lgd~~~A~Ne~Q~am~~y~~ALr  499 (564)
T KOG1174|consen  438 TPAVNLIAELCQVEGPTKDIIKLLEKH-LIIFPDVNL-HN-HLGDIMRAQNEPQKAMEYYYKALR  499 (564)
T ss_pred             HHHHHHHHHHHHhhCccchHHHHHHHH-HhhccccHH-HH-HHHHHHHHhhhHHHHHHHHHHHHh
Confidence            345555666677778888888888877 777776655 66 777887777888888877777664

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.05  E-value=6.3e-09  Score=90.33  Aligned_cols=223  Identities=15%  Similarity=0.102  Sum_probs=184.6

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhc
Q 044988           87 NQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMS  166 (538)
Q Consensus        87 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  166 (538)
                      +.+..+|.+.|-+.+|..-|+.-++.  .|-+.||..|-+.|.+..++..|+.++.+-++. ++-|+.......+.+-..
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-fP~~VT~l~g~ARi~eam  303 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-FPFDVTYLLGQARIHEAM  303 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-CCchhhhhhhhHHHHHHH
Confidence            56788899999999999999888775  678889999999999999999999999888876 466666677788888888


Q ss_pred             CCCCChhHHHHHhhcCCCC---CchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHH
Q 044988          167 GGECGVGCARLLFDDMPAR---SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSL  240 (538)
Q Consensus       167 g~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~  240 (538)
                      ++   .++|.++++...+.   ++.....+..+|.-.++++.|+..++++.+   .+...|+.+.-+|.-.+++|-++--
T Consensus       304 ~~---~~~a~~lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~speLf~NigLCC~yaqQ~D~~L~s  380 (478)
T KOG1129|consen  304 EQ---QEDALQLYKLVLKLHPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSPELFCNIGLCCLYAQQIDLVLPS  380 (478)
T ss_pred             Hh---HHHHHHHHHHHHhcCCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCCChHHHhhHHHHHHhhcchhhhHHH
Confidence            88   99999999887753   556666666778888999999999988654   6778899998888889999999999


Q ss_pred             HHHHHHCCCCCC--HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          241 FNEMRRARVGLD--QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       241 ~~~m~~~g~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                      |++.+..--.|+  ...|-.+-......|++..|.+.|+.....     .+.+...+|.|.-.-.+.|++++|..+++..
T Consensus       381 f~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~-----d~~h~ealnNLavL~~r~G~i~~Arsll~~A  455 (478)
T KOG1129|consen  381 FQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTS-----DAQHGEALNNLAVLAARSGDILGARSLLNAA  455 (478)
T ss_pred             HHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhcc-----CcchHHHHHhHHHHHhhcCchHHHHHHHHHh
Confidence            999887544454  335666666677889999999999998886     7777888889998899999999999999887


Q ss_pred             CC
Q 044988          319 QR  320 (538)
Q Consensus       319 ~~  320 (538)
                      ..
T Consensus       456 ~s  457 (478)
T KOG1129|consen  456 KS  457 (478)
T ss_pred             hh
Confidence            65

>PRK12370 invasion protein regulator; Provisional

Probab=99.05  E-value=2.2e-08  Score=100.68  Aligned_cols=172  Identities=14%  Similarity=0.037  Sum_probs=76.3

Q ss_pred             cHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC--C-CchhHHHHHHHHHhcCCHHHHHHHH
Q 044988          134 FREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA--R-SVVSWNSLLKGYVKRGDIDGAWKIF  210 (538)
Q Consensus       134 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~  210 (538)
                      +++|...+++.++.+ +.+...+..+..++...|+   .++|...|++..+  | +...|..+...+...|++++|...+
T Consensus       320 ~~~A~~~~~~Al~ld-P~~~~a~~~lg~~~~~~g~---~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~  395 (553)
T PRK12370        320 MIKAKEHAIKATELD-HNNPQALGLLGLINTIHSE---YIVGSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQTI  395 (553)
T ss_pred             HHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHccC---HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            455555555555543 3334445555555555555   5555555555433  2 2334444445555555555555555


Q ss_pred             ccCCC--CChH-HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCC
Q 044988          211 DEMPH--RNVV-SWTTMISGCAQNGKSRQALSLFNEMRRARVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVG  286 (538)
Q Consensus       211 ~~m~~--~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~  286 (538)
                      ++..+  |+.. .+..++..+...|++++|...++++.+.. .| +...+..+..++...|+.++|...+..+...    
T Consensus       396 ~~Al~l~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~----  470 (553)
T PRK12370        396 NECLKLDPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQ----  470 (553)
T ss_pred             HHHHhcCCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhc----
Confidence            55432  2211 12222223334455555555555544322 12 2222333444444555555555555444332    


Q ss_pred             CCCcchhHHHHHHHHHHhCCCHHHHHHHHHh
Q 044988          287 REPVLVSLNNALIHMYASCGEIEEAYGVFRK  317 (538)
Q Consensus       287 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  317 (538)
                       .|......+.+...|...|  +.|...++.
T Consensus       471 -~~~~~~~~~~l~~~~~~~g--~~a~~~l~~  498 (553)
T PRK12370        471 -EITGLIAVNLLYAEYCQNS--ERALPTIRE  498 (553)
T ss_pred             -cchhHHHHHHHHHHHhccH--HHHHHHHHH
Confidence             3333333344444444444  244444443

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.04  E-value=4.8e-06  Score=79.56  Aligned_cols=414  Identities=12%  Similarity=0.086  Sum_probs=266.4

Q ss_pred             hHHHHHHHHHHccCChhHHHHHHhcCCC--C-CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHH
Q 044988           53 YILAKLLAFYVTSGYLINAHKVFEKTEN--P-STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCA  129 (538)
Q Consensus        53 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  129 (538)
                      ..|..++.+|- .+++...+++.+.+.+  | ...|.....-.+...|+-++|.+....-.+.. ..+.+.|+.+.-.+.
T Consensus         9 ~lF~~~lk~yE-~kQYkkgLK~~~~iL~k~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d-~~S~vCwHv~gl~~R   86 (700)
T KOG1156|consen    9 ALFRRALKCYE-TKQYKKGLKLIKQILKKFPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRND-LKSHVCWHVLGLLQR   86 (700)
T ss_pred             HHHHHHHHHHH-HHHHHhHHHHHHHHHHhCCccchhHHhccchhhcccchHHHHHHHHHHhccC-cccchhHHHHHHHHh
Confidence            45556666553 4555555555555442  1 22344444444567889999999888777643 456778888888888


Q ss_pred             ccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHH
Q 044988          130 RCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKI  209 (538)
Q Consensus       130 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~  209 (538)
                      ...++++|.+.|......+ +.|..++.-+...-+..|+..+.-.....+-+........|..+..++--.|+...|..+
T Consensus        87 ~dK~Y~eaiKcy~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~i  165 (700)
T KOG1156|consen   87 SDKKYDEAIKCYRNALKIE-KDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLRPSQRASWIGFAVAQHLLGEYKMALEI  165 (700)
T ss_pred             hhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            8899999999999999876 667788888888888888832233333333333334667899999999999999999988


Q ss_pred             HccCCC-----CChHHHHHHH------HHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHH-HHHHHHHccCChHHHHHHHH
Q 044988          210 FDEMPH-----RNVVSWTTMI------SGCAQNGKSRQALSLFNEMRRARVGLDQVALV-AALSACAEIGDLKLGKWIHS  277 (538)
Q Consensus       210 ~~~m~~-----~~~~~~~~li------~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~-~li~~~~~~~~~~~a~~~~~  277 (538)
                      ++...+     |+...|....      ......|..++|++.+..-...  ..|...|. .-...+.+.+++++|..++.
T Consensus       166 l~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~--i~Dkla~~e~ka~l~~kl~~lEeA~~~y~  243 (700)
T KOG1156|consen  166 LEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQ--IVDKLAFEETKADLLMKLGQLEEAVKVYR  243 (700)
T ss_pred             HHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhH--HHHHHHHhhhHHHHHHHHhhHHhHHHHHH
Confidence            877542     4555444332      3345678888888877655432  22333332 33344678899999999999


Q ss_pred             HHHHhccCCCCCcchhHHHHHHHHHHhCCC-HHHHHHHHHhcCC-------C--------CcchHHHHHHHHHhcCCccH
Q 044988          278 YVEENFSVGREPVLVSLNNALIHMYASCGE-IEEAYGVFRKMQR-------R--------NTVSWTSMITGFAKQGYAQE  341 (538)
Q Consensus       278 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-~~~a~~~~~~m~~-------~--------~~~~~~~li~~~~~~~~~~~  341 (538)
                      .+...     .|.+...|..+..++.+..+ .+....+|....+       |        +...+...++-|.+..-...
T Consensus       244 ~Ll~r-----nPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg  318 (700)
T KOG1156|consen  244 RLLER-----NPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKG  318 (700)
T ss_pred             HHHhh-----CchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCcchhHHHHHHHHHHHhhcC
Confidence            99986     88888888888888863333 3333366665543       1        11122222222322221111


Q ss_pred             HHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc-C------------CCccHH--HHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          342 ALLTFLGVLSACSHGGFVDEGRQFFECMNQNW-G------------IKPRIE--HYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       342 a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-~------------~~p~~~--~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      +..+|..+.+-+-.-...+-..++.-.+.... |            -+|...  ++-.++..|-+.|+++.|..+++...
T Consensus       319 ~p~vf~dl~SLyk~p~k~~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~AI  398 (700)
T KOG1156|consen  319 VPSVFKDLRSLYKDPEKVAFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAI  398 (700)
T ss_pred             CCchhhhhHHHHhchhHhHHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHh
Confidence            11445555444443322221111111111100 1            145544  44567888999999999999999875


Q ss_pred             -CCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          407 -MKPND-AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       407 -~~p~~-~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                       -.|+. ..|..=.+.+...|+++.|..++++. .+++-.+.. ..+--+.-..++.+.++|.++.....+.|.
T Consensus       399 dHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea-~elD~aDR~-INsKcAKYmLrAn~i~eA~~~~skFTr~~~  470 (700)
T KOG1156|consen  399 DHTPTLIELYLVKARIFKHAGLLDEAAAWLDEA-QELDTADRA-INSKCAKYMLRANEIEEAEEVLSKFTREGF  470 (700)
T ss_pred             ccCchHHHHHHHHHHHHHhcCChHHHHHHHHHH-HhccchhHH-HHHHHHHHHHHccccHHHHHHHHHhhhccc
Confidence             44663 34444456789999999999999999 777666655 333566778899999999999999987775

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.00  E-value=1.2e-06  Score=75.47  Aligned_cols=394  Identities=13%  Similarity=0.092  Sum_probs=196.3

Q ss_pred             hhHHHHHHHHHHccCChhHHHHHHhcCCC--C-CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHH-HHH
Q 044988           52 NYILAKLLAFYVTSGYLINAHKVFEKTEN--P-STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFL-LSV  127 (538)
Q Consensus        52 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l-i~~  127 (538)
                      ..-+.+.+..+.+..++++|++++..-.+  | +....+.|..+|-...++..|-++++++-..  -|...-|... ...
T Consensus        10 EGeftaviy~lI~d~ry~DaI~~l~s~~Er~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQS   87 (459)
T KOG4340|consen   10 EGEFTAVVYRLIRDARYADAIQLLGSELERSPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQS   87 (459)
T ss_pred             CCchHHHHHHHHHHhhHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHH
Confidence            33466666666777777777777765443  2 4445666667777777777777777777653  4554444432 233


Q ss_pred             HHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHH--HHhcCCCCChhHHHHHhhcCCC-CCchhHHHHHHHHHhcCCHH
Q 044988          128 CARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNL--YLMSGGECGVGCARLLFDDMPA-RSVVSWNSLLKGYVKRGDID  204 (538)
Q Consensus       128 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~g~~~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~~g~~~  204 (538)
                      +-+.+.+..|+.+...|...   |+...-..-+.+  ....++   +..+..++++.+. .+..+.+......-+.|+++
T Consensus        88 LY~A~i~ADALrV~~~~~D~---~~L~~~~lqLqaAIkYse~D---l~g~rsLveQlp~en~Ad~~in~gCllykegqyE  161 (459)
T KOG4340|consen   88 LYKACIYADALRVAFLLLDN---PALHSRVLQLQAAIKYSEGD---LPGSRSLVEQLPSENEADGQINLGCLLYKEGQYE  161 (459)
T ss_pred             HHHhcccHHHHHHHHHhcCC---HHHHHHHHHHHHHHhccccc---CcchHHHHHhccCCCccchhccchheeeccccHH
Confidence            45566677777776666442   221111111111  223444   5556666666653 34444444444455666666


Q ss_pred             HHHHHHccCCC----CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHH---HHHHHH
Q 044988          205 GAWKIFDEMPH----RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKL---GKWIHS  277 (538)
Q Consensus       205 ~A~~~~~~m~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~---a~~~~~  277 (538)
                      .|.+-|+...+    .....||..+..| +.|+++.|+++..+..++|++-.+. ++        .|-.-+   +..+-+
T Consensus       162 aAvqkFqaAlqvsGyqpllAYniALaHy-~~~qyasALk~iSEIieRG~r~HPE-lg--------IGm~tegiDvrsvgN  231 (459)
T KOG4340|consen  162 AAVQKFQAALQVSGYQPLLAYNLALAHY-SSRQYASALKHISEIIERGIRQHPE-LG--------IGMTTEGIDVRSVGN  231 (459)
T ss_pred             HHHHHHHHHHhhcCCCchhHHHHHHHHH-hhhhHHHHHHHHHHHHHhhhhcCCc-cC--------ccceeccCchhcccc
Confidence            66666665443    2334555544443 3456666666666666665432111 00        000000   000000


Q ss_pred             HHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC-----CCcchHHHHHHHHHhcCCccHHH---------
Q 044988          278 YVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR-----RNTVSWTSMITGFAKQGYAQEAL---------  343 (538)
Q Consensus       278 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-----~~~~~~~~li~~~~~~~~~~~a~---------  343 (538)
                      ...-     ....-+..+|.-...+.+.|+++.|.+.+..|+.     -|++|...+.-.-. .+++.+..         
T Consensus       232 t~~l-----h~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~g~~KLqFLL~~  305 (459)
T KOG4340|consen  232 TLVL-----HQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTEGFEKLQFLLQQ  305 (459)
T ss_pred             hHHH-----HHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccccHHHHHHHHhc
Confidence            0000     0001122334444556788999999999999985     36677665532221 12222211         


Q ss_pred             -----HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCC-CccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHH
Q 044988          344 -----LTFLGVLSACSHGGFVDEGRQFFECMNQNWGI-KPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSL  417 (538)
Q Consensus       344 -----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l  417 (538)
                           .+|..++-.||+..-++.|-+++.+-... .. -.+...|+.|=....-.-..++|.+-++.+...-....-...
T Consensus       306 nPfP~ETFANlLllyCKNeyf~lAADvLAEn~~l-Tyk~L~~Yly~LLdaLIt~qT~pEea~KKL~~La~~l~~kLRklA  384 (459)
T KOG4340|consen  306 NPFPPETFANLLLLYCKNEYFDLAADVLAENAHL-TYKFLTPYLYDLLDALITCQTAPEEAFKKLDGLAGMLTEKLRKLA  384 (459)
T ss_pred             CCCChHHHHHHHHHHhhhHHHhHHHHHHhhCcch-hHHHhhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence                 67777888888887777777777543321 11 123334443322222344566666655544210000111111


Q ss_pred             HHH-HHhcCCHH----HHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          418 LLG-CRIHNNAE----LASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       418 ~~~-~~~~~~~~----~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +.. -.+..+-+    .|++-+++. .+.--+.   .. .-++.|++..++.-+.++|..-.+
T Consensus       385 i~vQe~r~~~dd~a~R~ai~~Yd~~-LE~YLPV---lM-a~AkiyW~~~Dy~~vEk~Fr~Sve  442 (459)
T KOG4340|consen  385 IQVQEARHNRDDEAIRKAVNEYDET-LEKYLPV---LM-AQAKIYWNLEDYPMVEKIFRKSVE  442 (459)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHHH-HHHHHHH---HH-HHHHhhccccccHHHHHHHHHHHh
Confidence            111 11222212    222223332 2211111   22 445778888899999888887654

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.98  E-value=1.4e-07  Score=86.81  Aligned_cols=93  Identities=13%  Similarity=-0.142  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHH
Q 044988          221 WTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIH  300 (538)
Q Consensus       221 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~  300 (538)
                      |..+...|...|++++|...|++..+.. +.+...|..+...+...|+++.|...++...+.     .|.+..++..+..
T Consensus        67 ~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l-----~P~~~~a~~~lg~  140 (296)
T PRK11189         67 HYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAYEAFDSVLEL-----DPTYNYAYLNRGI  140 (296)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----CCCCHHHHHHHHH
Confidence            4444444444555555555554444421 112344444444444444444444444444443     3333444444444


Q ss_pred             HHHhCCCHHHHHHHHHhcC
Q 044988          301 MYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       301 ~~~~~g~~~~a~~~~~~m~  319 (538)
                      ++...|++++|.+.|++..
T Consensus       141 ~l~~~g~~~eA~~~~~~al  159 (296)
T PRK11189        141 ALYYGGRYELAQDDLLAFY  159 (296)
T ss_pred             HHHHCCCHHHHHHHHHHHH
Confidence            4444444444444444433

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=98.95  E-value=7.6e-07  Score=86.77  Aligned_cols=251  Identities=14%  Similarity=0.074  Sum_probs=122.2

Q ss_pred             HHHHHHccCChhHHHHHHhcCCC--CCcc-hHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHH-c---
Q 044988           58 LLAFYVTSGYLINAHKVFEKTEN--PSTA-IWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCA-R---  130 (538)
Q Consensus        58 l~~~~~~~g~~~~a~~~~~~~~~--~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~-~---  130 (538)
                      ...++...|++++|++.++....  +|.. ........+.+.|+.++|..+|..+.+.+  |+...|-..+..+. -   
T Consensus        10 ~~~il~e~g~~~~AL~~L~~~~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn~~Yy~~L~~~~g~~~~   87 (517)
T PF12569_consen   10 KNSILEEAGDYEEALEHLEKNEKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDNYDYYRGLEEALGLQLQ   87 (517)
T ss_pred             HHHHHHHCCCHHHHHHHHHhhhhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHhhhcc
Confidence            34556677888888888766543  3433 34455667777788888888888887764  55555554444433 1   


Q ss_pred             --cCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChh-HHHHHhhcCCCCCc-hhHHHHHHHHHhcCCHHHH
Q 044988          131 --CGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVG-CARLLFDDMPARSV-VSWNSLLKGYVKRGDIDGA  206 (538)
Q Consensus       131 --~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~-~a~~~~~~~~~~~~-~~~~~li~~~~~~g~~~~A  206 (538)
                        ..+.+...++++++...-  |.......+.-.+.....   +. .+...+..+..+.+ ..++.+-..|......+-.
T Consensus        88 ~~~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~---F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i  162 (517)
T PF12569_consen   88 LSDEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDE---FKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAII  162 (517)
T ss_pred             cccccHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHH---HHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHH
Confidence              124556666777665543  332222222222211111   21 22223333333332 3344444444433333333


Q ss_pred             HHHHccCC------------------CCChH--HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHc
Q 044988          207 WKIFDEMP------------------HRNVV--SWTTMISGCAQNGKSRQALSLFNEMRRARVGLD-QVALVAALSACAE  265 (538)
Q Consensus       207 ~~~~~~m~------------------~~~~~--~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~  265 (538)
                      .+++....                  .|...  ++.-+...|...|++++|+.++++..+.  .|+ ...|..-...+-+
T Consensus       163 ~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h--tPt~~ely~~KarilKh  240 (517)
T PF12569_consen  163 ESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH--TPTLVELYMTKARILKH  240 (517)
T ss_pred             HHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc--CCCcHHHHHHHHHHHHH
Confidence            33332211                  01111  2233344455555555555555555553  333 3344444445555


Q ss_pred             cCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCC
Q 044988          266 IGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRN  322 (538)
Q Consensus       266 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  322 (538)
                      .|++.+|....+...+.     ...|-.+.+-.+..+.++|++++|.+++..-.+++
T Consensus       241 ~G~~~~Aa~~~~~Ar~L-----D~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~  292 (517)
T PF12569_consen  241 AGDLKEAAEAMDEAREL-----DLADRYINSKCAKYLLRAGRIEEAEKTASLFTRED  292 (517)
T ss_pred             CCCHHHHHHHHHHHHhC-----ChhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCC
Confidence            55555555555555554     44444444445555555555555555555544433

N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.94  E-value=3.3e-06  Score=84.42  Aligned_cols=404  Identities=11%  Similarity=0.084  Sum_probs=232.9

Q ss_pred             HHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC------------CCCc----
Q 044988           20 TRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE------------NPST----   83 (538)
Q Consensus        20 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~------------~~~~----   83 (538)
                      -..|..-+-+.++.......++...+.|.. ++.++|+|...|..+++-.+-  ++.+-+            +.|+    
T Consensus       841 ~deLv~EvEkRNRLklLlp~LE~~i~eG~~-d~a~hnAlaKIyIDSNNnPE~--fLkeN~yYDs~vVGkYCEKRDP~lA~  917 (1666)
T KOG0985|consen  841 VDELVEEVEKRNRLKLLLPWLESLIQEGSQ-DPATHNALAKIYIDSNNNPER--FLKENPYYDSKVVGKYCEKRDPHLAC  917 (1666)
T ss_pred             hHHHHHHHHhhhhHHHHHHHHHHHHhccCc-chHHHhhhhheeecCCCChHH--hcccCCcchhhHHhhhhcccCCceEE
Confidence            345566677778888888889999999866 899999999999877653321  111111            1111    


Q ss_pred             -------------------chHHHHHHHHhcCCCchHHHHHH-----------HHhHhCCCC--CCcchHHHHHHHHHcc
Q 044988           84 -------------------AIWNQMIRGHARSETPEKSVYLY-----------KQMIDKETE--PDEYTYSFLLSVCARC  131 (538)
Q Consensus        84 -------------------~~~~~li~~~~~~~~~~~a~~~~-----------~~m~~~~~~--p~~~~~~~li~~~~~~  131 (538)
                                         ..|....+-+.+..+.+--.+++           ++..+.+++  -|+...+...+++...
T Consensus       918 vaYerGqcD~elI~vcNeNSlfK~~aRYlv~R~D~~LW~~VL~e~n~~rRqLiDqVv~tal~E~~dPe~vS~tVkAfMta  997 (1666)
T KOG0985|consen  918 VAYERGQCDLELINVCNENSLFKSQARYLVERSDPDLWAKVLNEENPYRRQLIDQVVQTALPETQDPEEVSVTVKAFMTA  997 (1666)
T ss_pred             EeecccCCcHHHHHhcCchhHHHHHHHHHHhccChHHHHHHHhccChHHHHHHHHHHHhcCCccCChHHHHHHHHHHHhc
Confidence                               11222333333334433222222           222222221  2444555566666666


Q ss_pred             CCcHHHHHHHHHHHHhC--CCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHH
Q 044988          132 GLFREGEQVHGRVLASG--YCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKI  209 (538)
Q Consensus       132 ~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~  209 (538)
                      +-+.+-.++++++.-.+  +..+....|.|+-...+..    ...+.+..+++..-|..   .+...+...+-+++|..+
T Consensus       998 dLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAikad----~trVm~YI~rLdnyDa~---~ia~iai~~~LyEEAF~i 1070 (1666)
T KOG0985|consen  998 DLPNELIELLEKIVLDNSVFSENRNLQNLLILTAIKAD----RTRVMEYINRLDNYDAP---DIAEIAIENQLYEEAFAI 1070 (1666)
T ss_pred             CCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHhhcC----hHHHHHHHHHhccCCch---hHHHHHhhhhHHHHHHHH
Confidence            66666677776665432  2223334444444444443    34444444444432111   112223344455666666


Q ss_pred             HccCCC-------------------------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 044988          210 FDEMPH-------------------------RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACA  264 (538)
Q Consensus       210 ~~~m~~-------------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  264 (538)
                      |++...                         ..+..|..+..+-.+.|...+|++-|-+.      -|...|..++..+.
T Consensus      1071 fkkf~~n~~A~~VLie~i~~ldRA~efAe~~n~p~vWsqlakAQL~~~~v~dAieSyika------dDps~y~eVi~~a~ 1144 (1666)
T KOG0985|consen 1071 FKKFDMNVSAIQVLIENIGSLDRAYEFAERCNEPAVWSQLAKAQLQGGLVKDAIESYIKA------DDPSNYLEVIDVAS 1144 (1666)
T ss_pred             HHHhcccHHHHHHHHHHhhhHHHHHHHHHhhCChHHHHHHHHHHHhcCchHHHHHHHHhc------CCcHHHHHHHHHHH
Confidence            655321                         24467889999988899998888877543      36778999999999


Q ss_pred             ccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHH-
Q 044988          265 EIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL-  343 (538)
Q Consensus       265 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~-  343 (538)
                      +.|.+++..+++....+.    ...+.+.  +.|+-+|++.++..+.++++   ..||......+.+-|...+.++.|. 
T Consensus      1145 ~~~~~edLv~yL~MaRkk----~~E~~id--~eLi~AyAkt~rl~elE~fi---~gpN~A~i~~vGdrcf~~~~y~aAkl 1215 (1666)
T KOG0985|consen 1145 RTGKYEDLVKYLLMARKK----VREPYID--SELIFAYAKTNRLTELEEFI---AGPNVANIQQVGDRCFEEKMYEAAKL 1215 (1666)
T ss_pred             hcCcHHHHHHHHHHHHHh----hcCccch--HHHHHHHHHhchHHHHHHHh---cCCCchhHHHHhHHHhhhhhhHHHHH
Confidence            999999999999988887    5555555  47999999999988877765   3467777777777777888777776 


Q ss_pred             -----HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHH
Q 044988          344 -----LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLL  418 (538)
Q Consensus       344 -----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~  418 (538)
                           .-|..+...+...|+++.|.+.-++.       .+..+|...-.+|...+.+.-|.-.  .+.+-....-..-++
T Consensus      1216 ~y~~vSN~a~La~TLV~LgeyQ~AVD~aRKA-------ns~ktWK~VcfaCvd~~EFrlAQiC--GL~iivhadeLeeli 1286 (1666)
T KOG0985|consen 1216 LYSNVSNFAKLASTLVYLGEYQGAVDAARKA-------NSTKTWKEVCFACVDKEEFRLAQIC--GLNIIVHADELEELI 1286 (1666)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHHHHhhhc-------cchhHHHHHHHHHhchhhhhHHHhc--CceEEEehHhHHHHH
Confidence                 33445556666667776666554332       2344555555555544433322110  000112233344455


Q ss_pred             HHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHh
Q 044988          419 LGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAA  459 (538)
Q Consensus       419 ~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~  459 (538)
                      .-|...|-+++-+.+++.. .++.......|. -|+-.|.+
T Consensus      1287 ~~Yq~rGyFeElIsl~Ea~-LGLERAHMgmfT-ELaiLYsk 1325 (1666)
T KOG0985|consen 1287 EYYQDRGYFEELISLLEAG-LGLERAHMGMFT-ELAILYSK 1325 (1666)
T ss_pred             HHHHhcCcHHHHHHHHHhh-hchhHHHHHHHH-HHHHHHHh
Confidence            5555566666666555555 555444444344 44444433

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=98.91  E-value=5.4e-07  Score=74.95  Aligned_cols=197  Identities=11%  Similarity=0.045  Sum_probs=146.5

Q ss_pred             HHHHHHHHhcCCCchHHHHHHHHhHhCCCCCC-cchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHH
Q 044988           86 WNQMIRGHARSETPEKSVYLYKQMIDKETEPD-EYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYL  164 (538)
Q Consensus        86 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  164 (538)
                      ...|.-.|.+.|+...|..-+++.++.  .|+ ..+|..+...|-+.|..+.|.+-|++.++.. +.+..+.|.....+|
T Consensus        38 rlqLal~YL~~gd~~~A~~nlekAL~~--DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~-p~~GdVLNNYG~FLC  114 (250)
T COG3063          38 RLQLALGYLQQGDYAQAKKNLEKALEH--DPSYYLAHLVRAHYYQKLGENDLADESYRKALSLA-PNNGDVLNNYGAFLC  114 (250)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC-CCccchhhhhhHHHH
Confidence            445566777888888888888887775  343 4477777777788888888888888877764 555667777777778


Q ss_pred             hcCCCCChhHHHHHhhcCCC-C----CchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHH
Q 044988          165 MSGGECGVGCARLLFDDMPA-R----SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQ  236 (538)
Q Consensus       165 ~~g~~~~~~~a~~~~~~~~~-~----~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~  236 (538)
                      ..|.   +++|...|++... |    -..+|..+.-+..+.|+++.|...|++-.+   ....+.-.+.....+.|++..
T Consensus       115 ~qg~---~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~  191 (250)
T COG3063         115 AQGR---PEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAP  191 (250)
T ss_pred             hCCC---hHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchH
Confidence            8887   8888877777654 3    345777777788888888888888888654   234466777788888899999


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhH
Q 044988          237 ALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSL  294 (538)
Q Consensus       237 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  294 (538)
                      |..+++.....+. ++..+....|..-...|+.+.+.+.-..+.+.     +|.+...
T Consensus       192 Ar~~~~~~~~~~~-~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~-----fP~s~e~  243 (250)
T COG3063         192 ARLYLERYQQRGG-AQAESLLLGIRIAKRLGDRAAAQRYQAQLQRL-----FPYSEEY  243 (250)
T ss_pred             HHHHHHHHHhccc-ccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh-----CCCcHHH
Confidence            9999988877665 88888888888888888888888777777665     5655443

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.90  E-value=2.7e-06  Score=82.21  Aligned_cols=248  Identities=14%  Similarity=0.176  Sum_probs=158.9

Q ss_pred             HHHHHhcCCHHHHHHHHccCCCCChH--HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHH
Q 044988          194 LKGYVKRGDIDGAWKIFDEMPHRNVV--SWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKL  271 (538)
Q Consensus       194 i~~~~~~g~~~~A~~~~~~m~~~~~~--~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~  271 (538)
                      +.+......|.+|+.+++.+...++.  -|..+...|++.|+++.|.++|.+.-         .++-.|..|.+.|+++.
T Consensus       739 ieaai~akew~kai~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e~~---------~~~dai~my~k~~kw~d  809 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTEAD---------LFKDAIDMYGKAGKWED  809 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHhcc---------hhHHHHHHHhccccHHH
Confidence            34556677888888888888765554  36777788888899999988886542         34556778888898888


Q ss_pred             HHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHH--------
Q 044988          272 GKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL--------  343 (538)
Q Consensus       272 a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~--------  343 (538)
                      |.++-....      +.......|-+-..-+-+.|++.+|++++-.+..|+.     .|..|-+.|..++.+        
T Consensus       810 a~kla~e~~------~~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~~-----aiqmydk~~~~ddmirlv~k~h~  878 (1636)
T KOG3616|consen  810 AFKLAEECH------GPEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDK-----AIQMYDKHGLDDDMIRLVEKHHG  878 (1636)
T ss_pred             HHHHHHHhc------CchhHHHHHHHhHHhHHhhcchhhhhheeEEccCchH-----HHHHHHhhCcchHHHHHHHHhCh
Confidence            876654432      4555666666666677788888888888888777764     356677777777665        


Q ss_pred             ----HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCH-----HH-
Q 044988          344 ----LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPND-----AV-  413 (538)
Q Consensus       344 ----~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~-----~~-  413 (538)
                          .+...+..-+...|++..|+..|-+.-          -|.+-+.+|-..+-+++|.++-+.-. -.|.     +. 
T Consensus       879 d~l~dt~~~f~~e~e~~g~lkaae~~flea~----------d~kaavnmyk~s~lw~dayriakteg-g~n~~k~v~flw  947 (1636)
T KOG3616|consen  879 DHLHDTHKHFAKELEAEGDLKAAEEHFLEAG----------DFKAAVNMYKASELWEDAYRIAKTEG-GANAEKHVAFLW  947 (1636)
T ss_pred             hhhhHHHHHHHHHHHhccChhHHHHHHHhhh----------hHHHHHHHhhhhhhHHHHHHHHhccc-cccHHHHHHHHH
Confidence                444555566666777777776665442          23445555666666666666554332 0010     11 


Q ss_pred             ------------------HHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          414 ------------------LGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       414 ------------------~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                                        ...-++..+..+.++-|..+-+-.   .+-..++... -++.-+...|++++|-+.+-+..+
T Consensus       948 aksiggdaavkllnk~gll~~~id~a~d~~afd~afdlari~---~k~k~~~vhl-k~a~~ledegk~edaskhyveaik 1023 (1636)
T KOG3616|consen  948 AKSIGGDAAVKLLNKHGLLEAAIDFAADNCAFDFAFDLARIA---AKDKMGEVHL-KLAMFLEDEGKFEDASKHYVEAIK 1023 (1636)
T ss_pred             HHhhCcHHHHHHHHhhhhHHHHhhhhhcccchhhHHHHHHHh---hhccCccchh-HHhhhhhhccchhhhhHhhHHHhh
Confidence                              111223344555666666665544   2333344455 666778889999999887766654


Q ss_pred             C
Q 044988          476 M  476 (538)
Q Consensus       476 ~  476 (538)
                      .
T Consensus      1024 l 1024 (1636)
T KOG3616|consen 1024 L 1024 (1636)
T ss_pred             c
Confidence            3

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=98.90  E-value=1.1e-06  Score=73.08  Aligned_cols=198  Identities=13%  Similarity=0.051  Sum_probs=158.2

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHH
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALI  299 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~  299 (538)
                      +...|.-+|...|+...|..-+++.++.. +-+..++..+...|.+.|+.+.|.+-|+...+.     .|.+-.+.|...
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl-----~p~~GdVLNNYG  110 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSL-----APNNGDVLNNYG  110 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhc-----CCCccchhhhhh
Confidence            45667788999999999999999998853 334667788888888999999999999999887     788888889999


Q ss_pred             HHHHhCCCHHHHHHHHHhcCC-CC----cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcC
Q 044988          300 HMYASCGEIEEAYGVFRKMQR-RN----TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWG  374 (538)
Q Consensus       300 ~~~~~~g~~~~a~~~~~~m~~-~~----~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  374 (538)
                      ..+|..|++++|...|++... |+    ..+|..+.-+.                    .+.|+.+.|...|++..+.  
T Consensus       111 ~FLC~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Ca--------------------l~~gq~~~A~~~l~raL~~--  168 (250)
T COG3063         111 AFLCAQGRPEEAMQQFERALADPAYGEPSDTLENLGLCA--------------------LKAGQFDQAEEYLKRALEL--  168 (250)
T ss_pred             HHHHhCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHH--------------------hhcCCchhHHHHHHHHHHh--
Confidence            999999999999999998765 42    23444444444                    4445778888999888764  


Q ss_pred             CCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          375 IKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       375 ~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                       .|+ ..+.-.+.....+.|++-.|...++...  ..++..+.-..|......|+.+.+-++=.++ ....|....
T Consensus       169 -dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~~~~~~~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL-~r~fP~s~e  242 (250)
T COG3063         169 -DPQFPPALLELARLHYKAGDYAPARLYLERYQQRGGAQAESLLLGIRIAKRLGDRAAAQRYQAQL-QRLFPYSEE  242 (250)
T ss_pred             -CcCCChHHHHHHHHHHhcccchHHHHHHHHHHhcccccHHHHHHHHHHHHHhccHHHHHHHHHHH-HHhCCCcHH
Confidence             554 6677888888999999999999998773  4577888777888889999999998888888 888888776

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.89  E-value=4.1e-06  Score=82.04  Aligned_cols=235  Identities=16%  Similarity=0.164  Sum_probs=155.7

Q ss_pred             ChhHHHHHHH--HHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchHHHHHHHHhHhC-C--------CCCCcc
Q 044988           51 KNYILAKLLA--FYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDK-E--------TEPDEY  119 (538)
Q Consensus        51 ~~~~~~~l~~--~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-~--------~~p~~~  119 (538)
                      |+.+-.++++  .|..-|+.+.|.+-.+.++  +...|..|.+.|++..+.+-|.-++-.|... |        -.|+ .
T Consensus       725 d~~TRkaml~FSfyvtiG~MD~AfksI~~Ik--S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e  801 (1416)
T KOG3617|consen  725 DESTRKAMLDFSFYVTIGSMDAAFKSIQFIK--SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-E  801 (1416)
T ss_pred             CHHHHHhhhceeEEEEeccHHHHHHHHHHHh--hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-c
Confidence            4455555554  4566788888877666553  4567888999999988888888777777432 1        1222 3


Q ss_pred             hHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC-CchhHHHHHHHHH
Q 044988          120 TYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPAR-SVVSWNSLLKGYV  198 (538)
Q Consensus       120 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~  198 (538)
                      +=..+.-.....|.+++|+.+|.+-++.+         .|=..|-..|.   +++|.++-+.-..- =..+|.....-+-
T Consensus       802 ~eakvAvLAieLgMlEeA~~lYr~ckR~D---------LlNKlyQs~g~---w~eA~eiAE~~DRiHLr~Tyy~yA~~Le  869 (1416)
T KOG3617|consen  802 DEAKVAVLAIELGMLEEALILYRQCKRYD---------LLNKLYQSQGM---WSEAFEIAETKDRIHLRNTYYNYAKYLE  869 (1416)
T ss_pred             hhhHHHHHHHHHhhHHHHHHHHHHHHHHH---------HHHHHHHhccc---HHHHHHHHhhccceehhhhHHHHHHHHH
Confidence            33333334567788889988888877643         24456667777   88887765543321 2245666666667


Q ss_pred             hcCCHHHHHHHHccCCC-----------------------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHH
Q 044988          199 KRGDIDGAWKIFDEMPH-----------------------RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVA  255 (538)
Q Consensus       199 ~~g~~~~A~~~~~~m~~-----------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~  255 (538)
                      ..++.+.|++.|++-..                       .|...|......+-..|+.+.|+.+|.....         
T Consensus       870 ar~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D---------  940 (1416)
T KOG3617|consen  870 ARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD---------  940 (1416)
T ss_pred             hhccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh---------
Confidence            77888888888877542                       2344455555666667888888888877654         


Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 044988          256 LVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       256 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  319 (538)
                      |..+++..|-.|+.++|.++-++-         ..-...| .|.+.|...|++.+|...|.+..
T Consensus       941 ~fs~VrI~C~qGk~~kAa~iA~es---------gd~AAcY-hlaR~YEn~g~v~~Av~FfTrAq  994 (1416)
T KOG3617|consen  941 YFSMVRIKCIQGKTDKAARIAEES---------GDKAACY-HLARMYENDGDVVKAVKFFTRAQ  994 (1416)
T ss_pred             hhhheeeEeeccCchHHHHHHHhc---------ccHHHHH-HHHHHhhhhHHHHHHHHHHHHHH
Confidence            455666667788888887765432         1223333 68889999999999999888764

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.88  E-value=1.2e-05  Score=76.21  Aligned_cols=115  Identities=10%  Similarity=0.062  Sum_probs=72.3

Q ss_pred             cHHHHHHHHHHhhhhcCCCcc--HHHHHHHHHHhhhcCChHHHHHHHH--------hCC-CCCCHHHHHHHHHHHHhcCC
Q 044988          358 FVDEGRQFFECMNQNWGIKPR--IEHYGCMVDLFSRAGLMDEAFSLVQ--------NMP-MKPNDAVLGSLLLGCRIHNN  426 (538)
Q Consensus       358 ~~~~a~~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~--------~~~-~~p~~~~~~~l~~~~~~~~~  426 (538)
                      .+..+..++....+.   .|.  ..+.-.+++.....|+++.|++++.        .+. +.-.+.+...+...+.+.++
T Consensus       356 ~~~ka~e~L~~~~~~---~p~~s~~v~L~~aQl~is~gn~~~A~~il~~~~~~~~ss~~~~~~~P~~V~aiv~l~~~~~~  432 (652)
T KOG2376|consen  356 KHKKAIELLLQFADG---HPEKSKVVLLLRAQLKISQGNPEVALEILSLFLESWKSSILEAKHLPGTVGAIVALYYKIKD  432 (652)
T ss_pred             HHhhhHHHHHHHhcc---CCchhHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhhhhhhhhccChhHHHHHHHHHHhccC
Confidence            456667777766654   343  4456667778889999999999998        332 22223333445555667676


Q ss_pred             HHHHHHHHHHch---hccCCCC---cccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          427 AELASQVAQKLV---AEIDPEQ---AAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       427 ~~~A~~~~~~~~---~~~~p~~---~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      .+.|..++..+.   ....+..   ...+. .++..-.+.|.-++|..+++++.+.
T Consensus       433 ~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~-~aa~f~lr~G~~~ea~s~leel~k~  487 (652)
T KOG2376|consen  433 NDSASAVLDSAIKWWRKQQTGSIALLSLMR-EAAEFKLRHGNEEEASSLLEELVKF  487 (652)
T ss_pred             CccHHHHHHHHHHHHHHhcccchHHHhHHH-HHhHHHHhcCchHHHHHHHHHHHHh
Confidence            666666666664   1222222   22233 4455566789999999999999874

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.87  E-value=3.8e-06  Score=78.57  Aligned_cols=89  Identities=17%  Similarity=0.132  Sum_probs=55.0

Q ss_pred             HHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCCh
Q 044988          386 VDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRW  463 (538)
Q Consensus       386 ~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~  463 (538)
                      ...+.+.|++..|+..|.++. ..| |...|.....+|.+.|.+..|+.-.+.. .++.|+....|. .=+.++.-..+|
T Consensus       365 Gne~Fk~gdy~~Av~~YteAIkr~P~Da~lYsNRAac~~kL~~~~~aL~Da~~~-ieL~p~~~kgy~-RKg~al~~mk~y  442 (539)
T KOG0548|consen  365 GNEAFKKGDYPEAVKHYTEAIKRDPEDARLYSNRAACYLKLGEYPEALKDAKKC-IELDPNFIKAYL-RKGAALRAMKEY  442 (539)
T ss_pred             HHHHHhccCHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhhHHHHHHHHHHH-HhcCchHHHHHH-HHHHHHHHHHHH
Confidence            444556666666666666653 223 3556666666666666666666666666 666666666666 555566666666


Q ss_pred             HHHHHHHHHHHhC
Q 044988          464 QDVAAVRQKMIKM  476 (538)
Q Consensus       464 ~~A~~~~~~m~~~  476 (538)
                      ++|.+.|.+-.+.
T Consensus       443 dkAleay~eale~  455 (539)
T KOG0548|consen  443 DKALEAYQEALEL  455 (539)
T ss_pred             HHHHHHHHHHHhc
Confidence            6666666665553

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.86  E-value=1.9e-06  Score=79.41  Aligned_cols=138  Identities=12%  Similarity=-0.058  Sum_probs=90.9

Q ss_pred             hhHHHHHhhcCCCC-------CchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHH
Q 044988          172 VGCARLLFDDMPAR-------SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLF  241 (538)
Q Consensus       172 ~~~a~~~~~~~~~~-------~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~  241 (538)
                      .+.+..-+.++...       ....|..+...+...|+.++|...|++..+   .+...|+.+...+...|++++|...|
T Consensus        42 ~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~~  121 (296)
T PRK11189         42 QEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEAF  121 (296)
T ss_pred             HHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            55566555555531       134567777778888888888888877653   34567888888888888888888888


Q ss_pred             HHHHHCCCCCC-HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHh
Q 044988          242 NEMRRARVGLD-QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRK  317 (538)
Q Consensus       242 ~~m~~~g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  317 (538)
                      ++..+.  .|+ ..++..+..++...|++++|...++...+.     .|.+.. .......+...++.++|...|.+
T Consensus       122 ~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~-----~P~~~~-~~~~~~l~~~~~~~~~A~~~l~~  190 (296)
T PRK11189        122 DSVLEL--DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD-----DPNDPY-RALWLYLAESKLDPKQAKENLKQ  190 (296)
T ss_pred             HHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----CCCCHH-HHHHHHHHHccCCHHHHHHHHHH
Confidence            888763  443 556667777777888888888888888775     343331 11112223345567777776654

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.86  E-value=6e-06  Score=79.89  Aligned_cols=182  Identities=13%  Similarity=0.160  Sum_probs=89.5

Q ss_pred             HHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCC
Q 044988          227 GCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCG  306 (538)
Q Consensus       227 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  306 (538)
                      +....+++.+|+.+++.++....  -..-|..+...|+..|+++.|+++|-..-             .++--|.+|.+.|
T Consensus       741 aai~akew~kai~ildniqdqk~--~s~yy~~iadhyan~~dfe~ae~lf~e~~-------------~~~dai~my~k~~  805 (1636)
T KOG3616|consen  741 AAIGAKEWKKAISILDNIQDQKT--ASGYYGEIADHYANKGDFEIAEELFTEAD-------------LFKDAIDMYGKAG  805 (1636)
T ss_pred             HHhhhhhhhhhHhHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHhcc-------------hhHHHHHHHhccc
Confidence            34445566666666666655322  22335556666667777777666654331             1244566677777


Q ss_pred             CHHHHHHHHHhcCCCC--cchHHHHHHHHHhcCCccHHHHHHHHH------HHHhcccCcHHHHHHHHHHhhhhcCCCcc
Q 044988          307 EIEEAYGVFRKMQRRN--TVSWTSMITGFAKQGYAQEALLTFLGV------LSACSHGGFVDEGRQFFECMNQNWGIKPR  378 (538)
Q Consensus       307 ~~~~a~~~~~~m~~~~--~~~~~~li~~~~~~~~~~~a~~~~~~l------l~~~~~~~~~~~a~~~~~~~~~~~~~~p~  378 (538)
                      +|+.|.++-.+...|.  +..|-+-..-+-.+|++.+|...|..+      +..|.+.|..+...++..+-      .|+
T Consensus       806 kw~da~kla~e~~~~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~~aiqmydk~~~~ddmirlv~k~------h~d  879 (1636)
T KOG3616|consen  806 KWEDAFKLAEECHGPEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPDKAIQMYDKHGLDDDMIRLVEKH------HGD  879 (1636)
T ss_pred             cHHHHHHHHHHhcCchhHHHHHHHhHHhHHhhcchhhhhheeEEccCchHHHHHHHhhCcchHHHHHHHHh------Chh
Confidence            7777777666665543  233444444455566665555333211      22222222222222222111      122


Q ss_pred             --HHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHH
Q 044988          379 --IEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQ  435 (538)
Q Consensus       379 --~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~  435 (538)
                        ..|...+..-|...|++..|..-|-+..      -|.+.+..|...+-+++|-++.+
T Consensus       880 ~l~dt~~~f~~e~e~~g~lkaae~~flea~------d~kaavnmyk~s~lw~dayriak  932 (1636)
T KOG3616|consen  880 HLHDTHKHFAKELEAEGDLKAAEEHFLEAG------DFKAAVNMYKASELWEDAYRIAK  932 (1636)
T ss_pred             hhhHHHHHHHHHHHhccChhHHHHHHHhhh------hHHHHHHHhhhhhhHHHHHHHHh
Confidence              2233444455555566666655554432      24444455555555555555444

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.81  E-value=1.1e-05  Score=71.17  Aligned_cols=91  Identities=13%  Similarity=0.011  Sum_probs=43.2

Q ss_pred             hHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHH---HH
Q 044988          120 TYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLL---KG  196 (538)
Q Consensus       120 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li---~~  196 (538)
                      -.--+.+.+...|++..|+.-|...++.+ +.+-.++-.-...|...|+   -..|+.-|.+..+..+..+.+-+   ..
T Consensus        40 khlElGk~lla~~Q~sDALt~yHaAve~d-p~~Y~aifrRaT~yLAmGk---sk~al~Dl~rVlelKpDF~~ARiQRg~v  115 (504)
T KOG0624|consen   40 KHLELGKELLARGQLSDALTHYHAAVEGD-PNNYQAIFRRATVYLAMGK---SKAALQDLSRVLELKPDFMAARIQRGVV  115 (504)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHcCC-chhHHHHHHHHHHHhhhcC---CccchhhHHHHHhcCccHHHHHHHhchh
Confidence            34445555555666666666665555432 1222233333445555555   44444444444432222222222   24


Q ss_pred             HHhcCCHHHHHHHHccCC
Q 044988          197 YVKRGDIDGAWKIFDEMP  214 (538)
Q Consensus       197 ~~~~g~~~~A~~~~~~m~  214 (538)
                      +.+.|.++.|..-|+.+.
T Consensus       116 llK~Gele~A~~DF~~vl  133 (504)
T KOG0624|consen  116 LLKQGELEQAEADFDQVL  133 (504)
T ss_pred             hhhcccHHHHHHHHHHHH
Confidence            455666666666665544

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.79  E-value=2.6e-05  Score=76.69  Aligned_cols=197  Identities=12%  Similarity=0.107  Sum_probs=125.9

Q ss_pred             HhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC-------------CCcchHHHHHHHH
Q 044988           27 LQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN-------------PSTAIWNQMIRGH   93 (538)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-------------~~~~~~~~li~~~   93 (538)
                      +...|+++.|..-.+.+.      +..+|..+..++.+..+++-|.-.+-.|..             ++ ..-..+.-..
T Consensus       738 yvtiG~MD~AfksI~~Ik------S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLA  810 (1416)
T KOG3617|consen  738 YVTIGSMDAAFKSIQFIK------SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLA  810 (1416)
T ss_pred             EEEeccHHHHHHHHHHHh------hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHH
Confidence            344577777766665443      456899999999998888877766666542             22 2222222223


Q ss_pred             hcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChh
Q 044988           94 ARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVG  173 (538)
Q Consensus        94 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~  173 (538)
                      .+.|-.++|..+|.+.++         |..|=+.|-..|.+++|.++-+.--+.-+   ..+|.....-+-..++   ++
T Consensus       811 ieLgMlEeA~~lYr~ckR---------~DLlNKlyQs~g~w~eA~eiAE~~DRiHL---r~Tyy~yA~~Lear~D---i~  875 (1416)
T KOG3617|consen  811 IELGMLEEALILYRQCKR---------YDLLNKLYQSQGMWSEAFEIAETKDRIHL---RNTYYNYAKYLEARRD---IE  875 (1416)
T ss_pred             HHHhhHHHHHHHHHHHHH---------HHHHHHHHHhcccHHHHHHHHhhccceeh---hhhHHHHHHHHHhhcc---HH
Confidence            466788888888888775         34455566777888888776543222111   1244445555555666   77


Q ss_pred             HHHHHhhcCCC-----------------------CCchhHHHHHHHHHhcCCHHHHHHHHccCCC---------------
Q 044988          174 CARLLFDDMPA-----------------------RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---------------  215 (538)
Q Consensus       174 ~a~~~~~~~~~-----------------------~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---------------  215 (538)
                      .|++.|++...                       +|...|.-...-+-..|+++.|+.+|....+               
T Consensus       876 ~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D~fs~VrI~C~qGk~~  955 (1416)
T KOG3617|consen  876 AALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKDYFSMVRIKCIQGKTD  955 (1416)
T ss_pred             HHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhhhhhheeeEeeccCch
Confidence            77766665432                       1444555555666678888888888776531               


Q ss_pred             ---------CChHHHHHHHHHHHHcCCHHHHHHHHHHHH
Q 044988          216 ---------RNVVSWTTMISGCAQNGKSRQALSLFNEMR  245 (538)
Q Consensus       216 ---------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  245 (538)
                               .|......+.+.|-+.|++.+|..+|.+.+
T Consensus       956 kAa~iA~esgd~AAcYhlaR~YEn~g~v~~Av~FfTrAq  994 (1416)
T KOG3617|consen  956 KAARIAEESGDKAACYHLARMYENDGDVVKAVKFFTRAQ  994 (1416)
T ss_pred             HHHHHHHhcccHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence                     344566678888888899999999988875

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=98.77  E-value=2.8e-07  Score=83.56  Aligned_cols=228  Identities=13%  Similarity=0.142  Sum_probs=140.7

Q ss_pred             HHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHH-HHHHHHHccCCh
Q 044988          191 NSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALV-AALSACAEIGDL  269 (538)
Q Consensus       191 ~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~-~li~~~~~~~~~  269 (538)
                      .-+.+++...|+.+.++.-...-..|.......+...+...++-+.++.-+++....+..++..++. .....+...|++
T Consensus        39 ~~~~Rs~iAlg~~~~vl~ei~~~~~~~l~av~~la~y~~~~~~~e~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~  118 (290)
T PF04733_consen   39 FYQYRSYIALGQYDSVLSEIKKSSSPELQAVRLLAEYLSSPSDKESALEELKELLADQAGESNEIVQLLAATILFHEGDY  118 (290)
T ss_dssp             HHHHHHHHHTT-HHHHHHHS-TTSSCCCHHHHHHHHHHCTSTTHHCHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHH
T ss_pred             HHHHHHHHHcCChhHHHHHhccCCChhHHHHHHHHHHHhCccchHHHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCH
Confidence            3445566666666665555544445555555555444443345555555555444333332332322 222345567888


Q ss_pred             HHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC-CcchHHHHHHHHHhcCCccHHHHHHHH
Q 044988          270 KLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR-NTVSWTSMITGFAKQGYAQEALLTFLG  348 (538)
Q Consensus       270 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~  348 (538)
                      +.|.+++..        +  .+.......+..|.+.++++.|.+.++.|.+- +..+...+..++..             
T Consensus       119 ~~AL~~l~~--------~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~~eD~~l~qLa~awv~-------------  175 (290)
T PF04733_consen  119 EEALKLLHK--------G--GSLELLALAVQILLKMNRPDLAEKELKNMQQIDEDSILTQLAEAWVN-------------  175 (290)
T ss_dssp             HHHHCCCTT--------T--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCCSCCHHHHHHHHHHHH-------------
T ss_pred             HHHHHHHHc--------c--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHH-------------
Confidence            877665431        1  34455556788899999999999999988763 33344444444432             


Q ss_pred             HHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCC
Q 044988          349 VLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNN  426 (538)
Q Consensus       349 ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~  426 (538)
                         ...-...+.+|..+|+++.+++  .+++.+.+.+..++...|++++|.+++++.. ..|+ ..++..++.+....|+
T Consensus       176 ---l~~g~e~~~~A~y~f~El~~~~--~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk  250 (290)
T PF04733_consen  176 ---LATGGEKYQDAFYIFEELSDKF--GSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGK  250 (290)
T ss_dssp             ---HHHTTTCCCHHHHHHHHHHCCS----SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-
T ss_pred             ---HHhCchhHHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCC
Confidence               1111236788889999987753  5678889999999999999999999998863 3344 5677777888788887


Q ss_pred             H-HHHHHHHHHchhccCCCCcc
Q 044988          427 A-ELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       427 ~-~~A~~~~~~~~~~~~p~~~~  447 (538)
                      . +.+.+++.++ ....|+++.
T Consensus       251 ~~~~~~~~l~qL-~~~~p~h~~  271 (290)
T PF04733_consen  251 PTEAAERYLSQL-KQSNPNHPL  271 (290)
T ss_dssp             TCHHHHHHHHHC-HHHTTTSHH
T ss_pred             ChhHHHHHHHHH-HHhCCCChH
Confidence            7 7788999999 777888654

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.75  E-value=0.00011  Score=79.76  Aligned_cols=333  Identities=11%  Similarity=0.016  Sum_probs=190.3

Q ss_pred             HHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC----CC---c-----hhHHHHHH
Q 044988          128 CARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA----RS---V-----VSWNSLLK  195 (538)
Q Consensus       128 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~----~~---~-----~~~~~li~  195 (538)
                      ....|+++.+..+++.+.......+..........+...|+   ++++...+.....    .+   .     .....+..
T Consensus       384 l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~---~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~  460 (903)
T PRK04841        384 LFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHR---YSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQ  460 (903)
T ss_pred             HHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCC---HHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHH
Confidence            34456666655555544211111222223334445556666   6666666554321    00   0     11112233


Q ss_pred             HHHhcCCHHHHHHHHccCCC----CCh----HHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CC-CCCHHHHHHHHHH
Q 044988          196 GYVKRGDIDGAWKIFDEMPH----RNV----VSWTTMISGCAQNGKSRQALSLFNEMRRA----RV-GLDQVALVAALSA  262 (538)
Q Consensus       196 ~~~~~g~~~~A~~~~~~m~~----~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~-~p~~~~~~~li~~  262 (538)
                      .+...|+++.|...+++...    .+.    ...+.+...+...|++++|...+++....    |- .+...++..+...
T Consensus       461 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~  540 (903)
T PRK04841        461 VAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEI  540 (903)
T ss_pred             HHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHH
Confidence            45678888888887776432    221    24455666778899999999999888652    11 1112344555667


Q ss_pred             HHccCChHHHHHHHHHHHHhccCCCCC---cchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCc
Q 044988          263 CAEIGDLKLGKWIHSYVEENFSVGREP---VLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYA  339 (538)
Q Consensus       263 ~~~~~~~~~a~~~~~~~~~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~  339 (538)
                      +...|+++.|...++.........+.+   .....+..+...+...|++++|...+.+...-..           ..+..
T Consensus       541 ~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~-----------~~~~~  609 (903)
T PRK04841        541 LFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLS-----------NYQPQ  609 (903)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhh-----------ccCch
Confidence            788999999999988877653322221   1223344566777888999999999887643100           00000


Q ss_pred             cHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc---CCCccH-H-HHHHHHHHhhhcCChHHHHHHHHhCCCC--CCH-
Q 044988          340 QEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW---GIKPRI-E-HYGCMVDLFSRAGLMDEAFSLVQNMPMK--PND-  411 (538)
Q Consensus       340 ~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~---~~~p~~-~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~--p~~-  411 (538)
                       .....+..+.......|+.+.|...+.......   +..... . .....+..+...|+.+.|.+++......  ... 
T Consensus       610 -~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~  688 (903)
T PRK04841        610 -QQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNH  688 (903)
T ss_pred             -HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccch
Confidence             000122223334445567777777776664321   111111 0 0111224455688999999998776411  111 


Q ss_pred             ---HHHHHHHHHHHhcCCHHHHHHHHHHchhcc------CCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 044988          412 ---AVLGSLLLGCRIHNNAELASQVAQKLVAEI------DPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       412 ---~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~------~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                         ..+..+..++...|++++|...++++. ..      .+....+.. .++.++.+.|+.++|...+.+..+..
T Consensus       689 ~~~~~~~~~a~~~~~~g~~~~A~~~l~~al-~~~~~~g~~~~~a~~~~-~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        689 FLQGQWRNIARAQILLGQFDEAEIILEELN-ENARSLRLMSDLNRNLI-LLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             hHHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HHHHHhCchHHHHHHHH-HHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence               113455667888999999999999885 21      122223355 77888999999999999999987643

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=98.75  E-value=1.9e-05  Score=75.55  Aligned_cols=190  Identities=15%  Similarity=0.122  Sum_probs=98.2

Q ss_pred             ccHHHHHHHHhccCChHHHHHHHHHHHHhCC-CCChh-HHHHHHHHHHccCChhHHHHHHhcCCC--C-CcchHHHHHHH
Q 044988           18 LTTRQIFSLLQIRNTTKTLFQIHSQIIINGF-SQKNY-ILAKLLAFYVTSGYLINAHKVFEKTEN--P-STAIWNQMIRG   92 (538)
Q Consensus        18 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~   92 (538)
                      ..+..+...+...++.+.+...+....+... .++.. ........+...|++++|...+++..+  | +...+.. ...
T Consensus         7 ~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~-~~~   85 (355)
T cd05804           7 LGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDYPRDLLALKL-HLG   85 (355)
T ss_pred             HHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHH-hHH
Confidence            3444555555556666665555555444332 22221 122223344566777777777766542  2 2223331 112


Q ss_pred             Hhc----CCCchHHHHHHHHhHhCCCCCCc-chHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcC
Q 044988           93 HAR----SETPEKSVYLYKQMIDKETEPDE-YTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSG  167 (538)
Q Consensus        93 ~~~----~~~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  167 (538)
                      +..    .+....+.+.++.  .....|+. .....+...+...|+++.|...+++..+.. +.+...+..+..++...|
T Consensus        86 ~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g  162 (355)
T cd05804          86 AFGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQG  162 (355)
T ss_pred             HHHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcC
Confidence            222    3334444444433  11112222 233344456677777777777777777764 444556666777777777


Q ss_pred             CCCChhHHHHHhhcCCCC-----Cc--hhHHHHHHHHHhcCCHHHHHHHHccCC
Q 044988          168 GECGVGCARLLFDDMPAR-----SV--VSWNSLLKGYVKRGDIDGAWKIFDEMP  214 (538)
Q Consensus       168 ~~~~~~~a~~~~~~~~~~-----~~--~~~~~li~~~~~~g~~~~A~~~~~~m~  214 (538)
                      +   +++|...+++..+.     +.  ..|..+...+...|++++|..++++..
T Consensus       163 ~---~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~  213 (355)
T cd05804         163 R---FKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHI  213 (355)
T ss_pred             C---HHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHh
Confidence            7   77777776665431     11  123345555666666666666666543

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=98.74  E-value=0.00011  Score=72.02  Aligned_cols=411  Identities=14%  Similarity=0.050  Sum_probs=238.0

Q ss_pred             CccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC----CCcchHHHHH
Q 044988           15 SKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN----PSTAIWNQMI   90 (538)
Q Consensus        15 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~----~~~~~~~~li   90 (538)
                      -++..|..+.-++..+|++..+-+.|++....-+. ....|..+...|...|.--.|..+.+.-.+    |+..+--.++
T Consensus       321 nd~ai~d~Lt~al~~~g~f~~lae~fE~~~~~~~~-~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lma  399 (799)
T KOG4162|consen  321 NDAAIFDHLTFALSRCGQFEVLAEQFEQALPFSFG-EHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLMA  399 (799)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhhh-hHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHHH
Confidence            35678888999999999999999999998876544 567888999999999999999999986553    3323333333


Q ss_pred             -HHHh-cCCCchHHHHHHHHhHhC--CC--CCCcchHHHHHHHHHccC-----------CcHHHHHHHHHHHHhCCCCch
Q 044988           91 -RGHA-RSETPEKSVYLYKQMIDK--ET--EPDEYTYSFLLSVCARCG-----------LFREGEQVHGRVLASGYCSNV  153 (538)
Q Consensus        91 -~~~~-~~~~~~~a~~~~~~m~~~--~~--~p~~~~~~~li~~~~~~~-----------~~~~a~~~~~~~~~~~~~~~~  153 (538)
                       ..|. +.+..+++++.-.+....  +.  ...+..|..+.-+|...-           ...++.+.+++..+.+ +.|.
T Consensus       400 sklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d-~~dp  478 (799)
T KOG4162|consen  400 SKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFD-PTDP  478 (799)
T ss_pred             HHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcC-CCCc
Confidence             3333 356777777777666551  11  123445555554443221           1345667777777665 2232


Q ss_pred             hHHhHHHHHHHhcCCCCChhHHHHHhhcCCC----CCchhHHHHHHHHHhcCCHHHHHHHHccCCCC---ChHHHHHHHH
Q 044988          154 FIRTNLMNLYLMSGGECGVGCARLLFDDMPA----RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR---NVVSWTTMIS  226 (538)
Q Consensus       154 ~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~----~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~li~  226 (538)
                      .+...+.--|+..++   ++.|.....+..+    .+...|..+.-.+...+++..|+.+.+...+.   |......-+.
T Consensus       479 ~~if~lalq~A~~R~---l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~  555 (799)
T KOG4162|consen  479 LVIFYLALQYAEQRQ---LTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIH  555 (799)
T ss_pred             hHHHHHHHHHHHHHh---HHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhh
Confidence            333334445556666   7777776665443    36677888877888888888888877764431   1111111222


Q ss_pred             HHHHcCCHHHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHh
Q 044988          227 GCAQNGKSRQALSLFNEMRRA--RVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYAS  304 (538)
Q Consensus       227 ~~~~~~~~~~a~~~~~~m~~~--g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  304 (538)
                      .-...++.++++.....+..-  ...|-..+           ++-....+....+.-.  .+.......++..+......
T Consensus       556 i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~-----------~~~g~~~~lk~~l~la--~~q~~~a~s~sr~ls~l~a~  622 (799)
T KOG4162|consen  556 IELTFNDREEALDTCIHKLALWEAEYGVQQT-----------LDEGKLLRLKAGLHLA--LSQPTDAISTSRYLSSLVAS  622 (799)
T ss_pred             hhhhcccHHHHHHHHHHHHHHHHhhhhHhhh-----------hhhhhhhhhhcccccC--cccccccchhhHHHHHHHHh
Confidence            233457777777777766541  00000000           0000000000000000  00011111122111111111


Q ss_pred             CC---CHHHHHHHHHhcCCCC------cchHHHHHHHHHhcCCccHHH--------------HHHHHHHHHhcccCcHHH
Q 044988          305 CG---EIEEAYGVFRKMQRRN------TVSWTSMITGFAKQGYAQEAL--------------LTFLGVLSACSHGGFVDE  361 (538)
Q Consensus       305 ~g---~~~~a~~~~~~m~~~~------~~~~~~li~~~~~~~~~~~a~--------------~~~~~ll~~~~~~~~~~~  361 (538)
                      .+   ..+.....+.....|+      ...|......+.+.+..++|.              ..|......+...|...+
T Consensus       623 ~~~~~~se~~Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~~~l~~~~~~~~G~~~~~~~~~~E  702 (799)
T KOG4162|consen  623 QLKSAGSELKLPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKIDPLSASVYYLRGLLLEVKGQLEE  702 (799)
T ss_pred             hhhhcccccccCcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhcchhhHHHHHHhhHHHHHHHhhHH
Confidence            11   1111111111111122      113334445555566666554              233333344555678888


Q ss_pred             HHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHH--HHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 044988          362 GRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFS--LVQNM-PMKP-NDAVLGSLLLGCRIHNNAELASQVAQK  436 (538)
Q Consensus       362 a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~--~~~~~-~~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~  436 (538)
                      |.+.|....   -+.|+ +.+..++..++.+.|+..-|..  ++..+ +..| +...|-.+...+.+.|+.++|.+.|..
T Consensus       703 A~~af~~Al---~ldP~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~a  779 (799)
T KOG4162|consen  703 AKEAFLVAL---ALDPDHVPSMTALAELLLELGSPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAECFQA  779 (799)
T ss_pred             HHHHHHHHH---hcCCCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchHHHHHHHHH
Confidence            888888776   45786 7788999999999998777777  77776 3444 588999999999999999999999999


Q ss_pred             chhccCCCCcc
Q 044988          437 LVAEIDPEQAA  447 (538)
Q Consensus       437 ~~~~~~p~~~~  447 (538)
                      + ..+.+.+|.
T Consensus       780 a-~qLe~S~PV  789 (799)
T KOG4162|consen  780 A-LQLEESNPV  789 (799)
T ss_pred             H-HhhccCCCc
Confidence            9 777776664

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=98.74  E-value=1.5e-06  Score=78.80  Aligned_cols=243  Identities=13%  Similarity=0.041  Sum_probs=121.9

Q ss_pred             HHccCChhHHHHHHhcCCCC----CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHH
Q 044988           62 YVTSGYLINAHKVFEKTENP----STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREG  137 (538)
Q Consensus        62 ~~~~g~~~~a~~~~~~~~~~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a  137 (538)
                      +.-.|++..++.-.+ ....    +......+.+++...|+++.++   .+..... .|.......+...+....+-+.+
T Consensus        11 ~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~vl---~ei~~~~-~~~l~av~~la~y~~~~~~~e~~   85 (290)
T PF04733_consen   11 QFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSVL---SEIKKSS-SPELQAVRLLAEYLSSPSDKESA   85 (290)
T ss_dssp             HHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHHH---HHS-TTS-SCCCHHHHHHHHHHCTSTTHHCH
T ss_pred             HHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHHH---HHhccCC-ChhHHHHHHHHHHHhCccchHHH
Confidence            344566666665444 1111    1223334556666666655433   3333322 45555554444444333333344


Q ss_pred             HHHHHHHHHhCCC-CchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCC
Q 044988          138 EQVHGRVLASGYC-SNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR  216 (538)
Q Consensus       138 ~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  216 (538)
                      ..-+++....... .+.........++...|+   +++|++++...  .+.......+..|.+.++++.|.+.++.|.+-
T Consensus        86 l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~---~~~AL~~l~~~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~  160 (290)
T PF04733_consen   86 LEELKELLADQAGESNEIVQLLAATILFHEGD---YEEALKLLHKG--GSLELLALAVQILLKMNRPDLAEKELKNMQQI  160 (290)
T ss_dssp             HHHHHHCCCTS---CHHHHHHHHHHHHCCCCH---HHHHHCCCTTT--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHhccccccHHHHHHHHHHHHHcCC---HHHHHHHHHcc--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            3333333222222 222333333344555666   77777666654  34455556666777777777777777776642


Q ss_pred             -ChHHHHHHHHHHH----HcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc
Q 044988          217 -NVVSWTTMISGCA----QNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL  291 (538)
Q Consensus       217 -~~~~~~~li~~~~----~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  291 (538)
                       +..+...+..++.    ..+.+.+|..+|+++.+ ...++..+.+.+..++...|++++|..++....+.     .|.+
T Consensus       161 ~eD~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~-~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~-----~~~~  234 (290)
T PF04733_consen  161 DEDSILTQLAEAWVNLATGGEKYQDAFYIFEELSD-KFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEK-----DPND  234 (290)
T ss_dssp             SCCHHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHC-CS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC------CCH
T ss_pred             CCcHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHh-ccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh-----ccCC
Confidence             1222333333332    23356777777777644 34566666666666677777777777776665543     4555


Q ss_pred             hhHHHHHHHHHHhCCCH-HHHHHHHHhcCC
Q 044988          292 VSLNNALIHMYASCGEI-EEAYGVFRKMQR  320 (538)
Q Consensus       292 ~~~~~~l~~~~~~~g~~-~~a~~~~~~m~~  320 (538)
                      ..+...++.+..-.|+. +.+.+.+.++..
T Consensus       235 ~d~LaNliv~~~~~gk~~~~~~~~l~qL~~  264 (290)
T PF04733_consen  235 PDTLANLIVCSLHLGKPTEAAERYLSQLKQ  264 (290)
T ss_dssp             HHHHHHHHHHHHHTT-TCHHHHHHHHHCHH
T ss_pred             HHHHHHHHHHHHHhCCChhHHHHHHHHHHH
Confidence            55555566665566655 556666666553

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=98.73  E-value=4e-05  Score=73.34  Aligned_cols=260  Identities=10%  Similarity=0.016  Sum_probs=158.9

Q ss_pred             hhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchH---HHHHHHHhcCCCchHHHHHHHHhHhCCCCCCc-chHHHH
Q 044988           52 NYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIW---NQMIRGHARSETPEKSVYLYKQMIDKETEPDE-YTYSFL  124 (538)
Q Consensus        52 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~---~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~~l  124 (538)
                      +..+..+...+...|+.+.+...+....   +++...+   ......+...|++++|.+.+++..+.  .|+. ..+.. 
T Consensus         6 ~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~--~P~~~~a~~~-   82 (355)
T cd05804           6 ALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDD--YPRDLLALKL-   82 (355)
T ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCcHHHHHH-
Confidence            3455566666667777777666655433   2232222   22233456789999999999998875  3443 34442 


Q ss_pred             HHHHH----ccCCcHHHHHHHHHHHHhCCCCc-hhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC---CCchhHHHHHHH
Q 044988          125 LSVCA----RCGLFREGEQVHGRVLASGYCSN-VFIRTNLMNLYLMSGGECGVGCARLLFDDMPA---RSVVSWNSLLKG  196 (538)
Q Consensus       125 i~~~~----~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~---~~~~~~~~li~~  196 (538)
                      ...+.    ..+..+.+.+.+..  ..+..|+ ......+...+...|+   +++|...+++..+   .+...+..+...
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~~~~~G~---~~~A~~~~~~al~~~p~~~~~~~~la~i  157 (355)
T cd05804          83 HLGAFGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFGLEEAGQ---YDRAEEAARRALELNPDDAWAVHAVAHV  157 (355)
T ss_pred             hHHHHHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHHHHHcCC---HHHHHHHHHHHHhhCCCCcHHHHHHHHH
Confidence            22222    24455555555544  1122233 3455667788999999   9999999998875   256678888899


Q ss_pred             HHhcCCHHHHHHHHccCCC-----CCh--HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC-CCCHHHH-H--HHHHHHHc
Q 044988          197 YVKRGDIDGAWKIFDEMPH-----RNV--VSWTTMISGCAQNGKSRQALSLFNEMRRARV-GLDQVAL-V--AALSACAE  265 (538)
Q Consensus       197 ~~~~g~~~~A~~~~~~m~~-----~~~--~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~-~p~~~~~-~--~li~~~~~  265 (538)
                      +...|++++|...+++...     ++.  ..|..+...+...|++++|..+|++...... .+..... .  .++.-+..
T Consensus       158 ~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  237 (355)
T cd05804         158 LEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLEL  237 (355)
T ss_pred             HHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHh
Confidence            9999999999999998654     222  2455788889999999999999999864322 2222221 1  22333334


Q ss_pred             cCChHHHHHHHHHHHHhccCC-CCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          266 IGDLKLGKWIHSYVEENFSVG-REPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       266 ~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      .|....+.+. +.+....... ..+...........++...|+.+.|...++.+..
T Consensus       238 ~g~~~~~~~w-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~  292 (355)
T cd05804         238 AGHVDVGDRW-EDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKG  292 (355)
T ss_pred             cCCCChHHHH-HHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence            4443333332 1111110000 0011222223567777889999999999988754

A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.69  E-value=1e-06  Score=82.99  Aligned_cols=231  Identities=13%  Similarity=0.081  Sum_probs=169.7

Q ss_pred             HHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCC
Q 044988          227 GCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCG  306 (538)
Q Consensus       227 ~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  306 (538)
                      -+.+.|++.+|.-.|+..++.. +-+...|..|-......++-..|+..+.+..+.     .|.+..+..+|.-.|...|
T Consensus       294 ~lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~L-----dP~NleaLmaLAVSytNeg  367 (579)
T KOG1125|consen  294 NLMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLEL-----DPTNLEALMALAVSYTNEG  367 (579)
T ss_pred             HHHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhc-----CCccHHHHHHHHHHHhhhh
Confidence            3567888888888888887653 335666777777777778888888888888886     7888888888888888888


Q ss_pred             CHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHH
Q 044988          307 EIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMV  386 (538)
Q Consensus       307 ~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~  386 (538)
                      .-..|...|+.-....+. |..+..+ ...++...   +     ..+.....+....++|-++....+..+|..+...|.
T Consensus       368 ~q~~Al~~L~~Wi~~~p~-y~~l~~a-~~~~~~~~---~-----~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LG  437 (579)
T KOG1125|consen  368 LQNQALKMLDKWIRNKPK-YVHLVSA-GENEDFEN---T-----KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLG  437 (579)
T ss_pred             hHHHHHHHHHHHHHhCcc-chhcccc-CccccccC---C-----cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhH
Confidence            888888888765321100 0000000 00000000   0     011111234555666666666546567888899999


Q ss_pred             HHhhhcCChHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChH
Q 044988          387 DLFSRAGLMDEAFSLVQNM-PMKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQ  464 (538)
Q Consensus       387 ~~~~~~g~~~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~  464 (538)
                      -.|--.|.+++|...|+.. .++|+ ..+||.|...++...+.++|+..|+++ .++.|....+.. .|+..|...|.++
T Consensus       438 VLy~ls~efdraiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rA-LqLqP~yVR~Ry-NlgIS~mNlG~yk  515 (579)
T KOG1125|consen  438 VLYNLSGEFDRAVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRA-LQLQPGYVRVRY-NLGISCMNLGAYK  515 (579)
T ss_pred             HHHhcchHHHHHHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHH-HhcCCCeeeeeh-hhhhhhhhhhhHH
Confidence            9999999999999999987 36665 679999999999999999999999999 999999999888 8999999999999


Q ss_pred             HHHHHHHHHHh
Q 044988          465 DVAAVRQKMIK  475 (538)
Q Consensus       465 ~A~~~~~~m~~  475 (538)
                      +|.+.|-....
T Consensus       516 EA~~hlL~AL~  526 (579)
T KOG1125|consen  516 EAVKHLLEALS  526 (579)
T ss_pred             HHHHHHHHHHH
Confidence            99998876653

>PF12854 PPR_1: PPR repeat

Probab=98.69  E-value=3e-08  Score=56.88  Aligned_cols=33  Identities=36%  Similarity=0.733  Sum_probs=29.5

Q ss_pred             CCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          374 GIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       374 ~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      |+.||..+|++||.+|++.|++++|.++|++|+
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            788999999999999999999999999998884

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.66  E-value=1.4e-05  Score=80.23  Aligned_cols=405  Identities=13%  Similarity=0.039  Sum_probs=213.0

Q ss_pred             hHHHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCC-CCCCcchHHHHHHHH
Q 044988           53 YILAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKE-TEPDEYTYSFLLSVC  128 (538)
Q Consensus        53 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~-~~p~~~~~~~li~~~  128 (538)
                      ..|..|-..|....+...|.+.|+...+   .+...+......|++..+++.|..+.-..-+.. ...-...|....-.|
T Consensus       493 paf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG~yy  572 (1238)
T KOG1127|consen  493 PAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRGPYY  572 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhccccc
Confidence            3566666666666666666666665553   344456666677777777777766632222110 000112233333445


Q ss_pred             HccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchh-HHHH--HHHHHhcCCHHH
Q 044988          129 ARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVS-WNSL--LKGYVKRGDIDG  205 (538)
Q Consensus       129 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~-~~~l--i~~~~~~g~~~~  205 (538)
                      ...++...+..-|+...+.. +.|...|..++.+|.++|.   +..|.++|.+...-++.. |...  .-..+..|.+.+
T Consensus       573 Lea~n~h~aV~~fQsALR~d-PkD~n~W~gLGeAY~~sGr---y~~AlKvF~kAs~LrP~s~y~~fk~A~~ecd~GkYke  648 (1238)
T KOG1127|consen  573 LEAHNLHGAVCEFQSALRTD-PKDYNLWLGLGEAYPESGR---YSHALKVFTKASLLRPLSKYGRFKEAVMECDNGKYKE  648 (1238)
T ss_pred             cCccchhhHHHHHHHHhcCC-chhHHHHHHHHHHHHhcCc---eehHHHhhhhhHhcCcHhHHHHHHHHHHHHHhhhHHH
Confidence            66666666666666666654 4555667777777777777   777777776655433222 2111  122344566666


Q ss_pred             HHHHHccCCC----------CChHHHHHHHHHHHHcCCHH--------------------------------HHHHHHHH
Q 044988          206 AWKIFDEMPH----------RNVVSWTTMISGCAQNGKSR--------------------------------QALSLFNE  243 (538)
Q Consensus       206 A~~~~~~m~~----------~~~~~~~~li~~~~~~~~~~--------------------------------~a~~~~~~  243 (538)
                      |...+.....          .-..++-.+...+.-.|-..                                .|..+|-.
T Consensus       649 ald~l~~ii~~~s~e~~~q~gLaE~~ir~akd~~~~gf~~kavd~~eksie~f~~~l~h~~~~~~~~Wi~asdac~~f~q  728 (1238)
T KOG1127|consen  649 ALDALGLIIYAFSLERTGQNGLAESVIRDAKDSAITGFQKKAVDFFEKSIESFIVSLIHSLQSDRLQWIVASDACYIFSQ  728 (1238)
T ss_pred             HHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHhhhhhHHHHHHHhHHHHHHHH
Confidence            6655554431          00111211111111112111                                22222222


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHccCCh---H---HHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHh----C----CCHH
Q 044988          244 MRRARVGLDQVALVAALSACAEIGDL---K---LGKWIHSYVEENFSVGREPVLVSLNNALIHMYAS----C----GEIE  309 (538)
Q Consensus       244 m~~~g~~p~~~~~~~li~~~~~~~~~---~---~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~----g~~~  309 (538)
                      .. .. .|+......+..-..+.+..   +   .+.+.+-.-.+      ...+...|..|+..|.+    +    .+..
T Consensus       729 ~e-~~-~vn~h~l~il~~q~e~~~~l~~~d~l~Lg~~c~~~hls------l~~~~~~WyNLGinylr~f~~l~et~~~~~  800 (1238)
T KOG1127|consen  729 EE-PS-IVNMHYLIILSKQLEKTGALKKNDLLFLGYECGIAHLS------LAIHMYPWYNLGINYLRYFLLLGETMKDAC  800 (1238)
T ss_pred             hc-cc-chHHHHHHHHHHHHHhcccCcchhHHHHHHHHhhHHHH------HhhccchHHHHhHHHHHHHHHcCCcchhHH
Confidence            21 01 22222222222212222222   1   11111111111      12223444445444443    2    2334


Q ss_pred             HHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHH--------------HHHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          310 EAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEAL--------------LTFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       310 ~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~--------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                      .|...+.+..+   .+..+|+.|.-. ...|.+.-|.              .+|..+.-.|....+++.|...|....  
T Consensus       801 ~Ai~c~KkaV~L~ann~~~WnaLGVl-sg~gnva~aQHCfIks~~sep~~~~~W~NlgvL~l~n~d~E~A~~af~~~q--  877 (1238)
T KOG1127|consen  801 TAIRCCKKAVSLCANNEGLWNALGVL-SGIGNVACAQHCFIKSRFSEPTCHCQWLNLGVLVLENQDFEHAEPAFSSVQ--  877 (1238)
T ss_pred             HHHHHHHHHHHHhhccHHHHHHHHHh-hccchhhhhhhhhhhhhhccccchhheeccceeEEecccHHHhhHHHHhhh--
Confidence            67777776554   577788877655 4445555554              344455556667789999999999887  


Q ss_pred             cCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhC-----C--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHch------
Q 044988          373 WGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNM-----P--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLV------  438 (538)
Q Consensus       373 ~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~-----~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~------  438 (538)
                       .+.| |...|--....-...|+.-++..+|..-     .  .-|+..-|-....-....|+.++-+...+++.      
T Consensus       878 -SLdP~nl~~WlG~Ali~eavG~ii~~~~lfaHs~el~~~~gka~~f~Yw~c~te~h~~Ng~~e~~I~t~~ki~sAs~al  956 (1238)
T KOG1127|consen  878 -SLDPLNLVQWLGEALIPEAVGRIIERLILFAHSDELCSKEGKAKKFQYWLCATEIHLQNGNIEESINTARKISSASLAL  956 (1238)
T ss_pred             -hcCchhhHHHHHHHHhHHHHHHHHHHHHHHHhhHHhhccccccchhhHHHHHHHHHHhccchHHHHHHhhhhhhhHHHH
Confidence             4466 5666665555556778888888888652     1  22454444444444566666655444433332      


Q ss_pred             ---hccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          439 ---AEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       439 ---~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                         .+..|+...+|. ..+......+.+++|.++..+..
T Consensus       957 ~~yf~~~p~~~fAy~-~~gstlEhL~ey~~a~ela~Rli  994 (1238)
T KOG1127|consen  957 SYYFLGHPQLCFAYA-ANGSTLEHLEEYRAALELATRLI  994 (1238)
T ss_pred             HHHHhcCcchhHHHH-HHHhHHHHHHHHHHHHHHHHHHH
Confidence               567788877787 77777778888888777766653

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.62  E-value=0.0003  Score=71.06  Aligned_cols=318  Identities=13%  Similarity=0.126  Sum_probs=180.4

Q ss_pred             HHHHHHHHHHHhCCC--CChhHHHHHHHHHHccCChhHHHHHHhcCC-CCCcch-----HHHHHHHHhcCCCchHHHHHH
Q 044988           35 TLFQIHSQIIINGFS--QKNYILAKLLAFYVTSGYLINAHKVFEKTE-NPSTAI-----WNQMIRGHARSETPEKSVYLY  106 (538)
Q Consensus        35 ~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-~~~~~~-----~~~li~~~~~~~~~~~a~~~~  106 (538)
                      .-+++.++..+.+++  .|+...+..+.++...+-+.+-+++++++. .|++.+     -|.||-...+ -+..+..+..
T Consensus       965 ~rRqLiDqVv~tal~E~~dPe~vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAik-ad~trVm~YI 1043 (1666)
T KOG0985|consen  965 YRRQLIDQVVQTALPETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTAIK-ADRTRVMEYI 1043 (1666)
T ss_pred             HHHHHHHHHHHhcCCccCChHHHHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHhh-cChHHHHHHH
Confidence            346778888877754  467778888899999999999999998876 444443     3344433333 3555666666


Q ss_pred             HHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCC
Q 044988          107 KQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARS  186 (538)
Q Consensus       107 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~  186 (538)
                      +++-..+ .|+      +...+...+-+++|..+|.+.     ..+....+.|+.   ..+.   ++.|.+.-++..+| 
T Consensus      1044 ~rLdnyD-a~~------ia~iai~~~LyEEAF~ifkkf-----~~n~~A~~VLie---~i~~---ldRA~efAe~~n~p- 1104 (1666)
T KOG0985|consen 1044 NRLDNYD-APD------IAEIAIENQLYEEAFAIFKKF-----DMNVSAIQVLIE---NIGS---LDRAYEFAERCNEP- 1104 (1666)
T ss_pred             HHhccCC-chh------HHHHHhhhhHHHHHHHHHHHh-----cccHHHHHHHHH---Hhhh---HHHHHHHHHhhCCh-
Confidence            6655432 222      233344555567777666654     233333333333   2233   56666655555443 


Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc
Q 044988          187 VVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEI  266 (538)
Q Consensus       187 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~  266 (538)
                       ..|..+..+-.+.|...+|++-|-+.  .|+..|.-++....+.|.+++-.+++...++..-.|...  +.+|-+|++.
T Consensus      1105 -~vWsqlakAQL~~~~v~dAieSyika--dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~AyAkt 1179 (1666)
T KOG0985|consen 1105 -AVWSQLAKAQLQGGLVKDAIESYIKA--DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIFAYAKT 1179 (1666)
T ss_pred             -HHHHHHHHHHHhcCchHHHHHHHHhc--CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHHHHHHh
Confidence             45777777777777777777766553  344567777777777777777777777666655555444  3566677777


Q ss_pred             CChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcC------------------------CCC
Q 044988          267 GDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQ------------------------RRN  322 (538)
Q Consensus       267 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~------------------------~~~  322 (538)
                      +++.+.+.+.           ..++..-...+.+-|...|.++.|.-+|..+.                        ..+
T Consensus      1180 ~rl~elE~fi-----------~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aRKAns 1248 (1666)
T KOG0985|consen 1180 NRLTELEEFI-----------AGPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAARKANS 1248 (1666)
T ss_pred             chHHHHHHHh-----------cCCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhccc
Confidence            7665544332           11122222244444445555555544443321                        023


Q ss_pred             cchHHHHHHHHHhcCCccHHH----------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhh
Q 044988          323 TVSWTSMITGFAKQGYAQEAL----------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSR  391 (538)
Q Consensus       323 ~~~~~~li~~~~~~~~~~~a~----------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~  391 (538)
                      ..+|.-+-.+|...+.+.-|.          .-...++..|...|-+++...+++...   |+.- ....|+.|.-.|.+
T Consensus      1249 ~ktWK~VcfaCvd~~EFrlAQiCGL~iivhadeLeeli~~Yq~rGyFeElIsl~Ea~L---GLERAHMgmfTELaiLYsk 1325 (1666)
T KOG0985|consen 1249 TKTWKEVCFACVDKEEFRLAQICGLNIIVHADELEELIEYYQDRGYFEELISLLEAGL---GLERAHMGMFTELAILYSK 1325 (1666)
T ss_pred             hhHHHHHHHHHhchhhhhHHHhcCceEEEehHhHHHHHHHHHhcCcHHHHHHHHHhhh---chhHHHHHHHHHHHHHHHh
Confidence            445555555555555554444          334455566666666666666665544   3332 23445555555554

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.58  E-value=5.3e-06  Score=85.86  Aligned_cols=204  Identities=13%  Similarity=0.135  Sum_probs=154.1

Q ss_pred             HHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 044988          255 ALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFA  334 (538)
Q Consensus       255 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~  334 (538)
                      .|..-|.-....++++.|+.+.+++...+.......-...|.++++.-..-|.-+...++|+++.+              
T Consensus      1460 ~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcq-------------- 1525 (1710)
T KOG1070|consen 1460 LWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQ-------------- 1525 (1710)
T ss_pred             HHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHH--------------
Confidence            344455555666677777777766666543333333445666666666666666667777766543              


Q ss_pred             hcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC---
Q 044988          335 KQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN---  410 (538)
Q Consensus       335 ~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~---  410 (538)
                          +-+|..+|..|...|.+.+..++|.++++.|.++++  -...+|..+++.+.+..+-+.|..++.+.. .-|-   
T Consensus      1526 ----ycd~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eH 1599 (1710)
T KOG1070|consen 1526 ----YCDAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEH 1599 (1710)
T ss_pred             ----hcchHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhh
Confidence                223335677777777777899999999999999876  457789999999999999999999998763 2233   


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCC
Q 044988          411 DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRK  480 (538)
Q Consensus       411 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~  480 (538)
                      .......+..-.+.|+.+++..+|+.. ..-.|.....|. .+++.-.++|+.+.++.+|++....++.+
T Consensus      1600 v~~IskfAqLEFk~GDaeRGRtlfEgl-l~ayPKRtDlW~-VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1600 VEFISKFAQLEFKYGDAERGRTLFEGL-LSAYPKRTDLWS-VYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             HHHHHHHHHHHhhcCCchhhHHHHHHH-HhhCccchhHHH-HHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            445556666778999999999999999 888999999899 99999999999999999999999988854

>PF12854 PPR_1: PPR repeat

Probab=98.56  E-value=6.7e-08  Score=55.44  Aligned_cols=32  Identities=25%  Similarity=0.394  Sum_probs=14.7

Q ss_pred             CCCCCcchHHHHHHHHHccCCcHHHHHHHHHH
Q 044988          113 ETEPDEYTYSFLLSVCARCGLFREGEQVHGRV  144 (538)
Q Consensus       113 ~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~  144 (538)
                      |+.||..||++||.+|++.|++++|.++|++|
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M   33 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM   33 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence            34444444444444444444444444444443

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=98.52  E-value=0.0001  Score=65.25  Aligned_cols=326  Identities=13%  Similarity=0.091  Sum_probs=211.5

Q ss_pred             cchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHH---HHHHccCCcHHHHHHHHHHHHhCCCCchh-HHhH
Q 044988           83 TAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLL---SVCARCGLFREGEQVHGRVLASGYCSNVF-IRTN  158 (538)
Q Consensus        83 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li---~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~  158 (538)
                      +.-.--+...+...|++..|+.-|....+    .|+..|.++.   ..|...|+-..|+.=+...++.  .||-. .--.
T Consensus        38 vekhlElGk~lla~~Q~sDALt~yHaAve----~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlel--KpDF~~ARiQ  111 (504)
T KOG0624|consen   38 VEKHLELGKELLARGQLSDALTHYHAAVE----GDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLEL--KPDFMAARIQ  111 (504)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHHc----CCchhHHHHHHHHHHHhhhcCCccchhhHHHHHhc--CccHHHHHHH
Confidence            33455677888889999999999998875    4444555554   4578889989998888888875  57643 3334


Q ss_pred             HHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHH
Q 044988          159 LMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQAL  238 (538)
Q Consensus       159 l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~  238 (538)
                      -...+.+.|.   ++.|..-|+...+.++.. +....++.+.-..++-            ......+..+...|+...|+
T Consensus       112 Rg~vllK~Ge---le~A~~DF~~vl~~~~s~-~~~~eaqskl~~~~e~------------~~l~~ql~s~~~~GD~~~ai  175 (504)
T KOG0624|consen  112 RGVVLLKQGE---LEQAEADFDQVLQHEPSN-GLVLEAQSKLALIQEH------------WVLVQQLKSASGSGDCQNAI  175 (504)
T ss_pred             hchhhhhccc---HHHHHHHHHHHHhcCCCc-chhHHHHHHHHhHHHH------------HHHHHHHHHHhcCCchhhHH
Confidence            4567889999   999999998877543211 1111111111111111            12223455566789999999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          239 SLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       239 ~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                      .....+.+- .+.|...|..-..+|...|++..|..-+..+.+.    ....+...| -+...+...|+.+.+....++.
T Consensus       176 ~~i~~llEi-~~Wda~l~~~Rakc~i~~~e~k~AI~Dlk~askL----s~DnTe~~y-kis~L~Y~vgd~~~sL~~iREC  249 (504)
T KOG0624|consen  176 EMITHLLEI-QPWDASLRQARAKCYIAEGEPKKAIHDLKQASKL----SQDNTEGHY-KISQLLYTVGDAENSLKEIREC  249 (504)
T ss_pred             HHHHHHHhc-CcchhHHHHHHHHHHHhcCcHHHHHHHHHHHHhc----cccchHHHH-HHHHHHHhhhhHHHHHHHHHHH
Confidence            999998873 2346666777778888999999998888887776    344444444 6778888899999998888887


Q ss_pred             CC--CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-----HHHHHHHHHHhhh
Q 044988          319 QR--RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-----IEHYGCMVDLFSR  391 (538)
Q Consensus       319 ~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-----~~~~~~l~~~~~~  391 (538)
                      .+  ||-..+-.   .|-+..+..+.+..    +......+++.++.+-.+...+.   .|.     ...+..+-.++..
T Consensus       250 LKldpdHK~Cf~---~YKklkKv~K~les----~e~~ie~~~~t~cle~ge~vlk~---ep~~~~ir~~~~r~~c~C~~~  319 (504)
T KOG0624|consen  250 LKLDPDHKLCFP---FYKKLKKVVKSLES----AEQAIEEKHWTECLEAGEKVLKN---EPEETMIRYNGFRVLCTCYRE  319 (504)
T ss_pred             HccCcchhhHHH---HHHHHHHHHHHHHH----HHHHHhhhhHHHHHHHHHHHHhc---CCcccceeeeeeheeeecccc
Confidence            76  33221111   11111111111100    12223456777777777777654   343     2234455566777


Q ss_pred             cCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          392 AGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       392 ~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      .|++.+|++...++. ..|| ..++---..+|.-...++.|+.-|+.+ .+.++++..
T Consensus       320 d~~~~eAiqqC~evL~~d~~dv~~l~dRAeA~l~dE~YD~AI~dye~A-~e~n~sn~~  376 (504)
T KOG0624|consen  320 DEQFGEAIQQCKEVLDIDPDDVQVLCDRAEAYLGDEMYDDAIHDYEKA-LELNESNTR  376 (504)
T ss_pred             cCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhhHHHHHHHHHHHHH-HhcCcccHH
Confidence            888888888887763 4555 667766777788888889999999988 888877755

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.51  E-value=4.5e-05  Score=76.71  Aligned_cols=132  Identities=8%  Similarity=0.074  Sum_probs=74.7

Q ss_pred             cCCCCCCCCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcC--------
Q 044988            7 IPANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKT--------   78 (538)
Q Consensus         7 ~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~--------   78 (538)
                      +..++...|   .|..+-..|+...+...|...|+........ +......+...|++..+++.|..+.-..        
T Consensus       485 lrld~~~ap---af~~LG~iYrd~~Dm~RA~kCf~KAFeLDat-daeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~  560 (1238)
T KOG1127|consen  485 LRLDVSLAP---AFAFLGQIYRDSDDMKRAKKCFDKAFELDAT-DAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFA  560 (1238)
T ss_pred             HhcccchhH---HHHHHHHHHHHHHHHHHHHHHHHHHhcCCch-hhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHH
Confidence            334454444   5666777777666777788888777665422 5566777777777777777776653221        


Q ss_pred             ----------------------------C---CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHH-
Q 044988           79 ----------------------------E---NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLS-  126 (538)
Q Consensus        79 ----------------------------~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~-  126 (538)
                                                  .   +.|...|..+..+|.+.|++..|+.+|.+...  +.|+. +|..... 
T Consensus       561 ~k~nW~~rG~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~--LrP~s-~y~~fk~A  637 (1238)
T KOG1127|consen  561 CKENWVQRGPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASL--LRPLS-KYGRFKEA  637 (1238)
T ss_pred             HHhhhhhccccccCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHh--cCcHh-HHHHHHHH
Confidence                                        1   12344555666666666666666666665554  22322 2222211 


Q ss_pred             -HHHccCCcHHHHHHHHHHH
Q 044988          127 -VCARCGLFREGEQVHGRVL  145 (538)
Q Consensus       127 -~~~~~~~~~~a~~~~~~~~  145 (538)
                       .-+..|.+.++...++...
T Consensus       638 ~~ecd~GkYkeald~l~~ii  657 (1238)
T KOG1127|consen  638 VMECDNGKYKEALDALGLII  657 (1238)
T ss_pred             HHHHHhhhHHHHHHHHHHHH
Confidence             1244555666655555544

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=98.50  E-value=0.0011  Score=62.60  Aligned_cols=128  Identities=5%  Similarity=0.081  Sum_probs=73.7

Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHh-CCCCCC-HHHHHHHHHHH
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQN-MPMKPN-DAVLGSLLLGC  421 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~-~~~~p~-~~~~~~l~~~~  421 (538)
                      +|...++.-.+..-+..|+.+|.+..+. +..+ .+.++++++.-|| .++.+-|.++|+- +..-+| ..-....++-+
T Consensus       368 v~~~~mn~irR~eGlkaaR~iF~kaR~~-~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkkf~d~p~yv~~YldfL  445 (656)
T KOG1914|consen  368 VYCQYMNFIRRAEGLKAARKIFKKARED-KRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKKFGDSPEYVLKYLDFL  445 (656)
T ss_pred             ehhHHHHHHHHhhhHHHHHHHHHHHhhc-cCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHhcCCChHHHHHHHHHH
Confidence            3445555555566667777777777666 4444 5666666766554 4556667777754 222233 33334555666


Q ss_pred             HhcCCHHHHHHHHHHch-hccCCCCc-ccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          422 RIHNNAELASQVAQKLV-AEIDPEQA-AGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       422 ~~~~~~~~A~~~~~~~~-~~~~p~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ...++-..|..+|++.. ..+.|+.. ..|. .+++-=..-|+...+.++-+++..
T Consensus       446 ~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~-r~l~yES~vGdL~si~~lekR~~~  500 (656)
T KOG1914|consen  446 SHLNDDNNARALFERVLTSVLSADKSKEIWD-RMLEYESNVGDLNSILKLEKRRFT  500 (656)
T ss_pred             HHhCcchhHHHHHHHHHhccCChhhhHHHHH-HHHHHHHhcccHHHHHHHHHHHHH
Confidence            66677777777777764 21233322 2244 455555566777777777666654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.48  E-value=0.00055  Score=74.47  Aligned_cols=329  Identities=12%  Similarity=0.008  Sum_probs=185.9

Q ss_pred             HHccCChhHHHHHHhcCCC----CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCC--C----CCCcc--hHHHHHHHHH
Q 044988           62 YVTSGYLINAHKVFEKTEN----PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKE--T----EPDEY--TYSFLLSVCA  129 (538)
Q Consensus        62 ~~~~g~~~~a~~~~~~~~~----~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~--~----~p~~~--~~~~li~~~~  129 (538)
                      ....|++..+...++.++.    .+..........+...|+++++..++......-  .    .+...  ....+...+.
T Consensus       384 l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~  463 (903)
T PRK04841        384 LFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAI  463 (903)
T ss_pred             HHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHH
Confidence            3445677777777766641    222233333444566788888888887765421  0    01111  1122233456


Q ss_pred             ccCCcHHHHHHHHHHHHhCCCCc----hhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC-------CC--chhHHHHHHH
Q 044988          130 RCGLFREGEQVHGRVLASGYCSN----VFIRTNLMNLYLMSGGECGVGCARLLFDDMPA-------RS--VVSWNSLLKG  196 (538)
Q Consensus       130 ~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~-------~~--~~~~~~li~~  196 (538)
                      ..|+++.|...++.....-...+    ....+.+...+...|+   ++.|...+++...       +.  ..++..+...
T Consensus       464 ~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~---~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~  540 (903)
T PRK04841        464 NDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGE---LARALAMMQQTEQMARQHDVYHYALWSLLQQSEI  540 (903)
T ss_pred             hCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCC---HHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHH
Confidence            77888888888888766311111    1244556667778888   8888887776552       11  1234455566


Q ss_pred             HHhcCCHHHHHHHHccCCC-------C----ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHC--CCCCC--HHHHHHHHH
Q 044988          197 YVKRGDIDGAWKIFDEMPH-------R----NVVSWTTMISGCAQNGKSRQALSLFNEMRRA--RVGLD--QVALVAALS  261 (538)
Q Consensus       197 ~~~~g~~~~A~~~~~~m~~-------~----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--g~~p~--~~~~~~li~  261 (538)
                      +...|+++.|...+++...       +    ....+..+...+...|++++|...+.+....  ...+.  ...+..+..
T Consensus       541 ~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~  620 (903)
T PRK04841        541 LFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAK  620 (903)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHH
Confidence            7788888888887766431       1    1123444555666778888888888876542  11121  233444555


Q ss_pred             HHHccCChHHHHHHHHHHHHhccCCCCCcchhH--HHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCc
Q 044988          262 ACAEIGDLKLGKWIHSYVEENFSVGREPVLVSL--NNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYA  339 (538)
Q Consensus       262 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~  339 (538)
                      .+...|+.+.|...+..........+.......  ....+..+...|+.+.|...+.....+.......           
T Consensus       621 ~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~-----------  689 (903)
T PRK04841        621 ISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHF-----------  689 (903)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchh-----------
Confidence            667788888888888777654222111111100  0112244456788888888887765432111000           


Q ss_pred             cHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh---cCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          340 QEALLTFLGVLSACSHGGFVDEGRQFFECMNQN---WGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       340 ~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~---~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                        ....+..+..++...|+.++|...++.....   .|..++ ..+...+..++.+.|+.++|...+.+..
T Consensus       690 --~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al  758 (903)
T PRK04841        690 --LQGQWRNIARAQILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEAL  758 (903)
T ss_pred             --HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence              0011122334445555666666666665442   132332 3466677788889999999998888763

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.44  E-value=4.2e-05  Score=79.51  Aligned_cols=218  Identities=11%  Similarity=0.103  Sum_probs=123.0

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHccCCC--------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 044988          188 VSWNSLLKGYVKRGDIDGAWKIFDEMPH--------RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAA  259 (538)
Q Consensus       188 ~~~~~li~~~~~~g~~~~A~~~~~~m~~--------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  259 (538)
                      ..|-..+......++.++|++++++...        .-.-.|.++++.-..-|.-+...++|+++.+.  .-....|..|
T Consensus      1459 i~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqy--cd~~~V~~~L 1536 (1710)
T KOG1070|consen 1459 ILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQY--CDAYTVHLKL 1536 (1710)
T ss_pred             hHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHh--cchHHHHHHH
Confidence            4455555555555555555555555432        11224555555555555566666666666552  1223345566


Q ss_pred             HHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CC---cchHHHHHHHHH
Q 044988          260 LSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RN---TVSWTSMITGFA  334 (538)
Q Consensus       260 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~---~~~~~~li~~~~  334 (538)
                      ...|.+.+..+.|.++++.|.+.     +.....+|...+..+.+.++-+.|..++.+..+  |.   +......+..-.
T Consensus      1537 ~~iy~k~ek~~~A~ell~~m~KK-----F~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEF 1611 (1710)
T KOG1070|consen 1537 LGIYEKSEKNDEADELLRLMLKK-----FGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEF 1611 (1710)
T ss_pred             HHHHHHhhcchhHHHHHHHHHHH-----hcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHh
Confidence            66666666666666666666665     335556666667777777776777777666554  22   222222222222


Q ss_pred             hcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC---CCCC-
Q 044988          335 KQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP---MKPN-  410 (538)
Q Consensus       335 ~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---~~p~-  410 (538)
                      +.                    |+.++++.+|+.....+  +-....|+.++++-.++|+.+.+..+|+++.   ..|- 
T Consensus      1612 k~--------------------GDaeRGRtlfEgll~ay--PKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kk 1669 (1710)
T KOG1070|consen 1612 KY--------------------GDAERGRTLFEGLLSAY--PKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKK 1669 (1710)
T ss_pred             hc--------------------CCchhhHHHHHHHHhhC--ccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhH
Confidence            33                    36666667777666542  2346677777777777777777777777763   2222 


Q ss_pred             -HHHHHHHHHHHHhcCCHHHHHHHH
Q 044988          411 -DAVLGSLLLGCRIHNNAELASQVA  434 (538)
Q Consensus       411 -~~~~~~l~~~~~~~~~~~~A~~~~  434 (538)
                       ...|...+..-...|+-..++.+=
T Consensus      1670 mKfffKkwLeyEk~~Gde~~vE~VK 1694 (1710)
T KOG1070|consen 1670 MKFFFKKWLEYEKSHGDEKNVEYVK 1694 (1710)
T ss_pred             hHHHHHHHHHHHHhcCchhhHHHHH
Confidence             345555555556666654444333

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.44  E-value=6.5e-06  Score=70.45  Aligned_cols=118  Identities=10%  Similarity=0.113  Sum_probs=97.9

Q ss_pred             CcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHH-HHhcCC--HHHHH
Q 044988          357 GFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLG-CRIHNN--AELAS  431 (538)
Q Consensus       357 ~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~-~~~~~~--~~~A~  431 (538)
                      ++.+++...++...+.  -+.|...|..|...|...|++++|...|++.. ..| +...+..+..+ +...|+  .++|.
T Consensus        53 ~~~~~~i~~l~~~L~~--~P~~~~~w~~Lg~~~~~~g~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~  130 (198)
T PRK10370         53 QTPEAQLQALQDKIRA--NPQNSEQWALLGEYYLWRNDYDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTR  130 (198)
T ss_pred             hhHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHH
Confidence            3566777777776654  13468899999999999999999999999874 445 46677777776 467777  59999


Q ss_pred             HHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          432 QVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       432 ~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      +++++. ....|++..++. .++..+.+.|++++|+..++++.+..-
T Consensus       131 ~~l~~a-l~~dP~~~~al~-~LA~~~~~~g~~~~Ai~~~~~aL~l~~  175 (198)
T PRK10370        131 EMIDKA-LALDANEVTALM-LLASDAFMQADYAQAIELWQKVLDLNS  175 (198)
T ss_pred             HHHHHH-HHhCCCChhHHH-HHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            999999 999999999888 999999999999999999999987533

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.43  E-value=4.6e-06  Score=80.82  Aligned_cols=206  Identities=15%  Similarity=0.138  Sum_probs=106.1

Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC--CCCcchHHHHHHHHhcCCC
Q 044988           21 RQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE--NPSTAIWNQMIRGHARSET   98 (538)
Q Consensus        21 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~~~   98 (538)
                      ..+...+.+.|-...|..++++         ...|..++-+|...|+..+|..+..+..  +|+...|..+.+......-
T Consensus       402 ~~laell~slGitksAl~I~Er---------lemw~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d~s~  472 (777)
T KOG1128|consen  402 RLLAELLLSLGITKSALVIFER---------LEMWDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHDPSL  472 (777)
T ss_pred             HHHHHHHHHcchHHHHHHHHHh---------HHHHHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhccChHH
Confidence            3444555555666666666653         4455566666666666666655544332  3555556666666555555


Q ss_pred             chHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHH
Q 044988           99 PEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLL  178 (538)
Q Consensus        99 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~  178 (538)
                      +++|+++++....+       +-..+.....+.++++++.+.++.-.+.+ +....+|-.+..+..+.++   +..|.+.
T Consensus       473 yEkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek---~q~av~a  541 (777)
T KOG1128|consen  473 YEKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEK---EQAAVKA  541 (777)
T ss_pred             HHHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhh---hHHHHHH
Confidence            66666665544321       11111111223456666666666555543 3344455555555555555   5555555


Q ss_pred             hhcCCC--C-CchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 044988          179 FDDMPA--R-SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRR  246 (538)
Q Consensus       179 ~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  246 (538)
                      |.....  | +...||.+-.+|.+.|+-.+|...+.+..+   .+...|...+....+.|.+++|++.+.++..
T Consensus       542 F~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~eda~~A~~rll~  615 (777)
T KOG1128|consen  542 FHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFEDAIKAYHRLLD  615 (777)
T ss_pred             HHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHHHHHHHHHHHH
Confidence            554442  2 334555555555555555555555555443   2222344444444555555555555555543

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=98.42  E-value=0.0011  Score=62.70  Aligned_cols=227  Identities=13%  Similarity=0.042  Sum_probs=147.1

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc------hhH
Q 044988          221 WTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL------VSL  294 (538)
Q Consensus       221 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~------~~~  294 (538)
                      .-.+.++..+..+++.|.+-+....+..  -+..-++..-.++...|.+......-....+.    |...-      ...
T Consensus       227 ek~lgnaaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~----gre~rad~klIak~  300 (539)
T KOG0548|consen  227 EKELGNAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEV----GRELRADYKLIAKA  300 (539)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHH----hHHHHHHHHHHHHH
Confidence            5567777888889999999998887754  44444555666678888777766655555444    22111      111


Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHhcCCC--CcchHHHHHHH--HHhc------CCccHHHHHHHHHHHHhcccCcHHHHHH
Q 044988          295 NNALIHMYASCGEIEEAYGVFRKMQRR--NTVSWTSMITG--FAKQ------GYAQEALLTFLGVLSACSHGGFVDEGRQ  364 (538)
Q Consensus       295 ~~~l~~~~~~~g~~~~a~~~~~~m~~~--~~~~~~~li~~--~~~~------~~~~~a~~~~~~ll~~~~~~~~~~~a~~  364 (538)
                      ...+..+|.+.++++.+...|.+...+  ++...+.+=.+  -.+.      -+++.|.... .-...+.+.|++..|..
T Consensus       301 ~~r~g~a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~lk~~Ek~~k~~e~~a~~~pe~A~e~r-~kGne~Fk~gdy~~Av~  379 (539)
T KOG0548|consen  301 LARLGNAYTKREDYEGAIKYYQKALTEHRTPDLLSKLKEAEKALKEAERKAYINPEKAEEER-EKGNEAFKKGDYPEAVK  379 (539)
T ss_pred             HHHhhhhhhhHHhHHHHHHHHHHHhhhhcCHHHHHHHHHHHHHHHHHHHHHhhChhHHHHHH-HHHHHHHhccCHHHHHH
Confidence            122344666778899999999886642  21122211100  0000      0111111111 22567788899999999


Q ss_pred             HHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhcc
Q 044988          365 FFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEI  441 (538)
Q Consensus       365 ~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  441 (538)
                      .|.+++..   .| |...|....-+|.+.|.+..|++=.+... ..|+ ...|..=..++....++++|.+.|++. .+.
T Consensus       380 ~YteAIkr---~P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~ea-le~  455 (539)
T KOG0548|consen  380 HYTEAIKR---DPEDARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEA-LEL  455 (539)
T ss_pred             HHHHHHhc---CCchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH-Hhc
Confidence            99999876   46 68899999999999999999988776653 3444 344544455566677999999999999 999


Q ss_pred             CCCCcccHHHHHHHHHHh
Q 044988          442 DPEQAAGYLALVANVYAA  459 (538)
Q Consensus       442 ~p~~~~~~~~~l~~~~~~  459 (538)
                      .|++.. +...+.+++..
T Consensus       456 dp~~~e-~~~~~~rc~~a  472 (539)
T KOG0548|consen  456 DPSNAE-AIDGYRRCVEA  472 (539)
T ss_pred             CchhHH-HHHHHHHHHHH
Confidence            999888 44255555443

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.42  E-value=5.4e-06  Score=78.25  Aligned_cols=227  Identities=14%  Similarity=0.028  Sum_probs=100.5

Q ss_pred             hcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChh
Q 044988           94 ARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVG  173 (538)
Q Consensus        94 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~  173 (538)
                      .+.|++.+|.-.|+...+.. +-+...|..|...-+..++-..|...+.+.++.. +-|..+...|.-.|...|.   -.
T Consensus       296 m~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~Ld-P~NleaLmaLAVSytNeg~---q~  370 (579)
T KOG1125|consen  296 MKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLELD-PTNLEALMALAVSYTNEGL---QN  370 (579)
T ss_pred             HhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcC-CccHHHHHHHHHHHhhhhh---HH
Confidence            44555555555555555442 2244455555555555555555555555555543 3344555555555555555   55


Q ss_pred             HHHHHhhcCCCCC-chhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH-CCCCC
Q 044988          174 CARLLFDDMPARS-VVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRR-ARVGL  251 (538)
Q Consensus       174 ~a~~~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-~g~~p  251 (538)
                      .|.++|+...... ...|..  .                  ..++...-+.  ..+.....+....++|-++.. .+..+
T Consensus       371 ~Al~~L~~Wi~~~p~y~~l~--~------------------a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~  428 (579)
T KOG1125|consen  371 QALKMLDKWIRNKPKYVHLV--S------------------AGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKI  428 (579)
T ss_pred             HHHHHHHHHHHhCccchhcc--c------------------cCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCC
Confidence            5555554432100 000000  0                  0000000000  011111222333333333332 23223


Q ss_pred             CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CC-cchHHH
Q 044988          252 DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RN-TVSWTS  328 (538)
Q Consensus       252 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~-~~~~~~  328 (538)
                      |......|--.|--.|++++|.+.|+.+++.     .|.+..+||.|...++...+.++|+..|++..+  |+ +.+...
T Consensus       429 DpdvQ~~LGVLy~ls~efdraiDcf~~AL~v-----~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyN  503 (579)
T KOG1125|consen  429 DPDVQSGLGVLYNLSGEFDRAVDCFEAALQV-----KPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYN  503 (579)
T ss_pred             ChhHHhhhHHHHhcchHHHHHHHHHHHHHhc-----CCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehh
Confidence            3333334443444455555555555555553     455555555555555555555555555555443  32 234444


Q ss_pred             HHHHHHhcCCccHHHHHHHHHHHH
Q 044988          329 MITGFAKQGYAQEALLTFLGVLSA  352 (538)
Q Consensus       329 li~~~~~~~~~~~a~~~~~~ll~~  352 (538)
                      |.-.|...|.+.+|...|...|..
T Consensus       504 lgIS~mNlG~ykEA~~hlL~AL~m  527 (579)
T KOG1125|consen  504 LGISCMNLGAYKEAVKHLLEALSM  527 (579)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHHh
Confidence            444555555555555444444443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.40  E-value=3.4e-05  Score=68.83  Aligned_cols=98  Identities=12%  Similarity=0.006  Sum_probs=61.5

Q ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc
Q 044988          216 RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD----QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL  291 (538)
Q Consensus       216 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  291 (538)
                      .....+..+...+.+.|++++|...|+++...  .|+    ...+..+..++...|+++.|...++.+.+.     .|.+
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~-----~p~~  103 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESR--YPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRL-----HPNH  103 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH-----CcCC
Confidence            34455666667777777788887777777653  232    134556666777777788887777777765     3322


Q ss_pred             hh---HHHHHHHHHHhC--------CCHHHHHHHHHhcCC
Q 044988          292 VS---LNNALIHMYASC--------GEIEEAYGVFRKMQR  320 (538)
Q Consensus       292 ~~---~~~~l~~~~~~~--------g~~~~a~~~~~~m~~  320 (538)
                      ..   .+..+..++...        |+++.|.+.|+++.+
T Consensus       104 ~~~~~a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  143 (235)
T TIGR03302       104 PDADYAYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIR  143 (235)
T ss_pred             CchHHHHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHH
Confidence            22   333444555443        667777777777654

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.40  E-value=5.6e-06  Score=66.90  Aligned_cols=106  Identities=10%  Similarity=-0.059  Sum_probs=87.6

Q ss_pred             HHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhcc
Q 044988          364 QFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEI  441 (538)
Q Consensus       364 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  441 (538)
                      .++++..+   +.|+.  +..+...+...|++++|...|+... ..| +...|..+..++...|++++|...|+++ ..+
T Consensus        14 ~~~~~al~---~~p~~--~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~A-l~l   87 (144)
T PRK15359         14 DILKQLLS---VDPET--VYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHA-LML   87 (144)
T ss_pred             HHHHHHHH---cCHHH--HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHH-Hhc
Confidence            45555553   35654  5567788889999999999998874 344 5778888888999999999999999999 899


Q ss_pred             CCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          442 DPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       442 ~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      .|+++..+. .++.++.+.|++++|+..+++..+.
T Consensus        88 ~p~~~~a~~-~lg~~l~~~g~~~eAi~~~~~Al~~  121 (144)
T PRK15359         88 DASHPEPVY-QTGVCLKMMGEPGLAREAFQTAIKM  121 (144)
T ss_pred             CCCCcHHHH-HHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            999999888 9999999999999999999998764

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.37  E-value=7.2e-05  Score=66.75  Aligned_cols=189  Identities=11%  Similarity=-0.023  Sum_probs=127.6

Q ss_pred             CCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc---hhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CC-cc
Q 044988          251 LDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL---VSLNNALIHMYASCGEIEEAYGVFRKMQR--RN-TV  324 (538)
Q Consensus       251 p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~-~~  324 (538)
                      .....+..+...+...|+++.|...++.+.+.     .|.+   ...+..+..++.+.|++++|...++++.+  |+ ..
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~-----~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~  105 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESR-----YPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPD  105 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCc
Confidence            34556777778889999999999999999886     3433   24566788999999999999999999875  32 21


Q ss_pred             ---hHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccH-HHHHHHHHHhhhcCChHHHHH
Q 044988          325 ---SWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRI-EHYGCMVDLFSRAGLMDEAFS  400 (538)
Q Consensus       325 ---~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~A~~  400 (538)
                         ++..+...+...            +.......|+.+.|.+.|+.+.+.   .|+. ..+..+.....    ..... 
T Consensus       106 ~~~a~~~~g~~~~~~------------~~~~~~~~~~~~~A~~~~~~~~~~---~p~~~~~~~a~~~~~~----~~~~~-  165 (235)
T TIGR03302       106 ADYAYYLRGLSNYNQ------------IDRVDRDQTAAREAFEAFQELIRR---YPNSEYAPDAKKRMDY----LRNRL-  165 (235)
T ss_pred             hHHHHHHHHHHHHHh------------cccccCCHHHHHHHHHHHHHHHHH---CCCChhHHHHHHHHHH----HHHHH-
Confidence               233333333222            011122346788899999998866   4543 23332221111    11110 


Q ss_pred             HHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCc---ccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          401 LVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQA---AGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       401 ~~~~~~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                                ......+...+.+.|++++|...++++ ....|+.+   ..+. .++.++.+.|++++|..+++.+...
T Consensus       166 ----------~~~~~~~a~~~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~a~~-~l~~~~~~lg~~~~A~~~~~~l~~~  232 (235)
T TIGR03302       166 ----------AGKELYVARFYLKRGAYVAAINRFETV-VENYPDTPATEEALA-RLVEAYLKLGLKDLAQDAAAVLGAN  232 (235)
T ss_pred             ----------HHHHHHHHHHHHHcCChHHHHHHHHHH-HHHCCCCcchHHHHH-HHHHHHHHcCCHHHHHHHHHHHHhh
Confidence                      011124556688999999999999999 77766653   4567 8899999999999999999888754

Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.33  E-value=0.00018  Score=62.43  Aligned_cols=197  Identities=11%  Similarity=-0.006  Sum_probs=141.7

Q ss_pred             hHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhH-HHHHH
Q 044988           85 IWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTN-LMNLY  163 (538)
Q Consensus        85 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~-l~~~~  163 (538)
                      -+.+++..+.+..+++.|++++..-.++. +.+....+.|..+|-...++..|-..++++-..  .|...-|.. -...+
T Consensus        12 eftaviy~lI~d~ry~DaI~~l~s~~Er~-p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~AQSL   88 (459)
T KOG4340|consen   12 EFTAVVYRLIRDARYADAIQLLGSELERS-PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQAQSL   88 (459)
T ss_pred             chHHHHHHHHHHhhHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHHHHH
Confidence            46777877888899999999998877763 336778888888889999999999999998775  344333321 23445


Q ss_pred             HhcCCCCChhHHHHHhhcCCCC-CchhHHHHHHH--HHhcCCHHHHHHHHccCC-CCChHHHHHHHHHHHHcCCHHHHHH
Q 044988          164 LMSGGECGVGCARLLFDDMPAR-SVVSWNSLLKG--YVKRGDIDGAWKIFDEMP-HRNVVSWTTMISGCAQNGKSRQALS  239 (538)
Q Consensus       164 ~~~g~~~~~~~a~~~~~~~~~~-~~~~~~~li~~--~~~~g~~~~A~~~~~~m~-~~~~~~~~~li~~~~~~~~~~~a~~  239 (538)
                      .+.+.   +.+|+++...|... +...-..-+.+  .-..+++..+..+.++.+ +.+..+.+.......+.|+++.|++
T Consensus        89 Y~A~i---~ADALrV~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvq  165 (459)
T KOG4340|consen   89 YKACI---YADALRVAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQ  165 (459)
T ss_pred             HHhcc---cHHHHHHHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHH
Confidence            56677   88888888888763 32222222222  245788888999999888 4666677777667778899999999


Q ss_pred             HHHHHHHC-CCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchh
Q 044988          240 LFNEMRRA-RVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVS  293 (538)
Q Consensus       240 ~~~~m~~~-g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  293 (538)
                      -|+...+- |..| ...|+..+ ++.+.++.+.|.+...++.+.    |+...+.
T Consensus       166 kFqaAlqvsGyqp-llAYniAL-aHy~~~qyasALk~iSEIieR----G~r~HPE  214 (459)
T KOG4340|consen  166 KFQAALQVSGYQP-LLAYNLAL-AHYSSRQYASALKHISEIIER----GIRQHPE  214 (459)
T ss_pred             HHHHHHhhcCCCc-hhHHHHHH-HHHhhhhHHHHHHHHHHHHHh----hhhcCCc
Confidence            99988775 5554 45666555 455678888998888888887    6655544

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.28  E-value=2.1e-05  Score=80.80  Aligned_cols=229  Identities=10%  Similarity=0.028  Sum_probs=142.0

Q ss_pred             HHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CCcchHHHHHHH
Q 044988          255 ALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RNTVSWTSMITG  332 (538)
Q Consensus       255 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~li~~  332 (538)
                      .+..|+..+...++++.|.++.+...+.     .|.....|-.+...+.+.++...+..+  .+..  +...-|+.+-..
T Consensus        33 a~~~Li~~~~~~~~~deai~i~~~~l~~-----~P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~~~~~~~~~~~ve~~  105 (906)
T PRK14720         33 ELDDLIDAYKSENLTDEAKDICEEHLKE-----HKKSISALYISGILSLSRRPLNDSNLL--NLIDSFSQNLKWAIVEHI  105 (906)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHh-----CCcceehHHHHHHHHHhhcchhhhhhh--hhhhhcccccchhHHHHH
Confidence            3444444444555555555555544443     444444444444455566665555555  2222  222223333333


Q ss_pred             HHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCH
Q 044988          333 FAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPND  411 (538)
Q Consensus       333 ~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~  411 (538)
                      |...++...-...+..+..+|.+.|+.+++..+|+++.+-   .| |..+.|.+...|... ++++|.+++.+..     
T Consensus       106 ~~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~---D~~n~~aLNn~AY~~ae~-dL~KA~~m~~KAV-----  176 (906)
T PRK14720        106 CDKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKA---DRDNPEIVKKLATSYEEE-DKEKAITYLKKAI-----  176 (906)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhc---CcccHHHHHHHHHHHHHh-hHHHHHHHHHHHH-----
Confidence            4444444444456677788888889999999999999965   45 688999999999999 9999999988753     


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH-------H------------HHHHHHHhcCChHHHHHHHHH
Q 044988          412 AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL-------A------------LVANVYAAAKRWQDVAAVRQK  472 (538)
Q Consensus       412 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~-------~------------~l~~~~~~~g~~~~A~~~~~~  472 (538)
                             ..+...+++..+.++|.++ ....|++...+.       .            -+-..|...++|++++.+++.
T Consensus       177 -------~~~i~~kq~~~~~e~W~k~-~~~~~~d~d~f~~i~~ki~~~~~~~~~~~~~~~l~~~y~~~~~~~~~i~iLK~  248 (906)
T PRK14720        177 -------YRFIKKKQYVGIEEIWSKL-VHYNSDDFDFFLRIERKVLGHREFTRLVGLLEDLYEPYKALEDWDEVIYILKK  248 (906)
T ss_pred             -------HHHHhhhcchHHHHHHHHH-HhcCcccchHHHHHHHHHHhhhccchhHHHHHHHHHHHhhhhhhhHHHHHHHH
Confidence                   2355666777888888887 777777666322       0            122556677889999999999


Q ss_pred             HHhCCCCCCCceeEEEECCEEEEEEeCCCCCcchHHHHHH
Q 044988          473 MIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKT  512 (538)
Q Consensus       473 m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  512 (538)
                      +.+..-.    -.| ...+.+..|...|..|+..++.+.+
T Consensus       249 iL~~~~~----n~~-a~~~l~~~y~~kY~~~~~~ee~l~~  283 (906)
T PRK14720        249 ILEHDNK----NNK-AREELIRFYKEKYKDHSLLEDYLKM  283 (906)
T ss_pred             HHhcCCc----chh-hHHHHHHHHHHHccCcchHHHHHHH
Confidence            9874332    112 1222223344446777777766554

>PLN02789 farnesyltranstransferase

Probab=98.28  E-value=0.0004  Score=64.03  Aligned_cols=222  Identities=12%  Similarity=0.065  Sum_probs=122.5

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHH-HHHHHHHHHccC-ChHHHHHHHHHHHHhccCCCCCcchhHHHHHH
Q 044988          222 TTMISGCAQNGKSRQALSLFNEMRRARVGLDQVA-LVAALSACAEIG-DLKLGKWIHSYVEENFSVGREPVLVSLNNALI  299 (538)
Q Consensus       222 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~-~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~  299 (538)
                      +.+-..+...++.++|+.++.++.+  +.|+..| +..--.++...| +++++...++.+.+.     .|.+..+|+...
T Consensus        41 ~~~ra~l~~~e~serAL~lt~~aI~--lnP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~-----npknyqaW~~R~  113 (320)
T PLN02789         41 DYFRAVYASDERSPRALDLTADVIR--LNPGNYTVWHFRRLCLEALDADLEEELDFAEDVAED-----NPKNYQIWHHRR  113 (320)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHHHHH--HCchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHH-----CCcchHHhHHHH
Confidence            3333444555666777777776665  3444332 333333333444 456666666666664     556656666555


Q ss_pred             HHHHhCCCH--HHHHHHHHhcCCC---CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcC
Q 044988          300 HMYASCGEI--EEAYGVFRKMQRR---NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWG  374 (538)
Q Consensus       300 ~~~~~~g~~--~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  374 (538)
                      ..+.+.|+.  +++..+++++.+.   |..+|+.....+...|                    +++++++.++++++. .
T Consensus       114 ~~l~~l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~--------------------~~~eeL~~~~~~I~~-d  172 (320)
T PLN02789        114 WLAEKLGPDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTLG--------------------GWEDELEYCHQLLEE-D  172 (320)
T ss_pred             HHHHHcCchhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhh--------------------hHHHHHHHHHHHHHH-C
Confidence            555555542  4556666665543   3334444333333333                    555666666666654 1


Q ss_pred             CCccHHHHHHHHHHhhhc---CCh----HHHHHHHHhC-CCCCC-HHHHHHHHHHHHhc----CCHHHHHHHHHHchhcc
Q 044988          375 IKPRIEHYGCMVDLFSRA---GLM----DEAFSLVQNM-PMKPN-DAVLGSLLLGCRIH----NNAELASQVAQKLVAEI  441 (538)
Q Consensus       375 ~~p~~~~~~~l~~~~~~~---g~~----~~A~~~~~~~-~~~p~-~~~~~~l~~~~~~~----~~~~~A~~~~~~~~~~~  441 (538)
                       .-|..+|+....++.+.   |+.    +++++...++ ...|+ ...|+.+...+...    ++..+|.+.+.+. ...
T Consensus       173 -~~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~-~~~  250 (320)
T PLN02789        173 -VRNNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEV-LSK  250 (320)
T ss_pred             -CCchhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHh-hcc
Confidence             22455555555444433   222    3455555333 33343 56677666666552    3345677777777 667


Q ss_pred             CCCCcccHHHHHHHHHHhcC------------------ChHHHHHHHHHHH
Q 044988          442 DPEQAAGYLALVANVYAAAK------------------RWQDVAAVRQKMI  474 (538)
Q Consensus       442 ~p~~~~~~~~~l~~~~~~~g------------------~~~~A~~~~~~m~  474 (538)
                      .|.++.+.. .|+++|+...                  ..++|.++++.+.
T Consensus       251 ~~~s~~al~-~l~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~  300 (320)
T PLN02789        251 DSNHVFALS-DLLDLLCEGLQPTAEFRDTVDTLAEELSDSTLAQAVCSELE  300 (320)
T ss_pred             cCCcHHHHH-HHHHHHHhhhccchhhhhhhhccccccccHHHHHHHHHHHH
Confidence            777777666 7888887632                  2367888888873

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.25  E-value=0.00021  Score=73.68  Aligned_cols=232  Identities=10%  Similarity=0.041  Sum_probs=156.6

Q ss_pred             CchhHHHHHHHHHhcCCHHHHHHHHccCCC--CChH-HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 044988          186 SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--RNVV-SWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSA  262 (538)
Q Consensus       186 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~-~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  262 (538)
                      +...|..|+..+...+++++|.++.+...+  |+.. .|-.+...+.+.++.+++..+  .+.               ..
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l---------------~~   92 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRPLNDSNLL--NLI---------------DS   92 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcchhhhhhh--hhh---------------hh
Confidence            556778888888888888888888876543  4333 344444456666665555544  222               22


Q ss_pred             HHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCc
Q 044988          263 CAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYA  339 (538)
Q Consensus       263 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~  339 (538)
                      .....++.....++..+..      .+.+..++..+..+|.+.|+.++|..+++++.+   .|+...|.+...|... +.
T Consensus        93 ~~~~~~~~~ve~~~~~i~~------~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL  165 (906)
T PRK14720         93 FSQNLKWAIVEHICDKILL------YGENKLALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DK  165 (906)
T ss_pred             cccccchhHHHHHHHHHHh------hhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hH
Confidence            2223333333333344433      344445666899999999999999999999887   4678889999999988 99


Q ss_pred             cHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHH
Q 044988          340 QEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLL  418 (538)
Q Consensus       340 ~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~  418 (538)
                      ++|...+...+..+...+++..+.++|.++...   .|+ ...+-.+.+.....-..            .--..++--+-
T Consensus       166 ~KA~~m~~KAV~~~i~~kq~~~~~e~W~k~~~~---~~~d~d~f~~i~~ki~~~~~~------------~~~~~~~~~l~  230 (906)
T PRK14720        166 EKAITYLKKAIYRFIKKKQYVGIEEIWSKLVHY---NSDDFDFFLRIERKVLGHREF------------TRLVGLLEDLY  230 (906)
T ss_pred             HHHHHHHHHHHHHHHhhhcchHHHHHHHHHHhc---CcccchHHHHHHHHHHhhhcc------------chhHHHHHHHH
Confidence            999999999999999999999999999999865   453 33333333322222111            12234444555


Q ss_pred             HHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHH
Q 044988          419 LGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYA  458 (538)
Q Consensus       419 ~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~  458 (538)
                      ..|...++++++..+++.+ .+..|.+..+.. -++.+|.
T Consensus       231 ~~y~~~~~~~~~i~iLK~i-L~~~~~n~~a~~-~l~~~y~  268 (906)
T PRK14720        231 EPYKALEDWDEVIYILKKI-LEHDNKNNKARE-ELIRFYK  268 (906)
T ss_pred             HHHhhhhhhhHHHHHHHHH-HhcCCcchhhHH-HHHHHHH
Confidence            6677778888888888888 888888877666 6666655

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.25  E-value=2.5e-05  Score=63.14  Aligned_cols=102  Identities=10%  Similarity=0.005  Sum_probs=84.9

Q ss_pred             HHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCH
Q 044988          351 SACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MK-PNDAVLGSLLLGCRIHNNA  427 (538)
Q Consensus       351 ~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~-p~~~~~~~l~~~~~~~~~~  427 (538)
                      .++...|++++|...|+.....   .| +...|..+..++.+.|++++|...|+... .. .+...+..+..++...|++
T Consensus        32 ~~~~~~g~~~~A~~~~~~al~~---~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~~~g~~  108 (144)
T PRK15359         32 YASWQEGDYSRAVIDFSWLVMA---QPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEPVYQTGVCLKMMGEP  108 (144)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHc---CCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCH
Confidence            3445556888888999998854   55 68899999999999999999999999884 33 4578888999999999999


Q ss_pred             HHHHHHHHHchhccCCCCcccHHHHHHHHH
Q 044988          428 ELASQVAQKLVAEIDPEQAAGYLALVANVY  457 (538)
Q Consensus       428 ~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~  457 (538)
                      ++|...|++. ....|+++..+. ..+.++
T Consensus       109 ~eAi~~~~~A-l~~~p~~~~~~~-~~~~~~  136 (144)
T PRK15359        109 GLAREAFQTA-IKMSYADASWSE-IRQNAQ  136 (144)
T ss_pred             HHHHHHHHHH-HHhCCCChHHHH-HHHHHH
Confidence            9999999999 999999998555 665543

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.23  E-value=1.9e-06  Score=50.32  Aligned_cols=34  Identities=29%  Similarity=0.629  Sum_probs=26.8

Q ss_pred             hHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCc
Q 044988           85 IWNQMIRGHARSETPEKSVYLYKQMIDKETEPDE  118 (538)
Q Consensus        85 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~  118 (538)
                      +||.+|.+|++.|++++|.++|++|.+.|+.||.
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            6788888888888888888888888887877763

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.22  E-value=2.4e-06  Score=49.90  Aligned_cols=34  Identities=35%  Similarity=0.629  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD  252 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~  252 (538)
                      .+||++|.+|++.|++++|.++|++|.+.|+.||
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~   34 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPD   34 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence            3799999999999999999999999999999997

This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.20  E-value=0.00055  Score=58.72  Aligned_cols=170  Identities=14%  Similarity=0.065  Sum_probs=98.5

Q ss_pred             HHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCC-C
Q 044988          139 QVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR-N  217 (538)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~-~  217 (538)
                      ++.+.+.......+......-...|+..|+   +++|.+......  +......-+..+.+..+++-|...+++|.+- +
T Consensus        94 ~l~E~~a~~~~~sn~i~~l~aa~i~~~~~~---~deAl~~~~~~~--~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~ide  168 (299)
T KOG3081|consen   94 SLYELVADSTDGSNLIDLLLAAIIYMHDGD---FDEALKALHLGE--NLEAAALNVQILLKMHRFDLAEKELKKMQQIDE  168 (299)
T ss_pred             HHHHHHHhhccchhHHHHHHhhHHhhcCCC---hHHHHHHHhccc--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHccch
Confidence            344444444334444444445556677777   777777776632  2333333344556667777777777777763 3


Q ss_pred             hHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchh
Q 044988          218 VVSWTTMISGCAQ----NGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVS  293 (538)
Q Consensus       218 ~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  293 (538)
                      ..|.+.|..++.+    .+...+|.-+|++|.+. ..|+..+.+-...++...+++++|..+++.....     .+.++.
T Consensus       169 d~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~k-----d~~dpe  242 (299)
T KOG3081|consen  169 DATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDK-----DAKDPE  242 (299)
T ss_pred             HHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhc-----cCCCHH
Confidence            4455656655554    34677788888877543 5677777777777777777787777777777765     333343


Q ss_pred             HHHHHHHHHHhCC-CHHHHHHHHHhcC
Q 044988          294 LNNALIHMYASCG-EIEEAYGVFRKMQ  319 (538)
Q Consensus       294 ~~~~l~~~~~~~g-~~~~a~~~~~~m~  319 (538)
                      +...++-.-.-.| +.+...+.+..+.
T Consensus       243 tL~Nliv~a~~~Gkd~~~~~r~l~QLk  269 (299)
T KOG3081|consen  243 TLANLIVLALHLGKDAEVTERNLSQLK  269 (299)
T ss_pred             HHHHHHHHHHHhCCChHHHHHHHHHHH
Confidence            3333333333333 3333444444444

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=98.20  E-value=2.9e-05  Score=72.89  Aligned_cols=120  Identities=17%  Similarity=0.187  Sum_probs=100.8

Q ss_pred             HHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcC
Q 044988          348 GVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHN  425 (538)
Q Consensus       348 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~  425 (538)
                      .++..+...++++.|..+|+++.+.   .|+.  ...++..+...++-.+|.+++++.. ..| +...+......+.+.+
T Consensus       174 ~Ll~~l~~t~~~~~ai~lle~L~~~---~pev--~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~k~  248 (395)
T PF09295_consen  174 TLLKYLSLTQRYDEAIELLEKLRER---DPEV--AVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLLSKK  248 (395)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHhc---CCcH--HHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcC
Confidence            3455556667899999999999876   4664  4457888888899999999998874 233 5666666677799999


Q ss_pred             CHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          426 NAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       426 ~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      +++.|+.+.+++ ....|++..+|. .|+.+|.+.|++++|+..++.+.
T Consensus       249 ~~~lAL~iAk~a-v~lsP~~f~~W~-~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  249 KYELALEIAKKA-VELSPSEFETWY-QLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             CHHHHHHHHHHH-HHhCchhHHHHH-HHHHHHHhcCCHHHHHHHHhcCc
Confidence            999999999999 999999999999 99999999999999999999886

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.19  E-value=9.9e-05  Score=71.95  Aligned_cols=214  Identities=12%  Similarity=0.131  Sum_probs=137.5

Q ss_pred             CCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHH-------------HHHHHHHhc
Q 044988          288 EPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLT-------------FLGVLSACS  354 (538)
Q Consensus       288 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~-------------~~~ll~~~~  354 (538)
                      .|+-...-..+...+.+.|-...|..+|+++     ..|...|..|...|+..+|...             |..+.+...
T Consensus       394 lpp~Wq~q~~laell~slGitksAl~I~Erl-----emw~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~  468 (777)
T KOG1128|consen  394 LPPIWQLQRLLAELLLSLGITKSALVIFERL-----EMWDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLH  468 (777)
T ss_pred             CCCcchHHHHHHHHHHHcchHHHHHHHHHhH-----HHHHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhcc
Confidence            4555555567888899999999999999886     4556666677777765555422             222222222


Q ss_pred             ccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCCHHHHHH
Q 044988          355 HGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNM-PMKP-NDAVLGSLLLGCRIHNNAELASQ  432 (538)
Q Consensus       355 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~-~~~p-~~~~~~~l~~~~~~~~~~~~A~~  432 (538)
                      ...-+++|.++++....+        .-..+.....+.++++++.+.|+.- ...| -..+|-.+..+..+.++++.|.+
T Consensus       469 d~s~yEkawElsn~~sar--------A~r~~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~av~  540 (777)
T KOG1128|consen  469 DPSLYEKAWELSNYISAR--------AQRSLALLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAAVK  540 (777)
T ss_pred             ChHHHHHHHHHhhhhhHH--------HHHhhccccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHHHH
Confidence            222234444444333221        1122222223456777777777653 2333 35678888888899999999999


Q ss_pred             HHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeEEEECCEEEEEEeCCCCCcchHHHHHH
Q 044988          433 VAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKT  512 (538)
Q Consensus       433 ~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  512 (538)
                      .|... ..+.|++...|. .+..+|.+.|+-.+|...+++..+-+.  .+...|       ..|.--.-.-++.++++..
T Consensus       541 aF~rc-vtL~Pd~~eaWn-Nls~ayi~~~~k~ra~~~l~EAlKcn~--~~w~iW-------ENymlvsvdvge~eda~~A  609 (777)
T KOG1128|consen  541 AFHRC-VTLEPDNAEAWN-NLSTAYIRLKKKKRAFRKLKEALKCNY--QHWQIW-------ENYMLVSVDVGEFEDAIKA  609 (777)
T ss_pred             HHHHH-hhcCCCchhhhh-hhhHHHHHHhhhHHHHHHHHHHhhcCC--CCCeee-------echhhhhhhcccHHHHHHH
Confidence            99999 999999999999 999999999999999999999988763  344566       2333333334455555555


Q ss_pred             HHHHHHHHHHcCcc
Q 044988          513 LGEITMQAMQEGYK  526 (538)
Q Consensus       513 l~~~~~~m~~~~~~  526 (538)
                      ..++. .|++.+-.
T Consensus       610 ~~rll-~~~~~~~d  622 (777)
T KOG1128|consen  610 YHRLL-DLRKKYKD  622 (777)
T ss_pred             HHHHH-Hhhhhccc
Confidence            54433 34444433

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.18  E-value=0.00075  Score=57.48  Aligned_cols=189  Identities=14%  Similarity=0.143  Sum_probs=136.1

Q ss_pred             cCCHHHHHHHHHHHHH---CC-CCCCHHH-HHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhC
Q 044988          231 NGKSRQALSLFNEMRR---AR-VGLDQVA-LVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASC  305 (538)
Q Consensus       231 ~~~~~~a~~~~~~m~~---~g-~~p~~~~-~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  305 (538)
                      ..+.+++++++.++..   .| ..|+..+ |-.++-+....|+.+.|..+++.+...     +|.+..+-..-.-.+-..
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~-----fp~S~RV~~lkam~lEa~   99 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDR-----FPGSKRVGKLKAMLLEAT   99 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHh-----CCCChhHHHHHHHHHHHh
Confidence            4678889999888875   35 6666655 455666777889999999999999987     465555543334456678


Q ss_pred             CCHHHHHHHHHhcCCCC---cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHH
Q 044988          306 GEIEEAYGVFRKMQRRN---TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHY  382 (538)
Q Consensus       306 g~~~~a~~~~~~m~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~  382 (538)
                      |++++|.++++.+.+.|   .+++..-+......|                    +.-+|++-+....+.  +..|...|
T Consensus       100 ~~~~~A~e~y~~lL~ddpt~~v~~KRKlAilka~G--------------------K~l~aIk~ln~YL~~--F~~D~EAW  157 (289)
T KOG3060|consen  100 GNYKEAIEYYESLLEDDPTDTVIRKRKLAILKAQG--------------------KNLEAIKELNEYLDK--FMNDQEAW  157 (289)
T ss_pred             hchhhHHHHHHHHhccCcchhHHHHHHHHHHHHcC--------------------CcHHHHHHHHHHHHH--hcCcHHHH
Confidence            99999999999998754   344444444444444                    333555555555554  36689999


Q ss_pred             HHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHh---cCCHHHHHHHHHHchhccCCCCcc
Q 044988          383 GCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRI---HNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       383 ~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~---~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      ..|...|...|++++|.-.++++. ..|- ...+..+...+.-   ..+.+.|.++|.+. .++.|.+..
T Consensus       158 ~eLaeiY~~~~~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~a-lkl~~~~~r  226 (289)
T KOG3060|consen  158 HELAEIYLSEGDFEKAAFCLEELLLIQPFNPLYFQRLAEVLYTQGGAENLELARKYYERA-LKLNPKNLR  226 (289)
T ss_pred             HHHHHHHHhHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH-HHhChHhHH
Confidence            999999999999999999999985 4555 4455566655333   33778899999999 999995543

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.18  E-value=0.00019  Score=61.44  Aligned_cols=111  Identities=11%  Similarity=0.063  Sum_probs=66.5

Q ss_pred             CcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCHHHHHHHH
Q 044988          357 GFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MK-PNDAVLGSLLLGCRIHNNAELASQVA  434 (538)
Q Consensus       357 ~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~-p~~~~~~~l~~~~~~~~~~~~A~~~~  434 (538)
                      |++..|...|++....  -++|...|+.+.-+|.+.|++++|..-|.+.. +. .+....+.+...+.-.|+.+.|..++
T Consensus       114 g~~~~A~~~~rkA~~l--~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~gd~~~A~~ll  191 (257)
T COG5010         114 GNFGEAVSVLRKAARL--APTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPNEPSIANNLGMSLLLRGDLEDAETLL  191 (257)
T ss_pred             cchHHHHHHHHHHhcc--CCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcCCHHHHHHHH
Confidence            3555555666665542  24456677777777777777777766665542 22 23455566666666667777777777


Q ss_pred             HHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHH
Q 044988          435 QKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQ  471 (538)
Q Consensus       435 ~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~  471 (538)
                      ... ....+.+...-. .|+.+....|++++|..+..
T Consensus       192 l~a-~l~~~ad~~v~~-NLAl~~~~~g~~~~A~~i~~  226 (257)
T COG5010         192 LPA-YLSPAADSRVRQ-NLALVVGLQGDFREAEDIAV  226 (257)
T ss_pred             HHH-HhCCCCchHHHH-HHHHHHhhcCChHHHHhhcc
Confidence            666 444454555444 56666666777766665543

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.17  E-value=3e-05  Score=62.34  Aligned_cols=107  Identities=19%  Similarity=0.223  Sum_probs=88.1

Q ss_pred             HHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhcc
Q 044988          365 FFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEI  441 (538)
Q Consensus       365 ~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  441 (538)
                      .++....   ..|+ ......+...+...|++++|.+.++.+. ..| +...|..+...+...|++++|...+++. ...
T Consensus         5 ~~~~~l~---~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~-~~~   80 (135)
T TIGR02552         5 TLKDLLG---LDSEQLEQIYALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALA-AAL   80 (135)
T ss_pred             hHHHHHc---CChhhHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH-Hhc
Confidence            3444443   3553 5567778888899999999999998874 334 5678888888899999999999999999 888


Q ss_pred             CCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          442 DPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       442 ~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      .|+++..+. .++.+|...|++++|...+++..+.
T Consensus        81 ~p~~~~~~~-~la~~~~~~g~~~~A~~~~~~al~~  114 (135)
T TIGR02552        81 DPDDPRPYF-HAAECLLALGEPESALKALDLAIEI  114 (135)
T ss_pred             CCCChHHHH-HHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            999988788 8999999999999999999998874

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.17  E-value=0.00012  Score=74.56  Aligned_cols=124  Identities=16%  Similarity=0.066  Sum_probs=79.8

Q ss_pred             HHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHH
Q 044988          346 FLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCR  422 (538)
Q Consensus       346 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~  422 (538)
                      +..|..+....|.+++|+.+++.+.+.   .|+ ......+..++.+.+++++|+..+++.. ..|+ ......+..++.
T Consensus        89 ~~~La~i~~~~g~~~ea~~~l~~~~~~---~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~a~~l~  165 (694)
T PRK15179         89 QVLVARALEAAHRSDEGLAVWRGIHQR---FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLEAKSWD  165 (694)
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHHHHhh---CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHHHHHHH
Confidence            333444444555666666777766643   565 4456666677777777777777776653 3455 344445555667


Q ss_pred             hcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          423 IHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       423 ~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      +.|++++|..+|+++ ....|+++.++. .++.++.+.|+.++|...|++..
T Consensus       166 ~~g~~~~A~~~y~~~-~~~~p~~~~~~~-~~a~~l~~~G~~~~A~~~~~~a~  215 (694)
T PRK15179        166 EIGQSEQADACFERL-SRQHPEFENGYV-GWAQSLTRRGALWRARDVLQAGL  215 (694)
T ss_pred             HhcchHHHHHHHHHH-HhcCCCcHHHHH-HHHHHHHHcCCHHHHHHHHHHHH
Confidence            777777777777777 556666666666 77777777777777777776664

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.16  E-value=4.2e-06  Score=48.43  Aligned_cols=33  Identities=30%  Similarity=0.630  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGL  251 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  251 (538)
                      .+|+.+|.+|++.|+++.|.++|++|.+.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            589999999999999999999999999999887

>PLN02789 farnesyltranstransferase

Probab=98.15  E-value=0.00057  Score=63.08  Aligned_cols=120  Identities=12%  Similarity=0.056  Sum_probs=54.3

Q ss_pred             HHHhcCCCchHHHHHHHHhHhCCCCCCc-chHHHHHHHHHccC-CcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCC
Q 044988           91 RGHARSETPEKSVYLYKQMIDKETEPDE-YTYSFLLSVCARCG-LFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGG  168 (538)
Q Consensus        91 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  168 (538)
                      ..+...++.++|+.++.++++.  .|+. .+|+.--.++...| ++++++..++++.+.. +.+..+|+....++.+.|.
T Consensus        45 a~l~~~e~serAL~lt~~aI~l--nP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n-pknyqaW~~R~~~l~~l~~  121 (320)
T PLN02789         45 AVYASDERSPRALDLTADVIRL--NPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN-PKNYQIWHHRRWLAEKLGP  121 (320)
T ss_pred             HHHHcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC-CcchHHhHHHHHHHHHcCc
Confidence            3344455555666666655543  2322 23443333444444 3455555555555543 3333344444333333333


Q ss_pred             CCChhHHHHHhhcCCC---CCchhHHHHHHHHHhcCCHHHHHHHHccCC
Q 044988          169 ECGVGCARLLFDDMPA---RSVVSWNSLLKGYVKRGDIDGAWKIFDEMP  214 (538)
Q Consensus       169 ~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  214 (538)
                      . ..+++...++++.+   .|..+|+...-.+...|+++++++.++++.
T Consensus       122 ~-~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I  169 (320)
T PLN02789        122 D-AANKELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWEDELEYCHQLL  169 (320)
T ss_pred             h-hhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            0 01333444443332   233444444444555555555555555544

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=98.14  E-value=7.1e-05  Score=59.55  Aligned_cols=95  Identities=12%  Similarity=0.009  Sum_probs=83.1

Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ....-.+...+...|++++|.++|+-+. ..| +..-|-.|..++...|++++|+..|..+ ..+.|+++.++. .++.+
T Consensus        35 l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A-~~L~~ddp~~~~-~ag~c  112 (157)
T PRK15363         35 LNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRA-AQIKIDAPQAPW-AAAEC  112 (157)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHH-HhcCCCCchHHH-HHHHH
Confidence            4455566667778999999999999874 344 4677888888999999999999999999 999999999999 99999


Q ss_pred             HHhcCChHHHHHHHHHHHh
Q 044988          457 YAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       457 ~~~~g~~~~A~~~~~~m~~  475 (538)
                      +...|+.+.|.+.|+....
T Consensus       113 ~L~lG~~~~A~~aF~~Ai~  131 (157)
T PRK15363        113 YLACDNVCYAIKALKAVVR  131 (157)
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            9999999999999998875

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.14  E-value=3.6e-06  Score=48.73  Aligned_cols=33  Identities=21%  Similarity=0.586  Sum_probs=22.7

Q ss_pred             chHHHHHHHHhcCCCchHHHHHHHHhHhCCCCC
Q 044988           84 AIWNQMIRGHARSETPEKSVYLYKQMIDKETEP  116 (538)
Q Consensus        84 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p  116 (538)
                      .+|+.+|.+|++.|+++.|.++|++|.+.|++|
T Consensus         2 ~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    2 HTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             cHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            466777777777777777777777777666665

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.13  E-value=0.0026  Score=59.67  Aligned_cols=190  Identities=15%  Similarity=0.117  Sum_probs=134.2

Q ss_pred             hhHHHHHhhcCCC------CCchhHHHHHHHHHhcCCHHHHHHHHccCCC--CChHHHHHHHHHHHHcCCHHHHHHHHHH
Q 044988          172 VGCARLLFDDMPA------RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--RNVVSWTTMISGCAQNGKSRQALSLFNE  243 (538)
Q Consensus       172 ~~~a~~~~~~~~~------~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~  243 (538)
                      +.++...-++++.      ++...+...+.+......-..+-.++.+..+  ....-|..-+ .+...|++++|+..++.
T Consensus       253 Ia~lr~ra~q~p~~~~~d~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~aa~YG~A~-~~~~~~~~d~A~~~l~~  331 (484)
T COG4783         253 IADLRNRAEQSPPYNKLDSPDFQLARARIRAKYEALPNQQAADLLAKRSKRGGLAAQYGRAL-QTYLAGQYDEALKLLQP  331 (484)
T ss_pred             HHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhccccccchHHHHHHHhCccchHHHHHHHH-HHHHhcccchHHHHHHH
Confidence            4455555555553      2444555555544333333333333332222  2222344444 44567999999999999


Q ss_pred             HHHCCCCCCHHHHH-HHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--
Q 044988          244 MRRARVGLDQVALV-AALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--  320 (538)
Q Consensus       244 m~~~g~~p~~~~~~-~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--  320 (538)
                      +...  .||...|. .....+.+.++.++|.+.++.+...     .|......-.+..+|.+.|++.+|..++++...  
T Consensus       332 L~~~--~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l-----~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~  404 (484)
T COG4783         332 LIAA--QPDNPYYLELAGDILLEANKAKEAIERLKKALAL-----DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFND  404 (484)
T ss_pred             HHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc-----CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcC
Confidence            8874  56555554 5556678999999999999999987     666677777899999999999999999998775  


Q ss_pred             -CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          321 -RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       321 -~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                       .|+..|..|..+|...|+..++.   .....++.-.|+++.|...+....+.
T Consensus       405 p~dp~~w~~LAqay~~~g~~~~a~---~A~AE~~~~~G~~~~A~~~l~~A~~~  454 (484)
T COG4783         405 PEDPNGWDLLAQAYAELGNRAEAL---LARAEGYALAGRLEQAIIFLMRASQQ  454 (484)
T ss_pred             CCCchHHHHHHHHHHHhCchHHHH---HHHHHHHHhCCCHHHHHHHHHHHHHh
Confidence             47889999999999999888775   33355667788888888888888775

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.11  E-value=0.00023  Score=60.98  Aligned_cols=160  Identities=17%  Similarity=0.087  Sum_probs=132.4

Q ss_pred             ChhHHHHHHHHHHccCChhHHHHHHhcCC-C--CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHH
Q 044988           51 KNYILAKLLAFYVTSGYLINAHKVFEKTE-N--PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSV  127 (538)
Q Consensus        51 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  127 (538)
                      |..+ ..+-..+...|+-+....+..... .  .+....+..+....+.|++..|+..|++..... ++|..+|+.+.-+
T Consensus        66 d~~i-~~~a~a~~~~G~a~~~l~~~~~~~~~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~-p~d~~~~~~lgaa  143 (257)
T COG5010          66 DLSI-AKLATALYLRGDADSSLAVLQKSAIAYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGAA  143 (257)
T ss_pred             hHHH-HHHHHHHHhcccccchHHHHhhhhccCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHHH
Confidence            3444 666777888898888888877754 2  344456668999999999999999999998754 6788999999999


Q ss_pred             HHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC---CCchhHHHHHHHHHhcCCHH
Q 044988          128 CARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA---RSVVSWNSLLKGYVKRGDID  204 (538)
Q Consensus       128 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~  204 (538)
                      |.+.|+++.|..-|.+..+.- +-+....+.+...|.-.|+   .+.|..++.....   .|...-..+.......|+++
T Consensus       144 ldq~Gr~~~Ar~ay~qAl~L~-~~~p~~~nNlgms~~L~gd---~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~  219 (257)
T COG5010         144 LDQLGRFDEARRAYRQALELA-PNEPSIANNLGMSLLLRGD---LEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFR  219 (257)
T ss_pred             HHHccChhHHHHHHHHHHHhc-cCCchhhhhHHHHHHHcCC---HHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChH
Confidence            999999999999999999874 5567788999999999999   9999999987653   37778888888999999999


Q ss_pred             HHHHHHccCCCC
Q 044988          205 GAWKIFDEMPHR  216 (538)
Q Consensus       205 ~A~~~~~~m~~~  216 (538)
                      .|..+-..-..+
T Consensus       220 ~A~~i~~~e~~~  231 (257)
T COG5010         220 EAEDIAVQELLS  231 (257)
T ss_pred             HHHhhccccccc
Confidence            999998775543

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.10  E-value=0.0034  Score=54.08  Aligned_cols=114  Identities=11%  Similarity=0.082  Sum_probs=74.2

Q ss_pred             CcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhh----cCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHH
Q 044988          357 GFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSR----AGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELA  430 (538)
Q Consensus       357 ~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A  430 (538)
                      .+.+.|.+.++.|.+-    -+..+.+.|..++.+    .+.+.+|.-+|++|.  ..|+..+.+....++...|++++|
T Consensus       151 ~r~d~A~~~lk~mq~i----ded~tLtQLA~awv~la~ggek~qdAfyifeE~s~k~~~T~~llnG~Av~~l~~~~~eeA  226 (299)
T KOG3081|consen  151 HRFDLAEKELKKMQQI----DEDATLTQLAQAWVKLATGGEKIQDAFYIFEELSEKTPPTPLLLNGQAVCHLQLGRYEEA  226 (299)
T ss_pred             HHHHHHHHHHHHHHcc----chHHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcccCCChHHHccHHHHHHHhcCHHHH
Confidence            3667777777777642    244566666665543    345777888888884  457777888887788888888888


Q ss_pred             HHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          431 SQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       431 ~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ..+++.+ ..-.++++.+..+++..+.....+.+-..+.+.+++.
T Consensus       227 e~lL~ea-L~kd~~dpetL~Nliv~a~~~Gkd~~~~~r~l~QLk~  270 (299)
T KOG3081|consen  227 ESLLEEA-LDKDAKDPETLANLIVLALHLGKDAEVTERNLSQLKL  270 (299)
T ss_pred             HHHHHHH-HhccCCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHh
Confidence            8888888 7777777776663443333333333444455566554

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.10  E-value=0.00011  Score=59.66  Aligned_cols=129  Identities=16%  Similarity=0.095  Sum_probs=94.8

Q ss_pred             HHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCH----HHH
Q 044988          341 EALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPND----AVL  414 (538)
Q Consensus       341 ~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~----~~~  414 (538)
                      +|-..|..++..+. .++...+...++.+.+.++-.| .....-.+...+...|++++|...|+.+. ..||.    ...
T Consensus        10 ~a~~~y~~~~~~~~-~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~   88 (145)
T PF09976_consen   10 QASALYEQALQALQ-AGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLAR   88 (145)
T ss_pred             HHHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHH
Confidence            33356666666664 7788999999999988742221 13445557788899999999999999885 22443    344


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHH
Q 044988          415 GSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKM  473 (538)
Q Consensus       415 ~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m  473 (538)
                      ..+...+...|++++|+..++.. . ..+-.+..+. +++++|.+.|++++|+..|++.
T Consensus        89 l~LA~~~~~~~~~d~Al~~L~~~-~-~~~~~~~~~~-~~Gdi~~~~g~~~~A~~~y~~A  144 (145)
T PF09976_consen   89 LRLARILLQQGQYDEALATLQQI-P-DEAFKALAAE-LLGDIYLAQGDYDEARAAYQKA  144 (145)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHhc-c-CcchHHHHHH-HHHHHHHHCCCHHHHHHHHHHh
Confidence            45667789999999999999875 2 2333344355 9999999999999999999863

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.09  E-value=0.00092  Score=62.55  Aligned_cols=115  Identities=18%  Similarity=0.195  Sum_probs=94.6

Q ss_pred             ccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHH
Q 044988          355 HGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELAS  431 (538)
Q Consensus       355 ~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~  431 (538)
                      ..|.++.|+..+..+...   .| |+..+....+.+.+.++..+|.+.++++. ..|+ ...+-.+..++.+.|++++|+
T Consensus       318 ~~~~~d~A~~~l~~L~~~---~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai  394 (484)
T COG4783         318 LAGQYDEALKLLQPLIAA---QPDNPYYLELAGDILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAI  394 (484)
T ss_pred             HhcccchHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHH
Confidence            446888889999998865   56 56667777889999999999999999885 5677 566677788899999999999


Q ss_pred             HHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          432 QVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       432 ~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      .+++.. ..-.|+++..|. .|+.+|...|+..+|.....+..
T Consensus       395 ~~L~~~-~~~~p~dp~~w~-~LAqay~~~g~~~~a~~A~AE~~  435 (484)
T COG4783         395 RILNRY-LFNDPEDPNGWD-LLAQAYAELGNRAEALLARAEGY  435 (484)
T ss_pred             HHHHHH-hhcCCCCchHHH-HHHHHHHHhCchHHHHHHHHHHH
Confidence            999999 888999999888 99999888887777776665554

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.08  E-value=0.017  Score=58.45  Aligned_cols=214  Identities=12%  Similarity=0.057  Sum_probs=131.2

Q ss_pred             ccCChHHHHHHHHHHHHhCCCCChhHHHHHHHH--HHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHH
Q 044988           29 IRNTTKTLFQIHSQIIINGFSQKNYILAKLLAF--YVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSV  103 (538)
Q Consensus        29 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~  103 (538)
                      ..+++..|..-...+.+.-  |+.. |..++.+  ..+.|+.++|..+++...   ..|..|...+-.+|...++.++|.
T Consensus        21 d~~qfkkal~~~~kllkk~--Pn~~-~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~   97 (932)
T KOG2053|consen   21 DSSQFKKALAKLGKLLKKH--PNAL-YAKVLKALSLFRLGKGDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAV   97 (932)
T ss_pred             hhHHHHHHHHHHHHHHHHC--CCcH-HHHHHHHHHHHHhcCchhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHH
Confidence            3466777888777776652  3332 3333443  357889999998887665   346678888888899999999999


Q ss_pred             HHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCC--CC-----ChhHHH
Q 044988          104 YLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGG--EC-----GVGCAR  176 (538)
Q Consensus       104 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~--~~-----~~~~a~  176 (538)
                      .+|++....  .|+......+..+|++.+++.+-.++--++-+. ++.+.+.+=++++.....-.  ..     -+.-|.
T Consensus        98 ~~Ye~~~~~--~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~  174 (932)
T KOG2053|consen   98 HLYERANQK--YPSEELLYHLFMAYVREKSYKKQQKAALQLYKN-FPKRAYYFWSVISLILQSIFSENELLDPILLALAE  174 (932)
T ss_pred             HHHHHHHhh--CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCcccchHHHHHHHHHHhccCCcccccchhHHHHH
Confidence            999998864  577778888888899888877666655555543 45555555555555544332  00     012344


Q ss_pred             HHhhcCCCCC-c----hhHHHHHHHHHhcCCHHHHHHHHcc-----CCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 044988          177 LLFDDMPARS-V----VSWNSLLKGYVKRGDIDGAWKIFDE-----MPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRR  246 (538)
Q Consensus       177 ~~~~~~~~~~-~----~~~~~li~~~~~~g~~~~A~~~~~~-----m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  246 (538)
                      +.++.+.+.+ .    .-...-...+...|++++|++++..     ....+...-+.-+..+...+++.+..++-.++..
T Consensus       175 ~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~  254 (932)
T KOG2053|consen  175 KMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLE  254 (932)
T ss_pred             HHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHH
Confidence            4444444332 1    1111122334556667777777632     1223333444555666667777777777777766


Q ss_pred             CC
Q 044988          247 AR  248 (538)
Q Consensus       247 ~g  248 (538)
                      .|
T Consensus       255 k~  256 (932)
T KOG2053|consen  255 KG  256 (932)
T ss_pred             hC
Confidence            54

>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi

Probab=98.04  E-value=0.00011  Score=69.07  Aligned_cols=117  Identities=13%  Similarity=0.187  Sum_probs=60.4

Q ss_pred             HHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCC
Q 044988           90 IRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGE  169 (538)
Q Consensus        90 i~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  169 (538)
                      +..+...++++.|+++|+++.+..  |+  ....+++.+...++-.+|.+++++.++.. +.+..........+.+.++ 
T Consensus       176 l~~l~~t~~~~~ai~lle~L~~~~--pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~-p~d~~LL~~Qa~fLl~k~~-  249 (395)
T PF09295_consen  176 LKYLSLTQRYDEAIELLEKLRERD--PE--VAVLLARVYLLMNEEVEAIRLLNEALKEN-PQDSELLNLQAEFLLSKKK-  249 (395)
T ss_pred             HHHHhhcccHHHHHHHHHHHHhcC--Cc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhcCC-
Confidence            333444455555555555555432  22  23334444444455555555555555432 3344444445555555555 


Q ss_pred             CChhHHHHHhhcCCC--C-CchhHHHHHHHHHhcCCHHHHHHHHccCC
Q 044988          170 CGVGCARLLFDDMPA--R-SVVSWNSLLKGYVKRGDIDGAWKIFDEMP  214 (538)
Q Consensus       170 ~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~  214 (538)
                        .+.|..+.++..+  | +..+|..|..+|.+.|+++.|+..++.++
T Consensus       250 --~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  250 --YELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             --HHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence              5555555555543  2 33456666666666666666666666655

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.98  E-value=0.00071  Score=61.91  Aligned_cols=156  Identities=14%  Similarity=0.192  Sum_probs=102.3

Q ss_pred             CHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhccc-CcHHHHHHHHHHhhhhcCCCcc----HHH
Q 044988          307 EIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHG-GFVDEGRQFFECMNQNWGIKPR----IEH  381 (538)
Q Consensus       307 ~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~~~p~----~~~  381 (538)
                      ++++|...+++           .+..|...|++..|-..+..+...|... |+++.|.+.|++..+.+.....    ..+
T Consensus        89 ~~~~Ai~~~~~-----------A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~  157 (282)
T PF14938_consen   89 DPDEAIECYEK-----------AIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAEC  157 (282)
T ss_dssp             THHHHHHHHHH-----------HHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             CHHHHHHHHHH-----------HHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHH
Confidence            66666666555           4677888899999888899999999888 9999999999987765422222    446


Q ss_pred             HHHHHHHhhhcCChHHHHHHHHhCC---C-----CCCHH-HHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH--
Q 044988          382 YGCMVDLFSRAGLMDEAFSLVQNMP---M-----KPNDA-VLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL--  450 (538)
Q Consensus       382 ~~~l~~~~~~~g~~~~A~~~~~~~~---~-----~p~~~-~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~--  450 (538)
                      +..+...+.+.|++++|.++|+++.   .     +.+.. .+-..+-++...||+-.|.+.+++. ....|....+-.  
T Consensus       158 ~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~-~~~~~~F~~s~E~~  236 (282)
T PF14938_consen  158 LLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERY-CSQDPSFASSREYK  236 (282)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH-GTTSTTSTTSHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhhCCCCCCcHHHH
Confidence            6778889999999999999999863   1     11221 2333444677789999999999999 777775544322  


Q ss_pred             --HHHHHHHHh--cCChHHHHHHHHHHH
Q 044988          451 --ALVANVYAA--AKRWQDVAAVRQKMI  474 (538)
Q Consensus       451 --~~l~~~~~~--~g~~~~A~~~~~~m~  474 (538)
                        ..|+.++-.  ...+++|+.-|+.+.
T Consensus       237 ~~~~l~~A~~~~D~e~f~~av~~~d~~~  264 (282)
T PF14938_consen  237 FLEDLLEAYEEGDVEAFTEAVAEYDSIS  264 (282)
T ss_dssp             HHHHHHHHHHTT-CCCHHHHCHHHTTSS
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHcccC
Confidence              234444432  234555555555543

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=97.94  E-value=0.00029  Score=60.34  Aligned_cols=143  Identities=10%  Similarity=0.078  Sum_probs=101.7

Q ss_pred             HHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchH
Q 044988           25 SLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEK  101 (538)
Q Consensus        25 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~  101 (538)
                      ..|...|+++.+....+.+.    .|.        .-+...++.+++...++...   +.|...|..+...|...|++++
T Consensus        24 ~~Y~~~g~~~~v~~~~~~~~----~~~--------~~~~~~~~~~~~i~~l~~~L~~~P~~~~~w~~Lg~~~~~~g~~~~   91 (198)
T PRK10370         24 GSYLLSPKWQAVRAEYQRLA----DPL--------HQFASQQTPEAQLQALQDKIRANPQNSEQWALLGEYYLWRNDYDN   91 (198)
T ss_pred             HHHHHcchHHHHHHHHHHHh----Ccc--------ccccCchhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCHHH
Confidence            44677788777644432211    111        01223556666666666544   3567788899999999999999


Q ss_pred             HHHHHHHhHhCCCCCCcchHHHHHHHH-HccCC--cHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHH
Q 044988          102 SVYLYKQMIDKETEPDEYTYSFLLSVC-ARCGL--FREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLL  178 (538)
Q Consensus       102 a~~~~~~m~~~~~~p~~~~~~~li~~~-~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~  178 (538)
                      |...|++..+.. +-+...+..+..++ ...|+  .++|.+++++..+.+ +.+..++..+...+...|+   +++|...
T Consensus        92 A~~a~~~Al~l~-P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~d-P~~~~al~~LA~~~~~~g~---~~~Ai~~  166 (198)
T PRK10370         92 ALLAYRQALQLR-GENAELYAALATVLYYQAGQHMTPQTREMIDKALALD-ANEVTALMLLASDAFMQAD---YAQAIEL  166 (198)
T ss_pred             HHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHcCC---HHHHHHH
Confidence            999999888753 33556777777654 56676  489999999999876 5577888889999999999   9999999


Q ss_pred             hhcCCC
Q 044988          179 FDDMPA  184 (538)
Q Consensus       179 ~~~~~~  184 (538)
                      ++++.+
T Consensus       167 ~~~aL~  172 (198)
T PRK10370        167 WQKVLD  172 (198)
T ss_pred             HHHHHh
Confidence            988765

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.90  E-value=0.0011  Score=67.68  Aligned_cols=126  Identities=10%  Similarity=-0.002  Sum_probs=60.9

Q ss_pred             hhHHHHHHHHHHccCChhHHHHHHhcCCC--C-CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCc-chHHHHHHH
Q 044988           52 NYILAKLLAFYVTSGYLINAHKVFEKTEN--P-STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDE-YTYSFLLSV  127 (538)
Q Consensus        52 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~  127 (538)
                      +..+-.|..+..+.|+.++|..+++...+  | +...+..+..++.+.+++++|+..+++....  .|+. .....+..+
T Consensus        86 ~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~~~~a~~  163 (694)
T PRK15179         86 ELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREILLEAKS  163 (694)
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHHHHHHHH
Confidence            44444444455555555555555554431  2 2233444445555555555555555555543  2322 233344444


Q ss_pred             HHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCC
Q 044988          128 CARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMP  183 (538)
Q Consensus       128 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~  183 (538)
                      +.+.|++++|..+|+++...+ +.+..++..+..++...|+   .++|...|++..
T Consensus       164 l~~~g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~---~~~A~~~~~~a~  215 (694)
T PRK15179        164 WDEIGQSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGA---LWRARDVLQAGL  215 (694)
T ss_pred             HHHhcchHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCC---HHHHHHHHHHHH
Confidence            555555555555555555421 2334455555555555555   555555555443

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.86  E-value=1.9e-05  Score=44.42  Aligned_cols=29  Identities=17%  Similarity=0.418  Sum_probs=21.1

Q ss_pred             hHHHHHHHHhcCCCchHHHHHHHHhHhCC
Q 044988           85 IWNQMIRGHARSETPEKSVYLYKQMIDKE  113 (538)
Q Consensus        85 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~  113 (538)
                      +||.+|++|++.|++++|.++|++|.+.|
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g   30 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERG   30 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCc
Confidence            67777777777777777777777777665

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.84  E-value=2.2e-05  Score=44.16  Aligned_cols=31  Identities=35%  Similarity=0.703  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARV  249 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  249 (538)
                      ++|+.++++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            3688888888888888888888888887664

Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.83  E-value=0.0034  Score=53.66  Aligned_cols=191  Identities=13%  Similarity=0.044  Sum_probs=134.5

Q ss_pred             cCChHHHHHHHHHHHHhccCC-CCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHH
Q 044988          266 IGDLKLGKWIHSYVEENFSVG-REPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALL  344 (538)
Q Consensus       266 ~~~~~~a~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~  344 (538)
                      ..+.++..+++..+......+ -.+.-..++..+.-+...+|+.+.|...++.+..+-+.++....              
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~--------------   90 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGK--------------   90 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHH--------------
Confidence            345667777777776654433 22333345555666667789999999999887653222222111              


Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHH
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGC  421 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~  421 (538)
                      ....+   +-..|.+++|.++++.+.+.   .| |..++--=+.+.-..|+.-+|++-+.+..  +..|...|.-+...|
T Consensus        91 lkam~---lEa~~~~~~A~e~y~~lL~d---dpt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~~D~EAW~eLaeiY  164 (289)
T KOG3060|consen   91 LKAML---LEATGNYKEAIEYYESLLED---DPTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFMNDQEAWHELAEIY  164 (289)
T ss_pred             HHHHH---HHHhhchhhHHHHHHHHhcc---CcchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            00011   11235788889999999876   45 67777766767777888888887776653  557899999999999


Q ss_pred             HhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcC---ChHHHHHHHHHHHhCCC
Q 044988          422 RIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAK---RWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       422 ~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~m~~~~~  478 (538)
                      ...|++++|.-.++++ .-+.|-++..|. .+++.+.-.|   +.+-|.++|.+..+...
T Consensus       165 ~~~~~f~kA~fClEE~-ll~~P~n~l~f~-rlae~~Yt~gg~eN~~~arkyy~~alkl~~  222 (289)
T KOG3060|consen  165 LSEGDFEKAAFCLEEL-LLIQPFNPLYFQ-RLAEVLYTQGGAENLELARKYYERALKLNP  222 (289)
T ss_pred             HhHhHHHHHHHHHHHH-HHcCCCcHHHHH-HHHHHHHHHhhHHHHHHHHHHHHHHHHhCh
Confidence            9999999999999999 889999999666 8888887666   46678888888776433

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.80  E-value=0.0015  Score=59.80  Aligned_cols=164  Identities=14%  Similarity=0.082  Sum_probs=97.2

Q ss_pred             ChHHHHHHHHHHHHhccCCCCCc-chhHHHHHHHHHHhC-CCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHH
Q 044988          268 DLKLGKWIHSYVEENFSVGREPV-LVSLNNALIHMYASC-GEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLT  345 (538)
Q Consensus       268 ~~~~a~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~-g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~  345 (538)
                      +++.|...+....+.....|.+. -...+..+...|... |+++.|.+.|++.           +..|...+....+..+
T Consensus        89 ~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A-----------~~~y~~e~~~~~a~~~  157 (282)
T PF14938_consen   89 DPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKA-----------AELYEQEGSPHSAAEC  157 (282)
T ss_dssp             THHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHH-----------HHHHHHTT-HHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----------HHHHHHCCChhhHHHH
Confidence            55555555554444322222221 123344555666666 7777777777664           5566667766666688


Q ss_pred             HHHHHHHhcccCcHHHHHHHHHHhhhhcC----CCccHH-HHHHHHHHhhhcCChHHHHHHHHhCC-CCC----C--HHH
Q 044988          346 FLGVLSACSHGGFVDEGRQFFECMNQNWG----IKPRIE-HYGCMVDLFSRAGLMDEAFSLVQNMP-MKP----N--DAV  413 (538)
Q Consensus       346 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~----~~p~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p----~--~~~  413 (538)
                      +..+...+...|++++|.++|+++....-    ..++.. .+-..+-++...|+...|.+.+++.. ..|    +  ...
T Consensus       158 ~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~  237 (282)
T PF14938_consen  158 LLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKF  237 (282)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHH
Confidence            88888889999999999999999876421    122222 33344556777899999999998864 222    2  456


Q ss_pred             HHHHHHHHHh--cCCHHHHHHHHHHchhccCC
Q 044988          414 LGSLLLGCRI--HNNAELASQVAQKLVAEIDP  443 (538)
Q Consensus       414 ~~~l~~~~~~--~~~~~~A~~~~~~~~~~~~p  443 (538)
                      ...|+.++-.  ...++.++.-|+.+ ..+.|
T Consensus       238 ~~~l~~A~~~~D~e~f~~av~~~d~~-~~ld~  268 (282)
T PF14938_consen  238 LEDLLEAYEEGDVEAFTEAVAEYDSI-SRLDN  268 (282)
T ss_dssp             HHHHHHHHHTT-CCCHHHHCHHHTTS-S---H
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHccc-CccHH
Confidence            6677777654  23567777777776 44444

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.79  E-value=0.048  Score=54.19  Aligned_cols=340  Identities=10%  Similarity=0.118  Sum_probs=183.9

Q ss_pred             HhcCCCchHHHHHHHHh--------HhCCCCCCcchHHH-----HHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHH
Q 044988           93 HARSETPEKSVYLYKQM--------IDKETEPDEYTYSF-----LLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNL  159 (538)
Q Consensus        93 ~~~~~~~~~a~~~~~~m--------~~~~~~p~~~~~~~-----li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  159 (538)
                      +.+..++++-..+....        ..-|++.+..-|..     +|..+...+.+..|.++-..+...-... ..++...
T Consensus       399 ~l~~~~~d~~~~v~~~lrVln~~r~~~~gIplT~~qy~~l~~~~vi~Rl~~r~~Y~vaIQva~~l~~p~~~~-~~Vl~~W  477 (829)
T KOG2280|consen  399 SLRTPNPDEYMRVCRELRVLNALRDVRIGIPLTHEQYRHLSEEVVIDRLVDRHLYSVAIQVAKLLNLPESQG-DRVLLEW  477 (829)
T ss_pred             ccccCChHHHHHHHHHHHHHhhhcccccCccccHHHHhhhchhhhhHHHHhcchhHHHHHHHHHhCCccccc-cHHHHHH
Confidence            34444555444444333        23466666555544     5667778888999988877664322112 5778888


Q ss_pred             HHHHHhcCCCCChhHHHHHhhcCCC--CCchhHHHHHHHHHhcCCHHHHHHHHccCCCC--------ChHHHHHHHHHHH
Q 044988          160 MNLYLMSGGECGVGCARLLFDDMPA--RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR--------NVVSWTTMISGCA  229 (538)
Q Consensus       160 ~~~~~~~g~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--------~~~~~~~li~~~~  229 (538)
                      ...+.+..+....+.+..+-+++..  .+..+|..+.+-.-..|+.+-|..+++.=+..        +..-+...+.-..
T Consensus       478 a~~kI~~~d~~d~~vld~I~~kls~~~~~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kai  557 (829)
T KOG2280|consen  478 ARRKIKQSDKMDEEVLDKIDEKLSAKLTPGISYAAIARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAI  557 (829)
T ss_pred             HHHHHhccCccchHHHHHHHHHhcccCCCceeHHHHHHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHH
Confidence            8888877653334555555566655  46678888888888999999999998875431        2223555566667


Q ss_pred             HcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHH
Q 044988          230 QNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIE  309 (538)
Q Consensus       230 ~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  309 (538)
                      ..|+.+-...++-++.+.   .+...|...+      .+...|..+|..+.+..   +..       .+-+.|-...+..
T Consensus       558 es~d~~Li~~Vllhlk~~---~~~s~l~~~l------~~~p~a~~lY~~~~r~~---~~~-------~l~d~y~q~dn~~  618 (829)
T KOG2280|consen  558 ESGDTDLIIQVLLHLKNK---LNRSSLFMTL------RNQPLALSLYRQFMRHQ---DRA-------TLYDFYNQDDNHQ  618 (829)
T ss_pred             hcCCchhHHHHHHHHHHH---HHHHHHHHHH------HhchhhhHHHHHHHHhh---chh-------hhhhhhhcccchh
Confidence            778877777777766542   1112221111      22334444444444320   110       1112222222222


Q ss_pred             HHHHHHHhc------CCCCcchHHHHHHHHHhcCC---ccHHH-----------------------HHHHHHHHHhcccC
Q 044988          310 EAYGVFRKM------QRRNTVSWTSMITGFAKQGY---AQEAL-----------------------LTFLGVLSACSHGG  357 (538)
Q Consensus       310 ~a~~~~~~m------~~~~~~~~~~li~~~~~~~~---~~~a~-----------------------~~~~~ll~~~~~~~  357 (538)
                      .+-.+.-+-      .++-.........++.+...   ..+|.                       .+.+.-+.-+...|
T Consensus       619 ~~a~~~~q~~~~~~~~~~r~~~lk~~a~~~a~sk~~s~e~ka~ed~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g  698 (829)
T KOG2280|consen  619 ALASFHLQASYAAETIEGRIPALKTAANAFAKSKEKSFEAKALEDQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIG  698 (829)
T ss_pred             hhhhhhhhhhhhhhhhcccchhHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHcc
Confidence            111111000      00001111112222222221   01111                       12223334444556


Q ss_pred             cHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHc
Q 044988          358 FVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKL  437 (538)
Q Consensus       358 ~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~  437 (538)
                      +..+|.++-.+.+     -||-..|..=+.+++..+++++-+++-+..+   .+.-|.-+..+|.+.|+.++|.+++.+.
T Consensus       699 ~~k~a~ql~~~Fk-----ipdKr~~wLk~~aLa~~~kweeLekfAkskk---sPIGy~PFVe~c~~~~n~~EA~KYiprv  770 (829)
T KOG2280|consen  699 QNKRAEQLKSDFK-----IPDKRLWWLKLTALADIKKWEELEKFAKSKK---SPIGYLPFVEACLKQGNKDEAKKYIPRV  770 (829)
T ss_pred             chHHHHHHHHhcC-----CcchhhHHHHHHHHHhhhhHHHHHHHHhccC---CCCCchhHHHHHHhcccHHHHhhhhhcc
Confidence            6666666655543     4677777777777777777777777666654   2455666777777777777777777776


Q ss_pred             hhccCCCCcccHHHHHHHHHHhcCChHHHHHHH
Q 044988          438 VAEIDPEQAAGYLALVANVYAAAKRWQDVAAVR  470 (538)
Q Consensus       438 ~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~  470 (538)
                       .++.         -...+|.+.|++.+|.++-
T Consensus       771 -~~l~---------ekv~ay~~~~~~~eAad~A  793 (829)
T KOG2280|consen  771 -GGLQ---------EKVKAYLRVGDVKEAADLA  793 (829)
T ss_pred             -CChH---------HHHHHHHHhccHHHHHHHH
Confidence             2211         2235677777777777653

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=97.75  E-value=0.00028  Score=52.28  Aligned_cols=92  Identities=18%  Similarity=0.258  Sum_probs=67.1

Q ss_pred             HHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHh
Q 044988          382 YGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAA  459 (538)
Q Consensus       382 ~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~  459 (538)
                      +..+...+...|++++|...++++. ..|+ ...+..+...+...+++++|.+.++.. ....|.+...+. .++.++..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~-~~~~~~~~~~~~-~~~~~~~~   80 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKA-LELDPDNAKAYY-NLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHH-HhCCCcchhHHH-HHHHHHHH
Confidence            4556666777788888888887663 2333 356666777777788888888888887 777777776566 77788888


Q ss_pred             cCChHHHHHHHHHHHh
Q 044988          460 AKRWQDVAAVRQKMIK  475 (538)
Q Consensus       460 ~g~~~~A~~~~~~m~~  475 (538)
                      .|++++|...++...+
T Consensus        81 ~~~~~~a~~~~~~~~~   96 (100)
T cd00189          81 LGKYEEALEAYEKALE   96 (100)
T ss_pred             HHhHHHHHHHHHHHHc
Confidence            8888888888877664

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.74  E-value=0.00036  Score=51.46  Aligned_cols=79  Identities=15%  Similarity=0.050  Sum_probs=66.3

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHhHhCCC-CCCcchHHHHHHHHHccC--------CcHHHHHHHHHHHHhCCCCchhHHh
Q 044988           87 NQMIRGHARSETPEKSVYLYKQMIDKET-EPDEYTYSFLLSVCARCG--------LFREGEQVHGRVLASGYCSNVFIRT  157 (538)
Q Consensus        87 ~~li~~~~~~~~~~~a~~~~~~m~~~~~-~p~~~~~~~li~~~~~~~--------~~~~a~~~~~~~~~~~~~~~~~~~~  157 (538)
                      ...|..+...+++.....+|+.+++.|+ .|+..+|+.++.+.++..        +.-..+.+|++|+..++.|+..+|+
T Consensus        29 i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYn  108 (120)
T PF08579_consen   29 IDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYN  108 (120)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHH
Confidence            4456667777999999999999999999 899999999999877653        2345678899999999999999999


Q ss_pred             HHHHHHHh
Q 044988          158 NLMNLYLM  165 (538)
Q Consensus       158 ~l~~~~~~  165 (538)
                      .++..+.+
T Consensus       109 ivl~~Llk  116 (120)
T PF08579_consen  109 IVLGSLLK  116 (120)
T ss_pred             HHHHHHHH
Confidence            99888754

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=97.72  E-value=0.0015  Score=53.07  Aligned_cols=90  Identities=17%  Similarity=0.198  Sum_probs=45.9

Q ss_pred             HHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCc----chHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCc--hhHHhHH
Q 044988           86 WNQMIRGHARSETPEKSVYLYKQMIDKETEPDE----YTYSFLLSVCARCGLFREGEQVHGRVLASGYCSN--VFIRTNL  159 (538)
Q Consensus        86 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~l  159 (538)
                      |..++..+ ..++...+...++.+.+..  |+.    ...-.+...+...|++++|...|+........|+  ......|
T Consensus        15 y~~~~~~~-~~~~~~~~~~~~~~l~~~~--~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~L   91 (145)
T PF09976_consen   15 YEQALQAL-QAGDPAKAEAAAEQLAKDY--PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRL   91 (145)
T ss_pred             HHHHHHHH-HCCCHHHHHHHHHHHHHHC--CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHH
Confidence            44444444 3666666666677666542  222    1222334556666777777777777766542221  1223334


Q ss_pred             HHHHHhcCCCCChhHHHHHhhc
Q 044988          160 MNLYLMSGGECGVGCARLLFDD  181 (538)
Q Consensus       160 ~~~~~~~g~~~~~~~a~~~~~~  181 (538)
                      ...+...|+   +++|+..++.
T Consensus        92 A~~~~~~~~---~d~Al~~L~~  110 (145)
T PF09976_consen   92 ARILLQQGQ---YDEALATLQQ  110 (145)
T ss_pred             HHHHHHcCC---HHHHHHHHHh
Confidence            444444444   4444444443

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.70  E-value=0.00044  Score=65.48  Aligned_cols=120  Identities=12%  Similarity=0.140  Sum_probs=86.6

Q ss_pred             CCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC-C-----CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcch
Q 044988           47 GFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN-P-----STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYT  120 (538)
Q Consensus        47 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-~-----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~  120 (538)
                      +.+.+.......++......+++++..++-+... |     -..+.+++++.|.+.|..+.++.++..=...|+-||..|
T Consensus        61 ~~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s  140 (429)
T PF10037_consen   61 KKPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFS  140 (429)
T ss_pred             CCCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhh
Confidence            3445566667777777777777777777665552 1     223556888888888888888888888888888888888


Q ss_pred             HHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhc
Q 044988          121 YSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMS  166 (538)
Q Consensus       121 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  166 (538)
                      ++.||..+.+.|++..|.++...|...+...+..++.-.+.+|.+.
T Consensus       141 ~n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  141 FNLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            8888888888888888888888887776666666665555555554

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.69  E-value=0.00049  Score=53.68  Aligned_cols=94  Identities=16%  Similarity=0.049  Sum_probs=53.9

Q ss_pred             HHHHHHHHhhhcCChHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC---cccHHHH
Q 044988          381 HYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ---AAGYLAL  452 (538)
Q Consensus       381 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~---~~~~~~~  452 (538)
                      ++..++..+.+.|++++|.+.|+.+. ..|+    ...+..+...+.+.|+++.|...++.+ ....|++   +..+. .
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~-~~~~p~~~~~~~~~~-~   81 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAV-VKKYPKSPKAPDALL-K   81 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHH-HHHCCCCCcccHHHH-H
Confidence            34455555666666666666666553 2232    234444555666666666666666666 5555553   22244 5


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhC
Q 044988          453 VANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       453 l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      ++.++.+.|++++|...++++.+.
T Consensus        82 ~~~~~~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        82 LGMSLQELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHHHHHHhCChHHHHHHHHHHHHH
Confidence            566666666666666666666654

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=97.66  E-value=0.0017  Score=52.02  Aligned_cols=96  Identities=13%  Similarity=0.060  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHH
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNAL  298 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l  298 (538)
                      .....+...+...|++++|...|+.....+ +.+...+..+...+...|+++.|...++...+.     .|.+...+..+
T Consensus        18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-----~p~~~~~~~~l   91 (135)
T TIGR02552        18 EQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAAL-----DPDDPRPYFHA   91 (135)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-----CCCChHHHHHH
Confidence            334455566666777777777777766543 234555566666666777777777777766664     45555555566


Q ss_pred             HHHHHhCCCHHHHHHHHHhcCC
Q 044988          299 IHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       299 ~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      ...|...|++++|...|++..+
T Consensus        92 a~~~~~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        92 AECLLALGEPESALKALDLAIE  113 (135)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            6777777777777777776654

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=97.63  E-value=0.00017  Score=49.82  Aligned_cols=64  Identities=20%  Similarity=0.186  Sum_probs=57.8

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcC-ChHHHHHHHHHHHh
Q 044988          410 NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAK-RWQDVAAVRQKMIK  475 (538)
Q Consensus       410 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~m~~  475 (538)
                      ++.+|..+...+...|++++|+..|+++ ....|+++..+. .++.+|.+.| ++++|++.+++..+
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~a-i~~~p~~~~~~~-~~g~~~~~~~~~~~~A~~~~~~al~   66 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKA-IELDPNNAEAYY-NLGLAYMKLGKDYEEAIEDFEKALK   66 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHH-HHHSTTHHHHHH-HHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHcCCCCHHHHH-HHHHHHHHhCccHHHHHHHHHHHHH
Confidence            4678888889999999999999999999 999999999888 9999999999 79999999988765

...

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.63  E-value=5.3e-05  Score=54.83  Aligned_cols=80  Identities=16%  Similarity=0.184  Sum_probs=36.1

Q ss_pred             CcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCH-HHHHHHHHHHHhcCCHHHHHHHHH
Q 044988          357 GFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPND-AVLGSLLLGCRIHNNAELASQVAQ  435 (538)
Q Consensus       357 ~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~-~~~~~l~~~~~~~~~~~~A~~~~~  435 (538)
                      |+++.|+.+++++.+.....|+...+..+..+|.+.|++++|..+++.....|.. ...-.+..++.+.|++++|+++++
T Consensus         3 ~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~l~   82 (84)
T PF12895_consen    3 GNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQKLKLDPSNPDIHYLLARCLLKLGKYEEAIKALE   82 (84)
T ss_dssp             T-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHCHTHHHCHHHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhCCHHHHHHHHh
Confidence            5556666666665554111112333444555555555555555555553222222 222223344555555555555554


Q ss_pred             H
Q 044988          436 K  436 (538)
Q Consensus       436 ~  436 (538)
                      +
T Consensus        83 ~   83 (84)
T PF12895_consen   83 K   83 (84)
T ss_dssp             H
T ss_pred             c
Confidence            3

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.61  E-value=0.048  Score=50.36  Aligned_cols=110  Identities=13%  Similarity=0.122  Sum_probs=83.2

Q ss_pred             HHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 044988          346 FLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHN  425 (538)
Q Consensus       346 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~  425 (538)
                      ....+.-|...|....|.++-.+.    . -|+..-|..-+.+|+..++|++-.++-..   +-.+..|..++.+|.+.|
T Consensus       180 l~~Ti~~li~~~~~k~A~kl~k~F----k-v~dkrfw~lki~aLa~~~~w~eL~~fa~s---kKsPIGyepFv~~~~~~~  251 (319)
T PF04840_consen  180 LNDTIRKLIEMGQEKQAEKLKKEF----K-VPDKRFWWLKIKALAENKDWDELEKFAKS---KKSPIGYEPFVEACLKYG  251 (319)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHc----C-CcHHHHHHHHHHHHHhcCCHHHHHHHHhC---CCCCCChHHHHHHHHHCC
Confidence            334455556667777777775554    3 48888999999999999999988886654   234588899999999999


Q ss_pred             CHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          426 NAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       426 ~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      +..+|..+..++     |+     . --+..|.+.|+|.+|.+.--+..
T Consensus       252 ~~~eA~~yI~k~-----~~-----~-~rv~~y~~~~~~~~A~~~A~~~k  289 (319)
T PF04840_consen  252 NKKEASKYIPKI-----PD-----E-ERVEMYLKCGDYKEAAQEAFKEK  289 (319)
T ss_pred             CHHHHHHHHHhC-----Ch-----H-HHHHHHHHCCCHHHHHHHHHHcC
Confidence            999999998886     32     2 44478999999999988754443

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.61  E-value=0.0012  Score=52.60  Aligned_cols=86  Identities=8%  Similarity=-0.001  Sum_probs=49.5

Q ss_pred             HHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCc
Q 044988          263 CAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYA  339 (538)
Q Consensus       263 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~  339 (538)
                      +...|++++|..+|+.+...     .|.+...|..|..++-..|++++|...|.....   .|+.++-.+..++...|+.
T Consensus        45 ly~~G~l~~A~~~f~~L~~~-----Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~L~lG~~  119 (157)
T PRK15363         45 LMEVKEFAGAARLFQLLTIY-----DAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECYLACDNV  119 (157)
T ss_pred             HHHCCCHHHHHHHHHHHHHh-----CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHcCCH
Confidence            34555666666666555554     555555555666666666666666666665432   3455555566666666655


Q ss_pred             cHHHHHHHHHHHHh
Q 044988          340 QEALLTFLGVLSAC  353 (538)
Q Consensus       340 ~~a~~~~~~ll~~~  353 (538)
                      +.|...|...+.-|
T Consensus       120 ~~A~~aF~~Ai~~~  133 (157)
T PRK15363        120 CYAIKALKAVVRIC  133 (157)
T ss_pred             HHHHHHHHHHHHHh
Confidence            55555555555555

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.61  E-value=0.00021  Score=48.67  Aligned_cols=58  Identities=12%  Similarity=0.252  Sum_probs=48.4

Q ss_pred             HHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          417 LLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       417 l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      +...+...|++++|.+.|+++ .+..|+++..+. .++.++...|++++|..+|+++.+.
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~-l~~~P~~~~a~~-~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQA-LKQDPDNPEAWY-LLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHH-HCCSTTHHHHHH-HHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHH-HHHCCCCHHHHH-HHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            445678889999999999999 888899888788 8999999999999999999888753

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.61  E-value=0.0026  Score=53.36  Aligned_cols=114  Identities=15%  Similarity=0.106  Sum_probs=69.4

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD--QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                      ..+..+...+...|++++|...|++..+....+.  ...+..+...+.+.|+++.|...+....+.     .|.+...+.
T Consensus        36 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~-----~p~~~~~~~  110 (172)
T PRK02603         36 FVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL-----NPKQPSALN  110 (172)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CcccHHHHH
Confidence            3556666667777777777777777765433222  345666666677777777777777777765     455555555


Q ss_pred             HHHHHHHhCCC--------------HHHHHHHHHhcCCCCcchHHHHHHHHHhcC
Q 044988          297 ALIHMYASCGE--------------IEEAYGVFRKMQRRNTVSWTSMITGFAKQG  337 (538)
Q Consensus       297 ~l~~~~~~~g~--------------~~~a~~~~~~m~~~~~~~~~~li~~~~~~~  337 (538)
                      .+...|...|+              +++|.+++++....++..|..++.-+...|
T Consensus       111 ~lg~~~~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~  165 (172)
T PRK02603        111 NIAVIYHKRGEKAEEAGDQDEAEALFDKAAEYWKQAIRLAPNNYIEAQNWLKTTG  165 (172)
T ss_pred             HHHHHHHHcCChHhHhhCHHHHHHHHHHHHHHHHHHHhhCchhHHHHHHHHHhcC
Confidence            66666666665              355555665555544444544444444444

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=97.59  E-value=0.065  Score=50.13  Aligned_cols=429  Identities=11%  Similarity=0.068  Sum_probs=207.4

Q ss_pred             HhccCChHHHHHHHHHHHHhCCCC-C----hhHHHHHHHHHHccCChhHHHHHHhcCCC--CCcchHHHHHHHH--hcCC
Q 044988           27 LQIRNTTKTLFQIHSQIIINGFSQ-K----NYILAKLLAFYVTSGYLINAHKVFEKTEN--PSTAIWNQMIRGH--ARSE   97 (538)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~~~~~-~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~~~~~~~~li~~~--~~~~   97 (538)
                      +.+.+++.++..+|..+.+..-.. .    ...-+.++++|... +.+..........+  | ...|-.+..++  -+.+
T Consensus        16 Lqkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl~-nld~Me~~l~~l~~~~~-~s~~l~LF~~L~~Y~~k   93 (549)
T PF07079_consen   16 LQKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFLN-NLDLMEKQLMELRQQFG-KSAYLPLFKALVAYKQK   93 (549)
T ss_pred             HHHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHHh-hHHHHHHHHHHHHHhcC-CchHHHHHHHHHHHHhh
Confidence            456789999999999998764221 1    22345777887643 34444333333332  3 33455554443  4788


Q ss_pred             CchHHHHHHHHhHhC--CCCCC---c---------chHHHHHHHHHccCCcHHHHHHHHHHHHhCCC----CchhHHhHH
Q 044988           98 TPEKSVYLYKQMIDK--ETEPD---E---------YTYSFLLSVCARCGLFREGEQVHGRVLASGYC----SNVFIRTNL  159 (538)
Q Consensus        98 ~~~~a~~~~~~m~~~--~~~p~---~---------~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~l  159 (538)
                      .+.+|++.+..-.+.  +..|.   .         .-=+..+..+...|++.+++.+++++...=++    -+..+|+.+
T Consensus        94 ~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~  173 (549)
T PF07079_consen   94 EYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRA  173 (549)
T ss_pred             hHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHH
Confidence            999999988877654  32221   1         11234566788999999999999998876444    778888887


Q ss_pred             HHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHc--CCHHHH
Q 044988          160 MNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQN--GKSRQA  237 (538)
Q Consensus       160 ~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~--~~~~~a  237 (538)
                      +-++.++--   ++.-    +.+...=..-|--++-.|.+.=+.-++... .+. .|......+++....-.  .+..--
T Consensus       174 vlmlsrSYf---LEl~----e~~s~dl~pdyYemilfY~kki~~~d~~~Y-~k~-~peeeL~s~imqhlfi~p~e~l~~~  244 (549)
T PF07079_consen  174 VLMLSRSYF---LELK----ESMSSDLYPDYYEMILFYLKKIHAFDQRPY-EKF-IPEEELFSTIMQHLFIVPKERLPPL  244 (549)
T ss_pred             HHHHhHHHH---HHHH----HhcccccChHHHHHHHHHHHHHHHHhhchH-Hhh-CcHHHHHHHHHHHHHhCCHhhccHH
Confidence            777765542   2211    111111112244444444332111111000 000 01112222222222111  111222


Q ss_pred             HHHHHHHHHCCCCCCHHHH-HHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHH
Q 044988          238 LSLFNEMRRARVGLDQVAL-VAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFR  316 (538)
Q Consensus       238 ~~~~~~m~~~g~~p~~~~~-~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  316 (538)
                      +++++...+.-+.|+.... ..++....+  +.+++..+-+.+.......-...-+..+..++....+.++...|.+.+.
T Consensus       245 mq~l~~We~~yv~p~~~LVi~~L~~~f~~--~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk~~~T~~a~q~l~  322 (549)
T PF07079_consen  245 MQILENWENFYVHPNYDLVIEPLKQQFMS--DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVKQVQTEEAKQYLA  322 (549)
T ss_pred             HHHHHHHHhhccCCchhHHHHHHHHHHhc--ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            2333333333344432211 111112211  2333322222222110000011122333444444445555555554444


Q ss_pred             hcC--CC---------------------CcchHHHHHHH---HHhcCCccHHH-HH----HHHHHHHhcccCcHHHHHHH
Q 044988          317 KMQ--RR---------------------NTVSWTSMITG---FAKQGYAQEAL-LT----FLGVLSACSHGGFVDEGRQF  365 (538)
Q Consensus       317 ~m~--~~---------------------~~~~~~~li~~---~~~~~~~~~a~-~~----~~~ll~~~~~~~~~~~a~~~  365 (538)
                      -+.  +|                     |...++.+-.-   +......+.-. ..    ....=+-+...+.-++|..+
T Consensus       323 lL~~ldp~~svs~Kllls~~~lq~Iv~~DD~~~Tklr~yL~lwe~~qs~DiDrqQLvh~L~~~Ak~lW~~g~~dekalnL  402 (549)
T PF07079_consen  323 LLKILDPRISVSEKLLLSPKVLQDIVCEDDESYTKLRDYLNLWEEIQSYDIDRQQLVHYLVFGAKHLWEIGQCDEKALNL  402 (549)
T ss_pred             HHHhcCCcchhhhhhhcCHHHHHHHHhcchHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHHHHHHHHhcCCccHHHHHH
Confidence            322  12                     22222222111   10000000000 11    11111122223447788888


Q ss_pred             HHHhhhhcCCCc-cHHHHHHHH----HHhhhcC---ChHHH---HHHHHhCCCC----CCHHHHHHHHHH--HHhcCCHH
Q 044988          366 FECMNQNWGIKP-RIEHYGCMV----DLFSRAG---LMDEA---FSLVQNMPMK----PNDAVLGSLLLG--CRIHNNAE  428 (538)
Q Consensus       366 ~~~~~~~~~~~p-~~~~~~~l~----~~~~~~g---~~~~A---~~~~~~~~~~----p~~~~~~~l~~~--~~~~~~~~  428 (538)
                      ++.+.+-   .| |..+-|...    .+|..+=   .+.+-   ...+++....    .+...-|.|.+|  +..+|++.
T Consensus       403 Lk~il~f---t~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~LaDAEyLysqgey~  479 (549)
T PF07079_consen  403 LKLILQF---TNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFLADAEYLYSQGEYH  479 (549)
T ss_pred             HHHHHHh---ccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHHhcccHH
Confidence            8887743   44 443333322    2332221   11211   2222333322    345566777777  67889999


Q ss_pred             HHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          429 LASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       429 ~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      ++.-.-.-+ .++.| ++.+|. +++-++....++++|..++.++.
T Consensus       480 kc~~ys~WL-~~iaP-S~~~~R-LlGl~l~e~k~Y~eA~~~l~~LP  522 (549)
T PF07079_consen  480 KCYLYSSWL-TKIAP-SPQAYR-LLGLCLMENKRYQEAWEYLQKLP  522 (549)
T ss_pred             HHHHHHHHH-HHhCC-cHHHHH-HHHHHHHHHhhHHHHHHHHHhCC
Confidence            998888887 88899 566599 99999999999999999998865

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.59  E-value=0.0011  Score=51.69  Aligned_cols=101  Identities=13%  Similarity=0.093  Sum_probs=78.9

Q ss_pred             HHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC----HHHHHHHHH
Q 044988          346 FLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN----DAVLGSLLL  419 (538)
Q Consensus       346 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~----~~~~~~l~~  419 (538)
                      +......+...|++++|...|..+.+.+.-.| ....+..+..++.+.|++++|.+.|+.+. ..|+    ...+..+..
T Consensus         5 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~   84 (119)
T TIGR02795         5 YYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGM   84 (119)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHH
Confidence            44455566677899999999999987621111 14567779999999999999999999874 3344    456777788


Q ss_pred             HHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          420 GCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       420 ~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      ++.+.|+.++|...++++ ....|++..
T Consensus        85 ~~~~~~~~~~A~~~~~~~-~~~~p~~~~  111 (119)
T TIGR02795        85 SLQELGDKEKAKATLQQV-IKRYPGSSA  111 (119)
T ss_pred             HHHHhCChHHHHHHHHHH-HHHCcCChh
Confidence            899999999999999999 888888766

Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=97.58  E-value=0.06  Score=53.00  Aligned_cols=64  Identities=19%  Similarity=0.230  Sum_probs=36.2

Q ss_pred             hcCChHHHHHHHHhCC------CC----CCHHHHHHHHHH--HHhcCCHHHHHHHHHHch--hccCCCCcccHHHHHHHH
Q 044988          391 RAGLMDEAFSLVQNMP------MK----PNDAVLGSLLLG--CRIHNNAELASQVAQKLV--AEIDPEQAAGYLALVANV  456 (538)
Q Consensus       391 ~~g~~~~A~~~~~~~~------~~----p~~~~~~~l~~~--~~~~~~~~~A~~~~~~~~--~~~~p~~~~~~~~~l~~~  456 (538)
                      +.|..++|..+++...      +.    ..+..|..+|.+  ....|..+.|++.--.+.  .++-|+... |. +|+-+
T Consensus       989 ~~g~~~dat~lles~~l~~~~ri~~n~WrgAEAyHFmilAQrql~eg~v~~Al~Tal~L~DYEd~lpP~ei-yS-llALa 1066 (1189)
T KOG2041|consen  989 KHGFLEDATDLLESGLLAEQSRILENTWRGAEAYHFMILAQRQLFEGRVKDALQTALILSDYEDFLPPAEI-YS-LLALA 1066 (1189)
T ss_pred             hcCcchhhhhhhhhhhhhhHHHHHHhhhhhHHHHHHHHHHHHHHHhchHHHHHHHHhhhccHhhcCCHHHH-HH-HHHHH
Confidence            3567777777666542      11    223455555554  566788888877655554  445555444 55 55433

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.53  E-value=0.0048  Score=54.55  Aligned_cols=101  Identities=16%  Similarity=0.174  Sum_probs=85.1

Q ss_pred             Cc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhc-C--CHHHHHHHHHHchhccCCCCcccH
Q 044988          376 KP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGCRIH-N--NAELASQVAQKLVAEIDPEQAAGY  449 (538)
Q Consensus       376 ~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~~~~-~--~~~~A~~~~~~~~~~~~p~~~~~~  449 (538)
                      .| |...|-.|...|.+.|+.+.|..-|.+.. . .+|...+..+..++... |  ...++..+++++ ...+|++..+.
T Consensus       152 nP~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~a-l~~D~~~iral  230 (287)
T COG4235         152 NPGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQA-LALDPANIRAL  230 (287)
T ss_pred             CCCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHH-HhcCCccHHHH
Confidence            45 78999999999999999999999998874 3 35566777777664322 2  457899999999 99999999977


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          450 LALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       450 ~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      . +|+..+...|++.+|...|+.|.+..-
T Consensus       231 ~-lLA~~afe~g~~~~A~~~Wq~lL~~lp  258 (287)
T COG4235         231 S-LLAFAAFEQGDYAEAAAAWQMLLDLLP  258 (287)
T ss_pred             H-HHHHHHHHcccHHHHHHHHHHHHhcCC
Confidence            7 999999999999999999999998644

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.51  E-value=0.00038  Score=50.29  Aligned_cols=78  Identities=21%  Similarity=0.257  Sum_probs=61.8

Q ss_pred             cCChHHHHHHHHhCC-CCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHH
Q 044988          392 AGLMDEAFSLVQNMP-MKP---NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVA  467 (538)
Q Consensus       392 ~g~~~~A~~~~~~~~-~~p---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~  467 (538)
                      .|+++.|+.+++++. ..|   +...+..+..++.+.|++++|..++++  .+..|.+..... .++.+|.+.|++++|+
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~--~~~~~~~~~~~~-l~a~~~~~l~~y~eAi   78 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK--LKLDPSNPDIHY-LLARCLLKLGKYEEAI   78 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC--HTHHHCHHHHHH-HHHHHHHHTT-HHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH--hCCCCCCHHHHH-HHHHHHHHhCCHHHHH
Confidence            588999999999884 234   455666688999999999999999988  455566655466 7799999999999999


Q ss_pred             HHHHH
Q 044988          468 AVRQK  472 (538)
Q Consensus       468 ~~~~~  472 (538)
                      +++++
T Consensus        79 ~~l~~   83 (84)
T PF12895_consen   79 KALEK   83 (84)
T ss_dssp             HHHHH
T ss_pred             HHHhc
Confidence            99986

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.47  E-value=0.00092  Score=58.62  Aligned_cols=102  Identities=17%  Similarity=0.189  Sum_probs=83.7

Q ss_pred             hcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHH
Q 044988          353 CSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAEL  429 (538)
Q Consensus       353 ~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~  429 (538)
                      +.+.+++++|+..|.+.++   +.| |.+-|..-..+|.+.|.++.|++-.+... +.|. ..+|..|..+|...|++++
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~---l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~  167 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIE---LDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHh---cCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHH
Confidence            3456789999999999885   477 57777788999999999999998888764 5565 5799999999999999999


Q ss_pred             HHHHHHHchhccCCCCcccHHHHHHHHHHh
Q 044988          430 ASQVAQKLVAEIDPEQAAGYLALVANVYAA  459 (538)
Q Consensus       430 A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~  459 (538)
                      |++.|++. .++.|++.+ |-+.|-.+=-+
T Consensus       168 A~~aykKa-LeldP~Ne~-~K~nL~~Ae~~  195 (304)
T KOG0553|consen  168 AIEAYKKA-LELDPDNES-YKSNLKIAEQK  195 (304)
T ss_pred             HHHHHHhh-hccCCCcHH-HHHHHHHHHHH
Confidence            99999999 999999998 65466444333

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.47  E-value=0.0018  Score=61.27  Aligned_cols=101  Identities=13%  Similarity=0.059  Sum_probs=84.8

Q ss_pred             HHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCH
Q 044988          351 SACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNA  427 (538)
Q Consensus       351 ~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~  427 (538)
                      ..+...|+++.|...|.+..+.   .| +...|..+..+|.+.|++++|+..++++. ..| +...|..+..+|...|++
T Consensus        10 ~~a~~~~~~~~Ai~~~~~Al~~---~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~~   86 (356)
T PLN03088         10 KEAFVDDDFALAVDLYTQAIDL---DPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEY   86 (356)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCCH
Confidence            4455678999999999999865   55 57788899999999999999999999884 445 467888888899999999


Q ss_pred             HHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          428 ELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       428 ~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ++|+..|+++ ..+.|++..... .+..+
T Consensus        87 ~eA~~~~~~a-l~l~P~~~~~~~-~l~~~  113 (356)
T PLN03088         87 QTAKAALEKG-ASLAPGDSRFTK-LIKEC  113 (356)
T ss_pred             HHHHHHHHHH-HHhCCCCHHHHH-HHHHH
Confidence            9999999999 999999998555 55444

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=97.46  E-value=0.097  Score=48.92  Aligned_cols=130  Identities=14%  Similarity=0.213  Sum_probs=89.5

Q ss_pred             HHHHHHHHHhcccCcHHHHHHHHHHhhhhcC-CCccHHHHHHHHHHhhhcCChHHHHHHHHh-CCCCCCHHHH-HHHHHH
Q 044988          344 LTFLGVLSACSHGGFVDEGRQFFECMNQNWG-IKPRIEHYGCMVDLFSRAGLMDEAFSLVQN-MPMKPNDAVL-GSLLLG  420 (538)
Q Consensus       344 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~-~~~~p~~~~~-~~l~~~  420 (538)
                      .+|...+++-.+..-++.|+.+|-++.+. + +.+++.++++++.-++ .|+...|.++|+- |..-||...| +..+..
T Consensus       398 ~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~-~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~f~d~~~y~~kyl~f  475 (660)
T COG5107         398 FVFCVHLNYVLRKRGLEAARKLFIKLRKE-GIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLKFPDSTLYKEKYLLF  475 (660)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHhcc-CCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHhCCCchHHHHHHHHH
Confidence            44555666666777788888888888777 5 5678888888888555 5777888888864 3344554433 456666


Q ss_pred             HHhcCCHHHHHHHHHHchhccCCCC-cccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          421 CRIHNNAELASQVAQKLVAEIDPEQ-AAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       421 ~~~~~~~~~A~~~~~~~~~~~~p~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      +..-++-+.|..+|+.....+..+. ...|. .+++--..-|+...+..+=++|...
T Consensus       476 Li~inde~naraLFetsv~r~~~~q~k~iy~-kmi~YEs~~G~lN~v~sLe~rf~e~  531 (660)
T COG5107         476 LIRINDEENARALFETSVERLEKTQLKRIYD-KMIEYESMVGSLNNVYSLEERFREL  531 (660)
T ss_pred             HHHhCcHHHHHHHHHHhHHHHHHhhhhHHHH-HHHHHHHhhcchHHHHhHHHHHHHH
Confidence            7778888888888886642222221 22355 6667677788888888888887753

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.44  E-value=0.0029  Score=57.64  Aligned_cols=136  Identities=13%  Similarity=0.180  Sum_probs=100.8

Q ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          293 SLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       293 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                      .+|..++...-+.+..+.|+.+|.+..+....+|...+.. +              .+ -+...++.+.|..+|+...+.
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~-A--------------~~-E~~~~~d~~~A~~Ife~glk~   65 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAY-A--------------LM-EYYCNKDPKRARKIFERGLKK   65 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHH-H--------------HH-HHHTCS-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHH-H--------------HH-HHHhCCCHHHHHHHHHHHHHH
Confidence            3577788888888889999999999887555555443321 1              01 122235777899999999987


Q ss_pred             cCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          373 WGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPND----AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       373 ~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~----~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      +  ..+...|...++.+.+.|+.+.|..+|++.. .-|..    ..|...+..-.+.|+.+.+.++.+++ .+..|++..
T Consensus        66 f--~~~~~~~~~Y~~~l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~-~~~~~~~~~  142 (280)
T PF05843_consen   66 F--PSDPDFWLEYLDFLIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRA-EELFPEDNS  142 (280)
T ss_dssp             H--TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHH-HHHTTTS-H
T ss_pred             C--CCCHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHHhhhhhH
Confidence            5  4567788899999999999999999999875 22333    59999999999999999999999999 888888665

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.44  E-value=0.0019  Score=54.27  Aligned_cols=95  Identities=14%  Similarity=0.115  Sum_probs=75.3

Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALV  453 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l  453 (538)
                      ...+..+...+...|++++|...|++.. ..|+    ...+..+...+.+.|++++|...++++ ....|++...+. .+
T Consensus        35 a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~-~l  112 (172)
T PRK02603         35 AFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQA-LELNPKQPSALN-NI  112 (172)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCcccHHHHH-HH
Confidence            5567888888999999999999998774 2232    357778888899999999999999999 888999888777 88


Q ss_pred             HHHHHhcCC--------------hHHHHHHHHHHHh
Q 044988          454 ANVYAAAKR--------------WQDVAAVRQKMIK  475 (538)
Q Consensus       454 ~~~~~~~g~--------------~~~A~~~~~~m~~  475 (538)
                      +.+|...|+              +++|.+++++...
T Consensus       113 g~~~~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~  148 (172)
T PRK02603        113 AVIYHKRGEKAEEAGDQDEAEALFDKAAEYWKQAIR  148 (172)
T ss_pred             HHHHHHcCChHhHhhCHHHHHHHHHHHHHHHHHHHh
Confidence            888888776              4556666655554

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.42  E-value=0.0012  Score=62.43  Aligned_cols=89  Identities=19%  Similarity=0.123  Sum_probs=78.4

Q ss_pred             HHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCCh
Q 044988          386 VDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRW  463 (538)
Q Consensus       386 ~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~  463 (538)
                      ...+...|++++|+++|+++. ..| +...|..+..++...|++++|+..++++ ..+.|++...|. .++.+|...|++
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~A-l~l~P~~~~a~~-~lg~~~~~lg~~   86 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLDPNNAELYADRAQANIKLGNFTEAVADANKA-IELDPSLAKAYL-RKGTACMKLEEY   86 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCcCCHHHHH-HHHHHHHHhCCH
Confidence            455667899999999999884 444 4677788888899999999999999999 999999999888 999999999999


Q ss_pred             HHHHHHHHHHHhC
Q 044988          464 QDVAAVRQKMIKM  476 (538)
Q Consensus       464 ~~A~~~~~~m~~~  476 (538)
                      ++|+..|++..+.
T Consensus        87 ~eA~~~~~~al~l   99 (356)
T PLN03088         87 QTAKAALEKGASL   99 (356)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999998864

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.41  E-value=0.0073  Score=50.47  Aligned_cols=114  Identities=13%  Similarity=0.056  Sum_probs=65.5

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGL--DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p--~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                      ..|..+...+...|++++|+..|++.......|  ...++..+...+...|+.++|...+....+.     .|.....+.
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~-----~~~~~~~~~  110 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER-----NPFLPQALN  110 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CcCcHHHHH
Confidence            345666666667777777777777776542222  1235666666777777777777777777665     444445555


Q ss_pred             HHHHHHH-------hCCCHHHHH-------HHHHhcCCCCcchHHHHHHHHHhcC
Q 044988          297 ALIHMYA-------SCGEIEEAY-------GVFRKMQRRNTVSWTSMITGFAKQG  337 (538)
Q Consensus       297 ~l~~~~~-------~~g~~~~a~-------~~~~~m~~~~~~~~~~li~~~~~~~  337 (538)
                      .+...+.       ..|+++.|.       .++++....++..+......+...|
T Consensus       111 ~la~i~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~a~~~~p~~~~~~~~~~~~~~  165 (168)
T CHL00033        111 NMAVICHYRGEQAIEQGDSEIAEAWFDQAAEYWKQAIALAPGNYIEAQNWLKITG  165 (168)
T ss_pred             HHHHHHHHhhHHHHHcccHHHHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHhc
Confidence            5665665       666666444       4444444444444433333333333

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.38  E-value=0.0082  Score=46.20  Aligned_cols=109  Identities=16%  Similarity=0.118  Sum_probs=76.0

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHH
Q 044988          224 MISGCAQNGKSRQALSLFNEMRRARVGLD--QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHM  301 (538)
Q Consensus       224 li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  301 (538)
                      +..++-..|+.++|+.+|++....|....  ...+..+.+.+...|++++|..+++.....+.....  +......+..+
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~--~~~l~~f~Al~   84 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDEL--NAALRVFLALA   84 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccc--cHHHHHHHHHH
Confidence            44567778999999999999999887665  345666777788899999999999988876211111  33333345567


Q ss_pred             HHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 044988          302 YASCGEIEEAYGVFRKMQRRNTVSWTSMITGFA  334 (538)
Q Consensus       302 ~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~  334 (538)
                      +...|+.++|.+.+-...-++...|..-|..|.
T Consensus        85 L~~~gr~~eAl~~~l~~la~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   85 LYNLGRPKEALEWLLEALAETLPRYRRAIRFYA  117 (120)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            788899999998887655555445555555443

>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C

Probab=97.38  E-value=0.0028  Score=46.61  Aligned_cols=93  Identities=16%  Similarity=0.059  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHH
Q 044988          221 WTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIH  300 (538)
Q Consensus       221 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~  300 (538)
                      |..+...+...|++++|...+++..+.. +.+...+..+...+...++++.|...++...+.     .+.+...+..+..
T Consensus         3 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~~~~~~~   76 (100)
T cd00189           3 LLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALEL-----DPDNAKAYYNLGL   76 (100)
T ss_pred             HHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-----CCcchhHHHHHHH
Confidence            4455566666777777777777766532 222345555666666667777777777766664     3444455566677


Q ss_pred             HHHhCCCHHHHHHHHHhcC
Q 044988          301 MYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       301 ~~~~~g~~~~a~~~~~~m~  319 (538)
                      .+...|+++.|...+.+..
T Consensus        77 ~~~~~~~~~~a~~~~~~~~   95 (100)
T cd00189          77 AYYKLGKYEEALEAYEKAL   95 (100)
T ss_pred             HHHHHHhHHHHHHHHHHHH
Confidence            7777777777777776654

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=97.37  E-value=0.00021  Score=49.19  Aligned_cols=52  Identities=15%  Similarity=0.348  Sum_probs=37.2

Q ss_pred             HhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          422 RIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       422 ~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ...|++++|+++|+++ ....|++..... .++.+|.+.|++++|.++++++..
T Consensus         2 l~~~~~~~A~~~~~~~-l~~~p~~~~~~~-~la~~~~~~g~~~~A~~~l~~~~~   53 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKA-LQRNPDNPEARL-LLAQCYLKQGQYDEAEELLERLLK   53 (68)
T ss_dssp             HHTTHHHHHHHHHHHH-HHHTTTSHHHHH-HHHHHHHHTT-HHHHHHHHHCCHG
T ss_pred             hhccCHHHHHHHHHHH-HHHCCCCHHHHH-HHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3567777777777777 777777777666 777777777777777777777665

...

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.32  E-value=0.047  Score=53.23  Aligned_cols=255  Identities=15%  Similarity=0.129  Sum_probs=148.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHccCC-----------CCChHHHHHHHHHHHHcCC--HHHHHHHHHHHHHCCCCCCHHH
Q 044988          189 SWNSLLKGYVKRGDIDGAWKIFDEMP-----------HRNVVSWTTMISGCAQNGK--SRQALSLFNEMRRARVGLDQVA  255 (538)
Q Consensus       189 ~~~~li~~~~~~g~~~~A~~~~~~m~-----------~~~~~~~~~li~~~~~~~~--~~~a~~~~~~m~~~g~~p~~~~  255 (538)
                      .+.+-+..|...|.+++|.++----.           .-+...++..-.+|.+..+  +-+.+.-++++++.|-.|+...
T Consensus       558 p~~~~m~q~Ieag~f~ea~~iaclgVv~~DW~~LA~~ALeAL~f~~ARkAY~rVRdl~~L~li~EL~~~k~rge~P~~iL  637 (1081)
T KOG1538|consen  558 PQSAPMYQYIERGLFKEAYQIACLGVTDTDWRELAMEALEALDFETARKAYIRVRDLRYLELISELEERKKRGETPNDLL  637 (1081)
T ss_pred             cccccchhhhhccchhhhhcccccceecchHHHHHHHHHhhhhhHHHHHHHHHHhccHHHHHHHHHHHHHhcCCCchHHH
Confidence            44555556777777777765422111           0122345555566666554  3455566777888888898764


Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--------------C
Q 044988          256 LVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--------------R  321 (538)
Q Consensus       256 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--------------~  321 (538)
                      .   ...|+-.|.+.+|.++|..-       |..      |..+..|.....++.|.+++..-..              .
T Consensus       638 l---A~~~Ay~gKF~EAAklFk~~-------G~e------nRAlEmyTDlRMFD~aQE~~~~g~~~eKKmL~RKRA~WAr  701 (1081)
T KOG1538|consen  638 L---ADVFAYQGKFHEAAKLFKRS-------GHE------NRALEMYTDLRMFDYAQEFLGSGDPKEKKMLIRKRADWAR  701 (1081)
T ss_pred             H---HHHHHhhhhHHHHHHHHHHc-------Cch------hhHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHhh
Confidence            3   34466678888888777543       222      2334444444445555544433211              1


Q ss_pred             CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHH
Q 044988          322 NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSL  401 (538)
Q Consensus       322 ~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~  401 (538)
                      ++.--.+....+...|+.++|+       ..+...|-.+-+.++-+++-.     .+..+...+..-+.+...+.-|-++
T Consensus       702 ~~kePkaAAEmLiSaGe~~KAi-------~i~~d~gW~d~lidI~rkld~-----~ere~l~~~a~ylk~l~~~gLAaeI  769 (1081)
T KOG1538|consen  702 NIKEPKAAAEMLISAGEHVKAI-------EICGDHGWVDMLIDIARKLDK-----AEREPLLLCATYLKKLDSPGLAAEI  769 (1081)
T ss_pred             hcCCcHHHHHHhhcccchhhhh-------hhhhcccHHHHHHHHHhhcch-----hhhhHHHHHHHHHhhccccchHHHH
Confidence            1111122334455556665553       444555555555555444432     2344555555555566677778888


Q ss_pred             HHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHH---------HHHHHHhcCChHHHHHHHHH
Q 044988          402 VQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLAL---------VANVYAAAKRWQDVAAVRQK  472 (538)
Q Consensus       402 ~~~~~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~---------l~~~~~~~g~~~~A~~~~~~  472 (538)
                      |..|.   |   ..+++......+++++|..+.++. -++.|+....|...         --.+|.++|+..||..++++
T Consensus       770 F~k~g---D---~ksiVqlHve~~~W~eAFalAe~h-Pe~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQ  842 (1081)
T KOG1538|consen  770 FLKMG---D---LKSLVQLHVETQRWDEAFALAEKH-PEFKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQ  842 (1081)
T ss_pred             HHHhc---c---HHHHhhheeecccchHhHhhhhhC-ccccccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHH
Confidence            88875   2   134566677788888888888888 77777654433312         23578889999999999998


Q ss_pred             HHhCCC
Q 044988          473 MIKMGV  478 (538)
Q Consensus       473 m~~~~~  478 (538)
                      +....+
T Consensus       843 Ltnnav  848 (1081)
T KOG1538|consen  843 LTNNAV  848 (1081)
T ss_pred             hhhhhh
Confidence            865433

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.29  E-value=0.00084  Score=46.92  Aligned_cols=58  Identities=16%  Similarity=0.204  Sum_probs=49.9

Q ss_pred             HHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          419 LGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       419 ~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      ..+.+.+++++|.++++.+ ....|+++..+. ..+.++.+.|++++|.+.++...+.+.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~-l~~~p~~~~~~~-~~a~~~~~~g~~~~A~~~l~~~l~~~p   60 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERA-LELDPDDPELWL-QRARCLFQLGRYEEALEDLERALELSP   60 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHH-HHhCcccchhhH-HHHHHHHHhccHHHHHHHHHHHHHHCC
Confidence            4678889999999999999 888999998788 889999999999999999998886433

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.28  E-value=0.027  Score=51.84  Aligned_cols=285  Identities=11%  Similarity=-0.054  Sum_probs=144.8

Q ss_pred             HHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC---CCchhHHHHHHHHHhcCCHH
Q 044988          128 CARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA---RSVVSWNSLLKGYVKRGDID  204 (538)
Q Consensus       128 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~  204 (538)
                      +.+..++..|+..+...++.+ +.+..-|..-...+...|+   +++|.--.+.-.+   .......-.-+++...++..
T Consensus        59 ~yk~k~Y~nal~~yt~Ai~~~-pd~a~yy~nRAa~~m~~~~---~~~a~~dar~~~r~kd~~~k~~~r~~~c~~a~~~~i  134 (486)
T KOG0550|consen   59 FYKQKTYGNALKNYTFAIDMC-PDNASYYSNRAATLMMLGR---FEEALGDARQSVRLKDGFSKGQLREGQCHLALSDLI  134 (486)
T ss_pred             HHHHhhHHHHHHHHHHHHHhC-ccchhhhchhHHHHHHHHh---HhhcccchhhheecCCCccccccchhhhhhhhHHHH
Confidence            344455566666666666654 3334445555555555555   5544433322221   11112222233334444444


Q ss_pred             HHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-CCCCHHHHHHHHH-HHHccCChHHHHHHHHHHHHh
Q 044988          205 GAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR-VGLDQVALVAALS-ACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       205 ~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p~~~~~~~li~-~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      +|.+.++.     ...|           ....++..++...... -+|.-.++..+-. ++.-.|+.+.|..+--.+.+.
T Consensus       135 ~A~~~~~~-----~~~~-----------~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkl  198 (486)
T KOG0550|consen  135 EAEEKLKS-----KQAY-----------KAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSEAIDILKL  198 (486)
T ss_pred             HHHHHhhh-----hhhh-----------HHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHHHHHHHhc
Confidence            44444441     1111           1122233333322221 1244445444433 345678888888877777775


Q ss_pred             ccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHH
Q 044988          283 FSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEG  362 (538)
Q Consensus       283 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a  362 (538)
                           .+.+......-..++--.++.+.+...|++...-++....+-. ++..    -+.+..+..-.+-..+.|.+..|
T Consensus       199 -----d~~n~~al~vrg~~~yy~~~~~ka~~hf~qal~ldpdh~~sk~-~~~~----~k~le~~k~~gN~~fk~G~y~~A  268 (486)
T KOG0550|consen  199 -----DATNAEALYVRGLCLYYNDNADKAINHFQQALRLDPDHQKSKS-ASMM----PKKLEVKKERGNDAFKNGNYRKA  268 (486)
T ss_pred             -----ccchhHHHHhcccccccccchHHHHHHHhhhhccChhhhhHHh-Hhhh----HHHHHHHHhhhhhHhhccchhHH
Confidence                 3443333222233344567888999999888764332221100 0000    00001111222334577888899


Q ss_pred             HHHHHHhhhh--cCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHH-HHH--HHHHHHHhcCCHHHHHHHHHHc
Q 044988          363 RQFFECMNQN--WGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDA-VLG--SLLLGCRIHNNAELASQVAQKL  437 (538)
Q Consensus       363 ~~~~~~~~~~--~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~-~~~--~l~~~~~~~~~~~~A~~~~~~~  437 (538)
                      .+++.+.+..  .+..|+...|.....+..+.|+.++|+.--++.. ..|.. ...  .-..++...+++++|.+-++++
T Consensus       269 ~E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al-~iD~syikall~ra~c~l~le~~e~AV~d~~~a  347 (486)
T KOG0550|consen  269 YECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEAL-KIDSSYIKALLRRANCHLALEKWEEAVEDYEKA  347 (486)
T ss_pred             HHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhh-hcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9998887732  0223345567777777888899999988887765 33432 222  2233466778888888888888


Q ss_pred             hhccCCC
Q 044988          438 VAEIDPE  444 (538)
Q Consensus       438 ~~~~~p~  444 (538)
                       .+...+
T Consensus       348 -~q~~~s  353 (486)
T KOG0550|consen  348 -MQLEKD  353 (486)
T ss_pred             -Hhhccc
Confidence             444333

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.25  E-value=0.0025  Score=60.43  Aligned_cols=118  Identities=14%  Similarity=0.056  Sum_probs=94.6

Q ss_pred             CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhC--CCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHh
Q 044988           80 NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDK--ETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRT  157 (538)
Q Consensus        80 ~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~--~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  157 (538)
                      ..+......+++.+....+.+.+..++.+.+..  ....-..|.+++++.|...|..+.+..++..=...|+-||.++++
T Consensus        63 ~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~n  142 (429)
T PF10037_consen   63 PVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSFN  142 (429)
T ss_pred             CCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhHH
Confidence            456667777888888888889999999988864  333445677899999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCCChhHHHHHhhcCCC----CCchhHHHHHHHHHhc
Q 044988          158 NLMNLYLMSGGECGVGCARLLFDDMPA----RSVVSWNSLLKGYVKR  200 (538)
Q Consensus       158 ~l~~~~~~~g~~~~~~~a~~~~~~~~~----~~~~~~~~li~~~~~~  200 (538)
                      .||..+.+.|+   +..|.++...|..    .+..++...+.+|.+-
T Consensus       143 ~Lmd~fl~~~~---~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  143 LLMDHFLKKGN---YKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHhhccc---HHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            99999999999   9999888877653    2445555555555444

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of small ribosomal proteins possessing one of three conserved sequence blocks found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins. This leaves open the possibility that they may be functional partners of GTP-binding ribosomal proteins [].

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.24  E-value=0.0038  Score=52.17  Aligned_cols=94  Identities=12%  Similarity=-0.078  Sum_probs=74.9

Q ss_pred             cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHH
Q 044988          378 RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLAL  452 (538)
Q Consensus       378 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~  452 (538)
                      ....|..+...+...|++++|...|++.. ..|+    ..++..+...+...|++++|+..++++ ..+.|.....+. .
T Consensus        34 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~A-l~~~~~~~~~~~-~  111 (168)
T CHL00033         34 EAFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQA-LERNPFLPQALN-N  111 (168)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCcCcHHHHH-H
Confidence            35677888888889999999999998873 2233    347888888899999999999999999 888888887666 7


Q ss_pred             HHHHHH-------hcCChHHHHHHHHHH
Q 044988          453 VANVYA-------AAKRWQDVAAVRQKM  473 (538)
Q Consensus       453 l~~~~~-------~~g~~~~A~~~~~~m  473 (538)
                      ++.++.       +.|++++|...+++.
T Consensus       112 la~i~~~~~~~~~~~g~~~~A~~~~~~a  139 (168)
T CHL00033        112 MAVICHYRGEQAIEQGDSEIAEAWFDQA  139 (168)
T ss_pred             HHHHHHHhhHHHHHcccHHHHHHHHHHH
Confidence            777777       888888766666554

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.23  E-value=0.1  Score=46.40  Aligned_cols=58  Identities=5%  Similarity=-0.018  Sum_probs=38.8

Q ss_pred             HHHHHhcCCCchHHHHHHHHhHhCCCCCCcc-hH---HHHHHHHHccCCcHHHHHHHHHHHHhC
Q 044988           89 MIRGHARSETPEKSVYLYKQMIDKETEPDEY-TY---SFLLSVCARCGLFREGEQVHGRVLASG  148 (538)
Q Consensus        89 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-~~---~~li~~~~~~~~~~~a~~~~~~~~~~~  148 (538)
                      ....+.+.|++++|.+.|+.+...  -|+.. ..   -.+..++.+.++++.|...+++.++..
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~--yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~   99 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNR--YPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN   99 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC
Confidence            344456678888888888888764  34332 21   344566777888888888888887763

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.23  E-value=0.0014  Score=59.80  Aligned_cols=126  Identities=11%  Similarity=0.017  Sum_probs=66.2

Q ss_pred             HHHHHhcccCcHHHHHHHHHH---hhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--------CCCCHHHHH
Q 044988          348 GVLSACSHGGFVDEGRQFFEC---MNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--------MKPNDAVLG  415 (538)
Q Consensus       348 ~ll~~~~~~~~~~~a~~~~~~---~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--------~~p~~~~~~  415 (538)
                      .+.+.|.-.|+++.|....+.   +.+.+|-.. ....+..|..++.-.|+++.|.+.|+..-        ......+.-
T Consensus       200 nLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r~vEAQscY  279 (639)
T KOG1130|consen  200 NLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNRTVEAQSCY  279 (639)
T ss_pred             ccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcchhHHHHHHH
Confidence            333344444666666655443   222333222 24456666677777777777777665431        112234445


Q ss_pred             HHHHHHHhcCCHHHHHHHHHHch-----hccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          416 SLLLGCRIHNNAELASQVAQKLV-----AEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       416 ~l~~~~~~~~~~~~A~~~~~~~~-----~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      +|...|.-..++++|+.++.+-.     .+-......++- .|+++|...|..++|+.+.+.-.
T Consensus       280 SLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~Racw-SLgna~~alg~h~kAl~fae~hl  342 (639)
T KOG1130|consen  280 SLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACW-SLGNAFNALGEHRKALYFAELHL  342 (639)
T ss_pred             HhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH-HHHHHHHhhhhHHHHHHHHHHHH
Confidence            56666666666777766665543     111111222244 56667777777777666554443

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.22  E-value=0.0018  Score=54.33  Aligned_cols=88  Identities=15%  Similarity=0.074  Sum_probs=51.8

Q ss_pred             CCcchHHHHHHHHhc-----CCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHcc----------------CCcHHHHH
Q 044988           81 PSTAIWNQMIRGHAR-----SETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARC----------------GLFREGEQ  139 (538)
Q Consensus        81 ~~~~~~~~li~~~~~-----~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~----------------~~~~~a~~  139 (538)
                      .+..+|..++..|.+     .|..+=....+..|.+.|+.-|..+|+.|+..+=+.                .+.+-|.+
T Consensus        45 k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~  124 (228)
T PF06239_consen   45 KDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAID  124 (228)
T ss_pred             ccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHH
Confidence            344444444444432     244444444555555555555555555555544321                13456777


Q ss_pred             HHHHHHHhCCCCchhHHhHHHHHHHhcCC
Q 044988          140 VHGRVLASGYCSNVFIRTNLMNLYLMSGG  168 (538)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  168 (538)
                      ++++|...|+.||..++..+++.+.+.+.
T Consensus       125 lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  125 LLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            88888888888888888888887777665

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=97.22  E-value=0.17  Score=46.54  Aligned_cols=229  Identities=17%  Similarity=0.169  Sum_probs=131.2

Q ss_pred             HcCCHHHHHHHHHHHHHCCCCCCHHH--HHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCC
Q 044988          230 QNGKSRQALSLFNEMRRARVGLDQVA--LVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGE  307 (538)
Q Consensus       230 ~~~~~~~a~~~~~~m~~~g~~p~~~~--~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  307 (538)
                      -.|+++.|.+-|+.|...   |...-  ...|.-..-+.|+.+.|..+-+..-+.     -|.-.-.+.+.+...|..|+
T Consensus       132 ~eG~~~~Ar~kfeAMl~d---PEtRllGLRgLyleAqr~GareaAr~yAe~Aa~~-----Ap~l~WA~~AtLe~r~~~gd  203 (531)
T COG3898         132 LEGDYEDARKKFEAMLDD---PETRLLGLRGLYLEAQRLGAREAARHYAERAAEK-----APQLPWAARATLEARCAAGD  203 (531)
T ss_pred             hcCchHHHHHHHHHHhcC---hHHHHHhHHHHHHHHHhcccHHHHHHHHHHHHhh-----ccCCchHHHHHHHHHHhcCC
Confidence            346666666666666531   11111  111111123455666665555555543     34444444566666666666


Q ss_pred             HHHHHHHHHhcCC-----CCcc--hHHHHHHHHHh---cCCccHHH--------------HHHHHHHHHhcccCcHHHHH
Q 044988          308 IEEAYGVFRKMQR-----RNTV--SWTSMITGFAK---QGYAQEAL--------------LTFLGVLSACSHGGFVDEGR  363 (538)
Q Consensus       308 ~~~a~~~~~~m~~-----~~~~--~~~~li~~~~~---~~~~~~a~--------------~~~~~ll~~~~~~~~~~~a~  363 (538)
                      |+.|+++.+.-..     ++..  .-..|+.+-..   ..+...|.              ..-.....++.+.|++.++-
T Consensus       204 Wd~AlkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~KL~pdlvPaav~AAralf~d~~~rKg~  283 (531)
T COG3898         204 WDGALKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANKLAPDLVPAAVVAARALFRDGNLRKGS  283 (531)
T ss_pred             hHHHHHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhhcCCccchHHHHHHHHHHhccchhhhh
Confidence            6666666654332     2211  00111111000   00111111              22333456777888999999


Q ss_pred             HHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC----CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHch
Q 044988          364 QFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP----MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLV  438 (538)
Q Consensus       364 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  438 (538)
                      .+++.+-+.   .|.+..+...+  +.+.|+.  +..-+++..    .+| +......+..+....|++..|..--+.. 
T Consensus       284 ~ilE~aWK~---ePHP~ia~lY~--~ar~gdt--a~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa-  355 (531)
T COG3898         284 KILETAWKA---EPHPDIALLYV--RARSGDT--ALDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAA-  355 (531)
T ss_pred             hHHHHHHhc---CCChHHHHHHH--HhcCCCc--HHHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHH-
Confidence            999998865   56665544433  3455543  333332221    344 4677777888899999999999988888 


Q ss_pred             hccCCCCcccHHHHHHHHHHhc-CChHHHHHHHHHHHhC
Q 044988          439 AEIDPEQAAGYLALVANVYAAA-KRWQDVAAVRQKMIKM  476 (538)
Q Consensus       439 ~~~~p~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~m~~~  476 (538)
                      ....|.... |. +|+++-.-. |+-.++...+-+-...
T Consensus       356 ~r~~pres~-~l-LlAdIeeAetGDqg~vR~wlAqav~A  392 (531)
T COG3898         356 AREAPRESA-YL-LLADIEEAETGDQGKVRQWLAQAVKA  392 (531)
T ss_pred             hhhCchhhH-HH-HHHHHHhhccCchHHHHHHHHHHhcC
Confidence            888898877 88 888887654 9999999998887754

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.22  E-value=0.013  Score=53.44  Aligned_cols=146  Identities=12%  Similarity=0.085  Sum_probs=97.1

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHH
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRAR-VGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNA  297 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  297 (538)
                      .+|..++...-+.+..+.|..+|.+..+.+ +..+.....+.+. +...++.+.|..+|+...+.     .+.+..+|..
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~~~~~~vy~~~A~~E-~~~~~d~~~A~~Ife~glk~-----f~~~~~~~~~   75 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDKRCTYHVYVAYALME-YYCNKDPKRARKIFERGLKK-----FPSDPDFWLE   75 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCS-THHHHHHHHHH-HHTCS-HHHHHHHHHHHHHH-----HTT-HHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCCCCCHHHHHHHHHHH-HHhCCCHHHHHHHHHHHHHH-----CCCCHHHHHH
Confidence            468888999889889999999999998543 2333333333332 33357788899999999987     8888899999


Q ss_pred             HHHHHHhCCCHHHHHHHHHhcCCC--CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCC
Q 044988          298 LIHMYASCGEIEEAYGVFRKMQRR--NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGI  375 (538)
Q Consensus       298 l~~~~~~~g~~~~a~~~~~~m~~~--~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  375 (538)
                      .++.+...|+.+.|+.+|++....  ....                +...|...+..-.+.|+++.+..+.+++.+.   
T Consensus        76 Y~~~l~~~~d~~~aR~lfer~i~~l~~~~~----------------~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~---  136 (280)
T PF05843_consen   76 YLDFLIKLNDINNARALFERAISSLPKEKQ----------------SKKIWKKFIEFESKYGDLESVRKVEKRAEEL---  136 (280)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHHCCTSSCHHH----------------CHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH---
T ss_pred             HHHHHHHhCcHHHHHHHHHHHHHhcCchhH----------------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH---
Confidence            999999999999999999998762  2110                1133444444444455777888888887765   


Q ss_pred             CccHHHHHHHHHHh
Q 044988          376 KPRIEHYGCMVDLF  389 (538)
Q Consensus       376 ~p~~~~~~~l~~~~  389 (538)
                      .|+......+++-|
T Consensus       137 ~~~~~~~~~f~~ry  150 (280)
T PF05843_consen  137 FPEDNSLELFSDRY  150 (280)
T ss_dssp             TTTS-HHHHHHCCT
T ss_pred             hhhhhHHHHHHHHh
Confidence            34433344444433

The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=97.22  E-value=0.32  Score=49.72  Aligned_cols=376  Identities=10%  Similarity=0.065  Sum_probs=203.3

Q ss_pred             cHHHHHHHH--hccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC--CCcchHHHHHHHHh
Q 044988           19 TTRQIFSLL--QIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN--PSTAIWNQMIRGHA   94 (538)
Q Consensus        19 ~~~~ll~~~--~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~~~~~~~~li~~~~   94 (538)
                      .|..++.++  .+.|+.++|..+++.....+.. |..+...+-.+|...++.++|..++++...  |+......+..+|+
T Consensus        43 ~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~~P~eell~~lFmayv  121 (932)
T KOG2053|consen   43 LYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQKYPSEELLYHLFMAYV  121 (932)
T ss_pred             HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhhCCcHHHHHHHHHHHH
Confidence            456666654  4678889999888877766655 888999999999999999999999998874  66555556667788


Q ss_pred             cCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccC-C---------cHHHHHHHHHHHHhC-CCCchhHHhHHHHHH
Q 044988           95 RSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCG-L---------FREGEQVHGRVLASG-YCSNVFIRTNLMNLY  163 (538)
Q Consensus        95 ~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~-~---------~~~a~~~~~~~~~~~-~~~~~~~~~~l~~~~  163 (538)
                      +-+++.+-.+.--+|-+ ..+-++..|-.+++...+.. .         ..-|...++.+.+.+ -..+..-..-.....
T Consensus       122 R~~~yk~qQkaa~~LyK-~~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~iL  200 (932)
T KOG2053|consen  122 REKSYKKQQKAALQLYK-NFPKRAYYFWSVISLILQSIFSENELLDPILLALAEKMVQKLLEKKGKIESEAEIILYLLIL  200 (932)
T ss_pred             HHHHHHHHHHHHHHHHH-hCCcccchHHHHHHHHHHhccCCcccccchhHHHHHHHHHHHhccCCccchHHHHHHHHHHH
Confidence            88777654443333333 23446667777777765432 1         234556666666654 212222222233445


Q ss_pred             HhcCCCCChhHHHHHhhc-----CCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHH--------
Q 044988          164 LMSGGECGVGCARLLFDD-----MPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQ--------  230 (538)
Q Consensus       164 ~~~g~~~~~~~a~~~~~~-----~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~--------  230 (538)
                      ...|+   .++|..++..     ....+...-+.-+..+...+++.+..++-.++...+..-|...+..+.+        
T Consensus       201 ~~~~k---~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~~Ddy~~~~~sv~klLe~~~~~  277 (932)
T KOG2053|consen  201 ELQGK---YQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKGNDDYKIYTDSVFKLLELLNKE  277 (932)
T ss_pred             Hhccc---HHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhCCcchHHHHHHHHHHHHhcccc
Confidence            56777   8888888732     2223444555667778888888887777766553211113333322111        


Q ss_pred             --------cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH---ccCChHHHHHHHHHHHHhccCCCCCcchhHH----
Q 044988          231 --------NGKSRQALSLFNEMRRARVGLDQVALVAALSACA---EIGDLKLGKWIHSYVEENFSVGREPVLVSLN----  295 (538)
Q Consensus       231 --------~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~----  295 (538)
                              .+..+...+..++....   -....|-+-+.+..   ..|+.+++...|  +.+....+....|...|    
T Consensus       278 ~a~~~~s~~~~l~~~~ek~~~~i~~---~~Rgp~LA~lel~kr~~~~gd~ee~~~~y--~~kfg~kpcc~~Dl~~yl~~l  352 (932)
T KOG2053|consen  278 PAEAAHSLSKSLDECIEKAQKNIGS---KSRGPYLARLELDKRYKLIGDSEEMLSYY--FKKFGDKPCCAIDLNHYLGHL  352 (932)
T ss_pred             cchhhhhhhhhHHHHHHHHHHhhcc---cccCcHHHHHHHHHHhcccCChHHHHHHH--HHHhCCCcHhHhhHHHhhccC
Confidence                    11122222222222221   12233444444443   346666654333  22221111111122111    


Q ss_pred             -----HHHHHHHHhCC-CHHHHHHHHH----------------hcCCCCcchHH-HHHHHHHhcCCcc------------
Q 044988          296 -----NALIHMYASCG-EIEEAYGVFR----------------KMQRRNTVSWT-SMITGFAKQGYAQ------------  340 (538)
Q Consensus       296 -----~~l~~~~~~~g-~~~~a~~~~~----------------~m~~~~~~~~~-~li~~~~~~~~~~------------  340 (538)
                           ..++..+.... +.....+++.                .|.......|. .++..|.+.=...            
T Consensus       353 ~~~q~~~l~~~l~~~~~~~s~~~k~l~~h~c~l~~~rl~G~~~~l~ad~i~a~~~kl~~~ye~gls~~K~ll~TE~~~g~  432 (932)
T KOG2053|consen  353 NIDQLKSLMSKLVLADDDSSGDEKVLQQHLCVLLLLRLLGLYEKLPADSILAYVRKLKLTYEKGLSLSKDLLPTEYSFGD  432 (932)
T ss_pred             CHHHHHHHHHHhhccCCcchhhHHHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHhccccccccccccccccHH
Confidence                 23344443322 2222222211                11112333333 3333443331220            


Q ss_pred             H-HHHHHHHHHHHhcccCcHH---HHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          341 E-ALLTFLGVLSACSHGGFVD---EGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       341 ~-a~~~~~~ll~~~~~~~~~~---~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      + +.-+.+.++..|-+.++..   +|+-+++.....  -+.|..+--.+|..|.-.|-+..|.++|+.+.
T Consensus       433 ~~llLav~~Lid~~rktnd~~~l~eaI~LLE~glt~--s~hnf~~KLlLiriY~~lGa~p~a~~~y~tLd  500 (932)
T KOG2053|consen  433 ELLLLAVNHLIDLWRKTNDLTDLFEAITLLENGLTK--SPHNFQTKLLLIRIYSYLGAFPDAYELYKTLD  500 (932)
T ss_pred             HHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhc--CCccHHHHHHHHHHHHHhcCChhHHHHHHhcc
Confidence            1 1155667778888887765   455555555433  12355566678999999999999999999885

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.22  E-value=0.01  Score=58.89  Aligned_cols=150  Identities=9%  Similarity=-0.015  Sum_probs=97.9

Q ss_pred             CCCcchhHHHHHHHHHHhC-----CCHHHHHHHHHhcCC--CC-cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCc
Q 044988          287 REPVLVSLNNALIHMYASC-----GEIEEAYGVFRKMQR--RN-TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGF  358 (538)
Q Consensus       287 ~~~~~~~~~~~l~~~~~~~-----g~~~~a~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~  358 (538)
                      ..|.+...|..++.+....     ++.+.|..+|++..+  |+ ...|..+..++.....+..            ....+
T Consensus       332 ~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~------------~~~~~  399 (517)
T PRK10153        332 GLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQP------------LDEKQ  399 (517)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCC------------ccHHH
Confidence            4667777777777765432     236688888888776  33 2334333333322211110            00113


Q ss_pred             HHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHc
Q 044988          359 VDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGSLLLGCRIHNNAELASQVAQKL  437 (538)
Q Consensus       359 ~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~  437 (538)
                      +..+.+.............+...|..+.-.+...|++++|...++++. ..|+...|..+...+...|+.++|.+.++++
T Consensus       400 l~~a~~~~~~a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A  479 (517)
T PRK10153        400 LAALSTELDNIVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMSWLNYVLLGKVYELKGDNRLAADAYSTA  479 (517)
T ss_pred             HHHHHHHHHHhhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            344445444433321123355778877777777899999999998874 6788888999999999999999999999999


Q ss_pred             hhccCCCCcccHH
Q 044988          438 VAEIDPEQAAGYL  450 (538)
Q Consensus       438 ~~~~~p~~~~~~~  450 (538)
                       ..+.|..++ |.
T Consensus       480 -~~L~P~~pt-~~  490 (517)
T PRK10153        480 -FNLRPGENT-LY  490 (517)
T ss_pred             -HhcCCCCch-HH
Confidence             999999988 44

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=97.21  E-value=0.00076  Score=59.13  Aligned_cols=92  Identities=14%  Similarity=0.150  Sum_probs=78.4

Q ss_pred             hhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHH
Q 044988          389 FSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDV  466 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A  466 (538)
                      +.+.+++.+|+..|.+.. +.| |++.|..=..+|.+.|.++.|++-.+.. ..++|....+|. .|+.+|...|++++|
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~A-l~iDp~yskay~-RLG~A~~~~gk~~~A  168 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESA-LSIDPHYSKAYG-RLGLAYLALGKYEEA  168 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHH-HhcChHHHHHHH-HHHHHHHccCcHHHH
Confidence            457899999999998874 454 4667777778899999999999999999 999999999999 999999999999999


Q ss_pred             HHHHHHHHhCCCCCCCce
Q 044988          467 AAVRQKMIKMGVRKPPGQ  484 (538)
Q Consensus       467 ~~~~~~m~~~~~~~~~~~  484 (538)
                      ++.|++..+  +.|...+
T Consensus       169 ~~aykKaLe--ldP~Ne~  184 (304)
T KOG0553|consen  169 IEAYKKALE--LDPDNES  184 (304)
T ss_pred             HHHHHhhhc--cCCCcHH
Confidence            999998876  4444333

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=97.18  E-value=0.0016  Score=44.26  Aligned_cols=61  Identities=16%  Similarity=0.148  Sum_probs=37.5

Q ss_pred             HHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCc
Q 044988          385 MVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQA  446 (538)
Q Consensus       385 l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~  446 (538)
                      +...+...|++++|.+.|+.+. ..|+ ...+..+..++...|++++|...|+++ .+..|+++
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a-~~~~P~~p   65 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERA-LELDPDNP   65 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHH-HHHSTT-H
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHHCcCCC
Confidence            3445666677777777776663 3343 455666666677777777777777777 66666653

>PRK15331 chaperone protein SicA; Provisional

Probab=97.16  E-value=0.0064  Score=48.87  Aligned_cols=100  Identities=11%  Similarity=0.054  Sum_probs=80.1

Q ss_pred             CCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          374 GIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       374 ~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                      |+.++ ....-...--+-..|++++|..+|+-+.  -.-|..-|..|..++...+++++|+..|..+ .-+.++++..+.
T Consensus        31 gis~~~le~iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A-~~l~~~dp~p~f  109 (165)
T PRK15331         31 GIPQDMMDGLYAHAYEFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVA-FTLLKNDYRPVF  109 (165)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHcccCCCCccc
Confidence            55554 2222333444557899999999999874  2345666778888899999999999999999 888899998888


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          451 ALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       451 ~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                       ..+.+|...|+.+.|...|.....
T Consensus       110 -~agqC~l~l~~~~~A~~~f~~a~~  133 (165)
T PRK15331        110 -FTGQCQLLMRKAAKARQCFELVNE  133 (165)
T ss_pred             -hHHHHHHHhCCHHHHHHHHHHHHh
Confidence             999999999999999999998876

>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses

Probab=97.04  E-value=0.0031  Score=52.90  Aligned_cols=36  Identities=28%  Similarity=0.337  Sum_probs=32.0

Q ss_pred             CchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCC
Q 044988           98 TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGL  133 (538)
Q Consensus        98 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~  133 (538)
                      +-+-|++++++|...|+-||..|+..++..+.+.+.
T Consensus       118 Qq~c~i~lL~qME~~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  118 QQECAIDLLEQMENNGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             HHHHHHHHHHHHHHcCCCCcHHHHHHHHHHhccccH
Confidence            456789999999999999999999999999977654

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.04  E-value=0.028  Score=55.81  Aligned_cols=137  Identities=9%  Similarity=0.064  Sum_probs=96.0

Q ss_pred             CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhc-------
Q 044988          321 RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRA-------  392 (538)
Q Consensus       321 ~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~-------  392 (538)
                      .+...|...+.+.....+.+.               ++...|..+|++..+.   .|+ ...|..+..+|...       
T Consensus       335 ~~~~Ay~~~lrg~~~~~~~~~---------------~~~~~A~~lle~Ai~l---dP~~a~a~A~la~~~~~~~~~~~~~  396 (517)
T PRK10153        335 HQGAALTLFYQAHHYLNSGDA---------------KSLNKASDLLEEILKS---EPDFTYAQAEKALADIVRHSQQPLD  396 (517)
T ss_pred             CCHHHHHHHHHHHHHHhcCCH---------------HHHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHHHhcCCcc
Confidence            466677777666543332221               2578999999999865   786 45555554444322       


Q ss_pred             -CChHHHHHHHHhCC----CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHH
Q 044988          393 -GLMDEAFSLVQNMP----MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVA  467 (538)
Q Consensus       393 -g~~~~A~~~~~~~~----~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~  467 (538)
                       +++..+.+..++..    ...+...|..+...+...|++++|...++++ ..+.|+ ...|. .++.++...|+.++|.
T Consensus       397 ~~~l~~a~~~~~~a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rA-l~L~ps-~~a~~-~lG~~~~~~G~~~eA~  473 (517)
T PRK10153        397 EKQLAALSTELDNIVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKA-IDLEMS-WLNYV-LLGKVYELKGDNRLAA  473 (517)
T ss_pred             HHHHHHHHHHHHHhhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHH-HHcCCC-HHHHH-HHHHHHHHcCCHHHHH
Confidence             12344455544421    2344577777777777889999999999999 999996 45588 9999999999999999


Q ss_pred             HHHHHHHhCCC
Q 044988          468 AVRQKMIKMGV  478 (538)
Q Consensus       468 ~~~~~m~~~~~  478 (538)
                      +.+++....+.
T Consensus       474 ~~~~~A~~L~P  484 (517)
T PRK10153        474 DAYSTAFNLRP  484 (517)
T ss_pred             HHHHHHHhcCC
Confidence            99999876443

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.03  E-value=0.28  Score=45.45  Aligned_cols=104  Identities=18%  Similarity=0.130  Sum_probs=56.7

Q ss_pred             HHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc
Q 044988          299 IHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR  378 (538)
Q Consensus       299 ~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~  378 (538)
                      +.-+...|+...|.++-.+-.-|+..-|...+.+|+..+++++                    -..+-.   .    +-.
T Consensus       184 i~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~~w~e--------------------L~~fa~---s----kKs  236 (319)
T PF04840_consen  184 IRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENKDWDE--------------------LEKFAK---S----KKS  236 (319)
T ss_pred             HHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCCHHH--------------------HHHHHh---C----CCC
Confidence            4445556666666666666665666666666666666664432                    222211   1    112


Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQK  436 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~  436 (538)
                      +.-|...+.++.+.|+..+|..+..++.       +..-+..|.+.|++.+|.+..-+
T Consensus       237 PIGyepFv~~~~~~~~~~eA~~yI~k~~-------~~~rv~~y~~~~~~~~A~~~A~~  287 (319)
T PF04840_consen  237 PIGYEPFVEACLKYGNKKEASKYIPKIP-------DEERVEMYLKCGDYKEAAQEAFK  287 (319)
T ss_pred             CCChHHHHHHHHHCCCHHHHHHHHHhCC-------hHHHHHHHHHCCCHHHHHHHHHH
Confidence            2455566666666666666666666643       12334455566666666554443

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=96.98  E-value=0.021  Score=42.40  Aligned_cols=79  Identities=13%  Similarity=0.034  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHccC--------ChHHHHHHHHHHHHhccCCCCCcc
Q 044988          221 WTTMISGCAQNGKSRQALSLFNEMRRARV-GLDQVALVAALSACAEIG--------DLKLGKWIHSYVEENFSVGREPVL  291 (538)
Q Consensus       221 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~-~p~~~~~~~li~~~~~~~--------~~~~a~~~~~~~~~~~~~~~~~~~  291 (538)
                      -...|..+...+++.....+|+.+++.|+ -|+..+|+.++.+.++..        ..-....+|+.+...    ...|+
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~----~lKP~  103 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSN----KLKPN  103 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHh----ccCCc
Confidence            34455556666888888888888888888 788888888887766432        122344556666555    56666


Q ss_pred             hhHHHHHHHHHH
Q 044988          292 VSLNNALIHMYA  303 (538)
Q Consensus       292 ~~~~~~l~~~~~  303 (538)
                      ..+|+.++..+.
T Consensus       104 ~etYnivl~~Ll  115 (120)
T PF08579_consen  104 DETYNIVLGSLL  115 (120)
T ss_pred             HHHHHHHHHHHH
Confidence            666666655544

Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs [, , ].

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=96.96  E-value=0.0037  Score=42.86  Aligned_cols=51  Identities=16%  Similarity=0.185  Sum_probs=36.4

Q ss_pred             ccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          265 EIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       265 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      ..|+++.|...++.+.+.     .|.+..++..++.+|.+.|++++|.++++++..
T Consensus         3 ~~~~~~~A~~~~~~~l~~-----~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~   53 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQR-----NPDNPEARLLLAQCYLKQGQYDEAEELLERLLK   53 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHH-----TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHG
T ss_pred             hccCHHHHHHHHHHHHHH-----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            456677777777777665     666666666777788888888888888877765

...

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=96.91  E-value=0.0036  Score=57.25  Aligned_cols=51  Identities=16%  Similarity=0.098  Sum_probs=34.2

Q ss_pred             HHHhcCCCchHHHHHHHHhHhCCCCCCc----chHHHHHHHHHccCCcHHHHHHHH
Q 044988           91 RGHARSETPEKSVYLYKQMIDKETEPDE----YTYSFLLSVCARCGLFREGEQVHG  142 (538)
Q Consensus        91 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~~~~~li~~~~~~~~~~~a~~~~~  142 (538)
                      .-+|+.|+....+.+|+...+-|. -|-    ..|..|..+|.-.+++++|.+++.
T Consensus        25 ERLck~gdcraGv~ff~aA~qvGT-eDl~tLSAIYsQLGNAyfyL~DY~kAl~yH~   79 (639)
T KOG1130|consen   25 ERLCKMGDCRAGVDFFKAALQVGT-EDLSTLSAIYSQLGNAYFYLKDYEKALKYHT   79 (639)
T ss_pred             HHHHhccchhhhHHHHHHHHHhcc-hHHHHHHHHHHHhcchhhhHhhHHHHHhhhh
Confidence            346788888888888888887662 332    245555666666677777777643

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=96.90  E-value=0.21  Score=44.38  Aligned_cols=55  Identities=11%  Similarity=0.044  Sum_probs=33.8

Q ss_pred             HHHHHhcCCHHHHHHHHHHchhccCCCCcc---cHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          418 LLGCRIHNNAELASQVAQKLVAEIDPEQAA---GYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       418 ~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~---~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      ..-|.+.|.+..|..-++.+ .+.-|+.+.   +.. .++.+|...|..++|.++...+.
T Consensus       182 a~~Y~~~~~y~AA~~r~~~v-~~~Yp~t~~~~eal~-~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        182 AEYYTKRGAYVAVVNRVEQM-LRDYPDTQATRDALP-LMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHcCchHHHHHHHHHH-HHHCCCCchHHHHHH-HHHHHHHHcCChHHHHHHHHHHh
Confidence            34466667777777777776 555555443   233 55667777777777777665544

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=96.83  E-value=0.078  Score=51.78  Aligned_cols=100  Identities=16%  Similarity=0.162  Sum_probs=65.0

Q ss_pred             HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHH
Q 044988          253 QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITG  332 (538)
Q Consensus       253 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~  332 (538)
                      ..+...+..-+.+...+..|.++|..+-..             ..+++.....++|++|..+-++.++--...|-.-..-
T Consensus       747 re~l~~~a~ylk~l~~~gLAaeIF~k~gD~-------------ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqw  813 (1081)
T KOG1538|consen  747 REPLLLCATYLKKLDSPGLAAEIFLKMGDL-------------KSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQW  813 (1081)
T ss_pred             hhHHHHHHHHHhhccccchHHHHHHHhccH-------------HHHhhheeecccchHhHhhhhhCccccccccchHHHH
Confidence            334444444455666777777777776554             4677778888889999888888876222223333444


Q ss_pred             HHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          333 FAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       333 ~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                      ++...++++|.       .+|.+.|+-.+|.++++++...
T Consensus       814 LAE~DrFeEAq-------kAfhkAGr~~EA~~vLeQLtnn  846 (1081)
T KOG1538|consen  814 LAENDRFEEAQ-------KAFHKAGRQREAVQVLEQLTNN  846 (1081)
T ss_pred             hhhhhhHHHHH-------HHHHHhcchHHHHHHHHHhhhh
Confidence            55556666654       5666778888888888877543

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=96.80  E-value=0.0032  Score=43.33  Aligned_cols=64  Identities=20%  Similarity=0.237  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcC-CHHHHHHHHHHchhccCC
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHN-NAELASQVAQKLVAEIDP  443 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~~~~p  443 (538)
                      ..+|..+...+...|++++|+..|++.. ..|+ ...|..+..++...| ++++|++.+++. .++.|
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~a-l~l~P   69 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKA-LKLDP   69 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHH-HHHST
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHH-HHcCc
Confidence            4566677777777777777777776653 3343 556666666777777 577777777777 65555

...

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=96.76  E-value=0.58  Score=45.12  Aligned_cols=426  Identities=10%  Similarity=0.090  Sum_probs=233.9

Q ss_pred             CCCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC--CCCcchHHHHH
Q 044988           13 TSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE--NPSTAIWNQMI   90 (538)
Q Consensus        13 ~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li   90 (538)
                      .|-+-.++..|++-+... ..++++..++++... ++.++..|..-+..-.+..+++....+|.+-.  .-+...|..-|
T Consensus        16 nP~di~sw~~lire~qt~-~~~~~R~~YEq~~~~-FP~s~r~W~~yi~~El~skdfe~VEkLF~RCLvkvLnlDLW~lYl   93 (656)
T KOG1914|consen   16 NPYDIDSWSQLIREAQTQ-PIDKVRETYEQLVNV-FPSSPRAWKLYIERELASKDFESVEKLFSRCLVKVLNLDLWKLYL   93 (656)
T ss_pred             CCccHHHHHHHHHHHccC-CHHHHHHHHHHHhcc-CCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHhHHHHHH
Confidence            345567888888887666 889999999988875 34467888888888888999999999998755  35677777776


Q ss_pred             HHHhc-CCCchH----HHHHHHHhHh-CCCCCCc-chHHHHHHH---------HHccCCcHHHHHHHHHHHHhCCCCchh
Q 044988           91 RGHAR-SETPEK----SVYLYKQMID-KETEPDE-YTYSFLLSV---------CARCGLFREGEQVHGRVLASGYCSNVF  154 (538)
Q Consensus        91 ~~~~~-~~~~~~----a~~~~~~m~~-~~~~p~~-~~~~~li~~---------~~~~~~~~~a~~~~~~~~~~~~~~~~~  154 (538)
                      .---+ .|+...    ..+.|+-... -|+.+-. ..|+..+..         +....+++...+++++++...+..=..
T Consensus        94 ~YVR~~~~~~~~~r~~m~qAy~f~l~kig~di~s~siW~eYi~FL~~vea~gk~ee~QRI~~vRriYqral~tPm~nlEk  173 (656)
T KOG1914|consen   94 SYVRETKGKLFGYREKMVQAYDFALEKIGMDIKSYSIWDEYINFLEGVEAVGKYEENQRITAVRRIYQRALVTPMHNLEK  173 (656)
T ss_pred             HHHHHHccCcchHHHHHHHHHHHHHHHhccCcccchhHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHhcCccccHHH
Confidence            54322 233322    2333443333 3444322 234444433         233446667777787776543221111


Q ss_pred             HHhHH------HHHHH-------hcCCCCChhHHHHHhhcCCC------C--------Cc-------hhHHHHHHHHHhc
Q 044988          155 IRTNL------MNLYL-------MSGGECGVGCARLLFDDMPA------R--------SV-------VSWNSLLKGYVKR  200 (538)
Q Consensus       155 ~~~~l------~~~~~-------~~g~~~~~~~a~~~~~~~~~------~--------~~-------~~~~~li~~~~~~  200 (538)
                      .|+..      ++...       +...   +-.|.++.+++..      +        .+       ..|-.+|.-=-..
T Consensus       174 LW~DY~~fE~~IN~~tarK~i~e~s~~---Ym~AR~~~qel~~lt~GL~r~~~~vp~~~T~~e~~qv~~W~n~I~wEksN  250 (656)
T KOG1914|consen  174 LWKDYEAFEQEINIITARKFIGERSPE---YMNARRVYQELQNLTRGLNRNAPAVPPKGTKDEIQQVELWKNWIKWEKSN  250 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCHH---HHHHHHHHHHHHHHHhhhcccCCCCCCCCChHHHHHHHHHHHHHHHHhcC
Confidence            22111      11000       1111   2333333333221      0        00       0122222110000


Q ss_pred             ------CCHH--HHHHHHcc----CC-CCChH-HHHHHH----HHHHHcCC-------HHHHHHHHHHHHHCCCCCCHHH
Q 044988          201 ------GDID--GAWKIFDE----MP-HRNVV-SWTTMI----SGCAQNGK-------SRQALSLFNEMRRARVGLDQVA  255 (538)
Q Consensus       201 ------g~~~--~A~~~~~~----m~-~~~~~-~~~~li----~~~~~~~~-------~~~a~~~~~~m~~~g~~p~~~~  255 (538)
                            |..-  ...-+++.    +. .|++. -|...+    ..+...|+       .+++..++++....-..-+..+
T Consensus       251 pL~t~~~~~~~~Rv~yayeQ~ll~l~~~peiWy~~s~yl~~~s~l~~~~~d~~~a~~~t~e~~~~yEr~I~~l~~~~~~L  330 (656)
T KOG1914|consen  251 PLRTLDGTMLTRRVMYAYEQCLLYLGYHPEIWYDYSMYLIEISDLLTEKGDVPDAKSLTDEAASIYERAIEGLLKENKLL  330 (656)
T ss_pred             CcccccccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhhHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence                  0000  00000000    00 01110 011111    11222222       4566666666654333334444


Q ss_pred             HHHHHHHHHccC---ChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC-----CcchHH
Q 044988          256 LVAALSACAEIG---DLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR-----NTVSWT  327 (538)
Q Consensus       256 ~~~li~~~~~~~---~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~-----~~~~~~  327 (538)
                      |..+..---..-   ..+....+++.+...    .......+|..+++.-.+..-+..|+.+|.+..+.     ++..++
T Consensus       331 y~~~a~~eE~~~~~n~~~~~~~~~~~ll~~----~~~~~tLv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~  406 (656)
T KOG1914|consen  331 YFALADYEESRYDDNKEKKVHEIYNKLLKI----EDIDLTLVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAA  406 (656)
T ss_pred             HHHHHhhHHHhcccchhhhhHHHHHHHHhh----hccCCceehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHH
Confidence            444433222122   245555666666665    33333445667888888888899999999998862     455666


Q ss_pred             HHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-
Q 044988          328 SMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-  406 (538)
Q Consensus       328 ~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-  406 (538)
                      +++.-|+.                     ++...|..+|+.-.+.+|-.  ..--...++-+...++-..|..+|++.. 
T Consensus       407 A~mEy~cs---------------------kD~~~AfrIFeLGLkkf~d~--p~yv~~YldfL~~lNdd~N~R~LFEr~l~  463 (656)
T KOG1914|consen  407 ALMEYYCS---------------------KDKETAFRIFELGLKKFGDS--PEYVLKYLDFLSHLNDDNNARALFERVLT  463 (656)
T ss_pred             HHHHHHhc---------------------CChhHHHHHHHHHHHhcCCC--hHHHHHHHHHHHHhCcchhHHHHHHHHHh
Confidence            66666554                     36788899999887775433  3334566777788899999999999885 


Q ss_pred             --CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCC--C---cccHHHHHHHHHHhcCChHHHHHHHHHH
Q 044988          407 --MKPN--DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPE--Q---AAGYLALVANVYAAAKRWQDVAAVRQKM  473 (538)
Q Consensus       407 --~~p~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~--~---~~~~~~~l~~~~~~~g~~~~A~~~~~~m  473 (538)
                        ..|+  ...|..++.--..-|+...+.++-++. ....|.  .   .. -. .+++-|.-.+.+..-..-++.|
T Consensus       464 s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~-~~af~~~qe~~~~~-~~-~~v~RY~~~d~~~c~~~elk~l  536 (656)
T KOG1914|consen  464 SVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRR-FTAFPADQEYEGNE-TA-LFVDRYGILDLYPCSLDELKFL  536 (656)
T ss_pred             ccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHH-HHhcchhhcCCCCh-HH-HHHHHHhhcccccccHHHHHhh
Confidence              2333  579999999999999999999999988 444441  1   11 22 4556666666554433333333

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=96.70  E-value=0.035  Score=42.79  Aligned_cols=87  Identities=16%  Similarity=0.069  Sum_probs=50.4

Q ss_pred             HHHHhcCCCchHHHHHHHHhHhCCCCCC--cchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCC---chhHHhHHHHHHH
Q 044988           90 IRGHARSETPEKSVYLYKQMIDKETEPD--EYTYSFLLSVCARCGLFREGEQVHGRVLASGYCS---NVFIRTNLMNLYL  164 (538)
Q Consensus        90 i~~~~~~~~~~~a~~~~~~m~~~~~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~  164 (538)
                      ..++-..|+.++|+.+|++....|....  ...+..+.+.+...|++++|..++++..... +.   +......+..++.
T Consensus         8 A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~-p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    8 AWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEF-PDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCccccHHHHHHHHHHHH
Confidence            3445567777777777777777665443  2355566666777777777777777776542 11   1222222333445


Q ss_pred             hcCCCCChhHHHHHhh
Q 044988          165 MSGGECGVGCARLLFD  180 (538)
Q Consensus       165 ~~g~~~~~~~a~~~~~  180 (538)
                      ..|+   .++|.+.+-
T Consensus        87 ~~gr---~~eAl~~~l   99 (120)
T PF12688_consen   87 NLGR---PKEALEWLL   99 (120)
T ss_pred             HCCC---HHHHHHHHH
Confidence            5555   555555443

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.70  E-value=0.17  Score=49.96  Aligned_cols=179  Identities=16%  Similarity=0.080  Sum_probs=122.1

Q ss_pred             HHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC-CCcchHHHHHHHHHhcCCccHHHHHHHHHHH-
Q 044988          274 WIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR-RNTVSWTSMITGFAKQGYAQEALLTFLGVLS-  351 (538)
Q Consensus       274 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~-  351 (538)
                      -+|..+...     .||..   ..++....-.|+-+.+.+.+.+..+ ++...--+.+..           -.|..++. 
T Consensus       178 G~f~L~lSl-----LPp~~---~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~L-----------L~y~~~~~~  238 (468)
T PF10300_consen  178 GLFNLVLSL-----LPPKV---LKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVL-----------LWYHLVVPS  238 (468)
T ss_pred             HHHHHHHHh-----CCHHH---HHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHH-----------HHHHHHHHH
Confidence            356666665     66654   3678888888999999998887655 232211111100           12222222 


Q ss_pred             Hhc---ccCcHHHHHHHHHHhhhhcCCCccHHHHHHH-HHHhhhcCChHHHHHHHHhCCC------CCCHHHHHHHHHHH
Q 044988          352 ACS---HGGFVDEGRQFFECMNQNWGIKPRIEHYGCM-VDLFSRAGLMDEAFSLVQNMPM------KPNDAVLGSLLLGC  421 (538)
Q Consensus       352 ~~~---~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l-~~~~~~~g~~~~A~~~~~~~~~------~p~~~~~~~l~~~~  421 (538)
                      .+.   .....+.|.++++.+.++   -|+...|... .+.+...|++++|++.|++...      +.....+--+...+
T Consensus       239 ~~~~~~~~~~~~~a~~lL~~~~~~---yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~  315 (468)
T PF10300_consen  239 FLGIDGEDVPLEEAEELLEEMLKR---YPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCH  315 (468)
T ss_pred             HcCCcccCCCHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHH
Confidence            222   245789999999999977   5886665544 4667789999999999997641      12234444556678


Q ss_pred             HhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCCh-------HHHHHHHHHHHh
Q 044988          422 RIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRW-------QDVAAVRQKMIK  475 (538)
Q Consensus       422 ~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~-------~~A~~~~~~m~~  475 (538)
                      .-..++++|.+.|..+ .+...-+...|.-..+-++...|+.       ++|.++|++...
T Consensus       316 ~~~~~w~~A~~~f~~L-~~~s~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp~  375 (468)
T PF10300_consen  316 MFQHDWEEAAEYFLRL-LKESKWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVPK  375 (468)
T ss_pred             HHHchHHHHHHHHHHH-HhccccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHHH
Confidence            8899999999999999 7777777776663556677788888       999999998863

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.65  E-value=0.029  Score=50.29  Aligned_cols=59  Identities=12%  Similarity=0.060  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHccCChHHHHHHHHHHHH
Q 044988          221 WTTMISGCAQNGKSRQALSLFNEMRRARVGLDQ----VALVAALSACAEIGDLKLGKWIHSYVEE  281 (538)
Q Consensus       221 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~----~~~~~li~~~~~~~~~~~a~~~~~~~~~  281 (538)
                      |...+..+.+.|++++|...|+.+.+.  .|+.    ..+..+...+...|+++.|...|..+.+
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~--yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~  208 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKK--YPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVK  208 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            333333334445555555555555542  2221    2333444444444444444444444444

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.62  E-value=0.019  Score=51.48  Aligned_cols=94  Identities=18%  Similarity=0.093  Sum_probs=55.6

Q ss_pred             HHHHHHHHhhhcCChHHHHHHHHhCC-CCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHH--HH
Q 044988          381 HYGCMVDLFSRAGLMDEAFSLVQNMP-MKPND----AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLA--LV  453 (538)
Q Consensus       381 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~----~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~--~l  453 (538)
                      .|......+.+.|++++|...|+.+. ..|+.    ..+--+...+...|++++|...|+.+ ....|+++.....  .+
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~v-v~~yP~s~~~~dAl~kl  223 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASV-VKNYPKSPKAADAMFKV  223 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHHCCCCcchhHHHHHH
Confidence            34444444455567777776666653 23432    34445556667777777777777777 5555654432221  34


Q ss_pred             HHHHHhcCChHHHHHHHHHHHh
Q 044988          454 ANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       454 ~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +.++...|++++|..+++++.+
T Consensus       224 g~~~~~~g~~~~A~~~~~~vi~  245 (263)
T PRK10803        224 GVIMQDKGDTAKAKAVYQQVIK  245 (263)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHH
Confidence            5666677777777777777665

>PRK15331 chaperone protein SicA; Provisional

Probab=96.59  E-value=0.063  Score=43.30  Aligned_cols=103  Identities=9%  Similarity=-0.024  Sum_probs=66.7

Q ss_pred             HHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcC---CCCcchHHHHHHHHHhcCCc
Q 044988          263 CAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQ---RRNTVSWTSMITGFAKQGYA  339 (538)
Q Consensus       263 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~---~~~~~~~~~li~~~~~~~~~  339 (538)
                      +...|++++|..+|..+...     .+.+...+..|..++-..++++.|...|....   ..|+.+.-.....+...|+.
T Consensus        47 ~y~~Gk~~eA~~~F~~L~~~-----d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~agqC~l~l~~~  121 (165)
T PRK15331         47 FYNQGRLDEAETFFRFLCIY-----DFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKA  121 (165)
T ss_pred             HHHCCCHHHHHHHHHHHHHh-----CcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCH
Confidence            45678888888888887775     56667777788888888888888888876432   35666666667777777766


Q ss_pred             cHHHHHHHHHHHHhcccCcHHHHHHHHHHhh
Q 044988          340 QEALLTFLGVLSACSHGGFVDEGRQFFECMN  370 (538)
Q Consensus       340 ~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~  370 (538)
                      +.|...|..++.-+....-.++|..+++.+.
T Consensus       122 ~~A~~~f~~a~~~~~~~~l~~~A~~~L~~l~  152 (165)
T PRK15331        122 AKARQCFELVNERTEDESLRAKALVYLEALK  152 (165)
T ss_pred             HHHHHHHHHHHhCcchHHHHHHHHHHHHHHH
Confidence            6666555555543322222334444444443

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.52  E-value=0.11  Score=42.40  Aligned_cols=154  Identities=8%  Similarity=0.028  Sum_probs=105.5

Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC----CCcchHHHHHHHHhcC
Q 044988           21 RQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN----PSTAIWNQMIRGHARS   96 (538)
Q Consensus        21 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~----~~~~~~~~li~~~~~~   96 (538)
                      ..+..+....=|++...+  +........|++.---.|.+.....|+..+|...|++...    .|....-.+.++....
T Consensus        60 ~~~~~a~~q~ldP~R~~R--ea~~~~~~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~  137 (251)
T COG4700          60 HTLLMALQQKLDPERHLR--EATEELAIAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAI  137 (251)
T ss_pred             HHHHHHHHHhcChhHHHH--HHHHHHhhchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhh
Confidence            345555555555554332  2222333467777777888999999999999999987663    5666667777788888


Q ss_pred             CCchHHHHHHHHhHhCCC-CCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHH
Q 044988           97 ETPEKSVYLYKQMIDKET-EPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCA  175 (538)
Q Consensus        97 ~~~~~a~~~~~~m~~~~~-~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a  175 (538)
                      +++..|...++.+.+... .-++.+...+.+.+...|...+|+..|+.....  -|+...-.-....+.+.|+   .+++
T Consensus       138 ~~~A~a~~tLe~l~e~~pa~r~pd~~Ll~aR~laa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr---~~ea  212 (251)
T COG4700         138 QEFAAAQQTLEDLMEYNPAFRSPDGHLLFARTLAAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGR---LREA  212 (251)
T ss_pred             ccHHHHHHHHHHHhhcCCccCCCCchHHHHHHHHhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcc---hhHH
Confidence            999999999999877531 013445667778888999999999999998886  3555444445566677776   6555


Q ss_pred             HHHhhc
Q 044988          176 RLLFDD  181 (538)
Q Consensus       176 ~~~~~~  181 (538)
                      ..-+..
T Consensus       213 ~aq~~~  218 (251)
T COG4700         213 NAQYVA  218 (251)
T ss_pred             HHHHHH
Confidence            544333

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=96.46  E-value=0.0092  Score=48.47  Aligned_cols=68  Identities=22%  Similarity=0.297  Sum_probs=52.4

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH-----hCCCCCCC
Q 044988          413 VLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI-----KMGVRKPP  482 (538)
Q Consensus       413 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~-----~~~~~~~~  482 (538)
                      ....++..+...|++++|.++++.+ ....|-+...|. .++.+|...|+..+|.++|+++.     +-|+.|++
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~-l~~dP~~E~~~~-~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~  136 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRA-LALDPYDEEAYR-LLMRALAAQGRRAEALRVYERYRRRLREELGIEPSP  136 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHH-HHHSTT-HHHHH-HHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----H
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHH-HhcCCCCHHHHH-HHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCH
Confidence            4556677788899999999999999 999999999888 89999999999999999998885     45776654

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.42  E-value=0.41  Score=39.30  Aligned_cols=127  Identities=13%  Similarity=0.029  Sum_probs=69.3

Q ss_pred             CCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC-----Cc
Q 044988          249 VGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR-----NT  323 (538)
Q Consensus       249 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~-----~~  323 (538)
                      ..|+...-..+..++...|+..+|...|++...-    .+..+....-.+.++....+++..|...++++.+-     .+
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG----~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~p  160 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALSG----IFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSP  160 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhcc----ccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCC
Confidence            3455555555666666666666666666666554    45556666566666666677777777776665541     12


Q ss_pred             chHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHH
Q 044988          324 VSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLV  402 (538)
Q Consensus       324 ~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~  402 (538)
                      .+.-.+...|...                    |.+..|+.-|+....-   -|+....-.....+.++|+.+++..-+
T Consensus       161 d~~Ll~aR~laa~--------------------g~~a~Aesafe~a~~~---ypg~~ar~~Y~e~La~qgr~~ea~aq~  216 (251)
T COG4700         161 DGHLLFARTLAAQ--------------------GKYADAESAFEVAISY---YPGPQARIYYAEMLAKQGRLREANAQY  216 (251)
T ss_pred             CchHHHHHHHHhc--------------------CCchhHHHHHHHHHHh---CCCHHHHHHHHHHHHHhcchhHHHHHH
Confidence            2222222333333                    3455555556655533   455444334444455666666554433

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.38  E-value=0.017  Score=54.54  Aligned_cols=96  Identities=11%  Similarity=0.057  Sum_probs=62.8

Q ss_pred             cHHHHHHHHHHhhhcCChHHHHHHHHhC-CCCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHH
Q 044988          378 RIEHYGCMVDLFSRAGLMDEAFSLVQNM-PMKPND----AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLAL  452 (538)
Q Consensus       378 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~-~~~p~~----~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~  452 (538)
                      +...++.+..+|...|++++|+..|++. ...|+.    .+|..+..+|...|+.++|+..++++ .++.+..   |. .
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrA-Lelsn~~---f~-~  148 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTA-LRDYNLK---FS-T  148 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhcchh---HH-H
Confidence            4667888888888888888888888774 456664    35778888888888888888888888 5542111   32 1


Q ss_pred             HHH--HHHhcCChHHHHHHHHHHHhCCC
Q 044988          453 VAN--VYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       453 l~~--~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      +..  .+....+.++..++++.+...|.
T Consensus       149 i~~DpdL~plR~~pef~eLlee~rk~G~  176 (453)
T PLN03098        149 ILNDPDLAPFRASPEFKELQEEARKGGE  176 (453)
T ss_pred             HHhCcchhhhcccHHHHHHHHHHHHhCC
Confidence            111  11223344566677777777665

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=96.37  E-value=0.92  Score=42.79  Aligned_cols=377  Identities=11%  Similarity=0.081  Sum_probs=207.3

Q ss_pred             HHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCc---chHHHHHHHHhcCCCchHHHHHHHHhHhCCC
Q 044988           38 QIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPST---AIWNQMIRGHARSETPEKSVYLYKQMIDKET  114 (538)
Q Consensus        38 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~---~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~  114 (538)
                      ++-+.+...  +.+...|-+|++-|...|..++.++++++|..|-+   ..|..-+++-...+++.....+|.+.+... 
T Consensus        30 rLRerIkdN--PtnI~S~fqLiq~~~tq~s~~~~re~yeq~~~pfp~~~~aw~ly~s~ELA~~df~svE~lf~rCL~k~-  106 (660)
T COG5107          30 RLRERIKDN--PTNILSYFQLIQYLETQESMDAEREMYEQLSSPFPIMEHAWRLYMSGELARKDFRSVESLFGRCLKKS-  106 (660)
T ss_pred             HHHHHhhcC--chhHHHHHHHHHHHhhhhhHHHHHHHHHHhcCCCccccHHHHHHhcchhhhhhHHHHHHHHHHHHhhh-
Confidence            444444332  44678899999999999999999999999987655   367777877777788888888998888753 


Q ss_pred             CCCcchHHHHHHHHHccCCc------HHHHHHHHHHHH-hCCCCc-hhHHhHHHHHHH---hcCC---CCChhHHHHHhh
Q 044988          115 EPDEYTYSFLLSVCARCGLF------REGEQVHGRVLA-SGYCSN-VFIRTNLMNLYL---MSGG---ECGVGCARLLFD  180 (538)
Q Consensus       115 ~p~~~~~~~li~~~~~~~~~------~~a~~~~~~~~~-~~~~~~-~~~~~~l~~~~~---~~g~---~~~~~~a~~~~~  180 (538)
                       .+...|...+..-.+....      ....+.|+-... .++.|- ...|+..+...-   ..|.   .+.++...+.+.
T Consensus       107 -l~ldLW~lYl~YIRr~n~~~tGq~r~~i~~ayefv~~~~~~e~~s~~~W~ey~~fle~~~~~~kwEeQqrid~iR~~Y~  185 (660)
T COG5107         107 -LNLDLWMLYLEYIRRVNNLITGQKRFKIYEAYEFVLGCAIFEPQSENYWDEYGLFLEYIEELGKWEEQQRIDKIRNGYM  185 (660)
T ss_pred             -ccHhHHHHHHHHHHhhCcccccchhhhhHHHHHHHHhcccccccccchHHHHHHHHHhccccccHHHHHHHHHHHHHHH
Confidence             4455566555544333211      112233333333 233333 223443333221   1111   112444555555


Q ss_pred             cCCCC----------CchhHHHHHHHH-Hh--cC----CHHHHHHHHccCC-----------------------------
Q 044988          181 DMPAR----------SVVSWNSLLKGY-VK--RG----DIDGAWKIFDEMP-----------------------------  214 (538)
Q Consensus       181 ~~~~~----------~~~~~~~li~~~-~~--~g----~~~~A~~~~~~m~-----------------------------  214 (538)
                      ++...          |-..|..=++-. ++  .|    -+-.|.+.+++..                             
T Consensus       186 ral~tP~~nleklW~dy~~fE~e~N~~TarKfvge~sp~ym~ar~~yqe~~nlt~Gl~v~~~~~~Rt~nK~~r~s~S~Wl  265 (660)
T COG5107         186 RALQTPMGNLEKLWKDYENFELELNKITARKFVGETSPIYMSARQRYQEIQNLTRGLSVKNPINLRTANKAARTSDSNWL  265 (660)
T ss_pred             HHHcCccccHHHHHHHHHHHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHHHHhccccccCchhhhhhccccccccchhh
Confidence            55431          101111000000 00  00    0111111111110                             


Q ss_pred             --------C-----CC------hHHHHHHH--------------HHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 044988          215 --------H-----RN------VVSWTTMI--------------SGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALS  261 (538)
Q Consensus       215 --------~-----~~------~~~~~~li--------------~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~  261 (538)
                              .     .+      ...|+..+              .-+...++-+.|+....+-..  ..|+...+  +-.
T Consensus       266 NwIkwE~en~l~L~~~~~~qRi~y~~~q~~~y~~~~~evw~dys~Y~~~isd~q~al~tv~rg~~--~spsL~~~--lse  341 (660)
T COG5107         266 NWIKWEMENGLKLGGRPHEQRIHYIHNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIE--MSPSLTMF--LSE  341 (660)
T ss_pred             hHhhHhhcCCcccCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhccHHHHHHHHHHhccc--CCCchhee--HHH
Confidence                    0     00      01122211              223345677788877665433  23442211  111


Q ss_pred             HHHccCChHHHHHHHHHHHHhc----------cCCCC---------------CcchhHHHHHHHHHHhCCCHHHHHHHHH
Q 044988          262 ACAEIGDLKLGKWIHSYVEENF----------SVGRE---------------PVLVSLNNALIHMYASCGEIEEAYGVFR  316 (538)
Q Consensus       262 ~~~~~~~~~~a~~~~~~~~~~~----------~~~~~---------------~~~~~~~~~l~~~~~~~g~~~~a~~~~~  316 (538)
                      .+.-..+-+.....|+.+.+..          ...+.               ..-..+|..+++.-.+..-++.|+.+|-
T Consensus       342 ~yel~nd~e~v~~~fdk~~q~L~r~ys~~~s~~~s~~D~N~e~~~Ell~kr~~k~t~v~C~~~N~v~r~~Gl~aaR~~F~  421 (660)
T COG5107         342 YYELVNDEEAVYGCFDKCTQDLKRKYSMGESESASKVDNNFEYSKELLLKRINKLTFVFCVHLNYVLRKRGLEAARKLFI  421 (660)
T ss_pred             HHhhcccHHHHhhhHHHHHHHHHHHHhhhhhhhhccccCCccccHHHHHHHHhhhhhHHHHHHHHHHHHhhHHHHHHHHH
Confidence            2222233333222222221110          00001               1123456677777778888999999999


Q ss_pred             hcCC-----CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHH-HHHHHHhh
Q 044988          317 KMQR-----RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHY-GCMVDLFS  390 (538)
Q Consensus       317 ~m~~-----~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~-~~l~~~~~  390 (538)
                      +..+     +++..+++++..++..                     +...|..+|+.-...   -||...| +-.+.-+.
T Consensus       422 k~rk~~~~~h~vyi~~A~~E~~~~~---------------------d~~ta~~ifelGl~~---f~d~~~y~~kyl~fLi  477 (660)
T COG5107         422 KLRKEGIVGHHVYIYCAFIEYYATG---------------------DRATAYNIFELGLLK---FPDSTLYKEKYLLFLI  477 (660)
T ss_pred             HHhccCCCCcceeeeHHHHHHHhcC---------------------CcchHHHHHHHHHHh---CCCchHHHHHHHHHHH
Confidence            8876     5677888888776643                     566777888876654   3554443 45566677


Q ss_pred             hcCChHHHHHHHHhCC--CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          391 RAGLMDEAFSLVQNMP--MKPN--DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       391 ~~g~~~~A~~~~~~~~--~~p~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      +.++-+.|..+|+...  +..+  ...|..+|.--..-|+...+..+-+++ .+..|....
T Consensus       478 ~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf-~e~~pQen~  537 (660)
T COG5107         478 RINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERF-RELVPQENL  537 (660)
T ss_pred             HhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHH-HHHcCcHhH
Confidence            8899999999998653  2223  568889999889999999999988888 788887644

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.35  E-value=1.4  Score=44.48  Aligned_cols=309  Identities=13%  Similarity=0.063  Sum_probs=171.9

Q ss_pred             hCCCCchhHHh-----HHHHHHHhcCCCCChhHHHHHhhcCCCCC---chhHHHHHHHHHhcC---CHHHHHHHHccCCC
Q 044988          147 SGYCSNVFIRT-----NLMNLYLMSGGECGVGCARLLFDDMPARS---VVSWNSLLKGYVKRG---DIDGAWKIFDEMPH  215 (538)
Q Consensus       147 ~~~~~~~~~~~-----~l~~~~~~~g~~~~~~~a~~~~~~~~~~~---~~~~~~li~~~~~~g---~~~~A~~~~~~m~~  215 (538)
                      .|++.+..-|.     .+++-+...+.   +..|.++-.-+..|.   ...|.....-+.+..   +-+.+..+-+++..
T Consensus       426 ~gIplT~~qy~~l~~~~vi~Rl~~r~~---Y~vaIQva~~l~~p~~~~~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~  502 (829)
T KOG2280|consen  426 IGIPLTHEQYRHLSEEVVIDRLVDRHL---YSVAIQVAKLLNLPESQGDRVLLEWARRKIKQSDKMDEEVLDKIDEKLSA  502 (829)
T ss_pred             cCccccHHHHhhhchhhhhHHHHhcch---hHHHHHHHHHhCCccccccHHHHHHHHHHHhccCccchHHHHHHHHHhcc
Confidence            35555544443     34555666666   788888777776664   455555666665553   22333344444444


Q ss_pred             --CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC----CCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCC---
Q 044988          216 --RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVG----LDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVG---  286 (538)
Q Consensus       216 --~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~----p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~---  286 (538)
                        ....+|..+.......|+++-|..+++.=...+.+    .+..-+...+.-+...|+.+....++-.+.......   
T Consensus       503 ~~~~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~~~~s~l~  582 (829)
T KOG2280|consen  503 KLTPGISYAAIARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNKLNRSSLF  582 (829)
T ss_pred             cCCCceeHHHHHHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence              45567888887777889988888887643222211    122234455556666777776666666555541100   


Q ss_pred             ----CCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHH----HHHHHHHHHhcccC-
Q 044988          287 ----REPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL----LTFLGVLSACSHGG-  357 (538)
Q Consensus       287 ----~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~----~~~~~ll~~~~~~~-  357 (538)
                          ..|....    +-.-+++..+-..-..+|+.-..+     ..+.....+.+...+.+    .......++|++.. 
T Consensus       583 ~~l~~~p~a~~----lY~~~~r~~~~~~l~d~y~q~dn~-----~~~a~~~~q~~~~~~~~~~r~~~lk~~a~~~a~sk~  653 (829)
T KOG2280|consen  583 MTLRNQPLALS----LYRQFMRHQDRATLYDFYNQDDNH-----QALASFHLQASYAAETIEGRIPALKTAANAFAKSKE  653 (829)
T ss_pred             HHHHhchhhhH----HHHHHHHhhchhhhhhhhhcccch-----hhhhhhhhhhhhhhhhhcccchhHHHHHHHHhhhhh
Confidence                0111111    111122222222222222221110     00000111110000000    22223334444433 


Q ss_pred             ---------cHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHH
Q 044988          358 ---------FVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAE  428 (538)
Q Consensus       358 ---------~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~~~~  428 (538)
                               +..+-.++.+.+...+|......+.+--+.-+...|+..+|.++-++.+ -||...|---+.+++..++++
T Consensus       654 ~s~e~ka~ed~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk-ipdKr~~wLk~~aLa~~~kwe  732 (829)
T KOG2280|consen  654 KSFEAKALEDQMKLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK-IPDKRLWWLKLTALADIKKWE  732 (829)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC-CcchhhHHHHHHHHHhhhhHH
Confidence                     2334444555555555655555566666677778999999999999998 589988888899999999999


Q ss_pred             HHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          429 LASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       429 ~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +-+++-+.. .  .|   ..|. -...+|.+.|+.+||.+++.+...
T Consensus       733 eLekfAksk-k--sP---IGy~-PFVe~c~~~~n~~EA~KYiprv~~  772 (829)
T KOG2280|consen  733 ELEKFAKSK-K--SP---IGYL-PFVEACLKQGNKDEAKKYIPRVGG  772 (829)
T ss_pred             HHHHHHhcc-C--CC---CCch-hHHHHHHhcccHHHHhhhhhccCC
Confidence            888877766 2  13   3355 445899999999999999887653

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=96.34  E-value=0.91  Score=42.34  Aligned_cols=158  Identities=13%  Similarity=0.057  Sum_probs=92.8

Q ss_pred             HHHHhcCCHHHHHHHHccCCCCChH-HHHHHHHH--HHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHH-----------
Q 044988          195 KGYVKRGDIDGAWKIFDEMPHRNVV-SWTTMISG--CAQNGKSRQALSLFNEMRRARVGLDQVALVAAL-----------  260 (538)
Q Consensus       195 ~~~~~~g~~~~A~~~~~~m~~~~~~-~~~~li~~--~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li-----------  260 (538)
                      .++...|+.+.|.+.--...+-|.. .+...+++  +.-.++.+.+...|++.+.  ..|+...-...-           
T Consensus       177 ~cl~~~~~~~~a~~ea~~ilkld~~n~~al~vrg~~~yy~~~~~ka~~hf~qal~--ldpdh~~sk~~~~~~k~le~~k~  254 (486)
T KOG0550|consen  177 ECLAFLGDYDEAQSEAIDILKLDATNAEALYVRGLCLYYNDNADKAINHFQQALR--LDPDHQKSKSASMMPKKLEVKKE  254 (486)
T ss_pred             hhhhhcccchhHHHHHHHHHhcccchhHHHHhcccccccccchHHHHHHHhhhhc--cChhhhhHHhHhhhHHHHHHHHh
Confidence            4567778888888776665553332 34444433  3345778888888888776  345444322211           


Q ss_pred             --HHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCC
Q 044988          261 --SACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGY  338 (538)
Q Consensus       261 --~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~  338 (538)
                        +-..+.|++..|...|.+.+.. ++....++...|.....+..+.|+..+|+.-.+...+-|..    .|.+|.+.+ 
T Consensus       255 ~gN~~fk~G~y~~A~E~Yteal~i-dP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al~iD~s----yikall~ra-  328 (486)
T KOG0550|consen  255 RGNDAFKNGNYRKAYECYTEALNI-DPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKIDSS----YIKALLRRA-  328 (486)
T ss_pred             hhhhHhhccchhHHHHHHHHhhcC-CccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhcCHH----HHHHHHHHH-
Confidence              1234567777777777777665 22234445555556666666777777777777766654432    233333333 


Q ss_pred             ccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          339 AQEALLTFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       339 ~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                                  .++...++++.|.+-|+...+.
T Consensus       329 ------------~c~l~le~~e~AV~d~~~a~q~  350 (486)
T KOG0550|consen  329 ------------NCHLALEKWEEAVEDYEKAMQL  350 (486)
T ss_pred             ------------HHHHHHHHHHHHHHHHHHHHhh
Confidence                        2333345777777777777655

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=96.33  E-value=0.0079  Score=42.57  Aligned_cols=62  Identities=13%  Similarity=0.113  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHch---hccCCCC---cccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          412 AVLGSLLLGCRIHNNAELASQVAQKLV---AEIDPEQ---AAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       412 ~~~~~l~~~~~~~~~~~~A~~~~~~~~---~~~~p~~---~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      .+++.+...+...|++++|+..++++.   ....++.   ..++. .++.+|...|++++|++++++..
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~-~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLN-NLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHH-HHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH-HHHHHHHHcCCHHHHHHHHHHHH
Confidence            345555555666666666666666654   1111111   22333 56666777777777777666544

...

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.32  E-value=0.12  Score=44.69  Aligned_cols=122  Identities=14%  Similarity=0.089  Sum_probs=63.3

Q ss_pred             HHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC----CCchhHHHHH----
Q 044988          123 FLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA----RSVVSWNSLL----  194 (538)
Q Consensus       123 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~----~~~~~~~~li----  194 (538)
                      .++..+.-.|.+.-...++.+.++...+.++.....|++.-...||   .+.|...|++..+    -|..+.+.++    
T Consensus       182 ~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD---~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  182 SMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGD---IKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhccc---HHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            3344444444555555555555555444455555555555555555   5555555553332    1222222222    


Q ss_pred             -HHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 044988          195 -KGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRA  247 (538)
Q Consensus       195 -~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  247 (538)
                       ..|.-++++..|...|++++.   .|++.-|.-.-+..-.|+..+|++.++.|++.
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~  315 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ  315 (366)
T ss_pred             hhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence             234445566666666766554   33344444333334457777777777777764

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=96.28  E-value=0.09  Score=46.76  Aligned_cols=110  Identities=14%  Similarity=0.114  Sum_probs=83.6

Q ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH---ccCChHHHHHHHHHHHHhccCCCCCcch
Q 044988          216 RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACA---EIGDLKLGKWIHSYVEENFSVGREPVLV  292 (538)
Q Consensus       216 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~  292 (538)
                      .|...|-.|...|...|+++.|..-|.+..+.. .++...+..+..++.   ......++..+++.+.+.     .|.++
T Consensus       154 ~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~-----D~~~i  227 (287)
T COG4235         154 GDAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALAL-----DPANI  227 (287)
T ss_pred             CCchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhc-----CCccH
Confidence            367789999999999999999999999988741 234445555555543   233457888999999986     78888


Q ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHhcCC--CCcchHHHHHH
Q 044988          293 SLNNALIHMYASCGEIEEAYGVFRKMQR--RNTVSWTSMIT  331 (538)
Q Consensus       293 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~li~  331 (538)
                      .....|...+...|++.+|...|+.|.+  |....+..+|.
T Consensus       228 ral~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~~rr~~ie  268 (287)
T COG4235         228 RALSLLAFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLIE  268 (287)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHhcCCCCCchHHHHH
Confidence            8888899999999999999999999986  44445555544

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=96.23  E-value=0.014  Score=40.56  Aligned_cols=60  Identities=12%  Similarity=0.152  Sum_probs=43.2

Q ss_pred             HHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          387 DLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       387 ~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      ..|.+.+++++|.+.++.+. ..|+ ...|......+.+.|++++|.+.+++. ....|+++.
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~-l~~~p~~~~   64 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERA-LELSPDDPD   64 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHH-HHHCCCcHH
Confidence            45677788888888887764 3344 455666667778888888888888888 777777766

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.09  E-value=0.49  Score=41.19  Aligned_cols=141  Identities=13%  Similarity=0.058  Sum_probs=90.1

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhcc-CCCCCcchhHHHHH
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFS-VGREPVLVSLNNAL  298 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~~~~l  298 (538)
                      +.+.++..+...|.+.-.+..+++..+...+.+..-...+.+.-.+.||.+.|...++.+.+... ..+......+....
T Consensus       179 Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n~  258 (366)
T KOG2796|consen  179 VMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMNS  258 (366)
T ss_pred             HHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhhh
Confidence            44566666677788888888888888876666777778888888888999998888887765411 11233333333444


Q ss_pred             HHHHHhCCCHHHHHHHHHhcCCCC---cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCC
Q 044988          299 IHMYASCGEIEEAYGVFRKMQRRN---TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGI  375 (538)
Q Consensus       299 ~~~~~~~g~~~~a~~~~~~m~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  375 (538)
                      ...|.-.+++..|...+.++...|   ++..|.-.-.+.                    -.|+...|.+..+.+.+.   
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcll--------------------Ylg~l~DAiK~~e~~~~~---  315 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLL--------------------YLGKLKDALKQLEAMVQQ---  315 (366)
T ss_pred             hhheecccchHHHHHHHhhccccCCCchhhhchHHHHHH--------------------HHHHHHHHHHHHHHHhcc---
Confidence            556667788888888888887643   333222111111                    124667777888877754   


Q ss_pred             CccHHHHH
Q 044988          376 KPRIEHYG  383 (538)
Q Consensus       376 ~p~~~~~~  383 (538)
                      .|...+-+
T Consensus       316 ~P~~~l~e  323 (366)
T KOG2796|consen  316 DPRHYLHE  323 (366)
T ss_pred             CCccchhh
Confidence            55544333

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.03  E-value=0.87  Score=39.28  Aligned_cols=143  Identities=11%  Similarity=0.041  Sum_probs=80.1

Q ss_pred             hHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc----cHHHHHHHHHHhhhcCChHHHHH
Q 044988          325 SWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP----RIEHYGCMVDLFSRAGLMDEAFS  400 (538)
Q Consensus       325 ~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p----~~~~~~~l~~~~~~~g~~~~A~~  400 (538)
                      .|+.-...|...|.++.|-.+......+. ..-+++.|++++++........-    -...+......+.+..++++|-.
T Consensus        93 l~eKAs~lY~E~GspdtAAmaleKAak~l-env~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~lVrl~kf~Eaa~  171 (308)
T KOG1585|consen   93 LYEKASELYVECGSPDTAAMALEKAAKAL-ENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRVLVRLEKFTEAAT  171 (308)
T ss_pred             HHHHHHHHHHHhCCcchHHHHHHHHHHHh-hcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhHhhhhHHhhHHHH
Confidence            34444555666666665554444433332 23467777777776543211111    12345556667777778777766


Q ss_pred             HHHhCC-------CCCCH-HHHHHHHHHHHhcCCHHHHHHHHHHch---hccCCCCcccHHHHHHHHHHhcCChHHHHHH
Q 044988          401 LVQNMP-------MKPND-AVLGSLLLGCRIHNNAELASQVAQKLV---AEIDPEQAAGYLALVANVYAAAKRWQDVAAV  469 (538)
Q Consensus       401 ~~~~~~-------~~p~~-~~~~~l~~~~~~~~~~~~A~~~~~~~~---~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~  469 (538)
                      .+.+-.       .-|+. ..+...|-.+....++..|.+.++..-   .-..|++..+.. .|..+ ...|+.+++..+
T Consensus       172 a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~le-nLL~a-yd~gD~E~~~kv  249 (308)
T KOG1585|consen  172 AFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLE-NLLTA-YDEGDIEEIKKV  249 (308)
T ss_pred             HHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHH-HHHHH-hccCCHHHHHHH
Confidence            555432       12332 345566666777789999999998852   223445555455 45444 456777777665


Q ss_pred             H
Q 044988          470 R  470 (538)
Q Consensus       470 ~  470 (538)
                      +
T Consensus       250 l  250 (308)
T KOG1585|consen  250 L  250 (308)
T ss_pred             H
Confidence            4

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=96.01  E-value=0.013  Score=35.94  Aligned_cols=40  Identities=15%  Similarity=0.246  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHH
Q 044988          413 VLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVA  454 (538)
Q Consensus       413 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~  454 (538)
                      +|..+..++...|++++|+++++++ .+..|+++..+. .|+
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~-l~~~P~~~~a~~-~La   42 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRA-LALDPDDPEAWR-ALA   42 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHH-HHHCcCCHHHHH-Hhh
Confidence            5667888899999999999999999 888999888666 544

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=95.97  E-value=0.17  Score=43.69  Aligned_cols=51  Identities=16%  Similarity=0.172  Sum_probs=34.0

Q ss_pred             HHHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHH
Q 044988          349 VLSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAF  399 (538)
Q Consensus       349 ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~  399 (538)
                      +..-|.+.|.+..|..-++.+.+.+.-.+. ......++.+|.+.|..+.+.
T Consensus       147 ia~~Y~~~~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~a~  198 (203)
T PF13525_consen  147 IARFYYKRGKYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQAAD  198 (203)
T ss_dssp             HHHHHHCTT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHHHH
Confidence            445667777888888888888887532222 345677888888888877543

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.93  E-value=0.65  Score=37.22  Aligned_cols=129  Identities=12%  Similarity=0.154  Sum_probs=85.8

Q ss_pred             cccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhcC
Q 044988           17 ALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARS   96 (538)
Q Consensus        17 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~   96 (538)
                      ......++..+...+.+..+..+++.+.+.+. .++..++.++..|++.+ ..+..+.+..  .++......+++.|.+.
T Consensus         7 ~~~~~~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~~~-~~~ll~~l~~--~~~~yd~~~~~~~c~~~   82 (140)
T smart00299        7 PIDVSEVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAKYD-PQKEIERLDN--KSNHYDIEKVGKLCEKA   82 (140)
T ss_pred             cCCHHHHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHHHC-HHHHHHHHHh--ccccCCHHHHHHHHHHc
Confidence            34456788888888899999999999988874 67889999999998764 3455555552  23445556677777788


Q ss_pred             CCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHcc-CCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHH
Q 044988           97 ETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARC-GLFREGEQVHGRVLASGYCSNVFIRTNLMNLYL  164 (538)
Q Consensus        97 ~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~-~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  164 (538)
                      +.++++.-++.++..         +...+..+... ++++.|.++..+      ..+...|..++..+.
T Consensus        83 ~l~~~~~~l~~k~~~---------~~~Al~~~l~~~~d~~~a~~~~~~------~~~~~lw~~~~~~~l  136 (140)
T smart00299       83 KLYEEAVELYKKDGN---------FKDAIVTLIEHLGNYEKAIEYFVK------QNNPELWAEVLKALL  136 (140)
T ss_pred             CcHHHHHHHHHhhcC---------HHHHHHHHHHcccCHHHHHHHHHh------CCCHHHHHHHHHHHH
Confidence            888888888776532         33333334333 667777666554      124445555555443

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.92  E-value=0.1  Score=48.28  Aligned_cols=96  Identities=11%  Similarity=0.054  Sum_probs=76.6

Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ..+++.|..+|.+.+++.+|++..+...  .++|....-.-..++...|+++.|+..|+++ .++.|++..+-. -|+.+
T Consensus       257 ~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KALyRrG~A~l~~~e~~~A~~df~ka-~k~~P~Nka~~~-el~~l  334 (397)
T KOG0543|consen  257 LACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKALYRRGQALLALGEYDLARDDFQKA-LKLEPSNKAARA-ELIKL  334 (397)
T ss_pred             HHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhccHHHHHHHHHHH-HHhCCCcHHHHH-HHHHH
Confidence            4467788889999999999999988763  3466777777788899999999999999999 999999988555 77666


Q ss_pred             HHhcCChHH-HHHHHHHHHhC
Q 044988          457 YAAAKRWQD-VAAVRQKMIKM  476 (538)
Q Consensus       457 ~~~~g~~~~-A~~~~~~m~~~  476 (538)
                      --+..+..+ ..++|..|..+
T Consensus       335 ~~k~~~~~~kekk~y~~mF~k  355 (397)
T KOG0543|consen  335 KQKIREYEEKEKKMYANMFAK  355 (397)
T ss_pred             HHHHHHHHHHHHHHHHHHhhc
Confidence            666555544 47888888743

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=95.91  E-value=3  Score=44.54  Aligned_cols=134  Identities=15%  Similarity=0.079  Sum_probs=86.6

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHH------HHHHhcccCcHHHHHHHHHH
Q 044988          295 NNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLG------VLSACSHGGFVDEGRQFFEC  368 (538)
Q Consensus       295 ~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~------ll~~~~~~~~~~~a~~~~~~  368 (538)
                      |.-.++.--+.|.+.+|..++..=.+.-...|.+....+...+.+++|..+|..      .+.+|..+|++.+|..+..+
T Consensus       911 ~~e~~n~I~kh~Ly~~aL~ly~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~GklekAl~a~~~~~dWr~~l~~a~q  990 (1265)
T KOG1920|consen  911 FPECKNYIKKHGLYDEALALYKPDSEKQKVIYEAYADHLREELMSDEAALMYERCGKLEKALKAYKECGDWREALSLAAQ  990 (1265)
T ss_pred             cHHHHHHHHhcccchhhhheeccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhccHHHHHHHHHHhccHHHHHHHHHh
Confidence            344455555667777777666443333334455555666677777777755543      46778888888888888877


Q ss_pred             hhhhcCCCccH--HHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHc
Q 044988          369 MNQNWGIKPRI--EHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKL  437 (538)
Q Consensus       369 ~~~~~~~~p~~--~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~  437 (538)
                      +..    .-+.  .+-..|..-+...++.-+|-+++.+..-.|.     ..+..+++...+++|.++....
T Consensus       991 l~~----~~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~sd~~-----~av~ll~ka~~~~eAlrva~~~ 1052 (1265)
T KOG1920|consen  991 LSE----GKDELVILAEELVSRLVEQRKHYEAAKILLEYLSDPE-----EAVALLCKAKEWEEALRVASKA 1052 (1265)
T ss_pred             hcC----CHHHHHHHHHHHHHHHHHcccchhHHHHHHHHhcCHH-----HHHHHHhhHhHHHHHHHHHHhc
Confidence            642    1222  2236677778888998888888887653332     2334566677888888887766

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=95.89  E-value=0.39  Score=36.91  Aligned_cols=116  Identities=11%  Similarity=0.141  Sum_probs=70.4

Q ss_pred             cCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhh----------------------hcCChHHHHHHHHhCCCCCCHHH
Q 044988          356 GGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFS----------------------RAGLMDEAFSLVQNMPMKPNDAV  413 (538)
Q Consensus       356 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~----------------------~~g~~~~A~~~~~~~~~~p~~~~  413 (538)
                      .|.++++.++..+....    .+..-+|-+|--..                      .+|++.....-+-.+.  .+...
T Consensus        15 dG~V~qGveii~k~v~S----sni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis~C~NlKrVi~C~~~~n--~~se~   88 (161)
T PF09205_consen   15 DGDVKQGVEIIEKTVNS----SNIKEYNWVICNIIDAADCDYVVETLDSIGKIFDISKCGNLKRVIECYAKRN--KLSEY   88 (161)
T ss_dssp             TT-HHHHHHHHHHHHHH----S-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GGG-S-THHHHHHHHHTT-----HH
T ss_pred             hchHHHHHHHHHHHcCc----CCccccceeeeecchhhchhHHHHHHHHHhhhcCchhhcchHHHHHHHHHhc--chHHH
Confidence            46777788888777654    12222332222222                      3444444444444432  34556


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCC
Q 044988          414 LGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVR  479 (538)
Q Consensus       414 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  479 (538)
                      ++..+.....+|+-++-.++++.+ ......++.... -++.+|.+.|+..++.+++++..++|++
T Consensus        89 vD~ALd~lv~~~kkDqLdki~~~l-~kn~~~~p~~L~-kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   89 VDLALDILVKQGKKDQLDKIYNEL-KKNEEINPEFLV-KIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHH-HHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHH-hhccCCCHHHHH-HHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            677788899999999999999988 434444555456 8999999999999999999999999883

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=95.87  E-value=0.0064  Score=34.69  Aligned_cols=33  Identities=27%  Similarity=0.483  Sum_probs=28.8

Q ss_pred             HHHchhccCCCCcccHHHHHHHHHHhcCChHHHHH
Q 044988          434 AQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAA  468 (538)
Q Consensus       434 ~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~  468 (538)
                      |+++ .++.|+++.+|. .|+.+|...|++++|++
T Consensus         2 y~kA-ie~~P~n~~a~~-nla~~~~~~g~~~~A~~   34 (34)
T PF13431_consen    2 YKKA-IELNPNNAEAYN-NLANLYLNQGDYEEAIA   34 (34)
T ss_pred             hHHH-HHHCCCCHHHHH-HHHHHHHHCcCHHhhcC
Confidence            5666 889999999899 99999999999999863

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=95.87  E-value=0.79  Score=43.02  Aligned_cols=31  Identities=10%  Similarity=0.140  Sum_probs=25.5

Q ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHC
Q 044988          217 NVVSWTTMISGCAQNGKSRQALSLFNEMRRA  247 (538)
Q Consensus       217 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~  247 (538)
                      +--.+.+++.++.-.|+.++|.+.+++|.+.
T Consensus       304 dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l  334 (374)
T PF13281_consen  304 DYWDVATLLEASVLAGDYEKAIQAAEKAFKL  334 (374)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHhhc
Confidence            4445678888888899999999999999875

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=95.86  E-value=0.082  Score=48.93  Aligned_cols=64  Identities=17%  Similarity=0.081  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          411 DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       411 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      ...+..+..++.+.+++..|++..++. ++..|++..+.. .-+.+|...|+++.|+..|+++.+.
T Consensus       257 ~~~~lNlA~c~lKl~~~~~Ai~~c~kv-Le~~~~N~KALy-RrG~A~l~~~e~~~A~~df~ka~k~  320 (397)
T KOG0543|consen  257 LACHLNLAACYLKLKEYKEAIESCNKV-LELDPNNVKALY-RRGQALLALGEYDLARDDFQKALKL  320 (397)
T ss_pred             HHHhhHHHHHHHhhhhHHHHHHHHHHH-HhcCCCchhHHH-HHHHHHHhhccHHHHHHHHHHHHHh
Confidence            345667777899999999999999999 999999999888 8899999999999999999999973

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=95.84  E-value=1.1  Score=38.74  Aligned_cols=180  Identities=13%  Similarity=0.106  Sum_probs=99.6

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhH-HHHHHH
Q 044988          224 MISGCAQNGKSRQALSLFNEMRRARV--GLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSL-NNALIH  300 (538)
Q Consensus       224 li~~~~~~~~~~~a~~~~~~m~~~g~--~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~-~~~l~~  300 (538)
                      ....+...|++.+|...|+.+...-.  +--......+..++.+.|+++.|...++.+.+.     .|.+... +...+.
T Consensus        11 ~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~-----yP~~~~~~~A~Y~~   85 (203)
T PF13525_consen   11 KALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL-----YPNSPKADYALYML   85 (203)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH------TT-TTHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-----CCCCcchhhHHHHH
Confidence            34455667777777777777775421  112233445666667777777777777777665     3332221 111111


Q ss_pred             HHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHH
Q 044988          301 MYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIE  380 (538)
Q Consensus       301 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~  380 (538)
                      +.+....   ....+  ...             ...+...+|...|..++.-+-...-..+|...+..+....     ..
T Consensus        86 g~~~~~~---~~~~~--~~~-------------~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~l-----a~  142 (203)
T PF13525_consen   86 GLSYYKQ---IPGIL--RSD-------------RDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNRL-----AE  142 (203)
T ss_dssp             HHHHHHH---HHHHH---TT----------------HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHH-----HH
T ss_pred             HHHHHHh---Cccch--hcc-------------cChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHHH-----HH
Confidence            1111110   11111  111             1122334555778888888888888888888777776431     12


Q ss_pred             HHHHHHHHhhhcCChHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhcCCHHHHH
Q 044988          381 HYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN----DAVLGSLLLGCRIHNNAELAS  431 (538)
Q Consensus       381 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~----~~~~~~l~~~~~~~~~~~~A~  431 (538)
                      .--.+..-|.+.|.+..|..-++.+. .-|+    ....-.++.++.+.|..+.+.
T Consensus       143 ~e~~ia~~Y~~~~~y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~a~  198 (203)
T PF13525_consen  143 HELYIARFYYKRGKYKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQAAD  198 (203)
T ss_dssp             HHHHHHHHHHCTT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHHHH
Confidence            22346778999999999998888874 2244    245567788899999888544

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=95.83  E-value=0.17  Score=39.46  Aligned_cols=53  Identities=11%  Similarity=0.109  Sum_probs=37.1

Q ss_pred             CCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHH
Q 044988          248 RVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYA  303 (538)
Q Consensus       248 g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  303 (538)
                      ...|+..+..+++.+++..+++..|.++.+.+.+..   +++.+..+|..|++-..
T Consensus        47 pl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y---~I~i~~~~W~~Ll~W~~   99 (126)
T PF12921_consen   47 PLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKY---PIPIPKEFWRRLLEWAY   99 (126)
T ss_pred             CCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHH
Confidence            356777777778888777788888877777777663   35666677766665443

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production

Probab=95.70  E-value=0.042  Score=44.57  Aligned_cols=71  Identities=18%  Similarity=0.169  Sum_probs=51.4

Q ss_pred             hHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHH-----hCCCCchhHH
Q 044988           85 IWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLA-----SGYCSNVFIR  156 (538)
Q Consensus        85 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  156 (538)
                      ....++..+...|+++.|..+.+.+.... +.|...|..+|.++...|+...|.++|+.+.+     .|+.|+..+-
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~~  139 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPETR  139 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHHH
Confidence            44556677788999999999999998764 45777999999999999999999999888753     5888876653

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=95.55  E-value=2  Score=45.84  Aligned_cols=107  Identities=11%  Similarity=0.032  Sum_probs=63.5

Q ss_pred             CCCCHHHHHHHHHHH----HccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcc
Q 044988          249 VGLDQVALVAALSAC----AEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTV  324 (538)
Q Consensus       249 ~~p~~~~~~~li~~~----~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~  324 (538)
                      ..|+...+..+..+|    .....++.|.-.|...-+.             .--+.+|..+|+|.+|..+-.++..+-..
T Consensus       931 y~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gkl-------------ekAl~a~~~~~dWr~~l~~a~ql~~~~de  997 (1265)
T KOG1920|consen  931 YKPDSEKQKVIYEAYADHLREELMSDEAALMYERCGKL-------------EKALKAYKECGDWREALSLAAQLSEGKDE  997 (1265)
T ss_pred             eccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhccH-------------HHHHHHHHHhccHHHHHHHHHhhcCCHHH
Confidence            356666666655554    3456667776666655443             34567778888888888888877664333


Q ss_pred             hH---HHHHHHHHhcCCccHHHHH-------HHHHHHHhcccCcHHHHHHHHHH
Q 044988          325 SW---TSMITGFAKQGYAQEALLT-------FLGVLSACSHGGFVDEGRQFFEC  368 (538)
Q Consensus       325 ~~---~~li~~~~~~~~~~~a~~~-------~~~ll~~~~~~~~~~~a~~~~~~  368 (538)
                      ..   ..|+..+...++.-+|-..       ....+..+++...+++|..+-..
T Consensus       998 ~~~~a~~L~s~L~e~~kh~eAa~il~e~~sd~~~av~ll~ka~~~~eAlrva~~ 1051 (1265)
T KOG1920|consen  998 LVILAEELVSRLVEQRKHYEAAKILLEYLSDPEEAVALLCKAKEWEEALRVASK 1051 (1265)
T ss_pred             HHHHHHHHHHHHHHcccchhHHHHHHHHhcCHHHHHHHHhhHhHHHHHHHHHHh
Confidence            22   5566777777777766511       22233344445555555555443

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=95.41  E-value=0.17  Score=44.44  Aligned_cols=92  Identities=13%  Similarity=0.060  Sum_probs=45.8

Q ss_pred             ccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHH
Q 044988          265 EIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALL  344 (538)
Q Consensus       265 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~  344 (538)
                      +.|++..|...|...++....+...++..+|  |..++...|++++|..+|..+.+              ..++..+|-.
T Consensus       153 ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yW--LGe~~y~qg~y~~Aa~~f~~~~k--------------~~P~s~KApd  216 (262)
T COG1729         153 KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYW--LGESLYAQGDYEDAAYIFARVVK--------------DYPKSPKAPD  216 (262)
T ss_pred             HcCCHHHHHHHHHHHHHcCCCCcccchhHHH--HHHHHHhcccchHHHHHHHHHHH--------------hCCCCCCChH
Confidence            3444555555555555543333344444444  66666666666666666655543              1111122222


Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                      .+..+..+..+.|+.++|..+|+++.++
T Consensus       217 allKlg~~~~~l~~~d~A~atl~qv~k~  244 (262)
T COG1729         217 ALLKLGVSLGRLGNTDEACATLQQVIKR  244 (262)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            3333333444444555666666666555

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=95.37  E-value=0.065  Score=37.81  Aligned_cols=27  Identities=30%  Similarity=0.353  Sum_probs=21.1

Q ss_pred             hhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          292 VSLNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       292 ~~~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                      ..++..+..+|...|++++|.+.+++.
T Consensus        46 a~~~~~lg~~~~~~g~~~~A~~~~~~a   72 (78)
T PF13424_consen   46 ANTLNNLGECYYRLGDYEEALEYYQKA   72 (78)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            556677888888888888888888764

...

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=95.22  E-value=1.1  Score=43.63  Aligned_cols=156  Identities=12%  Similarity=0.109  Sum_probs=91.2

Q ss_pred             HHHhcCCCchHHHHHHH--HhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCC
Q 044988           91 RGHARSETPEKSVYLYK--QMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGG  168 (538)
Q Consensus        91 ~~~~~~~~~~~a~~~~~--~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  168 (538)
                      ....-.++++.+.+...  ++.. .+  ...-.+.+++.+-+.|..+.|+++..+-.            .-.....+.|+
T Consensus       269 k~av~~~d~~~v~~~i~~~~ll~-~i--~~~~~~~i~~fL~~~G~~e~AL~~~~D~~------------~rFeLAl~lg~  333 (443)
T PF04053_consen  269 KTAVLRGDFEEVLRMIAASNLLP-NI--PKDQGQSIARFLEKKGYPELALQFVTDPD------------HRFELALQLGN  333 (443)
T ss_dssp             HHHHHTT-HHH-----HHHHTGG-G----HHHHHHHHHHHHHTT-HHHHHHHSS-HH------------HHHHHHHHCT-
T ss_pred             HHHHHcCChhhhhhhhhhhhhcc-cC--ChhHHHHHHHHHHHCCCHHHHHhhcCChH------------HHhHHHHhcCC
Confidence            33455677777766664  2221 11  24457788888888888888887743321            22345567777


Q ss_pred             CCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 044988          169 ECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR  248 (538)
Q Consensus       169 ~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  248 (538)
                         ++.|.++.++..  +...|..|.....++|+++-|++.|.+..+     |..|+-.|.-.|+.+.-.++.+.....|
T Consensus       334 ---L~~A~~~a~~~~--~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d-----~~~L~lLy~~~g~~~~L~kl~~~a~~~~  403 (443)
T PF04053_consen  334 ---LDIALEIAKELD--DPEKWKQLGDEALRQGNIELAEECYQKAKD-----FSGLLLLYSSTGDREKLSKLAKIAEERG  403 (443)
T ss_dssp             ---HHHHHHHCCCCS--THHHHHHHHHHHHHTTBHHHHHHHHHHCT------HHHHHHHHHHCT-HHHHHHHHHHHHHTT
T ss_pred             ---HHHHHHHHHhcC--cHHHHHHHHHHHHHcCCHHHHHHHHHhhcC-----ccccHHHHHHhCCHHHHHHHHHHHHHcc
Confidence               888877776665  555788888888888888888888877654     5556666677777777777666666554


Q ss_pred             CCCCHHHHHHHHHHHHccCChHHHHHHHH
Q 044988          249 VGLDQVALVAALSACAEIGDLKLGKWIHS  277 (538)
Q Consensus       249 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~  277 (538)
                            -++..+.++.-.|++++..+++.
T Consensus       404 ------~~n~af~~~~~lgd~~~cv~lL~  426 (443)
T PF04053_consen  404 ------DINIAFQAALLLGDVEECVDLLI  426 (443)
T ss_dssp             -------HHHHHHHHHHHT-HHHHHHHHH
T ss_pred             ------CHHHHHHHHHHcCCHHHHHHHHH
Confidence                  13444555555666666555443

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=95.21  E-value=2.4  Score=38.71  Aligned_cols=161  Identities=14%  Similarity=0.054  Sum_probs=88.9

Q ss_pred             hcCCCchHHHHHHHHhHhCC--CCCCcc------hHHHHHHHHHccCCcHHHHHHHHHHHHh--------CCCCc-----
Q 044988           94 ARSETPEKSVYLYKQMIDKE--TEPDEY------TYSFLLSVCARCGLFREGEQVHGRVLAS--------GYCSN-----  152 (538)
Q Consensus        94 ~~~~~~~~a~~~~~~m~~~~--~~p~~~------~~~~li~~~~~~~~~~~a~~~~~~~~~~--------~~~~~-----  152 (538)
                      .++|+.+.|..++.+....-  ..|+..      .|+.-...+.+..+++.|...+++..+.        ...|+     
T Consensus         4 ~~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr   83 (278)
T PF08631_consen    4 WKQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSELR   83 (278)
T ss_pred             hhhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHHH
Confidence            45666677777666665422  122211      2333333333322666666665555443        11222     


Q ss_pred             hhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC--CC-chhHHHHHHHHHhcCCHHHHHHHHccCCC-C--ChHHHHHHHH
Q 044988          153 VFIRTNLMNLYLMSGGECGVGCARLLFDDMPA--RS-VVSWNSLLKGYVKRGDIDGAWKIFDEMPH-R--NVVSWTTMIS  226 (538)
Q Consensus       153 ~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~--~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~--~~~~~~~li~  226 (538)
                      ..+...++.+|...+.....++|.++++.+..  ++ +..+-.-++.+.+.++.+.+.+.+.+|.. .  ....+...+.
T Consensus        84 ~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~~~e~~~~~~l~  163 (278)
T PF08631_consen   84 LSILRLLANAYLEWDTYESVEKALNALRLLESEYGNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSVDHSESNFDSILH  163 (278)
T ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhcccccchHHHHHH
Confidence            24567777777777775556666666666643  23 44555556666667888888888888764 1  2334555555


Q ss_pred             HHHH--cCCHHHHHHHHHHHHHCCCCCCHH
Q 044988          227 GCAQ--NGKSRQALSLFNEMRRARVGLDQV  254 (538)
Q Consensus       227 ~~~~--~~~~~~a~~~~~~m~~~g~~p~~~  254 (538)
                      .+-.  ......|...+..+....+.|...
T Consensus       164 ~i~~l~~~~~~~a~~~ld~~l~~r~~~~~~  193 (278)
T PF08631_consen  164 HIKQLAEKSPELAAFCLDYLLLNRFKSSED  193 (278)
T ss_pred             HHHHHHhhCcHHHHHHHHHHHHHHhCCChh
Confidence            4422  234456777777776655565553

It is also involved in sporulation [].

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.20  E-value=0.13  Score=48.86  Aligned_cols=60  Identities=12%  Similarity=-0.037  Sum_probs=51.1

Q ss_pred             HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccH----HHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          344 LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRI----EHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       344 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      ..+..+..+|...|++++|...|++..+.   .|+.    .+|..+..+|...|+.++|++.+++..
T Consensus        76 ~a~~NLG~AL~~lGryeEAIa~f~rALeL---~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrAL  139 (453)
T PLN03098         76 EDAVNLGLSLFSKGRVKDALAQFETALEL---NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTAL  139 (453)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhh---CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            67888888999999999999999998854   6763    358899999999999999999998875

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=95.15  E-value=1.3  Score=40.49  Aligned_cols=202  Identities=9%  Similarity=0.049  Sum_probs=96.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHcc-------CCCC--ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHC-CCCC---CHHH
Q 044988          189 SWNSLLKGYVKRGDIDGAWKIFDE-------MPHR--NVVSWTTMISGCAQNGKSRQALSLFNEMRRA-RVGL---DQVA  255 (538)
Q Consensus       189 ~~~~li~~~~~~g~~~~A~~~~~~-------m~~~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p---~~~~  255 (538)
                      ++..+..+.+..|.+++++..--.       ..+.  -...|-.+..++-+..++.+++.+-..-... |..|   ....
T Consensus        45 ~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~l~~f~kt~~y~k~~l~lpgt~~~~~~gq~  124 (518)
T KOG1941|consen   45 VLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEKLCEFHKTISYCKTCLGLPGTRAGQLGGQV  124 (518)
T ss_pred             HhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHhcCCCCCcccccchh
Confidence            444555555666665555432211       1111  1123444455555555555555544433321 2222   1122


Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHHHhccCCC-CCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC-------CCcch-H
Q 044988          256 LVAALSACAEIGDLKLGKWIHSYVEENFSVGR-EPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR-------RNTVS-W  326 (538)
Q Consensus       256 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-------~~~~~-~  326 (538)
                      ..++-.++...+.++++.+.|+...+.....+ ......++..|...|.+..++++|.-+..+..+       .|... |
T Consensus       125 ~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~Kal~f~~kA~~lv~s~~l~d~~~ky  204 (518)
T KOG1941|consen  125 SLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYEKALFFPCKAAELVNSYGLKDWSLKY  204 (518)
T ss_pred             hhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhhHHhhhhHhHHHHHHhcCcCchhHHH
Confidence            33344455555566666666655555422211 122334455566666666666555444333221       11110 1


Q ss_pred             HHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh---cCCCcc-HHHHHHHHHHhhhcCChHHHHHHH
Q 044988          327 TSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQN---WGIKPR-IEHYGCMVDLFSRAGLMDEAFSLV  402 (538)
Q Consensus       327 ~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~---~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~  402 (538)
                      ..               .....+..++...|.+..|.+.-++..+.   .|-.|. ......+.+.|...|+.+.|+.-|
T Consensus       205 r~---------------~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDIyR~~gd~e~af~rY  269 (518)
T KOG1941|consen  205 RA---------------MSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADIYRSRGDLERAFRRY  269 (518)
T ss_pred             HH---------------HHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHhcccHhHHHHHH
Confidence            10               12223334445555665565555554332   133332 445667888899999999988888


Q ss_pred             HhC
Q 044988          403 QNM  405 (538)
Q Consensus       403 ~~~  405 (538)
                      +..
T Consensus       270 e~A  272 (518)
T KOG1941|consen  270 EQA  272 (518)
T ss_pred             HHH
Confidence            754

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=95.13  E-value=2.8  Score=38.99  Aligned_cols=243  Identities=14%  Similarity=0.052  Sum_probs=140.7

Q ss_pred             hcCCCCChhHHHHHhhcCCC-CCch--hHHHHHHHHHhcCCHHHHHHHHccCCC--CC-hHHHHHHHHHHHHcCCHHHHH
Q 044988          165 MSGGECGVGCARLLFDDMPA-RSVV--SWNSLLKGYVKRGDIDGAWKIFDEMPH--RN-VVSWTTMISGCAQNGKSRQAL  238 (538)
Q Consensus       165 ~~g~~~~~~~a~~~~~~~~~-~~~~--~~~~li~~~~~~g~~~~A~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~  238 (538)
                      -.|+   .+.|.+-|+.|.. |.+.  -...|.-..-+.|+.+.|...-++.-.  |. .-.+...+...|..|+++.|+
T Consensus       132 ~eG~---~~~Ar~kfeAMl~dPEtRllGLRgLyleAqr~GareaAr~yAe~Aa~~Ap~l~WA~~AtLe~r~~~gdWd~Al  208 (531)
T COG3898         132 LEGD---YEDARKKFEAMLDDPETRLLGLRGLYLEAQRLGAREAARHYAERAAEKAPQLPWAARATLEARCAAGDWDGAL  208 (531)
T ss_pred             hcCc---hHHHHHHHHHHhcChHHHHHhHHHHHHHHHhcccHHHHHHHHHHHHhhccCCchHHHHHHHHHHhcCChHHHH
Confidence            3455   6666666666653 2111  111122223456667776666655432  22 235677788888888888888


Q ss_pred             HHHHHHHHC-CCCCCHHH--HHHHHHHHH---ccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHH
Q 044988          239 SLFNEMRRA-RVGLDQVA--LVAALSACA---EIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAY  312 (538)
Q Consensus       239 ~~~~~m~~~-g~~p~~~~--~~~li~~~~---~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  312 (538)
                      ++++.-+.. -+.++..-  -..|+.+-.   -..+...|...-.+..+.     .|..+..-..-...+.+.|+..++-
T Consensus       209 kLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~KL-----~pdlvPaav~AAralf~d~~~rKg~  283 (531)
T COG3898         209 KLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANKL-----APDLVPAAVVAARALFRDGNLRKGS  283 (531)
T ss_pred             HHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhhc-----CCccchHHHHHHHHHHhccchhhhh
Confidence            888876653 34444332  222333221   123455666655555554     3333333345677888999999999


Q ss_pred             HHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhh
Q 044988          313 GVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSR  391 (538)
Q Consensus       313 ~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~  391 (538)
                      .+++.+-+..+..--..+..+.+.|+...                      .-++...+.-.++|| ..+...+..+-..
T Consensus       284 ~ilE~aWK~ePHP~ia~lY~~ar~gdta~----------------------dRlkRa~~L~slk~nnaes~~~va~aAld  341 (531)
T COG3898         284 KILETAWKAEPHPDIALLYVRARSGDTAL----------------------DRLKRAKKLESLKPNNAESSLAVAEAALD  341 (531)
T ss_pred             hHHHHHHhcCCChHHHHHHHHhcCCCcHH----------------------HHHHHHHHHHhcCccchHHHHHHHHHHHh
Confidence            99998876444333333334444453322                      222222222234554 5666677777778


Q ss_pred             cCChHHHHHHHHhC-CCCCCHHHHHHHHHH-HHhcCCHHHHHHHHHHc
Q 044988          392 AGLMDEAFSLVQNM-PMKPNDAVLGSLLLG-CRIHNNAELASQVAQKL  437 (538)
Q Consensus       392 ~g~~~~A~~~~~~~-~~~p~~~~~~~l~~~-~~~~~~~~~A~~~~~~~  437 (538)
                      .|++..|..--+.. ...|....|..|.+. -...||-.++...+-+.
T Consensus       342 a~e~~~ARa~Aeaa~r~~pres~~lLlAdIeeAetGDqg~vR~wlAqa  389 (531)
T COG3898         342 AGEFSAARAKAEAAAREAPRESAYLLLADIEEAETGDQGKVRQWLAQA  389 (531)
T ss_pred             ccchHHHHHHHHHHhhhCchhhHHHHHHHHHhhccCchHHHHHHHHHH
Confidence            88888777665554 246777777777776 45558888888888887

>PRK11906 transcriptional regulator; Provisional

Probab=95.07  E-value=1.2  Score=42.70  Aligned_cols=116  Identities=12%  Similarity=0.134  Sum_probs=79.8

Q ss_pred             cHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhh---------cCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcC
Q 044988          358 FVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSR---------AGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHN  425 (538)
Q Consensus       358 ~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~---------~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~  425 (538)
                      ..+.|..+|.+......+.|+ ...|..+..++..         .....+|.++.++..  -.-|+.....+..+....+
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld~~Da~a~~~~g~~~~~~~  352 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDITTVDGKILAIMGLITGLSG  352 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhhc
Confidence            567778888887733244665 4455444443322         223445566655543  3345666666666667777


Q ss_pred             CHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          426 NAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       426 ~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +++.|...|+++ ..+.|+...+|. ..+..+.-.|+.++|.+.+++..+
T Consensus       353 ~~~~a~~~f~rA-~~L~Pn~A~~~~-~~~~~~~~~G~~~~a~~~i~~alr  400 (458)
T PRK11906        353 QAKVSHILFEQA-KIHSTDIASLYY-YRALVHFHNEKIEEARICIDKSLQ  400 (458)
T ss_pred             chhhHHHHHHHH-hhcCCccHHHHH-HHHHHHHHcCCHHHHHHHHHHHhc
Confidence            789999999998 888999888888 888888889999999988888544

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.06  E-value=1.4  Score=35.24  Aligned_cols=43  Identities=7%  Similarity=0.128  Sum_probs=20.4

Q ss_pred             HHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHc
Q 044988           87 NQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCAR  130 (538)
Q Consensus        87 ~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  130 (538)
                      ..++..+...+.+......++.+...+ ..+...++.++..|++
T Consensus        11 ~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~   53 (140)
T smart00299       11 SEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAK   53 (140)
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHH
Confidence            344444444445555555555554443 2344444455554443

>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase

Probab=95.04  E-value=0.36  Score=37.62  Aligned_cols=41  Identities=7%  Similarity=0.204  Sum_probs=31.6

Q ss_pred             HHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHH
Q 044988          348 GVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDL  388 (538)
Q Consensus       348 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~  388 (538)
                      .++.+|+..|++..|.++.+...+.|+++.+..+|..|++=
T Consensus        57 AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W   97 (126)
T PF12921_consen   57 AIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEW   97 (126)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            33344444458888999999999999988888899988863

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=94.88  E-value=0.22  Score=43.67  Aligned_cols=113  Identities=18%  Similarity=0.087  Sum_probs=83.0

Q ss_pred             hHHHHHHhcCC--CCCcchHHHHHHHHhcC-----CCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccC---------
Q 044988           69 INAHKVFEKTE--NPSTAIWNQMIRGHARS-----ETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCG---------  132 (538)
Q Consensus        69 ~~a~~~~~~~~--~~~~~~~~~li~~~~~~-----~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~---------  132 (538)
                      -..+..|....  +.|-.+|-..+..+...     +.++=....++.|.+.|+.-|..+|+.|+..+-+..         
T Consensus        51 v~~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~  130 (406)
T KOG3941|consen   51 VHVEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQK  130 (406)
T ss_pred             cchhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHH
Confidence            34455666666  56777888888777543     556666777888999999999999999998765432         


Q ss_pred             -------CcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCC
Q 044988          133 -------LFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMP  183 (538)
Q Consensus       133 -------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~  183 (538)
                             +-+-+.+++++|...|+.||..+-..|++++.+.+-+  ..+..++.-.|+
T Consensus       131 ~F~HYP~QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p--~~K~~Rm~yWmP  186 (406)
T KOG3941|consen  131 VFLHYPQQQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFP--TKKVKRMLYWMP  186 (406)
T ss_pred             HHhhCchhhhHHHHHHHHHHHcCCCCchHHHHHHHHHhcccccc--HHHHHHHHHhhh
Confidence                   2345788999999999999999999999999888761  344444444443

>PF14432 DYW_deaminase: DYW family of nucleic acid deaminases

Probab=94.83  E-value=0.029  Score=42.97  Aligned_cols=44  Identities=39%  Similarity=0.763  Sum_probs=35.6

Q ss_pred             ceeEEEECCEEEEEEeCCCCCcchHHHHHHHHHHHHHHHHcCcccCCcccccCCCC
Q 044988          483 GQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYKPDISELFLGIEE  538 (538)
Q Consensus       483 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~m~~~~~~p~~~~~~~~~~~  538 (538)
                      +++|+.+    +.|++++..||+.        ++..+++..|+.|+...+.||+++
T Consensus         2 ~~~w~~~----h~F~sgd~shp~~--------~~~~~~~~~~~~~~~~~~~~~~~~   45 (116)
T PF14432_consen    2 GCSWIEV----HSFVSGDRSHPQS--------ELINKMKEEGYVPDTKEVGHDVDE   45 (116)
T ss_pred             CCCccce----EEEEeCCCcCccH--------HHHHHHHHcCCcchhhhhCCCchh
Confidence            5788755    8999999999998        344567788999999999887653

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.69  E-value=0.19  Score=44.15  Aligned_cols=90  Identities=20%  Similarity=0.181  Sum_probs=49.9

Q ss_pred             HHHHHHHHhhhcCChHHHHHHHHhCC-------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc---cHH
Q 044988          381 HYGCMVDLFSRAGLMDEAFSLVQNMP-------MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA---GYL  450 (538)
Q Consensus       381 ~~~~l~~~~~~~g~~~~A~~~~~~~~-------~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~---~~~  450 (538)
                      .|+.-++. .+.|++.+|...|....       ..||..-|  |..++...|+++.|..+|..+ ..-.|+.+.   .+.
T Consensus       144 ~Y~~A~~~-~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yW--LGe~~y~qg~y~~Aa~~f~~~-~k~~P~s~KApdall  219 (262)
T COG1729         144 LYNAALDL-YKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYW--LGESLYAQGDYEDAAYIFARV-VKDYPKSPKAPDALL  219 (262)
T ss_pred             HHHHHHHH-HHcCCHHHHHHHHHHHHHcCCCCcccchhHHH--HHHHHHhcccchHHHHHHHHH-HHhCCCCCCChHHHH
Confidence            45544443 33455666666665542       23444444  555566666666666666666 444444443   234


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          451 ALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       451 ~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                       -|+.+..+.|+.++|..+|+++.+
T Consensus       220 -Klg~~~~~l~~~d~A~atl~qv~k  243 (262)
T COG1729         220 -KLGVSLGRLGNTDEACATLQQVIK  243 (262)
T ss_pred             -HHHHHHHHhcCHHHHHHHHHHHHH
Confidence             455666666666666666666654

>KOG0890 consensus Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms; Chromatin structure and dynamics; Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=94.60  E-value=11  Score=43.83  Aligned_cols=301  Identities=12%  Similarity=0.039  Sum_probs=167.5

Q ss_pred             HHHHHHHhcCCCCChhHHHHHhhcCC----CC--CchhHHHHHHHHHhcCCHHHHHHHHcc-CCCCChHHHHHHHHHHHH
Q 044988          158 NLMNLYLMSGGECGVGCARLLFDDMP----AR--SVVSWNSLLKGYVKRGDIDGAWKIFDE-MPHRNVVSWTTMISGCAQ  230 (538)
Q Consensus       158 ~l~~~~~~~g~~~~~~~a~~~~~~~~----~~--~~~~~~~li~~~~~~g~~~~A~~~~~~-m~~~~~~~~~~li~~~~~  230 (538)
                      .+..+-.+++.   +..|...+++-.    +.  ...-|..+...|+..+++|...-+... ...|+.  + .-|.....
T Consensus      1388 tLa~aSfrc~~---y~RalmylEs~~~~ek~~~~~e~l~fllq~lY~~i~dpDgV~Gv~~~r~a~~sl--~-~qil~~e~ 1461 (2382)
T KOG0890|consen 1388 TLARASFRCKA---YARALMYLESHRSTEKEKETEEALYFLLQNLYGSIHDPDGVEGVSARRFADPSL--Y-QQILEHEA 1461 (2382)
T ss_pred             HHHHHHHhhHH---HHHHHHHHHHhccccchhHHHHHHHHHHHHHHHhcCCcchhhhHHHHhhcCccH--H-HHHHHHHh
Confidence            45556667777   888888887732    11  122333444477788887777777663 333332  2 33444566


Q ss_pred             cCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHH-HHHHHHHHhCCCH
Q 044988          231 NGKSRQALSLFNEMRRARVGLD-QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLN-NALIHMYASCGEI  308 (538)
Q Consensus       231 ~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~g~~  308 (538)
                      .|++..|...|+.+.+.  .|+ ..+++-++......+.++......+.....     .+.....+ +.=+.+-.+.+++
T Consensus      1462 ~g~~~da~~Cye~~~q~--~p~~~~~~~g~l~sml~~~~l~t~i~~~dg~~~~-----~se~~~~~~s~~~eaaW~l~qw 1534 (2382)
T KOG0890|consen 1462 SGNWADAAACYERLIQK--DPDKEKHHSGVLKSMLAIQHLSTEILHLDGLIIN-----RSEEVDELNSLGVEAAWRLSQW 1534 (2382)
T ss_pred             hccHHHHHHHHHHhhcC--CCccccchhhHHHhhhcccchhHHHhhhcchhhc-----cCHHHHHHHHHHHHHHhhhcch
Confidence            79999999999999875  344 667777777777777877777666655554     33333333 3334444677777


Q ss_pred             HHHHHHHHhcCCCCcchHHHH--HHHHHhcCCccHHH---------HHHHHHHHHhcccCcHHHHHHHHHHh--------
Q 044988          309 EEAYGVFRKMQRRNTVSWTSM--ITGFAKQGYAQEAL---------LTFLGVLSACSHGGFVDEGRQFFECM--------  369 (538)
Q Consensus       309 ~~a~~~~~~m~~~~~~~~~~l--i~~~~~~~~~~~a~---------~~~~~ll~~~~~~~~~~~a~~~~~~~--------  369 (538)
                      +.....+.   ..+..+|...  +..+.+..+-+.-.         ..+..-+.+|+..|.+..+.++.-++        
T Consensus      1535 D~~e~~l~---~~n~e~w~~~~~g~~ll~~~~kD~~~~~~~i~~~r~~~i~~lsa~s~~~Sy~~~Y~~~~kLH~l~el~~ 1611 (2382)
T KOG0890|consen 1535 DLLESYLS---DRNIEYWSVESIGKLLLRNKKKDEIATLDLIENSRELVIENLSACSIEGSYVRSYEILMKLHLLLELEN 1611 (2382)
T ss_pred             hhhhhhhh---cccccchhHHHHHHHHHhhcccchhhHHHHHHHHHHHhhhhHHHhhccchHHHHHHHHHHHHHHHHHHH
Confidence            77777665   3444444443  22222222222111         11222234444444433333332221        


Q ss_pred             --hhhcCCCccHH------HHHHHHHHhhhcCChHHHHHHHHhC----CCCCC-----HHHHHHHHHHHHhcCCHHHHHH
Q 044988          370 --NQNWGIKPRIE------HYGCMVDLFSRAGLMDEAFSLVQNM----PMKPN-----DAVLGSLLLGCRIHNNAELASQ  432 (538)
Q Consensus       370 --~~~~~~~p~~~------~~~~l~~~~~~~g~~~~A~~~~~~~----~~~p~-----~~~~~~l~~~~~~~~~~~~A~~  432 (538)
                        ....++.++..      -|..-+..-....+..+-+--+++.    ...|+     ...|-...+.+..+|.++.|..
T Consensus      1612 ~~~~l~~~s~~~~s~~~sd~W~~Rl~~tq~s~~~~epILa~RRs~l~~~~~~~~~~~~ge~wLqsAriaR~aG~~q~A~n 1691 (2382)
T KOG0890|consen 1612 SIEELKKVSYDEDSANNSDNWKNRLERTQPSFRIKEPILAFRRSMLDLRMRSNLKSRLGECWLQSARIARLAGHLQRAQN 1691 (2382)
T ss_pred             HHHHhhccCccccccccchhHHHHHHHhchhHHHHhHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHhcccHHHHHH
Confidence              11113333321      1111221111111122211111111    12222     5688888888999999999998


Q ss_pred             HHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          433 VAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       433 ~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      .+-.+ .+..++  ..+. -.+..+...|+...|+.++++......
T Consensus      1692 all~A-~e~r~~--~i~~-E~AK~lW~~gd~~~Al~~Lq~~l~~~~ 1733 (2382)
T KOG0890|consen 1692 ALLNA-KESRLP--EIVL-ERAKLLWQTGDELNALSVLQEILSKNF 1733 (2382)
T ss_pred             HHHhh-hhcccc--hHHH-HHHHHHHhhccHHHHHHHHHHHHHhhc
Confidence            88777 454433  3355 677899999999999999999986655

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=94.53  E-value=2.8  Score=37.51  Aligned_cols=139  Identities=14%  Similarity=0.097  Sum_probs=67.3

Q ss_pred             HhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHH
Q 044988          198 VKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKW  274 (538)
Q Consensus       198 ~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~  274 (538)
                      ...|++..|..+|+....   .+...--.++.+|...|+.+.|..++..+-..--.........-|..+.+.........
T Consensus       145 ~~~e~~~~a~~~~~~al~~~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~~~~~  224 (304)
T COG3118         145 IEAEDFGEAAPLLKQALQAAPENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATPEIQD  224 (304)
T ss_pred             hhccchhhHHHHHHHHHHhCcccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCCCHHH
Confidence            344555555555544332   22333444555555666666666665554322111111111122222222222222222


Q ss_pred             HHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC-----CcchHHHHHHHHHhcCCccHH
Q 044988          275 IHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR-----NTVSWTSMITGFAKQGYAQEA  342 (538)
Q Consensus       275 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~-----~~~~~~~li~~~~~~~~~~~a  342 (538)
                      +...+.      ..|.+...-..+...+...|+.+.|.+.+-.+.++     |...-..++..+...|..+.+
T Consensus       225 l~~~~a------adPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g~~Dp~  291 (304)
T COG3118         225 LQRRLA------ADPDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFGPADPL  291 (304)
T ss_pred             HHHHHH------hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcCCCCHH
Confidence            222222      24556666667888888888888888777665543     344555555555555544443

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=94.49  E-value=1.9  Score=35.41  Aligned_cols=125  Identities=8%  Similarity=0.091  Sum_probs=60.9

Q ss_pred             HHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcC
Q 044988          103 VYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDM  182 (538)
Q Consensus       103 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~  182 (538)
                      .+.+..+.+.+++|+...+..++..+.+.|.+....    .++..++-+|.......+-.+.... +....-+..++.++
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~----qllq~~Vi~DSk~lA~~LLs~~~~~-~~~~Ql~lDMLkRL   88 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLH----QLLQYHVIPDSKPLACQLLSLGNQY-PPAYQLGLDMLKRL   88 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHH----HHHhhcccCCcHHHHHHHHHhHccC-hHHHHHHHHHHHHh
Confidence            344555556777888888888888888887765543    3444444555433332222221111 11122333333333


Q ss_pred             CCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHH
Q 044988          183 PARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQ  236 (538)
Q Consensus       183 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~  236 (538)
                      .    ..+..++..+...|++-+|++..+.....+......++.+..+.+|...
T Consensus        89 ~----~~~~~iievLL~~g~vl~ALr~ar~~~~~~~~~~~~fLeAA~~~~D~~l  138 (167)
T PF07035_consen   89 G----TAYEEIIEVLLSKGQVLEALRYARQYHKVDSVPARKFLEAAANSNDDQL  138 (167)
T ss_pred             h----hhHHHHHHHHHhCCCHHHHHHHHHHcCCcccCCHHHHHHHHHHcCCHHH
Confidence            2    1234444555555555555555555433333333444444444444433

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=94.31  E-value=1.8  Score=33.44  Aligned_cols=56  Identities=25%  Similarity=0.277  Sum_probs=25.1

Q ss_pred             HHHHHHhcCCHHHHHHHHccCC---CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 044988          193 LLKGYVKRGDIDGAWKIFDEMP---HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR  248 (538)
Q Consensus       193 li~~~~~~g~~~~A~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  248 (538)
                      -+..+.++|+-+.-.+++..+.   ++++...-.+..+|.+.|+..++-+++.+..+.|
T Consensus        92 ALd~lv~~~kkDqLdki~~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG  150 (161)
T PF09205_consen   92 ALDILVKQGKKDQLDKIYNELKKNEEINPEFLVKIANAYKKLGNTREANELLKEACEKG  150 (161)
T ss_dssp             HHHHHHHTT-HHHHHHHHHHH-----S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHhccHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhc
Confidence            3444444455444444444432   2444444445555555555555555555554444

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=94.30  E-value=0.39  Score=42.18  Aligned_cols=104  Identities=10%  Similarity=0.137  Sum_probs=69.3

Q ss_pred             ccccHHHHHHHHh-----ccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHH
Q 044988           16 KALTTRQIFSLLQ-----IRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMI   90 (538)
Q Consensus        16 ~~~~~~~ll~~~~-----~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li   90 (538)
                      +-.+|-..+..+.     +.++++.....+..|.+.|+..|..+|+.|++.+-+..-...  .           .+....
T Consensus        66 dK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~--n-----------vfQ~~F  132 (406)
T KOG3941|consen   66 DKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQ--N-----------VFQKVF  132 (406)
T ss_pred             cHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccH--H-----------HHHHHH
Confidence            3444544444443     235667777778888888888888889888887765432111  1           111111


Q ss_pred             HHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCc
Q 044988           91 RGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLF  134 (538)
Q Consensus        91 ~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~  134 (538)
                      --|-+  +-+=+++++++|...|+.||..+-..|+.++.+.+..
T Consensus       133 ~HYP~--QQ~C~I~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  133 LHYPQ--QQNCAIKVLEQMEWHGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             hhCch--hhhHHHHHHHHHHHcCCCCchHHHHHHHHHhcccccc
Confidence            11211  2345789999999999999999999999999887753

>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=94.29  E-value=4.3  Score=39.70  Aligned_cols=160  Identities=14%  Similarity=0.118  Sum_probs=104.5

Q ss_pred             HHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHH
Q 044988          126 SVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDG  205 (538)
Q Consensus       126 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~  205 (538)
                      +...-.++++.+.++.+.-.-.. ..+..-.+.++..+-+.|.   .+.|+.+...-        ..-.....+.|+++.
T Consensus       269 k~av~~~d~~~v~~~i~~~~ll~-~i~~~~~~~i~~fL~~~G~---~e~AL~~~~D~--------~~rFeLAl~lg~L~~  336 (443)
T PF04053_consen  269 KTAVLRGDFEEVLRMIAASNLLP-NIPKDQGQSIARFLEKKGY---PELALQFVTDP--------DHRFELALQLGNLDI  336 (443)
T ss_dssp             HHHHHTT-HHH-----HHHHTGG-G--HHHHHHHHHHHHHTT----HHHHHHHSS-H--------HHHHHHHHHCT-HHH
T ss_pred             HHHHHcCChhhhhhhhhhhhhcc-cCChhHHHHHHHHHHHCCC---HHHHHhhcCCh--------HHHhHHHHhcCCHHH
Confidence            34456678888766654111110 1124457888899999999   99998876532        234556678999999


Q ss_pred             HHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccC
Q 044988          206 AWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSV  285 (538)
Q Consensus       206 A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~  285 (538)
                      |.++.++..  +...|..|.....+.|+++-|.+.|.+...         |..++-.|...|+.+...++.+.....   
T Consensus       337 A~~~a~~~~--~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~~~---  402 (443)
T PF04053_consen  337 ALEIAKELD--DPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAEER---  402 (443)
T ss_dssp             HHHHCCCCS--THHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHHT---
T ss_pred             HHHHHHhcC--cHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHHHc---
Confidence            999988766  566999999999999999999999988753         455666677788888877777776665   


Q ss_pred             CCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          286 GREPVLVSLNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       286 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                       +.      ++....++.-.|+.++..+++.+-
T Consensus       403 -~~------~n~af~~~~~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  403 -GD------INIAFQAALLLGDVEECVDLLIET  428 (443)
T ss_dssp             -T-------HHHHHHHHHHHT-HHHHHHHHHHT
T ss_pred             -cC------HHHHHHHHHHcCCHHHHHHHHHHc
Confidence             22      234444555668888888877664

This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=94.18  E-value=0.28  Score=44.64  Aligned_cols=123  Identities=11%  Similarity=0.028  Sum_probs=66.8

Q ss_pred             HHHhcccCcHHHHHHHHHHhhhhcCC--Cc--cHHHHHHHHHHhhhcCChHHHHHHHHhC-------CCCCCHHHHH---
Q 044988          350 LSACSHGGFVDEGRQFFECMNQNWGI--KP--RIEHYGCMVDLFSRAGLMDEAFSLVQNM-------PMKPNDAVLG---  415 (538)
Q Consensus       350 l~~~~~~~~~~~a~~~~~~~~~~~~~--~p--~~~~~~~l~~~~~~~g~~~~A~~~~~~~-------~~~p~~~~~~---  415 (538)
                      ..++.-.+.++++++.|+...+--.-  .|  ...++-.|...|.+..++++|.-...+.       .++.-..-|.   
T Consensus       129 ~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~  208 (518)
T KOG1941|consen  129 GNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYEKALFFPCKAAELVNSYGLKDWSLKYRAMS  208 (518)
T ss_pred             HHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhhHHhhhhHhHHHHHHhcCcCchhHHHHHHH
Confidence            33444445566666666654432111  11  2456777777788877777765444333       2221122222   


Q ss_pred             --HHHHHHHhcCCHHHHHHHHHHch-h----ccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHH
Q 044988          416 --SLLLGCRIHNNAELASQVAQKLV-A----EIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKM  473 (538)
Q Consensus       416 --~l~~~~~~~~~~~~A~~~~~~~~-~----~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m  473 (538)
                        .+.-++...|..-.|.+..++.. .    +-.|-...... .++++|-..|+.+.|..-|+..
T Consensus       209 lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~-~~aDIyR~~gd~e~af~rYe~A  272 (518)
T KOG1941|consen  209 LYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLL-CFADIYRSRGDLERAFRRYEQA  272 (518)
T ss_pred             HHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHH-HHHHHHHhcccHhHHHHHHHHH
Confidence              23335677777777777777664 2    22222222233 6778888888877777666543

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=94.17  E-value=1.1  Score=35.43  Aligned_cols=61  Identities=11%  Similarity=0.133  Sum_probs=46.8

Q ss_pred             HHHhhhcCChHHHHHHHHhCC--CC--C-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          386 VDLFSRAGLMDEAFSLVQNMP--MK--P-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       386 ~~~~~~~g~~~~A~~~~~~~~--~~--p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      .....+.|++++|.+.|+.+.  ..  | ....--.++.++.+.++++.|...+++. .++.|.++.
T Consensus        17 a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rF-irLhP~hp~   82 (142)
T PF13512_consen   17 AQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRF-IRLHPTHPN   82 (142)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHH-HHhCCCCCC
Confidence            344557899999999999885  11  1 1344556788899999999999999999 889998875

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=93.93  E-value=1.2  Score=39.77  Aligned_cols=119  Identities=12%  Similarity=0.128  Sum_probs=85.1

Q ss_pred             cccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHH---HHHHHHhcCCHHH
Q 044988          354 SHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGS---LLLGCRIHNNAEL  429 (538)
Q Consensus       354 ~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~---l~~~~~~~~~~~~  429 (538)
                      ...|+...|...|+.....   .| +...--.|+.+|...|+.+.|..++..++..-...-+..   -+..+.+.....+
T Consensus       145 ~~~e~~~~a~~~~~~al~~---~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~~  221 (304)
T COG3118         145 IEAEDFGEAAPLLKQALQA---APENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATPE  221 (304)
T ss_pred             hhccchhhHHHHHHHHHHh---CcccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCCC
Confidence            4556888888999888765   34 466777899999999999999999999974333222222   2333444444444


Q ss_pred             HHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          430 ASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       430 A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      ...+-++  ..-.|++...-. .++..+...|+.++|.+.+=.+..++.
T Consensus       222 ~~~l~~~--~aadPdd~~aa~-~lA~~~~~~g~~e~Ale~Ll~~l~~d~  267 (304)
T COG3118         222 IQDLQRR--LAADPDDVEAAL-ALADQLHLVGRNEAALEHLLALLRRDR  267 (304)
T ss_pred             HHHHHHH--HHhCCCCHHHHH-HHHHHHHHcCCHHHHHHHHHHHHHhcc
Confidence            4444444  355798888677 899999999999999998888776533

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=93.85  E-value=3.6  Score=39.74  Aligned_cols=98  Identities=11%  Similarity=0.149  Sum_probs=67.7

Q ss_pred             HHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCC--CCC--HHHHHHHHHHHHhc
Q 044988          349 VLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPM--KPN--DAVLGSLLLGCRIH  424 (538)
Q Consensus       349 ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~p~--~~~~~~l~~~~~~~  424 (538)
                      +..++-+.|+.++|.+.++++.+.+...-+..+...|+.++...+.+.++..++.+-..  -|.  ...|+..+-.+...
T Consensus       265 LAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALLkaRav  344 (539)
T PF04184_consen  265 LAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALLKARAV  344 (539)
T ss_pred             HHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHHHHHhh
Confidence            44455677899999999999987632222355778899999999999999999988741  233  34555554433333


Q ss_pred             CC---------------HHHHHHHHHHchhccCCCCcc
Q 044988          425 NN---------------AELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       425 ~~---------------~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      ++               -..|.+.+.++ .+.+|..+.
T Consensus       345 ~d~fs~e~a~rRGls~ae~~aveAi~RA-vefNPHVp~  381 (539)
T PF04184_consen  345 GDKFSPEAASRRGLSPAEMNAVEAIHRA-VEFNPHVPK  381 (539)
T ss_pred             ccccCchhhhhcCCChhHHHHHHHHHHH-HHhCCCCch
Confidence            32               13456778887 788888776

The molecular function of this protein is uncertain.

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=93.84  E-value=2.7  Score=41.68  Aligned_cols=155  Identities=12%  Similarity=0.094  Sum_probs=95.3

Q ss_pred             hHHHHHHHhcCCCCChhHHHHHhhcCCCC-Cc---------hhHHHHHHHHHh----cCCHHHHHHHHccCCC--CChHH
Q 044988          157 TNLMNLYLMSGGECGVGCARLLFDDMPAR-SV---------VSWNSLLKGYVK----RGDIDGAWKIFDEMPH--RNVVS  220 (538)
Q Consensus       157 ~~l~~~~~~~g~~~~~~~a~~~~~~~~~~-~~---------~~~~~li~~~~~----~g~~~~A~~~~~~m~~--~~~~~  220 (538)
                      ..++....=.|+   -+..++++.+..+. +.         -.|...+..++.    ....+.|.++++.+.+  |+...
T Consensus       192 ~kll~~vGF~gd---R~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~yP~s~l  268 (468)
T PF10300_consen  192 LKLLSFVGFSGD---RELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKRYPNSAL  268 (468)
T ss_pred             HHHHhhcCcCCc---HHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHhCCCcHH
Confidence            345555555566   66666666654432 11         234444443333    4567888888888876  77776


Q ss_pred             HHHHH-HHHHHcCCHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          221 WTTMI-SGCAQNGKSRQALSLFNEMRRAR---VGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       221 ~~~li-~~~~~~~~~~~a~~~~~~m~~~g---~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                      |...- +.+...|++++|++.|++.....   .+.....+--+.-++.-..++++|...+..+.+.     ...+..+|.
T Consensus       269 fl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~-----s~WSka~Y~  343 (468)
T PF10300_consen  269 FLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKE-----SKWSKAFYA  343 (468)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhc-----cccHHHHHH
Confidence            65543 55667789999999998765311   1122334445555667788888888888888876     233333332


Q ss_pred             -HHHHHHHhCCCH-------HHHHHHHHhcC
Q 044988          297 -ALIHMYASCGEI-------EEAYGVFRKMQ  319 (538)
Q Consensus       297 -~l~~~~~~~g~~-------~~a~~~~~~m~  319 (538)
                       ....++...|+.       ++|.++|.++.
T Consensus       344 Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  344 YLAAACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHHHHHHhhccchhhhhhHHHHHHHHHHHH
Confidence             334445567777       77888887765

In humans this protein is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. The human protein is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive []. Members of this family carry a tetratricopeptide repeat (IPR013105 from INTERPRO) at their C terminus.

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=93.80  E-value=0.95  Score=34.81  Aligned_cols=54  Identities=26%  Similarity=0.121  Sum_probs=40.6

Q ss_pred             HHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          262 ACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       262 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      +++..|+++.|.+.|......     .|...+.||.-..++.-.|+.++|.+-+++..+
T Consensus        52 alaE~g~Ld~AlE~F~qal~l-----~P~raSayNNRAQa~RLq~~~e~ALdDLn~Ale  105 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCL-----APERASAYNNRAQALRLQGDDEEALDDLNKALE  105 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHh-----cccchHhhccHHHHHHHcCChHHHHHHHHHHHH
Confidence            345667777777777777775     677778888888888888888888887777654

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=93.75  E-value=6.2  Score=37.24  Aligned_cols=35  Identities=23%  Similarity=0.221  Sum_probs=26.5

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC
Q 044988          410 NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ  445 (538)
Q Consensus       410 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~  445 (538)
                      |---+.+++.++.-.|+.++|.+..++| ....|+.
T Consensus       304 dYWd~ATl~Ea~vL~~d~~ka~~a~e~~-~~l~~~~  338 (374)
T PF13281_consen  304 DYWDVATLLEASVLAGDYEKAIQAAEKA-FKLKPPA  338 (374)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHH-hhcCCcc
Confidence            3444567788888889999999999998 6666654

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=93.63  E-value=8.2  Score=38.24  Aligned_cols=400  Identities=13%  Similarity=0.093  Sum_probs=196.9

Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHHhCCCCCh-hHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHh-c
Q 044988           21 RQIFSLLQIRNTTKTLFQIHSQIIINGFSQKN-YILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHA-R   95 (538)
Q Consensus        21 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~-~   95 (538)
                      +.|+.--....+...+..++..++..  .|-. .-|..-...-.+.|..+.+.++|++-.   +.+...|...+..++ .
T Consensus        49 t~li~~~~~~~~~~~~r~~y~~fL~k--yPl~~gyW~kfA~~E~klg~~~~s~~Vfergv~aip~SvdlW~~Y~~f~~n~  126 (577)
T KOG1258|consen   49 TTLIQENDSIEDVDALREVYDIFLSK--YPLCYGYWKKFADYEYKLGNAENSVKVFERGVQAIPLSVDLWLSYLAFLKNN  126 (577)
T ss_pred             HHHHhccCchhHHHHHHHHHHHHHhh--CccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcc
Confidence            33444333444455556666666543  2333 244555555556778888888887755   245555665555443 4


Q ss_pred             CCCchHHHHHHHHhHhC-CCC-CCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCC---
Q 044988           96 SETPEKSVYLYKQMIDK-ETE-PDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGEC---  170 (538)
Q Consensus        96 ~~~~~~a~~~~~~m~~~-~~~-p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~---  170 (538)
                      .|+.+...+.|+..... |.. -+...|...|..-..++++.....+++++++....-=...|..... +.......   
T Consensus       127 ~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~qks~k~v~~iyeRileiP~~~~~~~f~~f~~-~l~~~~~~~l~  205 (577)
T KOG1258|consen  127 NGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQKSWKRVANIYERILEIPLHQLNRHFDRFKQ-LLNQNEEKILL  205 (577)
T ss_pred             CCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhccccHHHHHHHHHHHHhhhhhHhHHHHHHHHH-HHhcCChhhhc
Confidence            56777777777777653 322 2444667777777777778888888887776421110111111000 00110000   


Q ss_pred             ChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCH-HHHHHHHccCCCCChH---HHHHH-------HHHHHHcCCHHHHHH
Q 044988          171 GVGCARLLFDDMPARSVVSWNSLLKGYVKRGDI-DGAWKIFDEMPHRNVV---SWTTM-------ISGCAQNGKSRQALS  239 (538)
Q Consensus       171 ~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~-~~A~~~~~~m~~~~~~---~~~~l-------i~~~~~~~~~~~a~~  239 (538)
                      ..+.+.++-......         ......+.. +.-....+....|...   ..+.+       -..+-......+...
T Consensus       206 ~~d~~~~l~~~~~~~---------~~~~~~~~~~e~~~~~v~~~~~~s~~l~~~~~~l~~~~~~~~~~~~~s~~~~~kr~  276 (577)
T KOG1258|consen  206 SIDELIQLRSDVAER---------SKITHSQEPLEELEIGVKDSTDPSKSLTEEKTILKRIVSIHEKVYQKSEEEEEKRW  276 (577)
T ss_pred             CHHHHHHHhhhHHhh---------hhcccccChhHHHHHHHhhccCccchhhHHHHHHHHHHHHHHHHHHhhHhHHHHHH
Confidence            011111110000000         000000111 1111111111111110   01111       111222222233333


Q ss_pred             HHHHHHHC---CCCC----CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHH
Q 044988          240 LFNEMRRA---RVGL----DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAY  312 (538)
Q Consensus       240 ~~~~m~~~---g~~p----~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  312 (538)
                      .|+.-.+.   .++|    +..+|..-+.--.+.|+.+.+.-.++.+.--     ...-..+|-..+......|+.+-|.
T Consensus       277 ~fE~~IkrpYfhvkpl~~aql~nw~~yLdf~i~~g~~~~~~~l~ercli~-----cA~Y~efWiky~~~m~~~~~~~~~~  351 (577)
T KOG1258|consen  277 GFEEGIKRPYFHVKPLDQAQLKNWRYYLDFEITLGDFSRVFILFERCLIP-----CALYDEFWIKYARWMESSGDVSLAN  351 (577)
T ss_pred             hhhhhccccccccCcccHHHHHHHHHHhhhhhhcccHHHHHHHHHHHHhH-----HhhhHHHHHHHHHHHHHcCchhHHH
Confidence            33332221   1222    3445555555556777777777777666543     4444455555666666667777777


Q ss_pred             HHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccH-HHHHHHHHH
Q 044988          313 GVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRI-EHYGCMVDL  388 (538)
Q Consensus       313 ~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~-~~~~~l~~~  388 (538)
                      .++....+   ++......+=..+                   +-..|+...|..+++.+...+   |+. ..-..-+..
T Consensus       352 ~~~~~~~~i~~k~~~~i~L~~a~f-------------------~e~~~n~~~A~~~lq~i~~e~---pg~v~~~l~~~~~  409 (577)
T KOG1258|consen  352 NVLARACKIHVKKTPIIHLLEARF-------------------EESNGNFDDAKVILQRIESEY---PGLVEVVLRKINW  409 (577)
T ss_pred             HHHHhhhhhcCCCCcHHHHHHHHH-------------------HHhhccHHHHHHHHHHHHhhC---CchhhhHHHHHhH
Confidence            77765543   2222111111111                   123467888888888887752   553 333333455


Q ss_pred             hhhcCChHHHH---HHHHhCC-CCCCHHHHHHH----HH-HHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHh
Q 044988          389 FSRAGLMDEAF---SLVQNMP-MKPNDAVLGSL----LL-GCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAA  459 (538)
Q Consensus       389 ~~~~g~~~~A~---~~~~~~~-~~p~~~~~~~l----~~-~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~  459 (538)
                      ..+.|..+.+.   +++.... .+-+..+...+    .+ .+.-.++.+.|..++.++ ....|+....|. .+++....
T Consensus       410 e~r~~~~~~~~~~~~l~s~~~~~~~~~~i~~~l~~~~~r~~~~i~~d~~~a~~~l~~~-~~~~~~~k~~~~-~~~~~~~~  487 (577)
T KOG1258|consen  410 ERRKGNLEDANYKNELYSSIYEGKENNGILEKLYVKFARLRYKIREDADLARIILLEA-NDILPDCKVLYL-ELIRFELI  487 (577)
T ss_pred             HHHhcchhhhhHHHHHHHHhcccccCcchhHHHHHHHHHHHHHHhcCHHHHHHHHHHh-hhcCCccHHHHH-HHHHHHHh
Confidence            56778877777   5554442 12222222222    22 245578899999999999 999999988787 66666655


Q ss_pred             cC
Q 044988          460 AK  461 (538)
Q Consensus       460 ~g  461 (538)
                      .+
T Consensus       488 ~~  489 (577)
T KOG1258|consen  488 QP  489 (577)
T ss_pred             CC
Confidence            54

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=93.55  E-value=0.66  Score=35.63  Aligned_cols=89  Identities=16%  Similarity=0.165  Sum_probs=53.0

Q ss_pred             HhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCc-c---cHHHHHHHHHHhcC
Q 044988          388 LFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQA-A---GYLALVANVYAAAK  461 (538)
Q Consensus       388 ~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~-~---~~~~~l~~~~~~~g  461 (538)
                      +++..|+++.|++.|.+..  .+.....||.-..++.-.|+.++|+.-+++. .++.-+.. +   .|+ .-+..|-..|
T Consensus        52 alaE~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~A-leLag~~trtacqa~v-QRg~lyRl~g  129 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKA-LELAGDQTRTACQAFV-QRGLLYRLLG  129 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHH-HHhcCccchHHHHHHH-HHHHHHHHhC
Confidence            4556677777777776542  2234566666667777777777777777766 33332221 1   244 4455666677


Q ss_pred             ChHHHHHHHHHHHhCCC
Q 044988          462 RWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       462 ~~~~A~~~~~~m~~~~~  478 (538)
                      +-+.|..=|+..-+.|-
T Consensus       130 ~dd~AR~DFe~AA~LGS  146 (175)
T KOG4555|consen  130 NDDAARADFEAAAQLGS  146 (175)
T ss_pred             chHHHHHhHHHHHHhCC
Confidence            77777777776665544

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=93.46  E-value=0.22  Score=28.08  Aligned_cols=31  Identities=26%  Similarity=0.107  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHchhccCCC
Q 044988          413 VLGSLLLGCRIHNNAELASQVAQKLVAEIDPE  444 (538)
Q Consensus       413 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~  444 (538)
                      .|..+...+...|++++|++.+++. ..+.|+
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~a-l~l~p~   33 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKA-LELDPN   33 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHH-HHHSTT
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH-HHHCcC
Confidence            3445555566666666666666666 555554

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PRK11906 transcriptional regulator; Provisional

Probab=93.26  E-value=3.8  Score=39.42  Aligned_cols=111  Identities=9%  Similarity=0.057  Sum_probs=82.6

Q ss_pred             CcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHH
Q 044988          357 GFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQV  433 (538)
Q Consensus       357 ~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~  433 (538)
                      .+..+|.+.-++..+.   .| |......+..++.-.|+++.|..+|++.. ..|| ..+|......+...|+.++|.+.
T Consensus       318 ~~~~~a~~~A~rAvel---d~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~~L~Pn~A~~~~~~~~~~~~~G~~~~a~~~  394 (458)
T PRK11906        318 LAAQKALELLDYVSDI---TTVDGKILAIMGLITGLSGQAKVSHILFEQAKIHSTDIASLYYYRALVHFHNEKIEEARIC  394 (458)
T ss_pred             HHHHHHHHHHHHHHhc---CCCCHHHHHHHHHHHHhhcchhhHHHHHHHHhhcCCccHHHHHHHHHHHHHcCCHHHHHHH
Confidence            3567777777777754   44 67888888888888899999999999985 6677 56666666778889999999999


Q ss_pred             HHHchhccCCCCcccHHH-HHHHHHHhcCChHHHHHHHHH
Q 044988          434 AQKLVAEIDPEQAAGYLA-LVANVYAAAKRWQDVAAVRQK  472 (538)
Q Consensus       434 ~~~~~~~~~p~~~~~~~~-~l~~~~~~~g~~~~A~~~~~~  472 (538)
                      +++. .++.|.....-.. ..++.|.. ...++|++++-+
T Consensus       395 i~~a-lrLsP~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  432 (458)
T PRK11906        395 IDKS-LQLEPRRRKAVVIKECVDMYVP-NPLKNNIKLYYK  432 (458)
T ss_pred             HHHH-hccCchhhHHHHHHHHHHHHcC-CchhhhHHHHhh
Confidence            9999 8999988763331 22234444 456777777644

>PF08631 SPO22: Meiosis protein SPO22/ZIP4 like; InterPro: IPR013940 SPO22 is a meiosis-specific protein with similarity to phospholipase A2, involved in completion of nuclear divisions during meiosis; induced early in meiosis []

Probab=93.25  E-value=6.5  Score=35.92  Aligned_cols=129  Identities=15%  Similarity=0.119  Sum_probs=72.7

Q ss_pred             hcCCHHHHHHHHccCCC------CCh------HHHHHHHHHHHHcC-CHHHHHHHHHHHHHC--------CCCCCH----
Q 044988          199 KRGDIDGAWKIFDEMPH------RNV------VSWTTMISGCAQNG-KSRQALSLFNEMRRA--------RVGLDQ----  253 (538)
Q Consensus       199 ~~g~~~~A~~~~~~m~~------~~~------~~~~~li~~~~~~~-~~~~a~~~~~~m~~~--------g~~p~~----  253 (538)
                      +.|+.+.|...+.+...      |+.      ..|+.-... .+.+ +++.|..++++..+.        ...|+.    
T Consensus         5 ~~~~~~~A~~~~~K~~~~~~~~~~~~~~~La~~~yn~G~~l-~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr   83 (278)
T PF08631_consen    5 KQGDLDLAEHMYSKAKDLLNSLDPDMAEELARVCYNIGKSL-LSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSELR   83 (278)
T ss_pred             hhCCHHHHHHHHHHhhhHHhcCCcHHHHHHHHHHHHHHHHH-HHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHHH
Confidence            45666666666655432      222      123333333 3444 777777777665432        233333    


Q ss_pred             -HHHHHHHHHHHccCChHH---HHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC---CcchH
Q 044988          254 -VALVAALSACAEIGDLKL---GKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR---NTVSW  326 (538)
Q Consensus       254 -~~~~~li~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~---~~~~~  326 (538)
                       .++..++.++...+..+.   |..+.+.+...     .+..+.++-.-+..+.+.++.+.+.+++.+|...   ....+
T Consensus        84 ~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e-----~~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~~~e~~~  158 (278)
T PF08631_consen   84 LSILRLLANAYLEWDTYESVEKALNALRLLESE-----YGNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSVDHSESNF  158 (278)
T ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHh-----CCCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhcccccchH
Confidence             356667777777776554   44555555443     4444455545567777788888888888888752   23444


Q ss_pred             HHHHHHH
Q 044988          327 TSMITGF  333 (538)
Q Consensus       327 ~~li~~~  333 (538)
                      ..++..+
T Consensus       159 ~~~l~~i  165 (278)
T PF08631_consen  159 DSILHHI  165 (278)
T ss_pred             HHHHHHH
Confidence            4444444

It is also involved in sporulation [].

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=93.20  E-value=0.19  Score=28.46  Aligned_cols=31  Identities=23%  Similarity=0.119  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHchhccCCC
Q 044988          413 VLGSLLLGCRIHNNAELASQVAQKLVAEIDPE  444 (538)
Q Consensus       413 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~  444 (538)
                      +|..+...+...|++++|+..++++ .++.|+
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~a-l~~~p~   33 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRA-LELDPD   33 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHH-HHHSTT
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHH-HHHCcC
Confidence            4555666666666666666666666 666654

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=92.88  E-value=8.8  Score=36.44  Aligned_cols=84  Identities=12%  Similarity=0.077  Sum_probs=53.0

Q ss_pred             CCcchHHHHHHHHHhc----CCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc---cHHHHHHHHHHhhhcC
Q 044988          321 RNTVSWTSMITGFAKQ----GYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP---RIEHYGCMVDLFSRAG  393 (538)
Q Consensus       321 ~~~~~~~~li~~~~~~----~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p---~~~~~~~l~~~~~~~g  393 (538)
                      ++...|..++..-...    ....+...++..+...+.+.|.++.|...+..+... +..+   ++.+.-.-+..+...|
T Consensus       120 ~~~~~~~~il~~R~~~l~~~~~~~~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~-~~~~~~~~~~v~~e~akllw~~g  198 (352)
T PF02259_consen  120 DDFSVWEPILSLRRLVLSLILLPEELAETWLKFAKLARKAGNFQLALSALNRLFQL-NPSSESLLPRVFLEYAKLLWAQG  198 (352)
T ss_pred             cchHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHCCCcHHHHHHHHHHhcc-CCcccCCCcchHHHHHHHHHHcC
Confidence            4555555555422221    123444477888888888999999999998888753 2111   2334445566666788


Q ss_pred             ChHHHHHHHHhC
Q 044988          394 LMDEAFSLVQNM  405 (538)
Q Consensus       394 ~~~~A~~~~~~~  405 (538)
                      +..+|+..++..
T Consensus       199 ~~~~Ai~~L~~~  210 (352)
T PF02259_consen  199 EQEEAIQKLREL  210 (352)
T ss_pred             CHHHHHHHHHHH
Confidence            888888877654

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=92.69  E-value=0.23  Score=39.99  Aligned_cols=54  Identities=11%  Similarity=0.223  Sum_probs=28.9

Q ss_pred             HHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHH
Q 044988           89 MIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHG  142 (538)
Q Consensus        89 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~  142 (538)
                      ++..+.+.+.+.....+++.+...+...+....+.++..|++.++.+....+++
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~   66 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK   66 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc
Confidence            445555556666666666666654434445555566666666655555555443

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=92.47  E-value=0.66  Score=41.55  Aligned_cols=61  Identities=20%  Similarity=0.259  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          413 VLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       413 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ++..++..+...|+++.+.+.++++ ....|-+...|. .++.+|.+.|+...|+..|+++.+
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~L-i~~dp~~E~~~~-~lm~~y~~~g~~~~ai~~y~~l~~  215 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERL-IELDPYDEPAYL-RLMEAYLVNGRQSAAIRAYRQLKK  215 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHH-HhcCccchHHHH-HHHHHHHHcCCchHHHHHHHHHHH
Confidence            4445566666677777777777777 777777777677 777777777777777777777654

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.21  E-value=13  Score=38.47  Aligned_cols=142  Identities=11%  Similarity=0.010  Sum_probs=83.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHccCCCCChH---HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc
Q 044988          190 WNSLLKGYVKRGDIDGAWKIFDEMPHRNVV---SWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEI  266 (538)
Q Consensus       190 ~~~li~~~~~~g~~~~A~~~~~~m~~~~~~---~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~  266 (538)
                      ...-+..+.+...++.|..+-+.-..+...   ........+.+.|++++|...|-+-... +.|.     .+|.-+...
T Consensus       337 le~kL~iL~kK~ly~~Ai~LAk~~~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~s-----~Vi~kfLda  410 (933)
T KOG2114|consen  337 LETKLDILFKKNLYKVAINLAKSQHLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEPS-----EVIKKFLDA  410 (933)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CChH-----HHHHHhcCH
Confidence            344566667777778888777664432222   2233345566788888888888765432 2332     234444444


Q ss_pred             CChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcc--hHHHHHHHHHhcCCccHHH
Q 044988          267 GDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTV--SWTSMITGFAKQGYAQEAL  343 (538)
Q Consensus       267 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~--~~~~li~~~~~~~~~~~a~  343 (538)
                      ..+..-..+++.+.+.    +....-++ ..|+.+|.+.++.+.-.+..+.-.+ +.+  -....+..+.+.+-.++|.
T Consensus       411 q~IknLt~YLe~L~~~----gla~~dht-tlLLncYiKlkd~~kL~efI~~~~~-g~~~fd~e~al~Ilr~snyl~~a~  483 (933)
T KOG2114|consen  411 QRIKNLTSYLEALHKK----GLANSDHT-TLLLNCYIKLKDVEKLTEFISKCDK-GEWFFDVETALEILRKSNYLDEAE  483 (933)
T ss_pred             HHHHHHHHHHHHHHHc----ccccchhH-HHHHHHHHHhcchHHHHHHHhcCCC-cceeeeHHHHHHHHHHhChHHHHH
Confidence            5555555566666665    55444444 4788888888888888888877652 222  1334455555555555544

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=92.17  E-value=5.2  Score=36.72  Aligned_cols=134  Identities=14%  Similarity=0.191  Sum_probs=86.5

Q ss_pred             hHHHHHHHHHHHHhCCCCChhHHHHHHHHHHc--c----CChhHHHHHHhcCCC-------CCcchHHHHHHHHhcCCCc
Q 044988           33 TKTLFQIHSQIIINGFSQKNYILAKLLAFYVT--S----GYLINAHKVFEKTEN-------PSTAIWNQMIRGHARSETP   99 (538)
Q Consensus        33 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~----g~~~~a~~~~~~~~~-------~~~~~~~~li~~~~~~~~~   99 (538)
                      +.....+++.+.+.|+..+..++-+..-....  .    .....|..+|+.|++       ++-.++..++..  ..+++
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~  155 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDV  155 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccH
Confidence            45567899999999999888777664444333  2    245678889998884       344456666544  33333


Q ss_pred             ----hHHHHHHHHhHhCCCCCCcc--hHHHHHHHHHccCC--cHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCC
Q 044988          100 ----EKSVYLYKQMIDKETEPDEY--TYSFLLSVCARCGL--FREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGG  168 (538)
Q Consensus       100 ----~~a~~~~~~m~~~~~~p~~~--~~~~li~~~~~~~~--~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  168 (538)
                          +.+..+|+.+.+.|...+..  ....++..+.....  ...+.++++.+.+.|+++....|..+.-...-.+.
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlLall~~~  232 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLLALLEDP  232 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHHHHhcCCc
Confidence                56777888888878766443  33334433322222  44778889999999988888777765554444444

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=92.14  E-value=0.52  Score=42.13  Aligned_cols=102  Identities=17%  Similarity=0.257  Sum_probs=75.6

Q ss_pred             HhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC-------CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCC
Q 044988           45 INGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN-------PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPD  117 (538)
Q Consensus        45 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~  117 (538)
                      ..|.+.+..+...++..-....++++++..+-++.+       |+... ...++.+. .-++++++.++..=.+.|+-||
T Consensus        57 ~~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~-~~~irlll-ky~pq~~i~~l~npIqYGiF~d  134 (418)
T KOG4570|consen   57 ERGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTI-HTWIRLLL-KYDPQKAIYTLVNPIQYGIFPD  134 (418)
T ss_pred             hcCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccH-HHHHHHHH-ccChHHHHHHHhCcchhccccc
Confidence            456666777777777777778888888888766652       22221 22233322 3367899999888888999999


Q ss_pred             cchHHHHHHHHHccCCcHHHHHHHHHHHHhC
Q 044988          118 EYTYSFLLSVCARCGLFREGEQVHGRVLASG  148 (538)
Q Consensus       118 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~  148 (538)
                      ..+++.+|+.+.+.+++..|.++.-.|....
T Consensus       135 qf~~c~l~D~flk~~n~~~aa~vvt~~~~qe  165 (418)
T KOG4570|consen  135 QFTFCLLMDSFLKKENYKDAASVVTEVMMQE  165 (418)
T ss_pred             hhhHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            9999999999999999999988888877664

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.82  E-value=2.1  Score=38.90  Aligned_cols=84  Identities=11%  Similarity=0.040  Sum_probs=37.4

Q ss_pred             HhcccCcHHHHHHHHHHhhhhcCCCccHHHHH----HHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcC
Q 044988          352 ACSHGGFVDEGRQFFECMNQNWGIKPRIEHYG----CMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHN  425 (538)
Q Consensus       352 ~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~----~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~  425 (538)
                      +|...|+...-...++++...+  .||...|.    .+.-++..+|-+++|.+.-++..  .+.|.-...++...+...|
T Consensus       146 a~fy~G~~~~~k~ai~kIip~w--n~dlp~~sYv~GmyaFgL~E~g~y~dAEk~A~ralqiN~~D~Wa~Ha~aHVlem~~  223 (491)
T KOG2610|consen  146 AHFYNGNQIGKKNAIEKIIPKW--NADLPCYSYVHGMYAFGLEECGIYDDAEKQADRALQINRFDCWASHAKAHVLEMNG  223 (491)
T ss_pred             HHHhccchhhhhhHHHHhcccc--CCCCcHHHHHHHHHHhhHHHhccchhHHHHHHhhccCCCcchHHHHHHHHHHHhcc
Confidence            4444555555555555544332  23322221    22223334555555555555442  1223333344444455555


Q ss_pred             CHHHHHHHHHHc
Q 044988          426 NAELASQVAQKL  437 (538)
Q Consensus       426 ~~~~A~~~~~~~  437 (538)
                      +..++.+.+.+-
T Consensus       224 r~Keg~eFM~~t  235 (491)
T KOG2610|consen  224 RHKEGKEFMYKT  235 (491)
T ss_pred             hhhhHHHHHHhc
Confidence            555555555544

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=91.78  E-value=0.33  Score=27.97  Aligned_cols=25  Identities=4%  Similarity=0.177  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          449 YLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       449 ~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      +. .|+.+|.+.|++++|++++++..
T Consensus         2 l~-~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    2 LN-NLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HH-HHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HH-HHHHHHHHcCCHHHHHHHHHHHH
Confidence            45 78889999999999999998844

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=91.71  E-value=0.78  Score=27.87  Aligned_cols=25  Identities=12%  Similarity=0.155  Sum_probs=10.4

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHH
Q 044988          222 TTMISGCAQNGKSRQALSLFNEMRR  246 (538)
Q Consensus       222 ~~li~~~~~~~~~~~a~~~~~~m~~  246 (538)
                      ..+...|...|++++|.++|++..+
T Consensus         5 ~~la~~~~~~G~~~~A~~~~~~~l~   29 (44)
T PF13428_consen    5 LALARAYRRLGQPDEAERLLRRALA   29 (44)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3333444444444444444444433

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=91.70  E-value=0.8  Score=36.29  Aligned_cols=52  Identities=13%  Similarity=0.102  Sum_probs=26.0

Q ss_pred             cCChHHHHHHHHhCC-CCCCHHHHHHH-HHHHHhcCCHHHHHHHHHHchhccCCC
Q 044988          392 AGLMDEAFSLVQNMP-MKPNDAVLGSL-LLGCRIHNNAELASQVAQKLVAEIDPE  444 (538)
Q Consensus       392 ~g~~~~A~~~~~~~~-~~p~~~~~~~l-~~~~~~~~~~~~A~~~~~~~~~~~~p~  444 (538)
                      .++.+++..+++.|. ..|+..-...+ ...+...|++++|.++|+.. .+..|.
T Consensus        23 ~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l-~~~~~~   76 (153)
T TIGR02561        23 SADPYDAQAMLDALRVLRPNLKELDMFDGWLLIARGNYDEAARILREL-LSSAGA   76 (153)
T ss_pred             cCCHHHHHHHHHHHHHhCCCccccchhHHHHHHHcCCHHHHHHHHHhh-hccCCC
Confidence            556666666666553 34443322222 22245566666666666665 443333

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.62  E-value=5.8  Score=32.48  Aligned_cols=120  Identities=9%  Similarity=0.030  Sum_probs=81.2

Q ss_pred             cccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHH---HH--HHHHhcCC
Q 044988          354 SHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGS---LL--LGCRIHNN  426 (538)
Q Consensus       354 ~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~---l~--~~~~~~~~  426 (538)
                      .+.+..++|+.-|..+.+. |...- +-............|+...|...|+++. ..|-+....-   |-  ..+...|.
T Consensus        69 A~~~k~d~Alaaf~~lekt-g~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlraa~lLvD~gs  147 (221)
T COG4649          69 AQENKTDDALAAFTDLEKT-GYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAAYLLVDNGS  147 (221)
T ss_pred             HHcCCchHHHHHHHHHHhc-CCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHHHHHHhcccc
Confidence            3445778888888888765 44321 2222333445678899999999999985 2222222222   22  23578889


Q ss_pred             HHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          427 AELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       427 ~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ++....-.+-+.....|-..+.-. .|+-+-.+.|++.+|.+.|+.+..
T Consensus       148 y~dV~srvepLa~d~n~mR~sArE-ALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         148 YDDVSSRVEPLAGDGNPMRHSARE-ALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             HHHHHHHhhhccCCCChhHHHHHH-HHhHHHHhccchHHHHHHHHHHHc
Confidence            999888888774445555555445 788888899999999999999875

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=91.49  E-value=0.86  Score=36.81  Aligned_cols=71  Identities=20%  Similarity=0.140  Sum_probs=43.2

Q ss_pred             hhcCChHHHHHHHHhCC-CCCCHHHHHHH-HHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCC
Q 044988          390 SRAGLMDEAFSLVQNMP-MKPNDAVLGSL-LLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKR  462 (538)
Q Consensus       390 ~~~g~~~~A~~~~~~~~-~~p~~~~~~~l-~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~  462 (538)
                      .+.++.+++..++..+. .+|.......+ ...+...|++.+|.++|+.+ .+-.|..+..-- +++.++...|+
T Consensus        21 l~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l-~~~~~~~p~~kA-LlA~CL~~~~D   93 (160)
T PF09613_consen   21 LRLGDPDDAEALLDALRVLRPEFPELDLFDGWLHIVRGDWDDALRLLREL-EERAPGFPYAKA-LLALCLYALGD   93 (160)
T ss_pred             HccCChHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhCCHHHHHHHHHHH-hccCCCChHHHH-HHHHHHHHcCC
Confidence            45677788888887774 55665544433 23367778888888888887 666665554222 44444444443

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=91.43  E-value=0.55  Score=27.04  Aligned_cols=26  Identities=12%  Similarity=0.189  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHH
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMR  245 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~  245 (538)
                      +|+.|...|.+.|++++|+.+|++..
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            46677777778888888888877744

>PRK11619 lytic murein transglycosylase; Provisional

Probab=91.32  E-value=20  Score=37.18  Aligned_cols=116  Identities=8%  Similarity=0.012  Sum_probs=75.0

Q ss_pred             CcHHHHHHHHHHhhhhcCCCcc--HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHH
Q 044988          357 GFVDEGRQFFECMNQNWGIKPR--IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGSLLLGCRIHNNAELASQV  433 (538)
Q Consensus       357 ~~~~~a~~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l~~~~~~~~~~~~A~~~  433 (538)
                      .+.+.|...+.......+..+.  ..++..+.......+...+|...++... ...+.....--+......++++.+...
T Consensus       255 ~d~~~A~~~~~~~~~~~~~~~~~~~~~~~~lA~~~a~~~~~~~a~~w~~~~~~~~~~~~~~e~r~r~Al~~~dw~~~~~~  334 (644)
T PRK11619        255 QDAENARLMIPSLVRAQKLNEDQRQELRDIVAWRLMGNDVTDEQAKWRDDVIMRSQSTSLLERRVRMALGTGDRRGLNTW  334 (644)
T ss_pred             hCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHhcccccCCcHHHHHHHHHHHHccCHHHHHHH
Confidence            3567888888877555344443  2334445444444433667777777653 223444455556666688899888888


Q ss_pred             HHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          434 AQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       434 ~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      +..| ............ -++.++...|+.++|...|+++.
T Consensus       335 i~~L-~~~~~~~~rw~Y-W~aRa~~~~g~~~~A~~~~~~~a  373 (644)
T PRK11619        335 LARL-PMEAKEKDEWRY-WQADLLLEQGRKAEAEEILRQLM  373 (644)
T ss_pred             HHhc-CHhhccCHhhHH-HHHHHHHHcCCHHHHHHHHHHHh
Confidence            8888 333334445456 78888888899999999888874

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=91.16  E-value=0.33  Score=27.55  Aligned_cols=25  Identities=32%  Similarity=0.458  Sum_probs=22.0

Q ss_pred             CCcchhHHHHHHHHHHhCCCHHHHH
Q 044988          288 EPVLVSLNNALIHMYASCGEIEEAY  312 (538)
Q Consensus       288 ~~~~~~~~~~l~~~~~~~g~~~~a~  312 (538)
                      .|.+...|+.+...|...|++++|+
T Consensus         9 ~P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    9 NPNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CCCCHHHHHHHHHHHHHCcCHHhhc
Confidence            7888888999999999999998886

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=90.84  E-value=3.1  Score=34.89  Aligned_cols=98  Identities=12%  Similarity=0.079  Sum_probs=64.8

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCc---chhH
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRARVGLD--QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPV---LVSL  294 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~~  294 (538)
                      .+..+...|++.|+.+.|++.|.++.+....|.  ...+..+|....-.+++..+......+......++...   ...+
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk~  117 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLKV  117 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHHH
Confidence            577788888888888888888888877654443  33466777777788888888888777776644332211   1122


Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHhcC
Q 044988          295 NNALIHMYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       295 ~~~l~~~~~~~g~~~~a~~~~~~m~  319 (538)
                      +..|  .+...+++..|-+.|-...
T Consensus       118 ~~gL--~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  118 YEGL--ANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHH--HHHHhchHHHHHHHHHccC
Confidence            2222  2335678888888887765

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=90.66  E-value=19  Score=35.80  Aligned_cols=83  Identities=12%  Similarity=0.257  Sum_probs=64.6

Q ss_pred             hccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHH-ccCChhHHHHHHhcCCC------CCcchHHHHHHHHhcCCCch
Q 044988           28 QIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYV-TSGYLINAHKVFEKTEN------PSTAIWNQMIRGHARSETPE  100 (538)
Q Consensus        28 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~a~~~~~~~~~------~~~~~~~~li~~~~~~~~~~  100 (538)
                      .+.|..+.+..+|+.-++. ++.+...|...+.... ..|+.+.....|++...      .+...|...|.--..++++.
T Consensus        90 ~klg~~~~s~~Vfergv~a-ip~SvdlW~~Y~~f~~n~~~d~~~lr~~fe~A~~~vG~dF~S~~lWdkyie~en~qks~k  168 (577)
T KOG1258|consen   90 YKLGNAENSVKVFERGVQA-IPLSVDLWLSYLAFLKNNNGDPETLRDLFERAKSYVGLDFLSDPLWDKYIEFENGQKSWK  168 (577)
T ss_pred             HHhhhHHHHHHHHHHHHHh-hhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcccchhccHHHHHHHHHHhccccHH
Confidence            4557778888889887764 5677778877776555 46788888888887663      35557888898888899999


Q ss_pred             HHHHHHHHhHh
Q 044988          101 KSVYLYKQMID  111 (538)
Q Consensus       101 ~a~~~~~~m~~  111 (538)
                      ....+|++.++
T Consensus       169 ~v~~iyeRile  179 (577)
T KOG1258|consen  169 RVANIYERILE  179 (577)
T ss_pred             HHHHHHHHHHh
Confidence            99999999986

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=90.37  E-value=12  Score=32.98  Aligned_cols=58  Identities=17%  Similarity=0.120  Sum_probs=39.1

Q ss_pred             HHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          349 VLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       349 ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      +.+-|.+.|.+..|..-++.|.+.+.-.+ ....+-.+..+|.+.|-.++|...-+-+.
T Consensus       173 IaryY~kr~~~~AA~nR~~~v~e~y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl~  231 (254)
T COG4105         173 IARYYLKRGAYVAAINRFEEVLENYPDTSAVREALARLEEAYYALGLTDEAKKTAKVLG  231 (254)
T ss_pred             HHHHHHHhcChHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhCChHHHHHHHHHHH
Confidence            34556667778888888888887642222 13455667778888888888877766554

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.74  E-value=13  Score=32.45  Aligned_cols=16  Identities=0%  Similarity=-0.176  Sum_probs=7.3

Q ss_pred             hcccCcHHHHHHHHHH
Q 044988          353 CSHGGFVDEGRQFFEC  368 (538)
Q Consensus       353 ~~~~~~~~~a~~~~~~  368 (538)
                      +....++..|..+++.
T Consensus       200 ~L~~~Dyv~aekc~r~  215 (308)
T KOG1585|consen  200 YLYAHDYVQAEKCYRD  215 (308)
T ss_pred             HhhHHHHHHHHHHhcc
Confidence            3333444445555444

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.65  E-value=28  Score=36.21  Aligned_cols=215  Identities=12%  Similarity=0.039  Sum_probs=137.4

Q ss_pred             CccccHHHHHHHHhccCChHHHHHHHHHHH----HhC------------CCCChhHHHHHHHHHHccCChhHHHHHHhcC
Q 044988           15 SKALTTRQIFSLLQIRNTTKTLFQIHSQII----ING------------FSQKNYILAKLLAFYVTSGYLINAHKVFEKT   78 (538)
Q Consensus        15 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~----~~~------------~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~   78 (538)
                      .+..+.++++.++...+++-.-.-+++.+.    ..+            ..........-++.+.+...++-|+.+.+.-
T Consensus       281 ~s~ss~~~i~~~~d~~n~~v~ys~vl~~l~d~l~~w~~~~~vltsdg~~~~L~ek~le~kL~iL~kK~ly~~Ai~LAk~~  360 (933)
T KOG2114|consen  281 LSNSSSNRIFKAYDLRNRYVLYSSVLEDLSDNLIEWSFDCLVLTSDGVVHELIEKDLETKLDILFKKNLYKVAINLAKSQ  360 (933)
T ss_pred             cCccchhheeehhhhcCcccchHHhHHHHHHHHHhcCCcEEEEecCCceeeeeeccHHHHHHHHHHhhhHHHHHHHHHhc
Confidence            456677788888888887644433333333    323            1122345566778888888889998887655


Q ss_pred             CCCCcchH----HHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchh
Q 044988           79 ENPSTAIW----NQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVF  154 (538)
Q Consensus        79 ~~~~~~~~----~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  154 (538)
                      .- +...-    ..-.+-+.+.|++++|...|-+-... +.|     ..+|.-|....++..-..+++.+.+.|+ .+..
T Consensus       361 ~~-d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~-le~-----s~Vi~kfLdaq~IknLt~YLe~L~~~gl-a~~d  432 (933)
T KOG2114|consen  361 HL-DEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF-LEP-----SEVIKKFLDAQRIKNLTSYLEALHKKGL-ANSD  432 (933)
T ss_pred             CC-CHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc-CCh-----HHHHHHhcCHHHHHHHHHHHHHHHHccc-ccch
Confidence            43 22222    22334456789999999988776643 233     3455666666667777788899999885 4555


Q ss_pred             HHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCc-hhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCC
Q 044988          155 IRTNLMNLYLMSGGECGVGCARLLFDDMPARSV-VSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGK  233 (538)
Q Consensus       155 ~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~-~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~  233 (538)
                      .-+.|+++|.+.++   .++..+..+....-.. .-....+..+.+.+-.+.|..+-.+... +......++   -..++
T Consensus       433 httlLLncYiKlkd---~~kL~efI~~~~~g~~~fd~e~al~Ilr~snyl~~a~~LA~k~~~-he~vl~ill---e~~~n  505 (933)
T KOG2114|consen  433 HTTLLLNCYIKLKD---VEKLTEFISKCDKGEWFFDVETALEILRKSNYLDEAELLATKFKK-HEWVLDILL---EDLHN  505 (933)
T ss_pred             hHHHHHHHHHHhcc---hHHHHHHHhcCCCcceeeeHHHHHHHHHHhChHHHHHHHHHHhcc-CHHHHHHHH---HHhcC
Confidence            66789999999999   8888877776662211 1234455566666666666665555433 333333333   34688


Q ss_pred             HHHHHHHHHHH
Q 044988          234 SRQALSLFNEM  244 (538)
Q Consensus       234 ~~~a~~~~~~m  244 (538)
                      +++|++++..+
T Consensus       506 y~eAl~yi~sl  516 (933)
T KOG2114|consen  506 YEEALRYISSL  516 (933)
T ss_pred             HHHHHHHHhcC
Confidence            99999988776

>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome

Probab=89.63  E-value=11  Score=31.53  Aligned_cols=100  Identities=17%  Similarity=0.128  Sum_probs=57.0

Q ss_pred             chhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhh
Q 044988          291 LVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMN  370 (538)
Q Consensus       291 ~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~  370 (538)
                      -...+..+...|++.|+.+.|.+.|.++.+....+ ...+             ..+..++..+...+++..+.....+..
T Consensus        35 ir~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~-~~~i-------------d~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   35 IRMALEDLADHYCKIGDLEEALKAYSRARDYCTSP-GHKI-------------DMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCH-HHHH-------------HHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            34556788899999999999999999987643221 1111             233344444455556666555555544


Q ss_pred             hhc--CCCcc----HHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          371 QNW--GIKPR----IEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       371 ~~~--~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      ...  +-.++    ..+|..|.  +...+++.+|-++|-...
T Consensus       101 ~~~~~~~d~~~~nrlk~~~gL~--~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  101 SLIEKGGDWERRNRLKVYEGLA--NLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHhccchHHHHHHHHHHHHHH--HHHhchHHHHHHHHHccC
Confidence            321  11112    12222222  335678888888887664

This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.

>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia

Probab=89.59  E-value=8.7  Score=31.20  Aligned_cols=74  Identities=20%  Similarity=0.196  Sum_probs=48.8

Q ss_pred             HHHHHhcccCcHHHHHHHHHHhhhhcCCCccHH-HHHHHHHHhhhcCChHHHHHHHHhCCCC-CCHHHHHHHHHHHHhc
Q 044988          348 GVLSACSHGGFVDEGRQFFECMNQNWGIKPRIE-HYGCMVDLFSRAGLMDEAFSLVQNMPMK-PNDAVLGSLLLGCRIH  424 (538)
Q Consensus       348 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~-p~~~~~~~l~~~~~~~  424 (538)
                      .++..-...++.+.+..++..+...   .|... .-..-...+...|++.+|..+|+++... |....-..|+..|...
T Consensus        15 e~~~~al~~~~~~D~e~lL~ALrvL---RP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~~~~p~~kALlA~CL~~   90 (160)
T PF09613_consen   15 EVLSVALRLGDPDDAEALLDALRVL---RPEFPELDLFDGWLHIVRGDWDDALRLLRELEERAPGFPYAKALLALCLYA   90 (160)
T ss_pred             HHHHHHHccCChHHHHHHHHHHHHh---CCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHH
Confidence            3444555677999999999998744   67533 2233345577899999999999999644 3333334455445443

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=89.40  E-value=1.8  Score=38.90  Aligned_cols=72  Identities=11%  Similarity=0.140  Sum_probs=36.0

Q ss_pred             HHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHHHHhcCCCchHHHHHHHHhHh-----CCCCCCcchHHHHHH
Q 044988           55 LAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIRGHARSETPEKSVYLYKQMID-----KETEPDEYTYSFLLS  126 (538)
Q Consensus        55 ~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~-----~~~~p~~~~~~~li~  126 (538)
                      +..++..+...|+++.+.+.+++...   -+...|..++.+|.+.|+...|+..|+.+.+     .|+.|...+......
T Consensus       156 l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y~~  235 (280)
T COG3629         156 LTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALYEE  235 (280)
T ss_pred             HHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHHHH
Confidence            34444455555555555555554442   2334555555555555555555555555543     244454444444333

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=89.16  E-value=28  Score=35.45  Aligned_cols=107  Identities=11%  Similarity=0.084  Sum_probs=59.0

Q ss_pred             hHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHh
Q 044988          120 TYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVK  199 (538)
Q Consensus       120 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~  199 (538)
                      .|+.+...++....++.|.+.|..--.         ....+.++.+..+   +++.+.+-..+++ +......+..++..
T Consensus       798 A~r~ig~~fa~~~~We~A~~yY~~~~~---------~e~~~ecly~le~---f~~LE~la~~Lpe-~s~llp~~a~mf~s  864 (1189)
T KOG2041|consen  798 AFRNIGETFAEMMEWEEAAKYYSYCGD---------TENQIECLYRLEL---FGELEVLARTLPE-DSELLPVMADMFTS  864 (1189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhccc---------hHhHHHHHHHHHh---hhhHHHHHHhcCc-ccchHHHHHHHHHh
Confidence            444444445555555555554433211         1124445555555   5555444444443 44456667777778


Q ss_pred             cCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 044988          200 RGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEM  244 (538)
Q Consensus       200 ~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  244 (538)
                      .|.-++|.+.|-+-..|..     .+..|...+++.+|.++-++.
T Consensus       865 vGMC~qAV~a~Lr~s~pka-----Av~tCv~LnQW~~avelaq~~  904 (1189)
T KOG2041|consen  865 VGMCDQAVEAYLRRSLPKA-----AVHTCVELNQWGEAVELAQRF  904 (1189)
T ss_pred             hchHHHHHHHHHhccCcHH-----HHHHHHHHHHHHHHHHHHHhc
Confidence            8888888777776655543     334556666777776665544

>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1

Probab=88.82  E-value=12  Score=30.80  Aligned_cols=133  Identities=14%  Similarity=0.100  Sum_probs=85.7

Q ss_pred             HHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhc--CCHHHHHHHHccCCC
Q 044988          138 EQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKR--GDIDGAWKIFDEMPH  215 (538)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~--g~~~~A~~~~~~m~~  215 (538)
                      .+.++.+.+.+++|+...+..+++.+.+.|+   +.....++.--.-+|.......+-.+...  .-..-|.+.+.++. 
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~---~~~L~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~-   89 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQ---FSQLHQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLG-   89 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCC---HHHHHHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhh-
Confidence            3455666778899999999999999999999   88887777665555544443333222221  11344555555544 


Q ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHH
Q 044988          216 RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEE  281 (538)
Q Consensus       216 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~  281 (538)
                         ..+..++..+...|++-+|+++.+.....    +......++.+..+.+|...-..+++.+.+
T Consensus        90 ---~~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~  148 (167)
T PF07035_consen   90 ---TAYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFFEE  148 (167)
T ss_pred             ---hhHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence               24566777788889999999888765322    122234566676677776666666666655

>PRK09687 putative lyase; Provisional

Probab=88.80  E-value=19  Score=32.94  Aligned_cols=80  Identities=3%  Similarity=-0.090  Sum_probs=40.9

Q ss_pred             CChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCc----hHHHHHHHHhHhCCCCCCcchHHHHH
Q 044988           50 QKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETP----EKSVYLYKQMIDKETEPDEYTYSFLL  125 (538)
Q Consensus        50 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~----~~a~~~~~~m~~~~~~p~~~~~~~li  125 (538)
                      ++..+....+..+...|..+-...+..-...+|...-...+.++.+.|+.    .++...+..+...  .|+...-...+
T Consensus        35 ~d~~vR~~A~~aL~~~~~~~~~~~l~~ll~~~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~~VR~~A~  112 (280)
T PRK09687         35 HNSLKRISSIRVLQLRGGQDVFRLAIELCSSKNPIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSACVRASAI  112 (280)
T ss_pred             CCHHHHHHHHHHHHhcCcchHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCHHHHHHHH
Confidence            45556666666666666533333333323345555555555666666653    3456666555332  35555555555


Q ss_pred             HHHHcc
Q 044988          126 SVCARC  131 (538)
Q Consensus       126 ~~~~~~  131 (538)
                      .++...
T Consensus       113 ~aLG~~  118 (280)
T PRK09687        113 NATGHR  118 (280)
T ss_pred             HHHhcc
Confidence            555443

>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A

Probab=88.57  E-value=0.88  Score=25.54  Aligned_cols=29  Identities=21%  Similarity=0.054  Sum_probs=14.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHchhccCC
Q 044988          414 LGSLLLGCRIHNNAELASQVAQKLVAEIDP  443 (538)
Q Consensus       414 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p  443 (538)
                      |..+...+...|++++|...|++. .++.|
T Consensus         4 ~~~lg~~y~~~~~~~~A~~~~~~a-~~~~~   32 (34)
T PF13181_consen    4 YYNLGKIYEQLGDYEEALEYFEKA-LELNP   32 (34)
T ss_dssp             HHHHHHHHHHTTSHHHHHHHHHHH-HHHHT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH-HhhCC
Confidence            344444455555555555555555 44444

...

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=88.51  E-value=1.4  Score=36.75  Aligned_cols=86  Identities=16%  Similarity=0.152  Sum_probs=56.5

Q ss_pred             hhhcCChHHHHHHHHhCC-CCCC------HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcC
Q 044988          389 FSRAGLMDEAFSLVQNMP-MKPN------DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAK  461 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~-~~p~------~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g  461 (538)
                      +.+.|++++|..-|.... .-|.      .+.|..-..+..+.+.++.|+.-..+. .++.|....+.. .-+.+|.+..
T Consensus       105 ~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKa-iel~pty~kAl~-RRAeayek~e  182 (271)
T KOG4234|consen  105 LFKNGDYEEANSKYQEALESCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKA-IELNPTYEKALE-RRAEAYEKME  182 (271)
T ss_pred             hhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhh-HhcCchhHHHHH-HHHHHHHhhh
Confidence            456677777776666542 1121      223333334566777778888777777 778887776555 6667788888


Q ss_pred             ChHHHHHHHHHHHhC
Q 044988          462 RWQDVAAVRQKMIKM  476 (538)
Q Consensus       462 ~~~~A~~~~~~m~~~  476 (538)
                      ++++|++=|+++.+.
T Consensus       183 k~eealeDyKki~E~  197 (271)
T KOG4234|consen  183 KYEEALEDYKKILES  197 (271)
T ss_pred             hHHHHHHHHHHHHHh
Confidence            888888888887764

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=88.47  E-value=15  Score=31.46  Aligned_cols=160  Identities=16%  Similarity=0.088  Sum_probs=81.7

Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHH
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNA  297 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  297 (538)
                      +.+||-+.--+...|+++.|.+.|+...+....-+-...+.-| ++.-.|++..|.+-+...-+.   +...|....|-.
T Consensus        99 ~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~y~Ya~lNRgi-~~YY~gR~~LAq~d~~~fYQ~---D~~DPfR~LWLY  174 (297)
T COG4785          99 PEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPTYNYAHLNRGI-ALYYGGRYKLAQDDLLAFYQD---DPNDPFRSLWLY  174 (297)
T ss_pred             HHHHHHHHHHHHhcccchHHHHHhhhHhccCCcchHHHhccce-eeeecCchHhhHHHHHHHHhc---CCCChHHHHHHH
Confidence            3478888888888899999999999887744332222222222 223457788777665555553   122222233322


Q ss_pred             HHHHHHhCCCHHHHHH-HHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc--C
Q 044988          298 LIHMYASCGEIEEAYG-VFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW--G  374 (538)
Q Consensus       298 l~~~~~~~g~~~~a~~-~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~  374 (538)
                      +.   .+.-++.+|.. +.++..+.|..-|...|-.|.-..-.+++                      +++.+...-  +
T Consensus       175 l~---E~k~dP~~A~tnL~qR~~~~d~e~WG~~iV~~yLgkiS~e~----------------------l~~~~~a~a~~n  229 (297)
T COG4785         175 LN---EQKLDPKQAKTNLKQRAEKSDKEQWGWNIVEFYLGKISEET----------------------LMERLKADATDN  229 (297)
T ss_pred             HH---HhhCCHHHHHHHHHHHHHhccHhhhhHHHHHHHHhhccHHH----------------------HHHHHHhhccch
Confidence            21   12234555554 44555555555555544443322211211                      111111100  0


Q ss_pred             ---CCccHHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          375 ---IKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       375 ---~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                         -..=..||--|..-+...|+.++|..+|+-..
T Consensus       230 ~~~Ae~LTEtyFYL~K~~l~~G~~~~A~~LfKLai  264 (297)
T COG4785         230 TSLAEHLTETYFYLGKYYLSLGDLDEATALFKLAV  264 (297)
T ss_pred             HHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHH
Confidence               00113466677777777777777777776543

>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.17  E-value=17  Score=31.61  Aligned_cols=117  Identities=12%  Similarity=0.179  Sum_probs=60.8

Q ss_pred             HHHHHhcCCccHHHHHHHHHHHHhccc-CcHHHHHHHHHHhhhhcCCC-ccHHHHHHH---HHHhhhcCChHHHHHHHHh
Q 044988          330 ITGFAKQGYAQEALLTFLGVLSACSHG-GFVDEGRQFFECMNQNWGIK-PRIEHYGCM---VDLFSRAGLMDEAFSLVQN  404 (538)
Q Consensus       330 i~~~~~~~~~~~a~~~~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~~~-p~~~~~~~l---~~~~~~~g~~~~A~~~~~~  404 (538)
                      |..|...|++..|......+...|-.. .+++.|+..|+..-+-+... .+...-..+   .+--+..+++.+|+++|++
T Consensus       100 ieIyt~~Grf~~aAk~~~~iaEiyEsdl~d~ekaI~~YE~Aae~yk~ees~ssANKC~lKvA~yaa~leqY~~Ai~iyeq  179 (288)
T KOG1586|consen  100 IEIYTDMGRFTMAAKHHIEIAEIYESDLQDFEKAIAHYEQAAEYYKGEESVSSANKCLLKVAQYAAQLEQYSKAIDIYEQ  179 (288)
T ss_pred             HHHHHhhhHHHHHHhhhhhHHHHHhhhHHHHHHHHHHHHHHHHHHcchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            445555566665554444555555433 56667777766654432211 122222222   2333456888999999988


Q ss_pred             CC---CCCCHHHHH---HHHHH--HHhc-CCHHHHHHHHHHchhccCCCCcc
Q 044988          405 MP---MKPNDAVLG---SLLLG--CRIH-NNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       405 ~~---~~p~~~~~~---~l~~~--~~~~-~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      +.   ...+..-|.   .++.+  |--. .+.-.+...+++- .++.|....
T Consensus       180 va~~s~~n~LLKys~KdyflkAgLChl~~~D~v~a~~ALeky-~~~dP~F~d  230 (288)
T KOG1586|consen  180 VARSSLDNNLLKYSAKDYFLKAGLCHLCKADEVNAQRALEKY-QELDPAFTD  230 (288)
T ss_pred             HHHHhccchHHHhHHHHHHHHHHHHhHhcccHHHHHHHHHHH-HhcCCcccc
Confidence            74   222222221   12222  2222 5666666677776 667777554

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.97  E-value=9.5  Score=37.83  Aligned_cols=147  Identities=20%  Similarity=0.123  Sum_probs=94.1

Q ss_pred             hCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHH---HHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHH
Q 044988          304 SCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTF---LGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIE  380 (538)
Q Consensus       304 ~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~---~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~  380 (538)
                      -.|+++.|..++-.+.++   .-+.++.-+.+.|-.++|+..-   ..-.....+.|+++.|.++..+..       +..
T Consensus       598 mrrd~~~a~~vLp~I~k~---~rt~va~Fle~~g~~e~AL~~s~D~d~rFelal~lgrl~iA~~la~e~~-------s~~  667 (794)
T KOG0276|consen  598 LRRDLEVADGVLPTIPKE---IRTKVAHFLESQGMKEQALELSTDPDQRFELALKLGRLDIAFDLAVEAN-------SEV  667 (794)
T ss_pred             hhccccccccccccCchh---hhhhHHhHhhhccchHhhhhcCCChhhhhhhhhhcCcHHHHHHHHHhhc-------chH
Confidence            346666666666655532   2344555566666666666110   011122235577777777765432       456


Q ss_pred             HHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhc
Q 044988          381 HYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAA  460 (538)
Q Consensus       381 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~  460 (538)
                      -|..|.++....|++..|.+.|.+..      -|..|+-.+...|+.+.-..+-... .+....+.. |.     +|...
T Consensus       668 Kw~~Lg~~al~~~~l~lA~EC~~~a~------d~~~LlLl~t~~g~~~~l~~la~~~-~~~g~~N~A-F~-----~~~l~  734 (794)
T KOG0276|consen  668 KWRQLGDAALSAGELPLASECFLRAR------DLGSLLLLYTSSGNAEGLAVLASLA-KKQGKNNLA-FL-----AYFLS  734 (794)
T ss_pred             HHHHHHHHHhhcccchhHHHHHHhhc------chhhhhhhhhhcCChhHHHHHHHHH-HhhcccchH-HH-----HHHHc
Confidence            78889999999999999999888764      2566777777788877666666655 333444433 33     67889


Q ss_pred             CChHHHHHHHHHH
Q 044988          461 KRWQDVAAVRQKM  473 (538)
Q Consensus       461 g~~~~A~~~~~~m  473 (538)
                      |+++++.+++.+-
T Consensus       735 g~~~~C~~lLi~t  747 (794)
T KOG0276|consen  735 GDYEECLELLIST  747 (794)
T ss_pred             CCHHHHHHHHHhc
Confidence            9999999988764

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=87.79  E-value=1.5  Score=24.56  Aligned_cols=28  Identities=14%  Similarity=0.194  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRR  246 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~  246 (538)
                      .+|..+...|...|++++|+..|++..+
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            3566677777777777777777777765

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=87.74  E-value=12  Score=29.68  Aligned_cols=55  Identities=13%  Similarity=0.031  Sum_probs=28.3

Q ss_pred             HHHcCCHHHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          228 CAQNGKSRQALSLFNEMRRAR--VGLDQVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       228 ~~~~~~~~~a~~~~~~m~~~g--~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      ..+.|++++|.+.|+.+...=  -+-....-..++.++.+.++++.|...++.+++.
T Consensus        20 ~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirL   76 (142)
T PF13512_consen   20 ALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRL   76 (142)
T ss_pred             HHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            344566666666666655431  0112233444555555555555555555555554

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=87.67  E-value=14  Score=30.32  Aligned_cols=133  Identities=8%  Similarity=0.037  Sum_probs=72.8

Q ss_pred             ccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCC-hhHHHHHHHHHHccCChhHHHHHHhcCCC--CCcchHHHHH----
Q 044988           18 LTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQK-NYILAKLLAFYVTSGYLINAHKVFEKTEN--PSTAIWNQMI----   90 (538)
Q Consensus        18 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~~~~~~~~li----   90 (538)
                      ..|..-+. +++.+..+.|..-|..+.+.|...= +-..-......+..|+...|...|+++-.  +.+....-+.    
T Consensus        60 d~flaAL~-lA~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlra  138 (221)
T COG4649          60 DAFLAALK-LAQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRA  138 (221)
T ss_pred             HHHHHHHH-HHHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHH
Confidence            33444333 3345566777777777777664421 22233344555667777777777776653  2222221111    


Q ss_pred             -HHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCC
Q 044988           91 -RGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCS  151 (538)
Q Consensus        91 -~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~  151 (538)
                       -.++.+|.++......+.+-..+.+.-...-..|.-+..+.|++..|.+.|..+......|
T Consensus       139 a~lLvD~gsy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~Da~ap  200 (221)
T COG4649         139 AYLLVDNGSYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIANDAQAP  200 (221)
T ss_pred             HHHHhccccHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHccccCc
Confidence             1235567777766666666544433333444455556667777777777777766543333

>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A

Probab=87.56  E-value=4  Score=26.04  Aligned_cols=48  Identities=6%  Similarity=0.007  Sum_probs=36.5

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeEEEECCEEEEEEeCCCCCcchHHHHHHHHHHHHHHHHcCc
Q 044988          452 LVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGY  525 (538)
Q Consensus       452 ~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~m~~~~~  525 (538)
                      .++-++.+.|++++|.+..+.+.+.                          .|...++...-..+.+.|++.|+
T Consensus         6 ~lAig~ykl~~Y~~A~~~~~~lL~~--------------------------eP~N~Qa~~L~~~i~~~i~kdgl   53 (53)
T PF14853_consen    6 YLAIGHYKLGEYEKARRYCDALLEI--------------------------EPDNRQAQSLKELIEDKIQKDGL   53 (53)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHHHH--------------------------TTS-HHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHhh--------------------------CCCcHHHHHHHHHHHHHHhccCC
Confidence            5677899999999999999999873                          44556666666667788888874

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=87.50  E-value=5.8  Score=38.44  Aligned_cols=70  Identities=14%  Similarity=0.054  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCC--CcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCC
Q 044988          411 DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPE--QAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPP  482 (538)
Q Consensus       411 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~  482 (538)
                      ..+-..+..++.+.|+.++|++.++++ .+..|.  ...... .|+.+|...+++.++..++.+-.+...+++.
T Consensus       259 ~y~KrRLAmCarklGr~~EAIk~~rdL-lke~p~~~~l~Ire-nLie~LLelq~Yad~q~lL~kYdDi~lpkSA  330 (539)
T PF04184_consen  259 VYAKRRLAMCARKLGRLREAIKMFRDL-LKEFPNLDNLNIRE-NLIEALLELQAYADVQALLAKYDDISLPKSA  330 (539)
T ss_pred             hhhHHHHHHHHHHhCChHHHHHHHHHH-HhhCCccchhhHHH-HHHHHHHhcCCHHHHHHHHHHhccccCCchH
Confidence            334455677788899999999999999 655554  233345 7889999999999999999987654444443

The molecular function of this protein is uncertain.

>KOG3364 consensus Membrane protein involved in organellar division [Cell wall/membrane/envelope biogenesis]

Probab=87.34  E-value=8.8  Score=29.99  Aligned_cols=71  Identities=13%  Similarity=0.121  Sum_probs=32.7

Q ss_pred             CccHHHHHHHHHHhhhcCCh---HHHHHHHHhCC--CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          376 KPRIEHYGCMVDLFSRAGLM---DEAFSLVQNMP--MKPN--DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       376 ~p~~~~~~~l~~~~~~~g~~---~~A~~~~~~~~--~~p~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      .++..+-..+..++.+..+.   .+.+.+++.+-  ..|+  ..-..-|.-++.+.+++++++++.+.+ .+..|++..
T Consensus        29 ~~s~~s~f~lAwaLV~S~~~~dv~~GI~iLe~l~~~~~~~~rRe~lyYLAvg~yRlkeY~~s~~yvd~l-l~~e~~n~Q  106 (149)
T KOG3364|consen   29 DVSKQSQFNLAWALVRSRDTEDVQEGIVILEDLLKSAHPERRRECLYYLAVGHYRLKEYSKSLRYVDAL-LETEPNNRQ  106 (149)
T ss_pred             cchHHHHHHHHHHHHcccchHHHHHhHHHHHHHhhhcCcccchhhhhhhHHHHHHHhhHHHHHHHHHHH-HhhCCCcHH
Confidence            34444444555555554432   23344444442  1122  112223333455556666666666655 555555544

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=87.20  E-value=18  Score=30.99  Aligned_cols=81  Identities=12%  Similarity=0.195  Sum_probs=43.9

Q ss_pred             ccCChhHHHHHHhcCC--CCC-cchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHH--HHHccCCcHHHH
Q 044988           64 TSGYLINAHKVFEKTE--NPS-TAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLS--VCARCGLFREGE  138 (538)
Q Consensus        64 ~~g~~~~a~~~~~~~~--~~~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~--~~~~~~~~~~a~  138 (538)
                      +.|-..-|+-=|.+..  .|+ +..||-|.--+...|+++.|.+.|+...+.+  |. .-|..+=+  ++--.|+++.|.
T Consensus        77 SlGL~~LAR~DftQaLai~P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELD--p~-y~Ya~lNRgi~~YY~gR~~LAq  153 (297)
T COG4785          77 SLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD--PT-YNYAHLNRGIALYYGGRYKLAQ  153 (297)
T ss_pred             hhhHHHHHhhhhhhhhhcCCCcHHHHHHHHHHHHhcccchHHHHHhhhHhccC--Cc-chHHHhccceeeeecCchHhhH
Confidence            3344444444443322  233 3467777777777888888888888777643  22 12222222  223346777776


Q ss_pred             HHHHHHHHh
Q 044988          139 QVHGRVLAS  147 (538)
Q Consensus       139 ~~~~~~~~~  147 (538)
                      +=+...-+.
T Consensus       154 ~d~~~fYQ~  162 (297)
T COG4785         154 DDLLAFYQD  162 (297)
T ss_pred             HHHHHHHhc
Confidence            665555544

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=87.02  E-value=17  Score=30.56  Aligned_cols=90  Identities=17%  Similarity=0.109  Sum_probs=63.4

Q ss_pred             HHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHH-----HHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHh
Q 044988          385 MVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSL-----LLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAA  459 (538)
Q Consensus       385 l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l-----~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~  459 (538)
                      +...+..+|++++|..-++.....|....+..+     .+.....|.+|.|+..++.. .  .+.-......+-++++..
T Consensus        95 lAk~~ve~~~~d~A~aqL~~~l~~t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~-~--~~~w~~~~~elrGDill~  171 (207)
T COG2976          95 LAKAEVEANNLDKAEAQLKQALAQTKDENLKALAALRLARVQLQQKKADAALKTLDTI-K--EESWAAIVAELRGDILLA  171 (207)
T ss_pred             HHHHHHhhccHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhcc-c--cccHHHHHHHHhhhHHHH
Confidence            456677889999999888876534544444444     34567888999999988876 2  122122122277889999


Q ss_pred             cCChHHHHHHHHHHHhCC
Q 044988          460 AKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       460 ~g~~~~A~~~~~~m~~~~  477 (538)
                      .|+-++|+.-|++..+.+
T Consensus       172 kg~k~~Ar~ay~kAl~~~  189 (207)
T COG2976         172 KGDKQEARAAYEKALESD  189 (207)
T ss_pred             cCchHHHHHHHHHHHHcc
Confidence            999999999999888765

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=86.77  E-value=31  Score=33.24  Aligned_cols=28  Identities=18%  Similarity=0.163  Sum_probs=19.6

Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHccCC
Q 044988          187 VVSWNSLLKGYVKRGDIDGAWKIFDEMP  214 (538)
Q Consensus       187 ~~~~~~li~~~~~~g~~~~A~~~~~~m~  214 (538)
                      ..++..++....+.++...|.+.+.-+.
T Consensus       298 i~~F~~~Ls~~Vk~~~T~~a~q~l~lL~  325 (549)
T PF07079_consen  298 IDRFGNLLSFKVKQVQTEEAKQYLALLK  325 (549)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            3467777777778888777777666544

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=86.62  E-value=7.3  Score=28.33  Aligned_cols=50  Identities=18%  Similarity=0.235  Sum_probs=41.6

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          233 KSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       233 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      +.-++.+-++.+....+.|+.....+.+++|-+.+++..|.++++.++..
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K   71 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDK   71 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            45567777777777788899999999999999999999999999888765

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>PF00637 Clathrin: Region in Clathrin and VPS; InterPro: IPR000547 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=86.52  E-value=0.54  Score=37.87  Aligned_cols=86  Identities=16%  Similarity=0.261  Sum_probs=62.6

Q ss_pred             HHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchH
Q 044988           22 QIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEK  101 (538)
Q Consensus        22 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~  101 (538)
                      .++..+...+.+..+..+++.+.+.+...++...+.++..|++.++.+...++++....   .-...+++.|.+.|.++.
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~---yd~~~~~~~c~~~~l~~~   88 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNN---YDLDKALRLCEKHGLYEE   88 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS---S-CTHHHHHHHTTTSHHH
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccc---cCHHHHHHHHHhcchHHH
Confidence            56777777888888889999999887777788999999999999888888888874332   333455666666666666


Q ss_pred             HHHHHHHhH
Q 044988          102 SVYLYKQMI  110 (538)
Q Consensus       102 a~~~~~~m~  110 (538)
                      |.-++.++.
T Consensus        89 a~~Ly~~~~   97 (143)
T PF00637_consen   89 AVYLYSKLG   97 (143)
T ss_dssp             HHHHHHCCT
T ss_pred             HHHHHHHcc
Confidence            666665543

These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. This entry represents the 7-fold alpha-alpha-superhelical ARM-type repeat found at the C-terminal of clathrin heavy chains and in VPS (vacuolar protein sorting-associated) proteins. In clathrin heavy chains, the C-terminal 7-fold ARM-type repeats interact to form the central hub of the triskelion. VPS proteins are required for vacuolar assembly and vacuolar traffick, and contain one clathrin-type repeat []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport; PDB: 3LVH_A 3LVG_C 1B89_A 3QIL_L.

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=86.52  E-value=6.9  Score=28.79  Aligned_cols=50  Identities=18%  Similarity=0.217  Sum_probs=38.0

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          233 KSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       233 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      +.-+..+-++.+....+.|+.....+.+.+|.+.+++..|.++++.++..
T Consensus        25 D~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K   74 (108)
T PF02284_consen   25 DGWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDK   74 (108)
T ss_dssp             -HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            34466777777777788999999999999999999999999999988887

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=86.23  E-value=5.5  Score=28.95  Aligned_cols=61  Identities=10%  Similarity=0.047  Sum_probs=44.7

Q ss_pred             CchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHH
Q 044988           98 TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNL  159 (538)
Q Consensus        98 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  159 (538)
                      +.-++.+-++.+....+.|++....+.+++|.+.+|+..|.++++-.+... ..+...|..+
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~-~~~~~~y~~~   82 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKC-GAHKEIYPYI   82 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cCchhhHHHH
Confidence            334566667777777888999999999999999999999999999877442 2233344444

Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=86.00  E-value=19  Score=33.17  Aligned_cols=136  Identities=18%  Similarity=0.251  Sum_probs=70.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc--cC----ChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCC
Q 044988          234 SRQALSLFNEMRRARVGLDQVALVAALSACAE--IG----DLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGE  307 (538)
Q Consensus       234 ~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~--~~----~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  307 (538)
                      +++.+.+++.|.+.|++-+..+|.+.......  ..    ....+..+|+.|++....-..+.+..+ ..|+..  ..++
T Consensus        78 ~~~~~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~-a~lLA~--~~~~  154 (297)
T PF13170_consen   78 FKEVLDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPF-AALLAM--TSED  154 (297)
T ss_pred             HHHHHHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhH-HHHHhc--cccc
Confidence            46677888899999999888887664443333  22    245678888888887332222223222 233222  3333


Q ss_pred             H----HHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccC--cHHHHHHHHHHhhhhcCCCccHHH
Q 044988          308 I----EEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGG--FVDEGRQFFECMNQNWGIKPRIEH  381 (538)
Q Consensus       308 ~----~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~--~~~~a~~~~~~~~~~~~~~p~~~~  381 (538)
                      .    +.++.+|+.+.+.+.           ..|+   .+.....++..+....  ...++..+++.+.+. |+++....
T Consensus       155 ~e~l~~~~E~~Y~~L~~~~f-----------~kgn---~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~-~~kik~~~  219 (297)
T PF13170_consen  155 VEELAERMEQCYQKLADAGF-----------KKGN---DLQFLSHILALSEGDDQEKVARVIELYNALKKN-GVKIKYMH  219 (297)
T ss_pred             HHHHHHHHHHHHHHHHHhCC-----------CCCc---HHHHHHHHHHhccccchHHHHHHHHHHHHHHHc-CCcccccc
Confidence            3    334444444433110           0000   0011111111111111  245777888888877 88887766


Q ss_pred             HHHHHH
Q 044988          382 YGCMVD  387 (538)
Q Consensus       382 ~~~l~~  387 (538)
                      |..+.-
T Consensus       220 yp~lGl  225 (297)
T PF13170_consen  220 YPTLGL  225 (297)
T ss_pred             ccHHHH
Confidence            666544

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.97  E-value=46  Score=34.47  Aligned_cols=147  Identities=12%  Similarity=0.120  Sum_probs=84.4

Q ss_pred             HHHHhcCCCchHHHHHHHHhHhCCCCC---CcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhc
Q 044988           90 IRGHARSETPEKSVYLYKQMIDKETEP---DEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMS  166 (538)
Q Consensus        90 i~~~~~~~~~~~a~~~~~~m~~~~~~p---~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  166 (538)
                      |+.+.+.+.+++|++.-+.-..  ..|   -.......|..+...|+++.|-...-.|...    +..-|--.+..+...
T Consensus       363 i~Wll~~k~yeeAl~~~k~~~~--~~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn----~~~eWe~~V~~f~e~  436 (846)
T KOG2066|consen  363 IDWLLEKKKYEEALDAAKASIG--NEERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLGN----NAAEWELWVFKFAEL  436 (846)
T ss_pred             HHHHHHhhHHHHHHHHHHhccC--CccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhcc----hHHHHHHHHHHhccc
Confidence            5566777888888887765543  334   2345677788888888888888877777543    344444444455554


Q ss_pred             CCCCChhHHHHHhhcCCC-CCchhHHHHHHHHHhcCCHHHHHHHHccCC-------------C-------CChHHHHHHH
Q 044988          167 GGECGVGCARLLFDDMPA-RSVVSWNSLLKGYVKRGDIDGAWKIFDEMP-------------H-------RNVVSWTTMI  225 (538)
Q Consensus       167 g~~~~~~~a~~~~~~~~~-~~~~~~~~li~~~~~~g~~~~A~~~~~~m~-------------~-------~~~~~~~~li  225 (538)
                      ++   ......++=.-.. -+...|..++..+.. .+...-.++..+-+             +       .+...-..|+
T Consensus       437 ~~---l~~Ia~~lPt~~~rL~p~vYemvLve~L~-~~~~~F~e~i~~Wp~~Lys~l~iisa~~~q~~q~Se~~~L~e~La  512 (846)
T KOG2066|consen  437 DQ---LTDIAPYLPTGPPRLKPLVYEMVLVEFLA-SDVKGFLELIKEWPGHLYSVLTIISATEPQIKQNSESTALLEVLA  512 (846)
T ss_pred             cc---cchhhccCCCCCcccCchHHHHHHHHHHH-HHHHHHHHHHHhCChhhhhhhHHHhhcchHHHhhccchhHHHHHH
Confidence            44   3322222211111 155677777777665 33333222222221             0       1222334477


Q ss_pred             HHHHHcCCHHHHHHHHHHHHH
Q 044988          226 SGCAQNGKSRQALSLFNEMRR  246 (538)
Q Consensus       226 ~~~~~~~~~~~a~~~~~~m~~  246 (538)
                      .-|...+++.+|+.++-..++
T Consensus       513 ~LYl~d~~Y~~Al~~ylklk~  533 (846)
T KOG2066|consen  513 HLYLYDNKYEKALPIYLKLQD  533 (846)
T ss_pred             HHHHHccChHHHHHHHHhccC
Confidence            778888888888888876643

>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.76  E-value=11  Score=32.62  Aligned_cols=33  Identities=9%  Similarity=0.136  Sum_probs=21.3

Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR  378 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~  378 (538)
                      .+..+...-+..+++.+|..+|+++... .+..+
T Consensus       156 C~lKvA~yaa~leqY~~Ai~iyeqva~~-s~~n~  188 (288)
T KOG1586|consen  156 CLLKVAQYAAQLEQYSKAIDIYEQVARS-SLDNN  188 (288)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH-hccch
Confidence            3444444445567889999999988765 44333

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=85.70  E-value=22  Score=30.62  Aligned_cols=221  Identities=19%  Similarity=0.145  Sum_probs=149.5

Q ss_pred             cCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHH
Q 044988          231 NGKSRQALSLFNEMRRARVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIE  309 (538)
Q Consensus       231 ~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  309 (538)
                      .+....+...+.......... ....+......+...+.+..+...+......   ...+.....+......+...+++.
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~  112 (291)
T COG0457          36 LGELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALEL---ELLPNLAEALLNLGLLLEALGKYE  112 (291)
T ss_pred             HhhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhh---hhccchHHHHHHHHHHHHHHhhHH
Confidence            456666777777666543321 3567777777888888888888887777652   024555556667777788888888


Q ss_pred             HHHHHHHhcCCCCcch---HHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCC--CccHHHHHH
Q 044988          310 EAYGVFRKMQRRNTVS---WTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGI--KPRIEHYGC  384 (538)
Q Consensus       310 ~a~~~~~~m~~~~~~~---~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~--~p~~~~~~~  384 (538)
                      .+.+.+......+...   .......                   .+...|+++.|...+...... ..  ......+..
T Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~~  172 (291)
T COG0457         113 EALELLEKALALDPDPDLAEALLALG-------------------ALYELGDYEEALELYEKALEL-DPELNELAEALLA  172 (291)
T ss_pred             HHHHHHHHHHcCCCCcchHHHHHHHH-------------------HHHHcCCHHHHHHHHHHHHhc-CCCccchHHHHHH
Confidence            8888888776522211   1111110                   445556788888888887432 11  123444455


Q ss_pred             HHHHhhhcCChHHHHHHHHhCC-CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcC
Q 044988          385 MVDLFSRAGLMDEAFSLVQNMP-MKPN--DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAK  461 (538)
Q Consensus       385 l~~~~~~~g~~~~A~~~~~~~~-~~p~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g  461 (538)
                      ....+...++.+++...+.... ..++  ...+..+...+...++.+.|...+... ....|.....+. .+...+...|
T Consensus       173 ~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~~  250 (291)
T COG0457         173 LGALLEALGRYEEALELLEKALKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKA-LELDPDNAEALY-NLALLLLELG  250 (291)
T ss_pred             hhhHHHHhcCHHHHHHHHHHHHhhCcccchHHHHHhhHHHHHcccHHHHHHHHHHH-HhhCcccHHHHh-hHHHHHHHcC
Confidence            5555778899999999998874 3333  677778888889999999999999999 777787444345 5556666777


Q ss_pred             ChHHHHHHHHHHHhC
Q 044988          462 RWQDVAAVRQKMIKM  476 (538)
Q Consensus       462 ~~~~A~~~~~~m~~~  476 (538)
                      .++++...+.+....
T Consensus       251 ~~~~~~~~~~~~~~~  265 (291)
T COG0457         251 RYEEALEALEKALEL  265 (291)
T ss_pred             CHHHHHHHHHHHHHh
Confidence            899999988887764

>PF13762 MNE1: Mitochondrial splicing apparatus component

Probab=84.86  E-value=14  Score=29.55  Aligned_cols=88  Identities=14%  Similarity=0.170  Sum_probs=60.5

Q ss_pred             HHhCCCCCh--hHHHHHHHHHHccCChhHHHHHHhcCCC---------CCcchHHHHHHHHhcCCC-chHHHHHHHHhHh
Q 044988           44 IINGFSQKN--YILAKLLAFYVTSGYLINAHKVFEKTEN---------PSTAIWNQMIRGHARSET-PEKSVYLYKQMID  111 (538)
Q Consensus        44 ~~~~~~~~~--~~~~~l~~~~~~~g~~~~a~~~~~~~~~---------~~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~  111 (538)
                      .+.+..++.  ...+.+++-.+..+++.-...+++.+..         .+..+|++++.+.++... ---+..+|.-|++
T Consensus        29 ~~~~~~~~~k~~fiN~iL~hl~~~~nf~~~v~~L~~l~~l~~~~~~~~~~~ssf~~if~SlsnSsSaK~~~~~Lf~~Lk~  108 (145)
T PF13762_consen   29 QEENASQSTKTIFINCILNHLASYQNFSGVVSILEHLHFLNTDNIIGWLDNSSFHIIFKSLSNSSSAKLTSLTLFNFLKK  108 (145)
T ss_pred             hhcccChhHHHHHHHHHHHHHHHccchHHHHHHHHHHHHhhHHHHhhhcccchHHHHHHHHccChHHHHHHHHHHHHHHH
Confidence            344455544  3557777777777888888877776652         355678888888765554 3456667777777


Q ss_pred             CCCCCCcchHHHHHHHHHcc
Q 044988          112 KETEPDEYTYSFLLSVCARC  131 (538)
Q Consensus       112 ~~~~p~~~~~~~li~~~~~~  131 (538)
                      .+.++++.-|..+|.++.+.
T Consensus       109 ~~~~~t~~dy~~li~~~l~g  128 (145)
T PF13762_consen  109 NDIEFTPSDYSCLIKAALRG  128 (145)
T ss_pred             cCCCCCHHHHHHHHHHHHcC
Confidence            77788888888888877664

>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models

Probab=84.53  E-value=1.4  Score=23.12  Aligned_cols=20  Identities=10%  Similarity=0.039  Sum_probs=14.6

Q ss_pred             HHHHHHHhcCChHHHHHHHH
Q 044988          452 LVANVYAAAKRWQDVAAVRQ  471 (538)
Q Consensus       452 ~l~~~~~~~g~~~~A~~~~~  471 (538)
                      .++.++...|++++|..+++
T Consensus         6 ~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    6 ALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHcCCHHHHHHHHh
Confidence            66777777777777777664

The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=84.51  E-value=25  Score=30.25  Aligned_cols=204  Identities=17%  Similarity=0.114  Sum_probs=122.4

Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRA-RVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                      ...+......+...+++..+...+...... ........+..........++...+...+......     .+.+.....
T Consensus        59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~  133 (291)
T COG0457          59 AGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALELLEKALAL-----DPDPDLAEA  133 (291)
T ss_pred             hHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHHHHHHHHcC-----CCCcchHHH
Confidence            345555566666666666666666665542 22334444555555555666666666666666554     111112222


Q ss_pred             HHHH-HHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCC
Q 044988          297 ALIH-MYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGI  375 (538)
Q Consensus       297 ~l~~-~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  375 (538)
                      .... .+...|+++.|...+.+....+.. .....             ..+......+...++.+.+...+......   
T Consensus       134 ~~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~-------------~~~~~~~~~~~~~~~~~~a~~~~~~~~~~---  196 (291)
T COG0457         134 LLALGALYELGDYEEALELYEKALELDPE-LNELA-------------EALLALGALLEALGRYEEALELLEKALKL---  196 (291)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhcCCC-ccchH-------------HHHHHhhhHHHHhcCHHHHHHHHHHHHhh---
Confidence            2333 677788888888888776432211 00000             11111111144456788888888888754   


Q ss_pred             Ccc--HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCC
Q 044988          376 KPR--IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPE  444 (538)
Q Consensus       376 ~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~  444 (538)
                      .++  ...+..+...+...++++.|...+.... ..|+ ...+..+...+...+..+.+...+++. ....|.
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~  268 (291)
T COG0457         197 NPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKA-LELDPD  268 (291)
T ss_pred             CcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHHHHHHHHHH-HHhCcc
Confidence            333  6778888888888999999999998774 3444 445555555555777899999999998 666665

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=84.24  E-value=20  Score=28.74  Aligned_cols=98  Identities=8%  Similarity=0.036  Sum_probs=57.0

Q ss_pred             ccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCC-cchHHHHHHHHHhcCCccHHH
Q 044988          265 EIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRN-TVSWTSMITGFAKQGYAQEAL  343 (538)
Q Consensus       265 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~-~~~~~~li~~~~~~~~~~~a~  343 (538)
                      ..++++++..+++.+.-.     .|.....-..-...+...|++++|.++|+++.+.. ...|..-+.+++-...-+.  
T Consensus        22 ~~~d~~D~e~lLdALrvL-----rP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~~~~p~~kAL~A~CL~al~Dp--   94 (153)
T TIGR02561        22 RSADPYDAQAMLDALRVL-----RPNLKELDMFDGWLLIARGNYDEAARILRELLSSAGAPPYGKALLALCLNAKGDA--   94 (153)
T ss_pred             hcCCHHHHHHHHHHHHHh-----CCCccccchhHHHHHHHcCCHHHHHHHHHhhhccCCCchHHHHHHHHHHHhcCCh--
Confidence            467777777777776665     44444433344556778899999999999988754 3356555555554433332  


Q ss_pred             HHHHHHHHHhcccCcHHHHHHHHHHhh
Q 044988          344 LTFLGVLSACSHGGFVDEGRQFFECMN  370 (538)
Q Consensus       344 ~~~~~ll~~~~~~~~~~~a~~~~~~~~  370 (538)
                       .|..........+....+..+.+.+.
T Consensus        95 -~Wr~~A~~~le~~~~~~a~~Lv~al~  120 (153)
T TIGR02561        95 -EWHVHADEVLARDADADAVALVRALL  120 (153)
T ss_pred             -HHHHHHHHHHHhCCCHhHHHHHHHHh
Confidence             23333333334445555555555554

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=83.76  E-value=3.2  Score=24.44  Aligned_cols=28  Identities=18%  Similarity=0.326  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRR  246 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~  246 (538)
                      .+++.+...|...|++++|..++++...
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            4677777888888888888888877754

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=83.55  E-value=37  Score=31.32  Aligned_cols=112  Identities=13%  Similarity=0.032  Sum_probs=49.3

Q ss_pred             cCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCH--HHHHH--HHHHHHccCChHHH
Q 044988          200 RGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQ--VALVA--ALSACAEIGDLKLG  272 (538)
Q Consensus       200 ~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~--~~~~~--li~~~~~~~~~~~a  272 (538)
                      .|+..+|-..++++.+   .|..++.-.=.+|.-+|+...-...+++.... ..||.  .+|..  ..-++...|-+++|
T Consensus       116 ~g~~h~a~~~wdklL~d~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~-wn~dlp~~sYv~GmyaFgL~E~g~y~dA  194 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDDYPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPK-WNADLPCYSYVHGMYAFGLEECGIYDDA  194 (491)
T ss_pred             cccccHHHHHHHHHHHhCchhhhhhhhhhhHHHhccchhhhhhHHHHhccc-cCCCCcHHHHHHHHHHhhHHHhccchhH
Confidence            3444444444444432   23344444445555555555555555554432 12222  12222  12222345555555


Q ss_pred             HHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHh
Q 044988          273 KWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRK  317 (538)
Q Consensus       273 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  317 (538)
                      +..-+...+.     .+.+.-...++...+...|+..++.++..+
T Consensus       195 Ek~A~ralqi-----N~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~  234 (491)
T KOG2610|consen  195 EKQADRALQI-----NRFDCWASHAKAHVLEMNGRHKEGKEFMYK  234 (491)
T ss_pred             HHHHHhhccC-----CCcchHHHHHHHHHHHhcchhhhHHHHHHh
Confidence            5555555443     333333333444555555555555555443

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=83.26  E-value=3.4  Score=22.95  Aligned_cols=27  Identities=19%  Similarity=0.336  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRR  246 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~  246 (538)
                      .|..+...+...|++++|++.|++..+
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            455566667777777777777776655

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=83.14  E-value=2.3  Score=23.45  Aligned_cols=24  Identities=21%  Similarity=0.321  Sum_probs=13.0

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHh
Q 044988          452 LVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       452 ~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .++.++.+.|++++|.+.|+++.+
T Consensus         5 ~~a~~~~~~g~~~~A~~~~~~~~~   28 (33)
T PF13174_consen    5 RLARCYYKLGDYDEAIEYFQRLIK   28 (33)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHH
Confidence            344555555555555555555543

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=82.97  E-value=6.9  Score=28.76  Aligned_cols=58  Identities=10%  Similarity=0.074  Sum_probs=37.4

Q ss_pred             HHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHH
Q 044988          101 KSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNL  159 (538)
Q Consensus       101 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  159 (538)
                      +..+-++.+....+.|++....+.+++|.+.+++..|.++++-++..- .+....|..+
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~-~~~~~~Y~~~   85 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKC-GNKKEIYPYI   85 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT-TT-TTHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cChHHHHHHH
Confidence            455566666667778888888888888888888888888888877652 2222245444

9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=82.91  E-value=3.1  Score=24.49  Aligned_cols=24  Identities=21%  Similarity=0.194  Sum_probs=10.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHc
Q 044988          414 LGSLLLGCRIHNNAELASQVAQKL  437 (538)
Q Consensus       414 ~~~l~~~~~~~~~~~~A~~~~~~~  437 (538)
                      ++.+...|...|++++|..+++++
T Consensus         5 ~~~la~~~~~~g~~~~A~~~~~~a   28 (42)
T PF13374_consen    5 LNNLANAYRAQGRYEEALELLEEA   28 (42)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhcchhhHHHHHH
Confidence            344444444444444444444444

>PF11207 DUF2989: Protein of unknown function (DUF2989); InterPro: IPR021372 Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed

Probab=82.90  E-value=24  Score=29.93  Aligned_cols=82  Identities=15%  Similarity=0.054  Sum_probs=46.7

Q ss_pred             HHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCC
Q 044988          228 CAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGE  307 (538)
Q Consensus       228 ~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  307 (538)
                      +.+.|+ +.|.+.|-.+...+.--+......+..-| ...+.+++..++-...+.... +...++..+.+|+..|.+.|+
T Consensus       117 Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~aLAtyY-~krD~~Kt~~ll~~~L~l~~~-~~~~n~eil~sLas~~~~~~~  193 (203)
T PF11207_consen  117 WSRFGD-QEALRRFLQLEGTPELETAELQYALATYY-TKRDPEKTIQLLLRALELSNP-DDNFNPEILKSLASIYQKLKN  193 (203)
T ss_pred             hhccCc-HHHHHHHHHHcCCCCCCCHHHHHHHHHHH-HccCHHHHHHHHHHHHHhcCC-CCCCCHHHHHHHHHHHHHhcc
Confidence            344455 56666666666555443433333333333 356667777777666665322 224556666677777777777


Q ss_pred             HHHHH
Q 044988          308 IEEAY  312 (538)
Q Consensus       308 ~~~a~  312 (538)
                      ++.|-
T Consensus       194 ~e~AY  198 (203)
T PF11207_consen  194 YEQAY  198 (203)
T ss_pred             hhhhh
Confidence            76653

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=82.75  E-value=51  Score=32.39  Aligned_cols=60  Identities=15%  Similarity=0.062  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      ...+++..+..+..+.-+..+-.+|..-|  -+...|..++.+|... ..+.-..+|+++.+.
T Consensus        68 ~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~  127 (711)
T COG1747          68 CLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEY  127 (711)
T ss_pred             HHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHh
Confidence            34444555555555555555555555522  3444455555555544 334444455555554

>KOG0890 consensus Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms; Chromatin structure and dynamics; Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=82.68  E-value=1.1e+02  Score=36.37  Aligned_cols=119  Identities=12%  Similarity=0.016  Sum_probs=64.2

Q ss_pred             HHHHHHhccCChHHHHHHHHHHHHhCCC--CChhHHHHHHHHHHccCChhHHHHHHhc-CCCCCcchHHHHHHHHhcCCC
Q 044988           22 QIFSLLQIRNTTKTLFQIHSQIIINGFS--QKNYILAKLLAFYVTSGYLINAHKVFEK-TENPSTAIWNQMIRGHARSET   98 (538)
Q Consensus        22 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~a~~~~~~-~~~~~~~~~~~li~~~~~~~~   98 (538)
                      ++..+--+++.+.+|...+++-.....+  .....+..+...|+.-+++|....+... ...|+  .++ -|-.....|+
T Consensus      1388 tLa~aSfrc~~y~RalmylEs~~~~ek~~~~~e~l~fllq~lY~~i~dpDgV~Gv~~~r~a~~s--l~~-qil~~e~~g~ 1464 (2382)
T KOG0890|consen 1388 TLARASFRCKAYARALMYLESHRSTEKEKETEEALYFLLQNLYGSIHDPDGVEGVSARRFADPS--LYQ-QILEHEASGN 1464 (2382)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHhcCCcchhhhHHHHhhcCcc--HHH-HHHHHHhhcc
Confidence            3444555566666666666653110000  1122333344477777777777666652 33332  222 2333456777


Q ss_pred             chHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHH
Q 044988           99 PEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRV  144 (538)
Q Consensus        99 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~  144 (538)
                      +..|...|+.+.+.+ ++...+++-++......|.++...-..+..
T Consensus      1465 ~~da~~Cye~~~q~~-p~~~~~~~g~l~sml~~~~l~t~i~~~dg~ 1509 (2382)
T KOG0890|consen 1465 WADAAACYERLIQKD-PDKEKHHSGVLKSMLAIQHLSTEILHLDGL 1509 (2382)
T ss_pred             HHHHHHHHHHhhcCC-CccccchhhHHHhhhcccchhHHHhhhcch
Confidence            777888888777654 333556666666666666666655544433

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=82.59  E-value=4.3  Score=36.60  Aligned_cols=98  Identities=20%  Similarity=0.166  Sum_probs=63.9

Q ss_pred             CCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC-CCc-----chHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHH
Q 044988          287 REPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR-RNT-----VSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVD  360 (538)
Q Consensus       287 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-~~~-----~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~  360 (538)
                      |.+....+...++..-....+++.+...+-++.. |+.     .+..+++..+.+-                     +++
T Consensus        59 g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irlllky---------------------~pq  117 (418)
T KOG4570|consen   59 GLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLLLKY---------------------DPQ  117 (418)
T ss_pred             CCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHHHcc---------------------ChH
Confidence            4444444445566666666778888887777664 221     1222223322222                     455


Q ss_pred             HHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          361 EGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       361 ~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      +++.++..=++ ||+-||..+++.+|+.+.+.+++.+|..+...|.
T Consensus       118 ~~i~~l~npIq-YGiF~dqf~~c~l~D~flk~~n~~~aa~vvt~~~  162 (418)
T KOG4570|consen  118 KAIYTLVNPIQ-YGIFPDQFTFCLLMDSFLKKENYKDAASVVTEVM  162 (418)
T ss_pred             HHHHHHhCcch-hccccchhhHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            66666665554 4999999999999999999999999988887664

>PRK09687 putative lyase; Provisional

Probab=82.46  E-value=39  Score=30.86  Aligned_cols=228  Identities=11%  Similarity=-0.032  Sum_probs=110.5

Q ss_pred             CCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCH----HHHHHHHHHHHHCCCCCCHHHHHH
Q 044988          183 PARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKS----RQALSLFNEMRRARVGLDQVALVA  258 (538)
Q Consensus       183 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~----~~a~~~~~~m~~~g~~p~~~~~~~  258 (538)
                      ..+|....-..+.++...|..+....+..-+..+|...-...+.++.+.|+.    .++...+..+...  .|+...-..
T Consensus        33 ~d~d~~vR~~A~~aL~~~~~~~~~~~l~~ll~~~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~~VR~~  110 (280)
T PRK09687         33 DDHNSLKRISSIRVLQLRGGQDVFRLAIELCSSKNPIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSACVRAS  110 (280)
T ss_pred             hCCCHHHHHHHHHHHHhcCcchHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCHHHHHH
Confidence            3445555555555565555543333333333345555555556666666653    4566666655332  345444445


Q ss_pred             HHHHHHccCChHH--HHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhc
Q 044988          259 ALSACAEIGDLKL--GKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQ  336 (538)
Q Consensus       259 li~~~~~~~~~~~--a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~  336 (538)
                      .+.++...+....  .......+...    -...+..+-...+.++.+.|+.+....+..-+..+|...-...+.++.+.
T Consensus       111 A~~aLG~~~~~~~~~~~~a~~~l~~~----~~D~~~~VR~~a~~aLg~~~~~~ai~~L~~~L~d~~~~VR~~A~~aLg~~  186 (280)
T PRK09687        111 AINATGHRCKKNPLYSPKIVEQSQIT----AFDKSTNVRFAVAFALSVINDEAAIPLLINLLKDPNGDVRNWAAFALNSN  186 (280)
T ss_pred             HHHHHhcccccccccchHHHHHHHHH----hhCCCHHHHHHHHHHHhccCCHHHHHHHHHHhcCCCHHHHHHHHHHHhcC
Confidence            5555544332110  11122222221    11223344446667777777654444444444445444333333333332


Q ss_pred             CCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHH
Q 044988          337 GYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGS  416 (538)
Q Consensus       337 ~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~  416 (538)
                      +.                   +...+...+..+..    .+|..+....+.++.+.|+. .|...+-+....++  ....
T Consensus       187 ~~-------------------~~~~~~~~L~~~L~----D~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~~~--~~~~  240 (280)
T PRK09687        187 KY-------------------DNPDIREAFVAMLQ----DKNEEIRIEAIIGLALRKDK-RVLSVLIKELKKGT--VGDL  240 (280)
T ss_pred             CC-------------------CCHHHHHHHHHHhc----CCChHHHHHHHHHHHccCCh-hHHHHHHHHHcCCc--hHHH
Confidence            21                   12233344444432    35666666777777777774 34444333322333  2345


Q ss_pred             HHHHHHhcCCHHHHHHHHHHchhccCCC
Q 044988          417 LLLGCRIHNNAELASQVAQKLVAEIDPE  444 (538)
Q Consensus       417 l~~~~~~~~~~~~A~~~~~~~~~~~~p~  444 (538)
                      .+.++...|+. +|...+.++ .+..|+
T Consensus       241 a~~ALg~ig~~-~a~p~L~~l-~~~~~d  266 (280)
T PRK09687        241 IIEAAGELGDK-TLLPVLDTL-LYKFDD  266 (280)
T ss_pred             HHHHHHhcCCH-hHHHHHHHH-HhhCCC
Confidence            66667777774 577777777 555553

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=82.37  E-value=2.6  Score=25.63  Aligned_cols=26  Identities=15%  Similarity=0.258  Sum_probs=22.5

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHhCC
Q 044988          452 LVANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       452 ~l~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                      .|+.+|...|+.+.|.++++++...|
T Consensus         4 dLA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         4 DLARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHcC
Confidence            57889999999999999999988543

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

Probab=82.17  E-value=19  Score=32.26  Aligned_cols=132  Identities=14%  Similarity=0.140  Sum_probs=74.0

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHH-------HHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          224 MISGCAQNGKSRQALSLFNEMRRARVGLDQVA-------LVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       224 li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~-------~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                      +.+...+.+++++|+..|.+....|+..|..+       ...+...|.+.|+.....+......+.+..-..|.......
T Consensus         9 ~a~~~v~~~~~~~ai~~yk~iL~kg~s~dek~~nEqE~tvlel~~lyv~~g~~~~l~~~i~~sre~m~~ftk~k~~Kiir   88 (421)
T COG5159           9 LANNAVKSNDIEKAIGEYKRILGKGVSKDEKTLNEQEATVLELFKLYVSKGDYCSLGDTITSSREAMEDFTKPKITKIIR   88 (421)
T ss_pred             HHHHhhhhhhHHHHHHHHHHHhcCCCChhhhhhhHHHHHHHHHHHHHHhcCCcchHHHHHHhhHHHHHHhcchhHHHHHH
Confidence            34455667788888888888888877766554       44566667777776554444333322211112333344444


Q ss_pred             HHHHHHHhC-CCHHHHHHHHHhcCC---C------CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcc
Q 044988          297 ALIHMYASC-GEIEEAYGVFRKMQR---R------NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSH  355 (538)
Q Consensus       297 ~l~~~~~~~-g~~~~a~~~~~~m~~---~------~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~  355 (538)
                      +|+..+... ..++....+.....+   +      ....-..++..+.+.|.+.+|+...+.+++-+.+
T Consensus        89 tLiekf~~~~dsl~dqi~v~~~~iewA~rEkr~fLr~~Le~Kli~l~y~~~~YsdalalIn~ll~ElKk  157 (421)
T COG5159          89 TLIEKFPYSSDSLEDQIKVLTALIEWADREKRKFLRLELECKLIYLLYKTGKYSDALALINPLLHELKK  157 (421)
T ss_pred             HHHHhcCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHh
Confidence            555554432 335555555544432   1      0112234677888888888888666666554443

>PF04190 DUF410: Protein of unknown function (DUF410) ; InterPro: IPR007317 This is a family of conserved eukaryotic proteins with undetermined function

Probab=81.92  E-value=39  Score=30.46  Aligned_cols=127  Identities=13%  Similarity=0.095  Sum_probs=65.7

Q ss_pred             HHCCCCCCHHHHHHHHHHHHccCChH-HHHHHHHHHHHhccCC-CCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCC
Q 044988          245 RRARVGLDQVALVAALSACAEIGDLK-LGKWIHSYVEENFSVG-REPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRN  322 (538)
Q Consensus       245 ~~~g~~p~~~~~~~li~~~~~~~~~~-~a~~~~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~  322 (538)
                      .+.+.++|......++..+...+.-+ .-..+.+.+.+.-..+ ...-++.....+...|.+.|++.+|+..|-.-..++
T Consensus        41 ~~~~~~~~~~~~~rl~~l~~~~~~~~p~r~~fi~~ai~WS~~~~~~~Gdp~LH~~~a~~~~~e~~~~~A~~Hfl~~~~~~  120 (260)
T PF04190_consen   41 EKSEDPVDEESIARLIELISLFPPEEPERKKFIKAAIKWSKFGSYKFGDPELHHLLAEKLWKEGNYYEAERHFLLGTDPS  120 (260)
T ss_dssp             HHTT---SHHHHHHHHHHHHHS-TT-TTHHHHHHHHHHHHHTSS-TT--HHHHHHHHHHHHHTT-HHHHHHHHHTS-HHH
T ss_pred             HHcCCCCCHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHHhhccHHHHHHHHHhcCChh
Confidence            33455666555555555544332211 1233333333332111 233456777889999999999999999887765555


Q ss_pred             cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhh
Q 044988          323 TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQ  371 (538)
Q Consensus       323 ~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  371 (538)
                      ...+..++.-....|...++-......+--|.-.+++..|...+....+
T Consensus       121 ~~~~~~ll~~~~~~~~~~e~dlfi~RaVL~yL~l~n~~~A~~~~~~f~~  169 (260)
T PF04190_consen  121 AFAYVMLLEEWSTKGYPSEADLFIARAVLQYLCLGNLRDANELFDTFTS  169 (260)
T ss_dssp             HHHHHHHHHHHHHHTSS--HHHHHHHHHHHHHHTTBHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            5555445655565666665544444444445555666666666655544

; PDB: 3LKU_E 2WPV_G.

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=81.43  E-value=2  Score=23.70  Aligned_cols=23  Identities=17%  Similarity=-0.045  Sum_probs=19.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHc
Q 044988          415 GSLLLGCRIHNNAELASQVAQKL  437 (538)
Q Consensus       415 ~~l~~~~~~~~~~~~A~~~~~~~  437 (538)
                      -.+..++.+.|++++|.+.|+++
T Consensus         4 ~~~a~~~~~~g~~~~A~~~~~~~   26 (33)
T PF13174_consen    4 YRLARCYYKLGDYDEAIEYFQRL   26 (33)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHH
Confidence            34667788899999999999986

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=81.38  E-value=3.3  Score=25.17  Aligned_cols=25  Identities=16%  Similarity=0.271  Sum_probs=18.3

Q ss_pred             HHHHHHccCCcHHHHHHHHHHHHhC
Q 044988          124 LLSVCARCGLFREGEQVHGRVLASG  148 (538)
Q Consensus       124 li~~~~~~~~~~~a~~~~~~~~~~~  148 (538)
                      +..+|...|+.+.|..+++++...|
T Consensus         5 LA~ayie~Gd~e~Ar~lL~evl~~~   29 (44)
T TIGR03504         5 LARAYIEMGDLEGARELLEEVIEEG   29 (44)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHcC
Confidence            5567777788888888877777544

This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	538
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	2e-07
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	8e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 52.9 bits (125), Expect = 2e-07
 Identities = 44/400 (11%), Positives = 106/400 (26%), Gaps = 28/400 (7%)

Query: 104 YLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLY 163
            L          P E   + LL            +   G+   +                
Sbjct: 78  CLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCC 137

Query: 164 LMSGGECGVGCARLLFDDMPAR-------SVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR 216
           L++     +  A  L      +       ++  +N+++ G+ ++G       +   +   
Sbjct: 138 LLTDQ---LPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDA 194

Query: 217 ----NVVSWTTMISGCAQNGKSRQALS-LFNEMRRARVGLDQVALVAALSACAEIGDLKL 271
               +++S+   +    +  +    +     +M +  + L  +     LS         +
Sbjct: 195 GLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRAT---V 251

Query: 272 GKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEA--------YGVFRKMQRRNT 323
            K +H          + P  V+ +  L  +YA  G +                + Q    
Sbjct: 252 LKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFEKQLHME 311

Query: 324 VSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW-GIKPRIEHY 382
           ++    +    K     + +      L            R   E  N+    +       
Sbjct: 312 LASRVCVVSVEKPTLPSKEVKHARKTLKTLRDQWEKALCRALRETKNRLEREVYEGRFSL 371

Query: 383 GCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEID 442
              + L     ++     ++Q +P +       +  L  R  +   +  Q     V  + 
Sbjct: 372 YPFLCLLDEREVVRMLLQVLQALPAQGESFTTLARELSARTFSRHVVQRQRVSGQVQAL- 430

Query: 443 PEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPP 482
                 YL L+A+     +                +R+ P
Sbjct: 431 QNHYRKYLCLLASDAEVPEPCLPRQYWEALGAPEALREQP 470

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 47.9 bits (112), Expect = 8e-06
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 7/82 (8%)

Query: 62  YVTSGYLINAHKVFEKTEN-------PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKET 114
            + +  L  AH +              +  ++N ++ G AR    ++ VY+   + D   
Sbjct: 137 CLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGL 196

Query: 115 EPDEYTYSFLLSVCARCGLFRE 136
            PD  +Y+  L    R      
Sbjct: 197 TPDLLSYAAALQCMGRQDQDAG 218

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 2e-04
 Identities = 71/544 (13%), Positives = 137/544 (25%), Gaps = 171/544 (31%)

Query: 110 IDKETEPDEYTYSFLLSVCARCGLFREG----------EQVHGRVLASGYCSNVFIRTNL 159
           +D ET   +Y Y  +LSV      F +           + +   +L+     ++ +  + 
Sbjct: 7   MDFETGEHQYQYKDILSV------FEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDA 60

Query: 160 MNLYLMSGGECGVGCARLLFD---DMPARSVVSW--NSLLKGYVKRGDIDGAWKIFDEMP 214
           ++                LF          V  +    L   Y     +    K     P
Sbjct: 61  VSG------------TLRLFWTLLSKQEEMVQKFVEEVLRINY---KFLMSPIKTEQRQP 105

Query: 215 HRNVVSWTTMISGCAQNGK-------SRQALSLFNEMRRARVGLDQ---VAL-------- 256
                 +         + +       SR  L  + ++R+A + L     V +        
Sbjct: 106 SMMTRMYIEQRDRLYNDNQVFAKYNVSR--LQPYLKLRQALLELRPAKNVLIDGVLGSGK 163

Query: 257 -VAALSACAEIGDLKLGK-------WIHSYVEENFSVGR----EPVLVSLNNALIHM--- 301
              AL  C      K+         W+        ++      E VL  L   L  +   
Sbjct: 164 TWVALDVCL---SYKVQCKMDFKIFWL--------NLKNCNSPETVLEMLQKLLYQIDPN 212

Query: 302 YASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDE 361
           + S  +            +    S  + +    K    +  LL    VL    +    + 
Sbjct: 213 WTSRSDHSSNI-------KLRIHSIQAELRRLLKSKPYENCLL----VLLNVQNAKAWN- 260

Query: 362 GRQF-FEC--------------MNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP 406
              F   C              ++        ++H        +   +         +  
Sbjct: 261 --AFNLSCKILLTTRFKQVTDFLSAATTTHISLDH---HSMTLTPDEVK-SLLLKYLDCR 314

Query: 407 MK--PNDAVLGS-LLLG----------CRI----HNNAELASQVAQKLVAEIDP-EQAAG 448
            +  P + +  +   L                  H N +  + + +  +  ++P E    
Sbjct: 315 PQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKM 374

Query: 449 YLALV---ANVYAAAKR----W-----QDVAAVRQKMIKMG-VRKPPGQSWVQINGV--- 492
           +  L     + +         W      DV  V  K+ K   V K P +S + I  +   
Sbjct: 375 FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLE 434

Query: 493 ----------LH----DFVAGDSTYKQASL--------IYKTLGEITMQAMQEGYKPDIS 530
                     LH    D      T+    L         Y  +G                
Sbjct: 435 LKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFR 494

Query: 531 ELFL 534
            +FL
Sbjct: 495 MVFL 498

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.9 bits (100), Expect = 3e-04
 Identities = 43/310 (13%), Positives = 85/310 (27%), Gaps = 100/310 (32%)

Query: 283 FSVGREPVLVSLNNAL----------IH-MYASCG------EIEEAYGVFRKMQRRNTVS 325
           ++V R    + L  AL          I  +    G      ++  +Y V  KM     + 
Sbjct: 129 YNVSRLQPYLKLRQALLELRPAKNVLIDGV-LGSGKTWVALDVCLSYKVQCKMD--FKIF 185

Query: 326 WTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCM 385
           W ++     K   + E +L  L  L                  ++ NW    R +H    
Sbjct: 186 WLNL-----KNCNSPETVLEMLQKL--LYQ-------------IDPNW--TSRSDH---S 220

Query: 386 VDLFSRAGLMDEAFSLVQNMPMKPN-----DAV-----LGSLLLGCRI---HNNAELASQ 432
            ++  R   +      +       N       V       +  L C+I       ++   
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDF 280

Query: 433 VAQKLVAEI---------DPEQAAGYLALVANVYAAAKRWQDVAAVRQK-------MIKM 476
           ++      I          P++    L    +      R QD+             +I  
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC-----RPQDLPREVLTTNPRRLSIIAE 335

Query: 477 GVRKPPG--QSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQEGYK-----PD- 528
            +R       +W  +N             K  ++I  +L  +     ++ +      P  
Sbjct: 336 SIRDGLATWDNWKHVN-----------CDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS 384

Query: 529 --ISELFLGI 536
             I  + L +
Sbjct: 385 AHIPTILLSL 394

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	538
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.96
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.96
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.95
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.95
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.92
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.91
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.9
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.89
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.86
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.83
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.83
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.82
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.8
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.8
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.79
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.79
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.77
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.77
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.76
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.74
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.74
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.73
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.73
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.73
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.73
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.73
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.72
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.72
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.7
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.7
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.69
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.67
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.65
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.63
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.62
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.58
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.56
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.55
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.53
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.52
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.51
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.5
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.48
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.48
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.48
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.48
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.47
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.47
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.46
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.45
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.45
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.45
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.45
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.44
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.44
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.43
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.42
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.41
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.4
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.38
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.38
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.36
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.36
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.34
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.33
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.33
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.32
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.29
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.29
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.29
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.28
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.27
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.27
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.24
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.23
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.2
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.19
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.19
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.19
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.17
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.06
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.06
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.05
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.05
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.01
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	98.97
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.96
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.94
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.91
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.91
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.89
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.87
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.83
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.82
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.82
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.79
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.78
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.78
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.76
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.76
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.74
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.74
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.73
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.72
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.7
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.7
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.7
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.67
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.67
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.65
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.64
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.63
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.62
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.61
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.6
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.59
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.56
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.56
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.56
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.55
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.55
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.54
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.53
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.51
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.51
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.49
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.49
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.48
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.48
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.47
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.46
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.45
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.43
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.42
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.41
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.38
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.38
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.37
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.36
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.34
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.33
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.33
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.31
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.3
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.3
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.29
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.28
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.26
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.26
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.23
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.23
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.21
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.2
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.19
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.18
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.18
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.17
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.16
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.16
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.13
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.11
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.11
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.1
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.09
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.08
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.08
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.06
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.05
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.03
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.03
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.02
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.0
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.99
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	97.98
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.97
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	97.96
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	97.94
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	97.93
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.93
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.93
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.92
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	97.9
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.86
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.85
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.83
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.83
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.77
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	97.74
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.73
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.68
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.65
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.61
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	97.59
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.57
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.56
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.53
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.52
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.5
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.48
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	97.37
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.36
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.36
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.16
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.12
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	97.01
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.92
2kat_A	115	Uncharacterized protein; NESG, structure, structur	96.89
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	96.86
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.84
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.74
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.72
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.69
1klx_A	138	Cysteine rich protein B; structural genomics, heli	96.65
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	96.63
1pc2_A	152	Mitochondria fission protein; unknown function; NM	96.59
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	96.59
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.58
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.57
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.53
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.29
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.15
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	95.92
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	95.65
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	95.41
1pc2_A	152	Mitochondria fission protein; unknown function; NM	95.4
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	95.23
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	95.12
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.11
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	95.03
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	94.99
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	94.97
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	94.85
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	94.47
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	94.38
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	94.37
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	94.1
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	94.05
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	93.34
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	92.4
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	92.35
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	91.62
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	90.8
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	90.4
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	90.37
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	90.2
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	89.85
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	88.58
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	88.48
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	88.33
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	88.01
3ltm_A	211	Alpha-REP4; protein engineering, heat-like repeat,	87.46
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	86.92
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	85.25
3ltj_A	201	Alpharep-4; protein engineering, heat-like repeat,	85.25
3ltm_A	211	Alpha-REP4; protein engineering, heat-like repeat,	85.13
3ltj_A	201	Alpharep-4; protein engineering, heat-like repeat,	84.98
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	84.46
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	84.14
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	83.4
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	82.7

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=3.6e-38  Score=322.83  Aligned_cols=446  Identities=12%  Similarity=0.025  Sum_probs=303.3

Q ss_pred             CccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC--CCCcchHHHHHHH
Q 044988           15 SKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE--NPSTAIWNQMIRG   92 (538)
Q Consensus        15 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~   92 (538)
                      ++...+..++..+.+.|+++.|..+++.+.+.  .|+..++..++.+|.+.|++++|+.+|+.+.  +++..+|+.++.+
T Consensus        82 ~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~  159 (597)
T 2xpi_A           82 SREDYLRLWRHDALMQQQYKCAAFVGEKVLDI--TGNPNDAFWLAQVYCCTGDYARAKCLLTKEDLYNRSSACRYLAAFC  159 (597)
T ss_dssp             CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGGGTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHccCchHHHHHHHHHHhh--CCCchHHHHHHHHHHHcCcHHHHHHHHHHHhccccchhHHHHHHHH
Confidence            45667888999999999999999999999865  4577888889999999999999999999884  6788899999999


Q ss_pred             HhcCCCchHHHHHHHHhHh-C--------------CCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHh
Q 044988           93 HARSETPEKSVYLYKQMID-K--------------ETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRT  157 (538)
Q Consensus        93 ~~~~~~~~~a~~~~~~m~~-~--------------~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  157 (538)
                      |.+.|++++|+++|+++.. .              +.+++..+|+.++.+|.+.|++++|.++|+++.+.+ +.+...+.
T Consensus       160 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-p~~~~~~~  238 (597)
T 2xpi_A          160 LVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVD-AKCYEAFD  238 (597)
T ss_dssp             HHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-chhhHHHH
Confidence            9999999999999985322 1              223357789999999999999999999999998875 33344444


Q ss_pred             HHHHHHHhcCCCCChhHHH--HH-hhcCCCC----CchhHHHHHHHHHhcCCHHHHHHHHccCCC--CChHHHHHHHHHH
Q 044988          158 NLMNLYLMSGGECGVGCAR--LL-FDDMPAR----SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--RNVVSWTTMISGC  228 (538)
Q Consensus       158 ~l~~~~~~~g~~~~~~~a~--~~-~~~~~~~----~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~  228 (538)
                      .+...+...+.   .+.+.  .+ +..+...    ....|+.++..|.+.|++++|.++|+++.+  ++..+|+.++..|
T Consensus       239 ~l~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~  315 (597)
T 2xpi_A          239 QLVSNHLLTAD---EEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKADTL  315 (597)
T ss_dssp             HHHHTTCSCHH---HHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHHHH
T ss_pred             HHHHhhcccch---hHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHHHH
Confidence            44332221111   11000  00 1111110    112233334444445555555555555444  4444555555555


Q ss_pred             HHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCH
Q 044988          229 AQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEI  308 (538)
Q Consensus       229 ~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  308 (538)
                      .+.|++++|..+|+++.+.+ +.+..++..++.++.+.|++++|..+++.+.+.     .|.+..+++.++..|.+.|++
T Consensus       316 ~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~  389 (597)
T 2xpi_A          316 FVRSRFIDVLAITTKILEID-PYNLDVYPLHLASLHESGEKNKLYLISNDLVDR-----HPEKAVTWLAVGIYYLCVNKI  389 (597)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHH-----CTTSHHHHHHHHHHHHHTTCH
T ss_pred             HHhcCHHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhh-----CcccHHHHHHHHHHHHHhccH
Confidence            55555555555555554432 123344444555555555555555555554443     344444444455555555555


Q ss_pred             HHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHH--------------HHHHHHHHHhcccCcHHHHHHHHHHhhh
Q 044988          309 EEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEAL--------------LTFLGVLSACSHGGFVDEGRQFFECMNQ  371 (538)
Q Consensus       309 ~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~--------------~~~~~ll~~~~~~~~~~~a~~~~~~~~~  371 (538)
                      ++|.++|+++.+   .+..+|+.++.+|.+.|++++|+              .++..++.+|.+.|++++|.++|+++.+
T Consensus       390 ~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  469 (597)
T 2xpi_A          390 SEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYA  469 (597)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            555555554432   23444555555555555555544              3444555666666788999999999987


Q ss_pred             hcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-------CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHchhccC
Q 044988          372 NWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-------MKPN--DAVLGSLLLGCRIHNNAELASQVAQKLVAEID  442 (538)
Q Consensus       372 ~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-------~~p~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~  442 (538)
                      ..  +.+..+|+.++.+|.+.|++++|.++|+++.       ..|+  ..+|..++.+|.+.|++++|.+.++++ .+..
T Consensus       470 ~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~-~~~~  546 (597)
T 2xpi_A          470 LF--QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQG-LLLS  546 (597)
T ss_dssp             HC--CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHS
T ss_pred             hC--CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHH-HHhC
Confidence            62  3468899999999999999999999999883       3677  789999999999999999999999999 8888


Q ss_pred             CCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          443 PEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       443 p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      |++..+|. .++.+|.+.|++++|.+.++++.+.
T Consensus       547 p~~~~~~~-~l~~~~~~~g~~~~A~~~~~~~l~~  579 (597)
T 2xpi_A          547 TNDANVHT-AIALVYLHKKIPGLAITHLHESLAI  579 (597)
T ss_dssp             SCCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCChHHHH-HHHHHHHHhCCHHHHHHHHHHHHhc
Confidence            99998888 9999999999999999999999874

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=6.1e-35  Score=298.86  Aligned_cols=428  Identities=9%  Similarity=-0.011  Sum_probs=299.8

Q ss_pred             ccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCC--------------
Q 044988           16 KALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENP--------------   81 (538)
Q Consensus        16 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~--------------   81 (538)
                      +..++..++.+|...|+++.|..+++.+...  ++++.+++.++.+|.+.|++++|+++|+++.+.              
T Consensus       116 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~  193 (597)
T 2xpi_A          116 NPNDAFWLAQVYCCTGDYARAKCLLTKEDLY--NRSSACRYLAAFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQD  193 (597)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHTCGG--GTCHHHHHHHHHHHHHTTCHHHHHHHHCSSCTTC----------CCC
T ss_pred             CchHHHHHHHHHHHcCcHHHHHHHHHHHhcc--ccchhHHHHHHHHHHHHhhHHHHHHHHhccCCccccccccccccccc
Confidence            4467888999999999999999999987644  678899999999999999999999999965543              


Q ss_pred             -----CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCC-cchHHHHHHHHHccCCcHHH--HHH-HHHHHHhCCCCc
Q 044988           82 -----STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPD-EYTYSFLLSVCARCGLFREG--EQV-HGRVLASGYCSN  152 (538)
Q Consensus        82 -----~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a--~~~-~~~~~~~~~~~~  152 (538)
                           +..+|+.++.+|.+.|++++|+++|++|.+.+  |+ ...+..+...+...+..+.+  ..+ +..+...+..+.
T Consensus       194 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~  271 (597)
T 2xpi_A          194 GGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVD--AKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFL  271 (597)
T ss_dssp             SSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHH
T ss_pred             cccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--chhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHH
Confidence                 37789999999999999999999999998854  44 33444444333222211111  111 333333333333


Q ss_pred             hhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC--CCchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHH
Q 044988          153 VFIRTNLMNLYLMSGGECGVGCARLLFDDMPA--RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISG  227 (538)
Q Consensus       153 ~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~--~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~  227 (538)
                      ..+|+.++..|.+.|+   +++|.++|+++.+  ++..+|+.++.+|.+.|++++|.++|+++.+   .+..+|+.++.+
T Consensus       272 ~~~~~~~~~~~~~~g~---~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~  348 (597)
T 2xpi_A          272 RSLYMLKLNKTSHEDE---LRRAEDYLSSINGLEKSSDLLLCKADTLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLAS  348 (597)
T ss_dssp             HHHHHTTSCTTTTHHH---HHHHHHHHHTSTTGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHH
T ss_pred             HHHHHHHHHHHcCcch---HHHHHHHHHHhhcCCchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHH
Confidence            4445555556666666   6666666666655  4556666666666666666666666666542   244556666666


Q ss_pred             HHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCC
Q 044988          228 CAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGE  307 (538)
Q Consensus       228 ~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  307 (538)
                      |.+.|++++|..+++++.+. .+.+..++..++..|.+.|++++|..+|+.+.+.     .|.+..+|+.++.+|.+.|+
T Consensus       349 ~~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~  422 (597)
T 2xpi_A          349 LHESGEKNKLYLISNDLVDR-HPEKAVTWLAVGIYYLCVNKISEARRYFSKSSTM-----DPQFGPAWIGFAHSFAIEGE  422 (597)
T ss_dssp             HHHHTCHHHHHHHHHHHHHH-CTTSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHTC
T ss_pred             HHHhCCHHHHHHHHHHHHhh-CcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHcCC
Confidence            66666666666666666543 2334555666666666666666666666666554     44455556666666666666


Q ss_pred             HHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHH--------------HHHHHHHHHhcccCcHHHHHHHHHHhh
Q 044988          308 IEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEAL--------------LTFLGVLSACSHGGFVDEGRQFFECMN  370 (538)
Q Consensus       308 ~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~--------------~~~~~ll~~~~~~~~~~~a~~~~~~~~  370 (538)
                      +++|.++|+++.+   ++..+|..++.+|.+.|++++|.              .+|..++..|.+.|++++|.++|+++.
T Consensus       423 ~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  502 (597)
T 2xpi_A          423 HDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALFQYDPLLLNELGVVAFNKSDMQTAINHFQNAL  502 (597)
T ss_dssp             HHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            6666666665542   34556666666666666666665              345556666667778888888888887


Q ss_pred             hhc---CCCcc--HHHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCC
Q 044988          371 QNW---GIKPR--IEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDP  443 (538)
Q Consensus       371 ~~~---~~~p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p  443 (538)
                      +..   +..|+  ..+|..++.+|.+.|++++|.+.++++. . +.+..+|..+..+|.+.|++++|.+.++++ .++.|
T Consensus       503 ~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~-l~~~p  581 (597)
T 2xpi_A          503 LLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTNDANVHTAIALVYLHKKIPGLAITHLHES-LAISP  581 (597)
T ss_dssp             HHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCT
T ss_pred             HhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHH-HhcCC
Confidence            642   45677  7899999999999999999999999874 3 347899999999999999999999999999 99999


Q ss_pred             CCcccHHHHHHHHHH
Q 044988          444 EQAAGYLALVANVYA  458 (538)
Q Consensus       444 ~~~~~~~~~l~~~~~  458 (538)
                      +++..+. .++.+|.
T Consensus       582 ~~~~~~~-~l~~~~~  595 (597)
T 2xpi_A          582 NEIMASD-LLKRALE  595 (597)
T ss_dssp             TCHHHHH-HHHHTTC
T ss_pred             CChHHHH-HHHHHHh
Confidence            9998787 8877664

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.96  E-value=1.7e-26  Score=222.81  Aligned_cols=369  Identities=12%  Similarity=0.059  Sum_probs=245.7

Q ss_pred             HHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHH
Q 044988           26 LLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKS  102 (538)
Q Consensus        26 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a  102 (538)
                      .+.+.|+++.|...+..+.+..+ .+...+..+...+...|++++|...++...   +.+...|..+..++.+.|++++|
T Consensus         8 ~~~~~g~~~~A~~~~~~~~~~~p-~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~p~~~~~~~~lg~~~~~~g~~~~A   86 (388)
T 1w3b_A            8 REYQAGDFEAAERHCMQLWRQEP-DNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQEA   86 (388)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHHH
Confidence            34445555555555555544421 123344444444455555555555544332   22334455555555555555555


Q ss_pred             HHHHHHhHhCCCCCC-cchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhc
Q 044988          103 VYLYKQMIDKETEPD-EYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDD  181 (538)
Q Consensus       103 ~~~~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~  181 (538)
                      +..|+++.+.  .|+ ..+|..+..++.+.|++++|...++++.+.. +.                              
T Consensus        87 ~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~------------------------------  133 (388)
T 1w3b_A           87 IEHYRHALRL--KPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN-PD------------------------------  133 (388)
T ss_dssp             HHHHHHHHHH--CTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC-TT------------------------------
T ss_pred             HHHHHHHHHc--CcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CC------------------------------
Confidence            5555555442  232 2244445555555555555555555544432 12                              


Q ss_pred             CCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCC--C-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHH
Q 044988          182 MPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--R-NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVA  258 (538)
Q Consensus       182 ~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~  258 (538)
                          +...+..+...+...|++++|.+.|+++.+  | +..+|..+...+...|++++|...|+++.+.+ +.+...+..
T Consensus       134 ----~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~  208 (388)
T 1w3b_A          134 ----LYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYIN  208 (388)
T ss_dssp             ----CTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             ----cHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHH
Confidence                223344455555555666666666665542  3 45678888888888899999999998888743 234667778


Q ss_pred             HHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHHHHHh
Q 044988          259 ALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTSMITGFAK  335 (538)
Q Consensus       259 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~  335 (538)
                      +...+...|++++|...+....+.     .|.+..++..+...|.+.|++++|.+.|+++.+  | +..+|..+...+.+
T Consensus       209 lg~~~~~~~~~~~A~~~~~~al~~-----~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~  283 (388)
T 1w3b_A          209 LGNVLKEARIFDRAVAAYLRALSL-----SPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKE  283 (388)
T ss_dssp             HHHHHHTTTCTTHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhh-----CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHH
Confidence            888888889999999988888886     677778888899999999999999999988764  2 34455555555555


Q ss_pred             cCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHH
Q 044988          336 QGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAV  413 (538)
Q Consensus       336 ~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~  413 (538)
                      .|                    ++++|...|+++.+.  .+.+..++..+...+.+.|++++|.+.++++. ..| +..+
T Consensus       284 ~g--------------------~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~  341 (388)
T 1w3b_A          284 KG--------------------SVAEAEDCYNTALRL--CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAA  341 (388)
T ss_dssp             HS--------------------CHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHH
T ss_pred             cC--------------------CHHHHHHHHHHHHhh--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHH
Confidence            44                    777777888888765  24468889999999999999999999999874 334 4788


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCC
Q 044988          414 LGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKR  462 (538)
Q Consensus       414 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~  462 (538)
                      +..+...+.+.|++++|...++++ .+..|+....+. .++.++.+.|+
T Consensus       342 ~~~l~~~~~~~g~~~~A~~~~~~a-~~~~p~~~~a~~-~lg~~~~~~~~  388 (388)
T 1w3b_A          342 HSNLASVLQQQGKLQEALMHYKEA-IRISPTFADAYS-NMGNTLKEMQD  388 (388)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHH-HTTCTTCHHHHH-HHHHHHHHTCC
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH-HhhCCCCHHHHH-hHHHHHHHccC
Confidence            899999999999999999999999 889999998888 88888777653

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.96  E-value=4.6e-28  Score=237.66  Aligned_cols=200  Identities=11%  Similarity=0.066  Sum_probs=153.7

Q ss_pred             HHHHHHHHHhCCCCChh-HHHHHHHHHHccCChhHHHHHHhcCC----CCCcchHHHHHHHHhcCCC---------chHH
Q 044988           37 FQIHSQIIINGFSQKNY-ILAKLLAFYVTSGYLINAHKVFEKTE----NPSTAIWNQMIRGHARSET---------PEKS  102 (538)
Q Consensus        37 ~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~----~~~~~~~~~li~~~~~~~~---------~~~a  102 (538)
                      ..+...+.+.+..+++. +++.+|++|++.|++++|.++|++|.    +||..+||+||.+|++.+.         ++.|
T Consensus        10 e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A   89 (501)
T 4g26_A           10 ENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRG   89 (501)
T ss_dssp             --------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHH
T ss_pred             HHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHH
Confidence            34445555555554443 46666777777777777777777665    4677777777777765544         5789


Q ss_pred             HHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcC
Q 044988          103 VYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDM  182 (538)
Q Consensus       103 ~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~  182 (538)
                      .++|++|.+.|+.||..||+++|.+|++.|++++|.++|++|.+.|+.||..+|+.+|.+|++.|+   +++|.++|++|
T Consensus        90 ~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~---~~~A~~l~~~M  166 (501)
T 4g26_A           90 FDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGD---ADKAYEVDAHM  166 (501)
T ss_dssp             HHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTC---HHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCC---HHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999888888888888887   66666666554


Q ss_pred             CCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 044988          183 PARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSA  262 (538)
Q Consensus       183 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  262 (538)
                      .+.                           -..||..||++||.+|++.|+.++|.++|++|.+.|+.|+..||+.++..
T Consensus       167 ~~~---------------------------G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~  219 (501)
T 4g26_A          167 VES---------------------------EVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEW  219 (501)
T ss_dssp             HHT---------------------------TCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHH
T ss_pred             Hhc---------------------------CCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHH
Confidence            321                           13689999999999999999999999999999999999999999999998


Q ss_pred             HHcc
Q 044988          263 CAEI  266 (538)
Q Consensus       263 ~~~~  266 (538)
                      ++..
T Consensus       220 F~s~  223 (501)
T 4g26_A          220 FKSE  223 (501)
T ss_dssp             HHSH
T ss_pred             HhcC
Confidence            8764

>4g26_A Pentatricopeptide repeat-containing protein AT2G3 mitochondrial; metallonuclease, prorp, ribonuclease, PIN, tRNA processing, NYN domain; 1.75A {Arabidopsis thaliana} PDB: 4g23_A* 4g25_A 4g24_A

Probab=99.95  E-value=1.2e-27  Score=234.77  Aligned_cols=188  Identities=16%  Similarity=0.151  Sum_probs=167.7

Q ss_pred             chHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCC---------cHHHHHHHHHHHHhCCCCchh
Q 044988           84 AIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGL---------FREGEQVHGRVLASGYCSNVF  154 (538)
Q Consensus        84 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~---------~~~a~~~~~~~~~~~~~~~~~  154 (538)
                      ..++.+|++|++.|++++|+++|++|.+.|+.||..||++||.+|++.+.         ++.|.++|++|.+.|+.||..
T Consensus        27 ~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~~  106 (501)
T 4g26_A           27 ALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEA  106 (501)
T ss_dssp             HHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCHH
Confidence            35888899999999999999999999999999999999999999987664         578899999999999999988


Q ss_pred             HHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCH
Q 044988          155 IRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKS  234 (538)
Q Consensus       155 ~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~  234 (538)
                      +|+++|.+|++.|+   +++|.++|++|.+.                           -..||..+|+++|.+|++.|++
T Consensus       107 tyn~lI~~~~~~g~---~~~A~~l~~~M~~~---------------------------g~~Pd~~tyn~lI~~~~~~g~~  156 (501)
T 4g26_A          107 TFTNGARLAVAKDD---PEMAFDMVKQMKAF---------------------------GIQPRLRSYGPALFGFCRKGDA  156 (501)
T ss_dssp             HHHHHHHHHHHHTC---HHHHHHHHHHHHHT---------------------------TCCCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHhcCC---HHHHHHHHHHHHHc---------------------------CCCCccceehHHHHHHHHCCCH
Confidence            88888888888888   77776666655321                           1358999999999999999999


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhC
Q 044988          235 RQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASC  305 (538)
Q Consensus       235 ~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  305 (538)
                      ++|.++|++|.+.|+.||..||+.+|.+|++.|++++|.++++.|.+.    +..++..+|+.++..|+..
T Consensus       157 ~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~----g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          157 DKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDL----VRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----TSSBCHHHHHHHHHHHHSH
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHh----CCCcCHHHHHHHHHHHhcC
Confidence            999999999999999999999999999999999999999999999999    9999999999999988864

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.95  E-value=1.5e-25  Score=216.31  Aligned_cols=348  Identities=16%  Similarity=0.124  Sum_probs=266.4

Q ss_pred             HHHhcCCCchHHHHHHHHhHhCCCCCC-cchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCC
Q 044988           91 RGHARSETPEKSVYLYKQMIDKETEPD-EYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGE  169 (538)
Q Consensus        91 ~~~~~~~~~~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  169 (538)
                      ..+.+.|++++|.+.++.+.+.  .|+ ...+..+...+...|++++|...++...+.. +.+..++..+..+|.+.|+ 
T Consensus         7 ~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~-p~~~~~~~~lg~~~~~~g~-   82 (388)
T 1w3b_A            7 HREYQAGDFEAAERHCMQLWRQ--EPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQ-   82 (388)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC-
T ss_pred             HHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHCCC-
Confidence            3445556666666666665543  233 3344444455555666666666666655543 4455566666666666666 


Q ss_pred             CChhHHHHHhhcCCC--C-CchhHHHHHHHHHhcCCHHHHHHHHccCCC--CC-hHHHHHHHHHHHHcCCHHHHHHHHHH
Q 044988          170 CGVGCARLLFDDMPA--R-SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--RN-VVSWTTMISGCAQNGKSRQALSLFNE  243 (538)
Q Consensus       170 ~~~~~a~~~~~~~~~--~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~  243 (538)
                        +++|...|+++.+  | +..+|..+..++.+.|++++|...|+++.+  |+ ...+..+...+...|++++|...|++
T Consensus        83 --~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~  160 (388)
T 1w3b_A           83 --LQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLK  160 (388)
T ss_dssp             --HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHH
Confidence              6666666665542  2 334566666677777777777777766542  43 45677888899999999999999999


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C
Q 044988          244 MRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--R  321 (538)
Q Consensus       244 m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~  321 (538)
                      +.+.. +-+..++..+...+...|+++.|...++.+.+.     .|.+...+..+...+...|++++|...|++..+  |
T Consensus       161 al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~-----~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p  234 (388)
T 1w3b_A          161 AIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTL-----DPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSP  234 (388)
T ss_dssp             HHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHCT
T ss_pred             HHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-----CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCc
Confidence            98753 335788899999999999999999999999997     677888889999999999999999999987754  3


Q ss_pred             -CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHH
Q 044988          322 -NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAF  399 (538)
Q Consensus       322 -~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~  399 (538)
                       +..++..+...+...|                    ++++|...|+++.+.   .| +..+|..+..+|.+.|++++|.
T Consensus       235 ~~~~~~~~l~~~~~~~g--------------------~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~  291 (388)
T 1w3b_A          235 NHAVVHGNLACVYYEQG--------------------LIDLAIDTYRRAIEL---QPHFPDAYCNLANALKEKGSVAEAE  291 (388)
T ss_dssp             TCHHHHHHHHHHHHHTT--------------------CHHHHHHHHHHHHHT---CSSCHHHHHHHHHHHHHHSCHHHHH
T ss_pred             CCHHHHHHHHHHHHHcC--------------------CHHHHHHHHHHHHhh---CCCCHHHHHHHHHHHHHcCCHHHHH
Confidence             4556666666665555                    777888888888865   45 4778999999999999999999


Q ss_pred             HHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          400 SLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       400 ~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +.|+++.  .+++..++..+...+...|++++|...++++ .+..|++...+. .++.+|.+.|++++|.+.++++.+
T Consensus       292 ~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~-~l~~~~~~~g~~~~A~~~~~~a~~  367 (388)
T 1w3b_A          292 DCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKA-LEVFPEFAAAHS-NLASVLQQQGKLQEALMHYKEAIR  367 (388)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHH-TTSCTTCHHHHH-HHHHHHHTTTCCHHHHHHHHHHHT
T ss_pred             HHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhcCCCcHHHHH-HHHHHHHHcCCHHHHHHHHHHHHh
Confidence            9999884  4567889999999999999999999999999 899999998788 999999999999999999999986

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.92  E-value=8e-23  Score=204.89  Aligned_cols=424  Identities=9%  Similarity=-0.037  Sum_probs=299.5

Q ss_pred             cHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhc
Q 044988           19 TTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHAR   95 (538)
Q Consensus        19 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~   95 (538)
                      .+......+...|+++.|...++.+.+..  |++.++..+..+|.+.|++++|+..|++..   +.+...|..+..++.+
T Consensus         8 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~   85 (514)
T 2gw1_A            8 ALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELKPDYSKVLLRRASANEG   85 (514)
T ss_dssp             HHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccChHHHHHHHHHHHHHHH
Confidence            45566677888899999999999988876  578888888889999999999999888765   3455678888888899


Q ss_pred             CCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHH
Q 044988           96 SETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCA  175 (538)
Q Consensus        96 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a  175 (538)
                      .|++++|+..|+++.+.+ +++......++..+........+.+.+..+...+..|+......-...............+
T Consensus        86 ~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (514)
T 2gw1_A           86 LGKFADAMFDLSVLSLNG-DFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSM  164 (514)
T ss_dssp             TTCHHHHHHHHHHHHHSS-SCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCHHHH
T ss_pred             HhhHHHHHHHHHHHHhcC-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHH
Confidence            999999999999888765 3455555555555544333333333333222221111111111100000111110001112


Q ss_pred             HHHhhcCC---------CC-CchhHHHHHHHHHh---cCCHHHHHHHHccCCC----------------C-ChHHHHHHH
Q 044988          176 RLLFDDMP---------AR-SVVSWNSLLKGYVK---RGDIDGAWKIFDEMPH----------------R-NVVSWTTMI  225 (538)
Q Consensus       176 ~~~~~~~~---------~~-~~~~~~~li~~~~~---~g~~~~A~~~~~~m~~----------------~-~~~~~~~li  225 (538)
                      ...+....         .| +...+......+..   .|++++|...|+++.+                | +..+|..+.
T Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  244 (514)
T 2gw1_A          165 ASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTG  244 (514)
T ss_dssp             HHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHH
Confidence            22222111         11 23344444444444   7899999998887543                1 234678888


Q ss_pred             HHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhC
Q 044988          226 SGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASC  305 (538)
Q Consensus       226 ~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  305 (538)
                      ..+...|++++|...|+++.+..  |+...+..+...+...|+++.|...++.+.+.     .|.+..++..+...|...
T Consensus       245 ~~~~~~~~~~~A~~~~~~~l~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~  317 (514)
T 2gw1_A          245 IFKFLKNDPLGAHEDIKKAIELF--PRVNSYIYMALIMADRNDSTEYYNYFDKALKL-----DSNNSSVYYHRGQMNFIL  317 (514)
T ss_dssp             HHHHHSSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTT-----CTTCTHHHHHHHHHHHHT
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhC--ccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhc-----CcCCHHHHHHHHHHHHHh
Confidence            89999999999999999998754  34778888888899999999999999998886     566777888899999999


Q ss_pred             CCHHHHHHHHHhcCC--C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHH
Q 044988          306 GEIEEAYGVFRKMQR--R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHY  382 (538)
Q Consensus       306 g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~  382 (538)
                      |++++|...|+++.+  | +...                    +..+...+...|++++|..+++.+.+..  +.+..++
T Consensus       318 ~~~~~A~~~~~~~~~~~~~~~~~--------------------~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~  375 (514)
T 2gw1_A          318 QNYDQAGKDFDKAKELDPENIFP--------------------YIQLACLAYRENKFDDCETLFSEAKRKF--PEAPEVP  375 (514)
T ss_dssp             TCTTHHHHHHHHHHHTCSSCSHH--------------------HHHHHHHTTTTTCHHHHHHHHHHHHHHS--TTCSHHH
T ss_pred             CCHHHHHHHHHHHHHhChhhHHH--------------------HHHHHHHHHHcCCHHHHHHHHHHHHHHc--ccCHHHH
Confidence            999999999988754  2 2333                    3444455566668888889999888652  2357788


Q ss_pred             HHHHHHhhhcCChHHHHHHHHhCC----CCCC----HHHHHHHHHHHHh---cCCHHHHHHHHHHchhccCCCCcccHHH
Q 044988          383 GCMVDLFSRAGLMDEAFSLVQNMP----MKPN----DAVLGSLLLGCRI---HNNAELASQVAQKLVAEIDPEQAAGYLA  451 (538)
Q Consensus       383 ~~l~~~~~~~g~~~~A~~~~~~~~----~~p~----~~~~~~l~~~~~~---~~~~~~A~~~~~~~~~~~~p~~~~~~~~  451 (538)
                      ..+...|.+.|++++|.+.++++.    ..|+    ...+..+...+..   .|++++|...++++ ....|++...+. 
T Consensus       376 ~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a-~~~~~~~~~~~~-  453 (514)
T 2gw1_A          376 NFFAEILTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKA-SKLDPRSEQAKI-  453 (514)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHH-HHHCTTCHHHHH-
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHH-HHhCcccHHHHH-
Confidence            999999999999999999998873    1222    4488889999999   99999999999999 888999998788 


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          452 LVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       452 ~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      .++.+|.+.|++++|...+++..+.
T Consensus       454 ~la~~~~~~g~~~~A~~~~~~a~~~  478 (514)
T 2gw1_A          454 GLAQMKLQQEDIDEAITLFEESADL  478 (514)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            9999999999999999999999874

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.91  E-value=1.4e-21  Score=197.03  Aligned_cols=420  Identities=10%  Similarity=0.021  Sum_probs=308.4

Q ss_pred             cccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHH
Q 044988           17 ALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGH   93 (538)
Q Consensus        17 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~   93 (538)
                      ...+..+...+...|+++.|...++.+.+... .++.++..+..+|.+.|++++|++.|++..   +.+...|..+..++
T Consensus        25 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~  103 (537)
T 3fp2_A           25 AVQLKNRGNHFFTAKNFNEAIKYYQYAIELDP-NEPVFYSNISACYISTGDLEKVIEFTTKALEIKPDHSKALLRRASAN  103 (537)
T ss_dssp             HHHHHHHHHHHHHTTCCC-CHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhCC-CCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCchHHHHHHHHHHH
Confidence            34566677788888899999999998888753 367788888888888999999999888765   34566788888888


Q ss_pred             hcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhC--CCCchhHHhHHHHHHHhcCCCCC
Q 044988           94 ARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASG--YCSNVFIRTNLMNLYLMSGGECG  171 (538)
Q Consensus        94 ~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~  171 (538)
                      ...|++++|+..|+.+..   .|+..  ...+..+...+....|...++.+....  ..+........+..+....+   
T Consensus       104 ~~~g~~~~A~~~~~~~~~---~~~~~--~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~---  175 (537)
T 3fp2_A          104 ESLGNFTDAMFDLSVLSL---NGDFD--GASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFD---  175 (537)
T ss_dssp             HHHTCHHHHHHHHHHHC----------------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSC---
T ss_pred             HHcCCHHHHHHHHHHHhc---CCCCC--hHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcC---
Confidence            888999999988863322   23222  122334444455677888887775531  01111122334455666667   


Q ss_pred             hhHHHHHhhcCCCCCch---hHHHHHHHHHh--------cCCHHHHHHHHccCCC--CC--------hHHHHHHHHHHHH
Q 044988          172 VGCARLLFDDMPARSVV---SWNSLLKGYVK--------RGDIDGAWKIFDEMPH--RN--------VVSWTTMISGCAQ  230 (538)
Q Consensus       172 ~~~a~~~~~~~~~~~~~---~~~~li~~~~~--------~g~~~~A~~~~~~m~~--~~--------~~~~~~li~~~~~  230 (538)
                      .+.+...+......+..   ....+...+..        .|++++|..+|+++.+  |+        ..+|..+...+..
T Consensus       176 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~  255 (537)
T 3fp2_A          176 SHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFL  255 (537)
T ss_dssp             HHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHh
Confidence            77777777776665443   33333333322        2578999999988764  33        2357777788899


Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHH
Q 044988          231 NGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEE  310 (538)
Q Consensus       231 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  310 (538)
                      .|++++|...|+++.+.  .|+...+..+...+...|+++.|...+..+.+.     .|.+..++..+...|...|++++
T Consensus       256 ~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~  328 (537)
T 3fp2_A          256 KNNLLDAQVLLQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDL-----NPEYPPTYYHRGQMYFILQDYKN  328 (537)
T ss_dssp             TTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             cccHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhcc-----CCCCHHHHHHHHHHHHhcCCHHH
Confidence            99999999999999884  566788888999999999999999999999987     67778888899999999999999


Q ss_pred             HHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHH
Q 044988          311 AYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVD  387 (538)
Q Consensus       311 a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~  387 (538)
                      |...|+++.+   .+...|..+...+...|                    ++++|..+++++.+..  +.+...+..+..
T Consensus       329 A~~~~~~a~~~~~~~~~~~~~la~~~~~~g--------------------~~~~A~~~~~~~~~~~--~~~~~~~~~l~~  386 (537)
T 3fp2_A          329 AKEDFQKAQSLNPENVYPYIQLACLLYKQG--------------------KFTESEAFFNETKLKF--PTLPEVPTFFAE  386 (537)
T ss_dssp             HHHHHHHHHHHCTTCSHHHHHHHHHHHHTT--------------------CHHHHHHHHHHHHHHC--TTCTHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHcC--------------------CHHHHHHHHHHHHHhC--CCChHHHHHHHH
Confidence            9999998764   23445555555555555                    7778888888888752  335778899999


Q ss_pred             HhhhcCChHHHHHHHHhCC--------CCCCHHHHHHHHHHHHhc----------CCHHHHHHHHHHchhccCCCCcccH
Q 044988          388 LFSRAGLMDEAFSLVQNMP--------MKPNDAVLGSLLLGCRIH----------NNAELASQVAQKLVAEIDPEQAAGY  449 (538)
Q Consensus       388 ~~~~~g~~~~A~~~~~~~~--------~~p~~~~~~~l~~~~~~~----------~~~~~A~~~~~~~~~~~~p~~~~~~  449 (538)
                      .|...|++++|.+.|+++.        .......+......+...          |++++|...++++ ....|++...+
T Consensus       387 ~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a-~~~~p~~~~~~  465 (537)
T 3fp2_A          387 ILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKA-CELDPRSEQAK  465 (537)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHH-HHHCTTCHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHH-HHhCCCCHHHH
Confidence            9999999999999998863        111223344555667777          9999999999999 88999999888


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          450 LALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       450 ~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      . .++.+|.+.|++++|.+.+++..+.
T Consensus       466 ~-~l~~~~~~~g~~~~A~~~~~~al~~  491 (537)
T 3fp2_A          466 I-GLAQLKLQMEKIDEAIELFEDSAIL  491 (537)
T ss_dssp             H-HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             H-HHHHHHHHhccHHHHHHHHHHHHHh
Confidence            8 9999999999999999999999874

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.90  E-value=2.9e-21  Score=190.17  Aligned_cols=348  Identities=11%  Similarity=0.067  Sum_probs=229.8

Q ss_pred             cchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHH
Q 044988           83 TAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNL  162 (538)
Q Consensus        83 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  162 (538)
                      ...|..+...+.+.|++++|+.+|+++.+.. +.+..+|..+..++...|++++|...++++.+.+ +.+..++..+..+
T Consensus        26 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  103 (450)
T 2y4t_A           26 VEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGHL  103 (450)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHH
Confidence            3445555556666666666666666665432 2344555566666666666666666666666554 3344555555555


Q ss_pred             HHhcCCCCChhHHHHHhhcCCCCCc------hhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHH
Q 044988          163 YLMSGGECGVGCARLLFDDMPARSV------VSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQ  236 (538)
Q Consensus       163 ~~~~g~~~~~~~a~~~~~~~~~~~~------~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~  236 (538)
                      |.+.|+   +++|...|+++.+.++      ..|..+...+..                   ..+..+...+...|++++
T Consensus       104 ~~~~g~---~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------------------~~~~~~a~~~~~~~~~~~  161 (450)
T 2y4t_A          104 LLKQGK---LDEAEDDFKKVLKSNPSENEEKEAQSQLIKSDEM-------------------QRLRSQALNAFGSGDYTA  161 (450)
T ss_dssp             HHHTTC---HHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHTCHHH
T ss_pred             HHHcCC---HHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHH-------------------HHHHHHHHHHHHcCCHHH
Confidence            555555   5555555555443211      333333332211                   112233445666777788


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHH
Q 044988          237 ALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFR  316 (538)
Q Consensus       237 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  316 (538)
                      |+..|+++.+.. +.+...+..+..++.+.|+++.|...++.+.+.     .|.+..++..++..|...|++++|...|+
T Consensus       162 A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  235 (450)
T 2y4t_A          162 AIAFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKL-----KNDNTEAFYKISTLYYQLGDHELSLSEVR  235 (450)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHH-----HCSCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            888777777642 335667777777777888888888888777775     55667777788888888888888888888


Q ss_pred             hcCC--CCcc-hHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-----HHHHHHHHHH
Q 044988          317 KMQR--RNTV-SWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-----IEHYGCMVDL  388 (538)
Q Consensus       317 ~m~~--~~~~-~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-----~~~~~~l~~~  388 (538)
                      ++.+  |+.. .+..+ ....       .......+...|...|++++|..+|+++.+.   .|+     ...+..+..+
T Consensus       236 ~~~~~~p~~~~~~~~~-~~~~-------~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~---~p~~~~~~~~~~~~l~~~  304 (450)
T 2y4t_A          236 ECLKLDQDHKRCFAHY-KQVK-------KLNKLIESAEELIRDGRYTDATSKYESVMKT---EPSIAEYTVRSKERICHC  304 (450)
T ss_dssp             HHHHHCTTCHHHHHHH-HHHH-------HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CCSSHHHHHHHHHHHHHH
T ss_pred             HHHHhCCChHHHHHHH-HHHH-------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---CCcchHHHHHHHHHHHHH
Confidence            7754  3222 22222 1000       0122334466777778999999999999876   454     4578899999


Q ss_pred             hhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHH-----------
Q 044988          389 FSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVAN-----------  455 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~-----------  455 (538)
                      +.+.|++++|.+.++++. ..| +...|..+..+|...|++++|...++++ .++.|+++..+. .++.           
T Consensus       305 ~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a-l~~~p~~~~~~~-~l~~~~~~~~~~~~~  382 (450)
T 2y4t_A          305 FSKDEKPVEAIRVCSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYETA-QEHNENDQQIRE-GLEKAQRLLKQSQKR  382 (450)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HTTSSSCHHHHH-HHHHHHHHHHHHHSC
T ss_pred             HHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHH-HHhCcchHHHHH-HHHHHHHHhhcccch
Confidence            999999999999999874 334 6899999999999999999999999999 999999998777 7773           


Q ss_pred             -HHHhcC-----ChHHHHHHHHHH
Q 044988          456 -VYAAAK-----RWQDVAAVRQKM  473 (538)
Q Consensus       456 -~~~~~g-----~~~~A~~~~~~m  473 (538)
                       .|...|     +.+++.+.++++
T Consensus       383 ~~y~~lg~~~~~~~~~~~~~y~~~  406 (450)
T 2y4t_A          383 DYYKILGVKRNAKKQEIIKAYRKL  406 (450)
T ss_dssp             CSGGGSCSSTTCCTTHHHHHHHHH
T ss_pred             hHHHHhCCCccCCHHHHHHHHHHH
Confidence             344445     566777777764

>2y4t_A DNAJ homolog subfamily C member 3; chaperone, endoplasmic reticulum, protein folding, tetratricopeptiderepeat, J domain, unfolded protein respons; 3.00A {Homo sapiens} PDB: 2y4u_A

Probab=99.89  E-value=1.2e-20  Score=185.60  Aligned_cols=306  Identities=11%  Similarity=0.025  Sum_probs=255.7

Q ss_pred             CCCCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHH
Q 044988           12 ATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQ   88 (538)
Q Consensus        12 ~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~   88 (538)
                      ..|.+...+..+...+...|+++.|..+++.+.+.. +.+..++..+..+|...|++++|+..|+++.   +.+...|..
T Consensus        21 ~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~   99 (450)
T 2y4t_A           21 QSMADVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQ   99 (450)
T ss_dssp             --CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHH
Confidence            344566788888999999999999999999999874 3468899999999999999999999999876   345678999


Q ss_pred             HHHHHhcCCCchHHHHHHHHhHhCCCCCCc----chHHHH------------HHHHHccCCcHHHHHHHHHHHHhCCCCc
Q 044988           89 MIRGHARSETPEKSVYLYKQMIDKETEPDE----YTYSFL------------LSVCARCGLFREGEQVHGRVLASGYCSN  152 (538)
Q Consensus        89 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~----~~~~~l------------i~~~~~~~~~~~a~~~~~~~~~~~~~~~  152 (538)
                      +...|.+.|++++|...|+++.+.  .|+.    ..+..+            ...+...|++++|...++++.+.. +.+
T Consensus       100 l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~  176 (450)
T 2y4t_A          100 RGHLLLKQGKLDEAEDDFKKVLKS--NPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWD  176 (450)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHhc--CCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCC
Confidence            999999999999999999999875  3543    455555            344888999999999999999875 567


Q ss_pred             hhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC---CCchhHHHHHHHHHhcCCHHHHHHHHccCCC--C-ChHHHHHH--
Q 044988          153 VFIRTNLMNLYLMSGGECGVGCARLLFDDMPA---RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--R-NVVSWTTM--  224 (538)
Q Consensus       153 ~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~l--  224 (538)
                      ..++..+..+|.+.|+   +++|...|+++.+   .+..+|..+...|...|++++|...|+++..  | +...+..+  
T Consensus       177 ~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~~~  253 (450)
T 2y4t_A          177 AELRELRAECFIKEGE---PRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQ  253 (450)
T ss_dssp             HHHHHHHHHHHHHTTC---GGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHCCC---HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCChHHHHHHHHH
Confidence            8899999999999999   9999999998864   4678999999999999999999999998753  4 33445444  


Q ss_pred             ----------HHHHHHcCCHHHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCC
Q 044988          225 ----------ISGCAQNGKSRQALSLFNEMRRARVGLD-----QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREP  289 (538)
Q Consensus       225 ----------i~~~~~~~~~~~a~~~~~~m~~~g~~p~-----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~  289 (538)
                                ...+.+.|++++|...|+++.+.  .|+     ...+..+...+.+.|++++|...++.+.+.     .|
T Consensus       254 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~-----~p  326 (450)
T 2y4t_A          254 VKKLNKLIESAEELIRDGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQM-----EP  326 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH-----CT
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----Cc
Confidence                      78899999999999999999884  454     447888889999999999999999999887     67


Q ss_pred             cchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHH
Q 044988          290 VLVSLNNALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTSMIT  331 (538)
Q Consensus       290 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~  331 (538)
                      .+..++..+..+|...|++++|...|+++.+  | +...+..+..
T Consensus       327 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~  371 (450)
T 2y4t_A          327 DNVNALKDRAEAYLIEEMYDEAIQDYETAQEHNENDQQIREGLEK  371 (450)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcchHHHHHHHHH
Confidence            7788889999999999999999999998865  3 3444554443

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.86  E-value=5.2e-20  Score=184.41  Aligned_cols=390  Identities=11%  Similarity=-0.023  Sum_probs=279.8

Q ss_pred             hhHHHHHHHHHHccCChhHHHHHHhcCC--CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHH
Q 044988           52 NYILAKLLAFYVTSGYLINAHKVFEKTE--NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCA  129 (538)
Q Consensus        52 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  129 (538)
                      ...+......+.+.|++++|+..|+++.  .|+...|..+..++.+.|++++|+..|+++.+.+ +.+..+|..+..++.
T Consensus         6 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~   84 (514)
T 2gw1_A            6 ALALKDKGNQFFRNKKYDDAIKYYNWALELKEDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANE   84 (514)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhcCccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHH
Confidence            4566777788888999999999998876  4788888888999999999999999999988754 334568888888999


Q ss_pred             ccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC----CCchhHHHH---HHHHHhcCC
Q 044988          130 RCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA----RSVVSWNSL---LKGYVKRGD  202 (538)
Q Consensus       130 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~----~~~~~~~~l---i~~~~~~g~  202 (538)
                      ..|++++|...|+++.+.+ +++......++..+.....   ...+.+.+..+..    ++...+...   .........
T Consensus        85 ~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (514)
T 2gw1_A           85 GLGKFADAMFDLSVLSLNG-DFNDASIEPMLERNLNKQA---MSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPS  160 (514)
T ss_dssp             HTTCHHHHHHHHHHHHHSS-SCCGGGTHHHHHHHHHHHH---HHHHTTC---------------------------CCCC
T ss_pred             HHhhHHHHHHHHHHHHhcC-CCccchHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCch
Confidence            9999999999999988876 4455555555555554444   4444333322211    000000000   000111111


Q ss_pred             HHHHHHHHccCC---------CC-ChHHHHHHHHHHHH---cCCHHHHHHHHHHHHH-----CCCC--------CCHHHH
Q 044988          203 IDGAWKIFDEMP---------HR-NVVSWTTMISGCAQ---NGKSRQALSLFNEMRR-----ARVG--------LDQVAL  256 (538)
Q Consensus       203 ~~~A~~~~~~m~---------~~-~~~~~~~li~~~~~---~~~~~~a~~~~~~m~~-----~g~~--------p~~~~~  256 (538)
                      ...+...+....         .| +...+......+..   .|++++|...|+++.+     ..-.        .+...+
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  240 (514)
T 2gw1_A          161 VTSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISL  240 (514)
T ss_dssp             HHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHH
T ss_pred             hHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHH
Confidence            122222222221         12 23445555555554   8999999999999987     3112        234567


Q ss_pred             HHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHH
Q 044988          257 VAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGF  333 (538)
Q Consensus       257 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~  333 (538)
                      ..+...+...|+++.|...++.+.+.     .|. ...+..+...|...|++++|...++++.+   .+...+..+...+
T Consensus       241 ~~~~~~~~~~~~~~~A~~~~~~~l~~-----~~~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~  314 (514)
T 2gw1_A          241 EHTGIFKFLKNDPLGAHEDIKKAIEL-----FPR-VNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMN  314 (514)
T ss_dssp             HHHHHHHHHSSCHHHHHHHHHHHHHH-----CCC-HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhh-----Ccc-HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHH
Confidence            78888899999999999999999987     344 78888999999999999999999998765   2445566666666


Q ss_pred             HhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCH
Q 044988          334 AKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPND  411 (538)
Q Consensus       334 ~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~  411 (538)
                      ...|                    ++++|...++++.+..  +.+..++..+...|...|++++|.+.++++.  .+.+.
T Consensus       315 ~~~~--------------------~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~  372 (514)
T 2gw1_A          315 FILQ--------------------NYDQAGKDFDKAKELD--PENIFPYIQLACLAYRENKFDDCETLFSEAKRKFPEAP  372 (514)
T ss_dssp             HHTT--------------------CTTHHHHHHHHHHHTC--SSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHSTTCS
T ss_pred             HHhC--------------------CHHHHHHHHHHHHHhC--hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcccCH
Confidence            6655                    6666678888877541  2357789999999999999999999999874  23456


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc------cHHHHHHHHHHh---cCChHHHHHHHHHHHhC
Q 044988          412 AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA------GYLALVANVYAA---AKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       412 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~------~~~~~l~~~~~~---~g~~~~A~~~~~~m~~~  476 (538)
                      ..+..+...+...|++++|...++++ ....|+++.      .+. .++.+|..   .|++++|...++++.+.
T Consensus       373 ~~~~~la~~~~~~~~~~~A~~~~~~a-~~~~~~~~~~~~~~~~~~-~l~~~~~~~~~~~~~~~A~~~~~~a~~~  444 (514)
T 2gw1_A          373 EVPNFFAEILTDKNDFDKALKQYDLA-IELENKLDGIYVGIAPLV-GKATLLTRNPTVENFIEATNLLEKASKL  444 (514)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHHTSSSCSSCSHHHH-HHHHHHHTSCCTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHH-HHhhhccchHHHHHHHHH-HHHHHHhhhhhcCCHHHHHHHHHHHHHh
Confidence            78889999999999999999999999 777777754      678 89999999   99999999999999874

>3fp2_A TPR repeat-containing protein YHR117W; TOM71, mitochondria translocation, allosteric REG phosphoprotein, TPR repeat, ATP-binding; 1.98A {Saccharomyces cerevisiae} PDB: 3fp3_A 3fp4_A 3lca_A

Probab=99.83  E-value=4.7e-19  Score=178.52  Aligned_cols=384  Identities=10%  Similarity=0.020  Sum_probs=283.6

Q ss_pred             hhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHH
Q 044988           52 NYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVC  128 (538)
Q Consensus        52 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  128 (538)
                      ...+..+...+.+.|++++|+..|++..   +.+...|..+..++.+.|++++|++.|+++.+.+ +.+..++..+..++
T Consensus        25 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~  103 (537)
T 3fp2_A           25 AVQLKNRGNHFFTAKNFNEAIKYYQYAIELDPNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASAN  103 (537)
T ss_dssp             HHHHHHHHHHHHHTTCCC-CHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHH
Confidence            4567778888999999999999998876   3467788999999999999999999999998754 34567888899999


Q ss_pred             HccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC------CchhHHHHHHHHHhcCC
Q 044988          129 ARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPAR------SVVSWNSLLKGYVKRGD  202 (538)
Q Consensus       129 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~------~~~~~~~li~~~~~~g~  202 (538)
                      ...|++++|...++ ....  .|+.  ....+..+...+.   ...|...++++...      ........+..+....+
T Consensus       104 ~~~g~~~~A~~~~~-~~~~--~~~~--~~~~~~~~~~~~~---~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  175 (537)
T 3fp2_A          104 ESLGNFTDAMFDLS-VLSL--NGDF--DGASIEPMLERNL---NKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFD  175 (537)
T ss_dssp             HHHTCHHHHHHHHH-HHC---------------CHHHHHH---HHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSC
T ss_pred             HHcCCHHHHHHHHH-HHhc--CCCC--ChHHHHHHHHHHH---HHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcC
Confidence            99999999999996 3322  2222  1222344455555   67778877776542      22234455666777888


Q ss_pred             HHHHHHHHccCCCCChH---HHHHHHHHHHH--------cCCHHHHHHHHHHHHHCCCCCC--------HHHHHHHHHHH
Q 044988          203 IDGAWKIFDEMPHRNVV---SWTTMISGCAQ--------NGKSRQALSLFNEMRRARVGLD--------QVALVAALSAC  263 (538)
Q Consensus       203 ~~~A~~~~~~m~~~~~~---~~~~li~~~~~--------~~~~~~a~~~~~~m~~~g~~p~--------~~~~~~li~~~  263 (538)
                      .+.+...+......+..   ....+...+..        .|++++|..+|+++.+.  .|+        ..++..+...+
T Consensus       176 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~~~~~g~~~  253 (537)
T 3fp2_A          176 SHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSA--NTVDDPLRENAALALCYTGIFH  253 (537)
T ss_dssp             HHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHH--CCCcchhhHHHHHHHHHHHHHH
Confidence            88888888887764433   33333333222        25789999999999874  344        23466677778


Q ss_pred             HccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCcc
Q 044988          264 AEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQ  340 (538)
Q Consensus       264 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~  340 (538)
                      ...|+++.|...++.+.+.     .|. ...+..+...|...|++++|...|+++.+   .+..+|..+...+...|   
T Consensus       254 ~~~~~~~~A~~~~~~~~~~-----~~~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---  324 (537)
T 3fp2_A          254 FLKNNLLDAQVLLQESINL-----HPT-PNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQ---  324 (537)
T ss_dssp             HHTTCHHHHHHHHHHHHHH-----CCC-HHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT---
T ss_pred             HhcccHHHHHHHHHHHHhc-----CCC-chHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcC---
Confidence            8899999999999999987     344 67788899999999999999999998764   34445555555555555   


Q ss_pred             HHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHH
Q 044988          341 EALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSL  417 (538)
Q Consensus       341 ~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l  417 (538)
                                       ++++|...|+++.+.   .| +...+..+..+|...|++++|.+.++++.  .+.+...+..+
T Consensus       325 -----------------~~~~A~~~~~~a~~~---~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l  384 (537)
T 3fp2_A          325 -----------------DYKNAKEDFQKAQSL---NPENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFF  384 (537)
T ss_dssp             -----------------CHHHHHHHHHHHHHH---CTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHH
T ss_pred             -----------------CHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHH
Confidence                             777788888888765   34 46789999999999999999999999874  33446788889


Q ss_pred             HHHHHhcCCHHHHHHHHHHchhccCCCCcccHH-----HHHHHHHHhc----------CChHHHHHHHHHHHhC
Q 044988          418 LLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL-----ALVANVYAAA----------KRWQDVAAVRQKMIKM  476 (538)
Q Consensus       418 ~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~-----~~l~~~~~~~----------g~~~~A~~~~~~m~~~  476 (538)
                      ...+...|++++|...++++ ....|++...+.     ..++.++.+.          |++++|...+++..+.
T Consensus       385 ~~~~~~~g~~~~A~~~~~~a-~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~  457 (537)
T 3fp2_A          385 AEILTDRGDFDTAIKQYDIA-KRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACEL  457 (537)
T ss_dssp             HHHHHHTTCHHHHHHHHHHH-HHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHH-HHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHh
Confidence            99999999999999999999 666666554332     1445778888          9999999999999874

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.83  E-value=9.9e-18  Score=159.29  Aligned_cols=333  Identities=11%  Similarity=0.043  Sum_probs=242.1

Q ss_pred             cchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHH
Q 044988           83 TAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNL  162 (538)
Q Consensus        83 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  162 (538)
                      +..+..+...+.+.|++++|+..|+++.+.. +.+..++..+...+...|++++|...++++.+.. +.+...+..+..+
T Consensus         3 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~   80 (359)
T 3ieg_A            3 VEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHL   80 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHH
Confidence            4567778888888999999999999888753 3456688888888888899999999998888874 4456777788888


Q ss_pred             HHhcCCCCChhHHHHHhhcCCCCCc---h---hHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHH
Q 044988          163 YLMSGGECGVGCARLLFDDMPARSV---V---SWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQ  236 (538)
Q Consensus       163 ~~~~g~~~~~~~a~~~~~~~~~~~~---~---~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~  236 (538)
                      +...|+   +++|...|++..+.++   .   .+..+....       .            ...+..+...+...|++++
T Consensus        81 ~~~~~~---~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~-------~------------~~~~~~~a~~~~~~~~~~~  138 (359)
T 3ieg_A           81 LLKQGK---LDEAEDDFKKVLKSNPSEQEEKEAESQLVKAD-------E------------MQRLRSQALDAFDGADYTA  138 (359)
T ss_dssp             HHHHTC---HHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHH-------H------------HHHHHHHHHHHHHTTCHHH
T ss_pred             HHHcCC---hHHHHHHHHHHHhcCCcccChHHHHHHHHHHH-------H------------HHHHHHHHHHHHHccCHHH
Confidence            888888   8888777776654322   1   111111110       0            1123334667788888899


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHH
Q 044988          237 ALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFR  316 (538)
Q Consensus       237 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  316 (538)
                      |...|+++.+.. +.+...+..+...+...|+++.|...++.+.+.     .|.+...+..+...|...|++++|...|+
T Consensus       139 A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~la~~~~~~~~~~~A~~~~~  212 (359)
T 3ieg_A          139 AITFLDKILEVC-VWDAELRELRAECFIKEGEPRKAISDLKAASKL-----KSDNTEAFYKISTLYYQLGDHELSLSEVR  212 (359)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT-----CSCCHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            998888887753 345677788888888889999998888888876     67777788888888999999999999888


Q ss_pred             hcCC--CC-cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-H----HHHHHHHHH
Q 044988          317 KMQR--RN-TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-I----EHYGCMVDL  388 (538)
Q Consensus       317 ~m~~--~~-~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~----~~~~~l~~~  388 (538)
                      +..+  |+ ...+..+...-        .......+...+...|++++|...++++.+.   .|+ .    ..+..+..+
T Consensus       213 ~a~~~~~~~~~~~~~~~~~~--------~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~~~~la~~  281 (359)
T 3ieg_A          213 ECLKLDQDHKRCFAHYKQVK--------KLNKLIESAEELIRDGRYTDATSKYESVMKT---EPSVAEYTVRSKERICHC  281 (359)
T ss_dssp             HHHHHCTTCHHHHHHHHHHH--------HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CCSSHHHHHHHHHHHHHH
T ss_pred             HHHhhCccchHHHHHHHHHH--------HHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---CCCchHHHHHHHHHHHHH
Confidence            7764  22 22222111100        0122233455667778999999999998876   343 2    345567889


Q ss_pred             hhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHH
Q 044988          389 FSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYA  458 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~  458 (538)
                      +...|++++|.+.+++.. ..| +..++..+...+...|++++|...++++ .+..|++...+. .+..+..
T Consensus       282 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a-~~~~p~~~~~~~-~l~~~~~  351 (359)
T 3ieg_A          282 FSKDEKPVEAIRICSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAA-QEHNENDQQIRE-GLEKAQR  351 (359)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HTTCTTCHHHHH-HHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhcCCCChHHHH-HHHHHHH
Confidence            999999999999998874 234 6788999999999999999999999999 999999888666 6655543

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.82  E-value=3.9e-17  Score=155.12  Aligned_cols=295  Identities=11%  Similarity=0.018  Sum_probs=214.7

Q ss_pred             cchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHH
Q 044988          118 EYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGY  197 (538)
Q Consensus       118 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~  197 (538)
                      ...+..+...+...|++++|...++++.+.. +.+..++..+..++...|+   +++|...|++..+.            
T Consensus         3 ~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~---~~~A~~~~~~~~~~------------   66 (359)
T 3ieg_A            3 VEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGK---SKAALPDLTKVIAL------------   66 (359)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC---HHHHHHHHHHHHHH------------
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccC---HHHHHHHHHHHHHh------------
Confidence            3456667777777888888888888877764 4445566666666666666   66666655443210            


Q ss_pred             HhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC----CHHHHHHH------------HH
Q 044988          198 VKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGL----DQVALVAA------------LS  261 (538)
Q Consensus       198 ~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p----~~~~~~~l------------i~  261 (538)
                                      ...+...|..+...+...|++++|...|+++.+.  .|    +...+..+            ..
T Consensus        67 ----------------~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~a~  128 (359)
T 3ieg_A           67 ----------------KMDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKS--NPSEQEEKEAESQLVKADEMQRLRSQAL  128 (359)
T ss_dssp             ----------------CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----------------CCCcchHHHHHHHHHHHcCChHHHHHHHHHHHhc--CCcccChHHHHHHHHHHHHHHHHHHHHH
Confidence                            1123445666666666667777777777666653  33    22222222            56


Q ss_pred             HHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCC
Q 044988          262 ACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGY  338 (538)
Q Consensus       262 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~  338 (538)
                      .+...|+++.|...++.+.+.     .|.+..++..+...+...|++++|...++++.+   .+...+..+...+...| 
T Consensus       129 ~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~-  202 (359)
T 3ieg_A          129 DAFDGADYTAAITFLDKILEV-----CVWDAELRELRAECFIKEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLG-  202 (359)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHT-
T ss_pred             HHHHccCHHHHHHHHHHHHHh-----CCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC-
Confidence            788999999999999999987     677788889999999999999999999998775   34455556666665555 


Q ss_pred             ccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHH------------HHHHHhhhcCChHHHHHHHHhC
Q 044988          339 AQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYG------------CMVDLFSRAGLMDEAFSLVQNM  405 (538)
Q Consensus       339 ~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~------------~l~~~~~~~g~~~~A~~~~~~~  405 (538)
                                         ++++|...|+...+.   .|+ ...+.            .+...+.+.|++++|.+.++++
T Consensus       203 -------------------~~~~A~~~~~~a~~~---~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~  260 (359)
T 3ieg_A          203 -------------------DHELSLSEVRECLKL---DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESV  260 (359)
T ss_dssp             -------------------CHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             -------------------CHHHHHHHHHHHHhh---CccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence                               666667777777654   232 22222            3367789999999999999987


Q ss_pred             C-CCCC-H----HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          406 P-MKPN-D----AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       406 ~-~~p~-~----~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      . ..|+ .    ..+..+...+...|++++|...++++ ....|+++..+. .++.+|.+.|++++|.+.+++..+.
T Consensus       261 ~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~g~~~~A~~~~~~a~~~  335 (359)
T 3ieg_A          261 MKTEPSVAEYTVRSKERICHCFSKDEKPVEAIRICSEV-LQMEPDNVNALK-DRAEAYLIEEMYDEAIQDYEAAQEH  335 (359)
T ss_dssp             HHHCCSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HhcCCCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHH-HHhCcccHHHHH-HHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            4 3344 2    23445777899999999999999999 888999999888 9999999999999999999999874

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.80  E-value=3.2e-18  Score=160.05  Aligned_cols=284  Identities=14%  Similarity=0.166  Sum_probs=125.8

Q ss_pred             ccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHH
Q 044988           64 TSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGR  143 (538)
Q Consensus        64 ~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~  143 (538)
                      +.|++++|.++++++..|  .+|..|+.++.+.|++++|++.|.+      .+|..+|..++.++...|++++|..+++.
T Consensus        15 ~~~~ld~A~~fae~~~~~--~vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~yl~~   86 (449)
T 1b89_A           15 HIGNLDRAYEFAERCNEP--AVWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVKYLQM   86 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhCCCh--HHHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            678899999999999555  4899999999999999999999964      36777999999999999999999998877


Q ss_pred             HHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHH
Q 044988          144 VLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTT  223 (538)
Q Consensus       144 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~  223 (538)
                      ..+.  .+++.+.+.++.+|.+.|+   ++++.++++.   |+..+|+.+...|...|.+++|...|..+     ..|..
T Consensus        87 ark~--~~~~~i~~~Li~~Y~Klg~---l~e~e~f~~~---pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a-----~n~~~  153 (449)
T 1b89_A           87 ARKK--ARESYVETELIFALAKTNR---LAELEEFING---PNNAHIQQVGDRCYDEKMYDAAKLLYNNV-----SNFGR  153 (449)
T ss_dssp             ------------------------C---HHHHTTTTTC---C----------------CTTTHHHHHHHT-----TCHHH
T ss_pred             HHHh--CccchhHHHHHHHHHHhCC---HHHHHHHHcC---CcHHHHHHHHHHHHHcCCHHHHHHHHHHh-----hhHHH
Confidence            7764  4567888999999999999   9888887763   67779999999999999999999999987     37999


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHH
Q 044988          224 MISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYA  303 (538)
Q Consensus       224 li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  303 (538)
                      ++.++.+.|++++|.+.+.++      .+..+|..++.+|...|+++.|......+         ...+.-...++..|.
T Consensus       154 LA~~L~~Lg~yq~AVea~~KA------~~~~~Wk~v~~aCv~~~ef~lA~~~~l~L---------~~~ad~l~~lv~~Ye  218 (449)
T 1b89_A          154 LASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHI---------VVHADELEELINYYQ  218 (449)
T ss_dssp             HHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHHHHHHHTTCHHHHHHTTTTT---------TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhccHHHHHHHHHHc------CCchhHHHHHHHHHHcCcHHHHHHHHHHH---------HhCHhhHHHHHHHHH
Confidence            999999999999999999988      27889999999999999999995543321         122222346888999


Q ss_pred             hCCCHHHHHHHHHhcCCC---CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc---
Q 044988          304 SCGEIEEAYGVFRKMQRR---NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP---  377 (538)
Q Consensus       304 ~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p---  377 (538)
                      +.|++++|..+++....-   ....|+-+.-+|++-+                  -+++.+..+.|.   .+-+++|   
T Consensus       219 k~G~~eEai~lLe~aL~le~ah~~~ftel~il~~ky~------------------p~k~~ehl~~~~---~~ini~k~~~  277 (449)
T 1b89_A          219 DRGYFEELITMLEAALGLERAHMGMFTELAILYSKFK------------------PQKMREHLELFW---SRVNIPKVLR  277 (449)
T ss_dssp             HTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTC------------------HHHHHHHHHHHS---TTSCHHHHHH
T ss_pred             HCCCHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHhcC------------------HHHHHHHHHHHH---HHhcCcHHHH
Confidence            999999999999987653   3445555555555432                  223333444433   2224444   


Q ss_pred             ---cHHHHHHHHHHhhhcCChHHHHHHHHh
Q 044988          378 ---RIEHYGCMVDLFSRAGLMDEAFSLVQN  404 (538)
Q Consensus       378 ---~~~~~~~l~~~~~~~g~~~~A~~~~~~  404 (538)
                         +...|..+.-.|...++++.|....-+
T Consensus       278 ~~~~~~~w~e~~~ly~~~~e~d~A~~tm~~  307 (449)
T 1b89_A          278 AAEQAHLWAELVFLYDKYEEYDNAIITMMN  307 (449)
T ss_dssp             HHHTTTCHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhchHHHHHHHHHh
Confidence               356788888889999999988765543

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.80  E-value=2.9e-17  Score=154.11  Aligned_cols=84  Identities=7%  Similarity=-0.013  Sum_probs=65.0

Q ss_pred             cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHH
Q 044988          378 RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVAN  455 (538)
Q Consensus       378 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~  455 (538)
                      +..++..+..+|...|++++|.+.+++..  .+.+...+..+...+...|++++|.+.++++ .++.|+++..+. .++.
T Consensus       235 ~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~-~l~~  312 (330)
T 3hym_B          235 WEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTA-LGLRRDDTFSVT-MLGH  312 (330)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHHTT-TTTCSCCHHHHH-HHHH
T ss_pred             HHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHHHH-HccCCCchHHHH-HHHH
Confidence            45678888888888888888888888763  2335677888888888889999999999988 888888888677 7777


Q ss_pred             HH-HhcCCh
Q 044988          456 VY-AAAKRW  463 (538)
Q Consensus       456 ~~-~~~g~~  463 (538)
                      ++ ...|+.
T Consensus       313 ~~~~~~g~~  321 (330)
T 3hym_B          313 CIEMYIGDS  321 (330)
T ss_dssp             HHHTTTTC-
T ss_pred             HHHHHhCch
Confidence            77 344543

>1b89_A Protein (clathrin heavy chain); triskelion, coated vesicles, endocytosis, SELF- assembly, alpha-alpha superhelix; 2.60A {Bos taurus} SCOP: a.118.1.3

Probab=99.79  E-value=3.8e-18  Score=159.57  Aligned_cols=280  Identities=13%  Similarity=0.145  Sum_probs=138.3

Q ss_pred             HhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchHHHHHH
Q 044988           27 LQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLY  106 (538)
Q Consensus        27 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~  106 (538)
                      +...+++++|.++++.+      +++.+|..|..++.+.|++++|++.|.+.  +|...|..++.++...|++++|+..+
T Consensus        13 l~~~~~ld~A~~fae~~------~~~~vWs~La~A~l~~g~~~eAIdsfika--~D~~~y~~V~~~ae~~g~~EeAi~yl   84 (449)
T 1b89_A           13 IEHIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYL   84 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHccCHHHHHHHHHhC------CChHHHHHHHHHHHHcCCHHHHHHHHHcC--CCHHHHHHHHHHHHhCCCHHHHHHHH
Confidence            34667889999999987      34469999999999999999999999664  67779999999999999999999988


Q ss_pred             HHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCC
Q 044988          107 KQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARS  186 (538)
Q Consensus       107 ~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~  186 (538)
                      +..++.  .+++.+.+.++.+|.+.|+++++.++++       .|+..+|..++..|...|.   +++|...|..+    
T Consensus        85 ~~ark~--~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~---yeeA~~~Y~~a----  148 (449)
T 1b89_A           85 QMARKK--ARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKM---YDAAKLLYNNV----  148 (449)
T ss_dssp             --------------------------CHHHHTTTTT-------CC----------------C---TTTHHHHHHHT----
T ss_pred             HHHHHh--CccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCC---HHHHHHHHHHh----
Confidence            877764  5668889999999999999999988874       4777899999999999999   99999999988    


Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc
Q 044988          187 VVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEI  266 (538)
Q Consensus       187 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~  266 (538)
                       ..|..++.++.+.|++++|.+.+.++.  ++.+|..++.+|+..|+++.|......+   .+.|+  -...++..|.+.
T Consensus       149 -~n~~~LA~~L~~Lg~yq~AVea~~KA~--~~~~Wk~v~~aCv~~~ef~lA~~~~l~L---~~~ad--~l~~lv~~Yek~  220 (449)
T 1b89_A          149 -SNFGRLASTLVHLGEYQAAVDGARKAN--STRTWKEVCFACVDGKEFRLAQMCGLHI---VVHAD--ELEELINYYQDR  220 (449)
T ss_dssp             -TCHHHHHHHHHTTTCHHHHHHHHHHHT--CHHHHHHHHHHHHHTTCHHHHHHTTTTT---TTCHH--HHHHHHHHHHHT
T ss_pred             -hhHHHHHHHHHHhccHHHHHHHHHHcC--CchhHHHHHHHHHHcCcHHHHHHHHHHH---HhCHh--hHHHHHHHHHHC
Confidence             489999999999999999999999983  8899999999999999999996655542   23444  355788999999


Q ss_pred             CChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhC--CCHHHHHHHHHhcCC--------CCcchHHHHHHHHHhc
Q 044988          267 GDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASC--GEIEEAYGVFRKMQR--------RNTVSWTSMITGFAKQ  336 (538)
Q Consensus       267 ~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--g~~~~a~~~~~~m~~--------~~~~~~~~li~~~~~~  336 (538)
                      |++++|..+++.....     .+.....|+-|.-+|++-  +++.+..+.|..-..        .+...|.-+...|...
T Consensus       221 G~~eEai~lLe~aL~l-----e~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~ini~k~~~~~~~~~~w~e~~~ly~~~  295 (449)
T 1b89_A          221 GYFEELITMLEAALGL-----ERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKY  295 (449)
T ss_dssp             TCHHHHHHHHHHHTTS-----TTCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHhCC-----cHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999998876     477888888888888865  345555555543332        2577899999999999


Q ss_pred             CCccHHH
Q 044988          337 GYAQEAL  343 (538)
Q Consensus       337 ~~~~~a~  343 (538)
                      ++++.|.
T Consensus       296 ~e~d~A~  302 (449)
T 1b89_A          296 EEYDNAI  302 (449)
T ss_dssp             TCHHHHH
T ss_pred             chHHHHH
Confidence            9999887

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.79  E-value=3.9e-17  Score=153.29  Aligned_cols=275  Identities=11%  Similarity=-0.014  Sum_probs=201.7

Q ss_pred             CCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHH
Q 044988           49 SQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLL  125 (538)
Q Consensus        49 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li  125 (538)
                      +.++..+..+...+...|++++|+++|+++.   +.+...+..++..+...|++++|..+++++.+.. +.+...+..+.
T Consensus        19 ~~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~   97 (330)
T 3hym_B           19 QENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVG   97 (330)
T ss_dssp             -CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHH
Confidence            3455566666666777777777777776654   2344456666667777777777777777776642 33455667777


Q ss_pred             HHHHccC-CcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC---CCchhHHHHHHHHHhcC
Q 044988          126 SVCARCG-LFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA---RSVVSWNSLLKGYVKRG  201 (538)
Q Consensus       126 ~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g  201 (538)
                      ..+...| ++++|...+++..+.. +.+...+..+..++...|+   +++|...|++..+   .+...+..+...+...|
T Consensus        98 ~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~---~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~  173 (330)
T 3hym_B           98 CYYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESE---HDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTN  173 (330)
T ss_dssp             HHHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTC---HHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTT
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccC---HHHHHHHHHHHHHhccccHHHHHHHHHHHHHHh
Confidence            7777777 7777777777777654 3445667777777777777   7777777776553   24556666777788888


Q ss_pred             CHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC--------CCCCHHHHHHHHHHHHccCChH
Q 044988          202 DIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR--------VGLDQVALVAALSACAEIGDLK  270 (538)
Q Consensus       202 ~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g--------~~p~~~~~~~li~~~~~~~~~~  270 (538)
                      ++++|...|++..+   .+...+..+...+...|++++|...|+++.+..        .+.+..++..+...+...|+++
T Consensus       174 ~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  253 (330)
T 3hym_B          174 NSKLAERFFSQALSIAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYA  253 (330)
T ss_dssp             CHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHH
T ss_pred             hHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHH
Confidence            88888888877543   456788889999999999999999999887631        1334578888899999999999


Q ss_pred             HHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHHHH
Q 044988          271 LGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTSMITGF  333 (538)
Q Consensus       271 ~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~  333 (538)
                      .|...++.+.+.     .|.+...+..+...|...|++++|.+.|++..+  | +...+..+..++
T Consensus       254 ~A~~~~~~a~~~-----~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~  314 (330)
T 3hym_B          254 EALDYHRQALVL-----IPQNASTYSAIGYIHSLMGNFENAVDYFHTALGLRRDDTFSVTMLGHCI  314 (330)
T ss_dssp             HHHHHHHHHHHH-----STTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTCSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhh-----CccchHHHHHHHHHHHHhccHHHHHHHHHHHHccCCCchHHHHHHHHHH
Confidence            999999999987     566778888999999999999999999999876  3 455666666666

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.77  E-value=4.4e-16  Score=154.63  Aligned_cols=376  Identities=11%  Similarity=-0.034  Sum_probs=289.3

Q ss_pred             HHHHHHHHHhCCCCChhHHHHHHHHHHc----cCChhHHHHHHhcCC-CCCcchHHHHHHHHhc----CCCchHHHHHHH
Q 044988           37 FQIHSQIIINGFSQKNYILAKLLAFYVT----SGYLINAHKVFEKTE-NPSTAIWNQMIRGHAR----SETPEKSVYLYK  107 (538)
Q Consensus        37 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~-~~~~~~~~~li~~~~~----~~~~~~a~~~~~  107 (538)
                      ...+....+.   -++..+..+...|..    .+++++|...|++.. ..+...+..|...|..    .+++++|..+|+
T Consensus        27 ~~~~~~~a~~---g~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~  103 (490)
T 2xm6_A           27 LEQLKQKAES---GEAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQGYTPAEYVLGLRYMNGEGVPQDYAQAVIWYK  103 (490)
T ss_dssp             HHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHC---CCHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence            3444444443   367778888888887    899999999998765 3566788888888888    899999999999


Q ss_pred             HhHhCCCCCCcchHHHHHHHHHc----cCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHh----cCCCCChhHHHHHh
Q 044988          108 QMIDKETEPDEYTYSFLLSVCAR----CGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLM----SGGECGVGCARLLF  179 (538)
Q Consensus       108 ~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~~~~a~~~~  179 (538)
                      +..+.|   +...+..|...|..    .+++++|...|++..+.|   +...+..|...|..    .++   .++|...|
T Consensus       104 ~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~d---~~~A~~~~  174 (490)
T 2xm6_A          104 KAALKG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RDSGQQSMGDAYFEGDGVTRD---YVMAREWY  174 (490)
T ss_dssp             HHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCC---HHHHHHHH
T ss_pred             HHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCC---HHHHHHHH
Confidence            998764   56677778888877    789999999999998876   56677888888887    667   99999999


Q ss_pred             hcCCC-CCchhHHHHHHHHHh----cCCHHHHHHHHccCCC-CChHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCCC
Q 044988          180 DDMPA-RSVVSWNSLLKGYVK----RGDIDGAWKIFDEMPH-RNVVSWTTMISGCAQ----NGKSRQALSLFNEMRRARV  249 (538)
Q Consensus       180 ~~~~~-~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~  249 (538)
                      ++..+ .+...+..+...|..    .++.++|..+|++..+ .+..++..+...|..    .+++++|..+|++..+.| 
T Consensus       175 ~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~-  253 (490)
T 2xm6_A          175 SKAAEQGNVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSGDELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQG-  253 (490)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTT-
T ss_pred             HHHHHCCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC-
Confidence            87664 367788888888887    8999999999988653 566778888888886    789999999999988754 


Q ss_pred             CCCHHHHHHHHHHHHc----cCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhC-----CCHHHHHHHHHhcCC
Q 044988          250 GLDQVALVAALSACAE----IGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASC-----GEIEEAYGVFRKMQR  320 (538)
Q Consensus       250 ~p~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-----g~~~~a~~~~~~m~~  320 (538)
                        +...+..+...+..    .++.++|...++...+.    +   +...+..+...|...     +++++|...|++..+
T Consensus       254 --~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~----~---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~  324 (490)
T 2xm6_A          254 --NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQ----G---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAE  324 (490)
T ss_dssp             --CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTT----T---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHH
T ss_pred             --CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHc----C---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHh
Confidence              44566666666766    78999999999888765    3   334556788888887     899999999988765


Q ss_pred             C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhh----cCCh
Q 044988          321 R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSR----AGLM  395 (538)
Q Consensus       321 ~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~  395 (538)
                      . +...+..+...|...|..                 .+.++|...|++..+.    .+...+..|...|..    .+++
T Consensus       325 ~~~~~a~~~lg~~y~~~g~~-----------------~~~~~A~~~~~~a~~~----~~~~a~~~Lg~~y~~g~g~~~~~  383 (490)
T 2xm6_A          325 QGDATAQANLGAIYFRLGSE-----------------EEHKKAVEWFRKAAAK----GEKAAQFNLGNALLQGKGVKKDE  383 (490)
T ss_dssp             TTCHHHHHHHHHHHHHSCCH-----------------HHHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHTSSSCCCH
T ss_pred             cCCHHHHHHHHHHHHhCCCc-----------------ccHHHHHHHHHHHHHC----CCHHHHHHHHHHHHcCCCCCCCH
Confidence            3 444555555555443311                 2778899999988864    357788888888888    8999


Q ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHchhccCCC---CcccHHHHHHHHH
Q 044988          396 DEAFSLVQNMPMKPNDAVLGSLLLGCRI----HNNAELASQVAQKLVAEIDPE---QAAGYLALVANVY  457 (538)
Q Consensus       396 ~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~~~~p~---~~~~~~~~l~~~~  457 (538)
                      ++|.+.|++.....+...+..+...+..    .++.++|...|+++ .+..|+   ++.... .++.++
T Consensus       384 ~~A~~~~~~A~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A-~~~~~~~~~~~~a~~-~l~~~~  450 (490)
T 2xm6_A          384 QQAAIWMRKAAEQGLSAAQVQLGEIYYYGLGVERDYVQAWAWFDTA-STNDMNLFGTENRNI-TEKKLT  450 (490)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHH-HHHHCCHHHHHHHHH-HHTTSC
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH-HHCCCCCcCCHHHHH-HHHhcC
Confidence            9999999987545578888888888888    89999999999999 666643   554344 444433

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.77  E-value=2.8e-15  Score=150.38  Aligned_cols=404  Identities=8%  Similarity=0.016  Sum_probs=240.9

Q ss_pred             cHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC--CCcchHHHHHHHH-hc
Q 044988           19 TTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN--PSTAIWNQMIRGH-AR   95 (538)
Q Consensus        19 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--~~~~~~~~li~~~-~~   95 (538)
                      .+..++.. ...++++.|..+++.+++.- +.+...|..++..+.+.|++++|..+|++...  |+...|...+... ..
T Consensus        15 ~w~~l~~~-~~~~~~~~a~~~~e~al~~~-P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~p~~~lw~~~~~~~~~~   92 (530)
T 2ooe_A           15 AWSILIRE-AQNQPIDKARKTYERLVAQF-PSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLSYVRET   92 (530)
T ss_dssp             HHHHHHHH-HHSSCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH-HHhCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcCCChHHHHHHHHHHHHH
Confidence            44445543 45566666666666666542 33455666666666666677777776666552  5555555555322 23


Q ss_pred             CCCchHHHH----HHHHhHhC-CCCC-CcchHHHHHHHHHc---------cCCcHHHHHHHHHHHHhCCCCchhHHhHHH
Q 044988           96 SETPEKSVY----LYKQMIDK-ETEP-DEYTYSFLLSVCAR---------CGLFREGEQVHGRVLASGYCSNVFIRTNLM  160 (538)
Q Consensus        96 ~~~~~~a~~----~~~~m~~~-~~~p-~~~~~~~li~~~~~---------~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  160 (538)
                      .|+.+.|.+    +|+..... |..| +...|...+....+         .|+++.|..+|++.++....+....|....
T Consensus        93 ~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~~~~~~~~~  172 (530)
T 2ooe_A           93 KGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYN  172 (530)
T ss_dssp             TTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTHHHHHHHHH
T ss_pred             ccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhHHHHHHHHH
Confidence            455555544    55554432 3333 23345555554433         456666666666666521111112222222


Q ss_pred             HHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHcc-------CC------CCC--------hH
Q 044988          161 NLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDE-------MP------HRN--------VV  219 (538)
Q Consensus       161 ~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~-------m~------~~~--------~~  219 (538)
                      ......|    ...+..++.                 .+.+++..|..++..       +.      .|+        ..
T Consensus       173 ~~e~~~~----~~~~~~~l~-----------------~~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~~~  231 (530)
T 2ooe_A          173 KYEEGIN----IHLAKKMIE-----------------DRSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVD  231 (530)
T ss_dssp             HHHHHHC----HHHHHHHHH-----------------TTHHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCHHHHHH
T ss_pred             HHHHhhc----hhHHHHHHH-----------------HhhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhHHHHHH
Confidence            2111111    001111111                 123345555544433       11      122        23


Q ss_pred             HHHHHHHHHHHc----CCH----HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc-------cCChH-------HHHHHHH
Q 044988          220 SWTTMISGCAQN----GKS----RQALSLFNEMRRARVGLDQVALVAALSACAE-------IGDLK-------LGKWIHS  277 (538)
Q Consensus       220 ~~~~li~~~~~~----~~~----~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~-------~~~~~-------~a~~~~~  277 (538)
                      .|...+......    ++.    .+|..+|++.... .+-+...|......+.+       .|+++       .|..+++
T Consensus       232 ~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~-~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~  310 (530)
T 2ooe_A          232 MWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLV-LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYE  310 (530)
T ss_dssp             HHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHH
Confidence            555555443332    232    4778888888874 23356677777776664       68877       8888998


Q ss_pred             HHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CC-c-chHHHHHHHHHhcCCccHHHHHHHHHHHHh
Q 044988          278 YVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RN-T-VSWTSMITGFAKQGYAQEALLTFLGVLSAC  353 (538)
Q Consensus       278 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~-~-~~~~~li~~~~~~~~~~~a~~~~~~ll~~~  353 (538)
                      ...+.    ..|.+...|..++..+.+.|++++|..+|+++.+  |+ . ..|...+..+                    
T Consensus       311 ~Al~~----~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~--------------------  366 (530)
T 2ooe_A          311 RAIST----LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFA--------------------  366 (530)
T ss_dssp             HHTTT----TCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHH--------------------
T ss_pred             HHHHH----hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHH--------------------
Confidence            88863    3677888898999999999999999999998765  22 1 2344444333                    


Q ss_pred             cccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHH-hhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHH
Q 044988          354 SHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDL-FSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAEL  429 (538)
Q Consensus       354 ~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~-~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~  429 (538)
                      .+.|+++.|..+|++..+.   .|+ ...|...+.. +...|+.++|..+|++.. ..| +...|..++..+.+.|+.++
T Consensus       367 ~~~~~~~~A~~~~~~Al~~---~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~  443 (530)
T 2ooe_A          367 RRAEGIKSGRMIFKKARED---ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNN  443 (530)
T ss_dssp             HHHHHHHHHHHHHHHHHTC---TTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHH
T ss_pred             HHhcCHHHHHHHHHHHHhc---cCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhh
Confidence            3445788888999988754   343 3333332222 346899999999998763 334 47888889999999999999


Q ss_pred             HHHHHHHchhccCCCCcc----cHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          430 ASQVAQKLVAEIDPEQAA----GYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       430 A~~~~~~~~~~~~p~~~~----~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      |..+|+++ ....|.++.    .|. ..+....+.|+.+.+..+.+++.+
T Consensus       444 Ar~~~~~a-l~~~~~~~~~~~~lw~-~~~~~e~~~G~~~~~~~~~~r~~~  491 (530)
T 2ooe_A          444 TRVLFERV-LTSGSLPPEKSGEIWA-RFLAFESNIGDLASILKVEKRRFT  491 (530)
T ss_dssp             HHHHHHHH-HHSCCSCGGGCHHHHH-HHHHHHHHSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH-HhccCCCHHHHHHHHH-HHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999 666555443    455 556777788999999999988875

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.76  E-value=1.1e-14  Score=151.83  Aligned_cols=409  Identities=12%  Similarity=0.119  Sum_probs=286.7

Q ss_pred             CCccccHHHHHHHHhccCChHHHHHHHHHHHHhC--CCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHH
Q 044988           14 SSKALTTRQIFSLLQIRNTTKTLFQIHSQIIING--FSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIR   91 (538)
Q Consensus        14 ~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~   91 (538)
                      ..++.--+...+++...|.+.++.++++...-.+  +.-+....+.|+....+. +.....+..++..+-+   ...+..
T Consensus       982 ~~~PeeVs~~vKaf~~aglp~EaieLLEKivl~~s~fs~n~~LqnlLi~tAIka-D~~Rv~eyI~kLd~~d---~~eIA~ 1057 (1630)
T 1xi4_A          982 TQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKA-DRTRVMEYINRLDNYD---APDIAN 1057 (1630)
T ss_pred             ccCHHHhHHHHHHHHhCCCHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHh-ChhhHHHHHHHhhhcc---HHHHHH
Confidence            3344455677788888888888888888888432  112345555566555554 3344444444443222   445677


Q ss_pred             HHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCC
Q 044988           92 GHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECG  171 (538)
Q Consensus        92 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  171 (538)
                      .+...|.+++|..+|++..     -.....+.++.   ..+++++|.++.++.      .+..+|..+..++...|+   
T Consensus      1058 Iai~lglyEEAf~IYkKa~-----~~~~A~~VLie---~i~nldrAiE~Aerv------n~p~vWsqLAKAql~~G~--- 1120 (1630)
T 1xi4_A         1058 IAISNELFEEAFAIFRKFD-----VNTSAVQVLIE---HIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKGM--- 1120 (1630)
T ss_pred             HHHhCCCHHHHHHHHHHcC-----CHHHHHHHHHH---HHhhHHHHHHHHHhc------CCHHHHHHHHHHHHhCCC---
Confidence            7888899999999998852     11122233322   667888888887754      346688899999999999   


Q ss_pred             hhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCC--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC
Q 044988          172 VGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARV  249 (538)
Q Consensus       172 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  249 (538)
                      +++|...|.+.  .|...|..++.++.+.|++++|.+.|....+  +++...+.++.+|++.+++++...+.    +   
T Consensus      1121 ~kEAIdsYiKA--dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~e~~Idt~LafaYAKl~rleele~fI----~--- 1191 (1630)
T 1xi4_A         1121 VKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFI----N--- 1191 (1630)
T ss_pred             HHHHHHHHHhc--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcccccccHHHHHHHHhhcCHHHHHHHH----h---
Confidence            99999999664  5777888899999999999999999976443  33334445888899988887543332    2   


Q ss_pred             CCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHH
Q 044988          250 GLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSM  329 (538)
Q Consensus       250 ~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~l  329 (538)
                      .|+...|..+...|...|+++.|..+|..+             ..|..++..|.+.|++++|.+.+++.  .+..+|..+
T Consensus      1192 ~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA-------------~ny~rLA~tLvkLge~q~AIEaarKA--~n~~aWkev 1256 (1630)
T 1xi4_A         1192 GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-------------SNFGRLASTLVHLGEYQAAVDGARKA--NSTRTWKEV 1256 (1630)
T ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHhh-------------hHHHHHHHHHHHhCCHHHHHHHHHHh--CCHHHHHHH
Confidence            456667778888899999999999988874             25678999999999999999999987  556888888


Q ss_pred             HHHHHhcCCccHHH----------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhc--CChH
Q 044988          330 ITGFAKQGYAQEAL----------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRA--GLMD  396 (538)
Q Consensus       330 i~~~~~~~~~~~a~----------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~--g~~~  396 (538)
                      ..+|...|++..|.          ..+..++..|...|.+++|..+++...   ++.| ....|+.|..+|++.  ++..
T Consensus      1257 ~~acve~~Ef~LA~~cgl~Iiv~~deLeeli~yYe~~G~feEAI~LlE~aL---~LeraH~gmftELaiLyaKy~peklm 1333 (1630)
T 1xi4_A         1257 CFACVDGKEFRLAQMCGLHIVVHADELEELINYYQDRGYFEELITMLEAAL---GLERAHMGMFTELAILYSKFKPQKMR 1333 (1630)
T ss_pred             HHHHhhhhHHHHHHHHHHhhhcCHHHHHHHHHHHHHcCCHHHHHHHHHHHh---ccChhHhHHHHHHHHHHHhCCHHHHH
Confidence            88898888888887          345677788999999999999998776   4455 355777777777654  5667


Q ss_pred             HHHHHHHhCC-CC------CCHHHHHHHHHHHHhcCCHHHHHHHHHHc--------h---hccCCCCcccHHHHHHHHHH
Q 044988          397 EAFSLVQNMP-MK------PNDAVLGSLLLGCRIHNNAELASQVAQKL--------V---AEIDPEQAAGYLALVANVYA  458 (538)
Q Consensus       397 ~A~~~~~~~~-~~------p~~~~~~~l~~~~~~~~~~~~A~~~~~~~--------~---~~~~p~~~~~~~~~l~~~~~  458 (538)
                      ++.++|..-. ..      -+...|.-+.-.|.+.|+++.|...+-+-        .   .-.++.++..|. -.+..|.
T Consensus      1334 Ehlk~f~~rini~k~~r~~e~~~lW~elv~LY~~~~e~dnA~~tm~~h~~~a~~~~~Fk~~i~kv~n~elyy-kai~Fyl 1412 (1630)
T 1xi4_A         1334 EHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYY-RAIQFYL 1412 (1630)
T ss_pred             HHHHHHHHhcccchHhHHHHHHHHHHHHHHHHHhcccHHHHHHHHHhccHhhhhhHHHHHHhcccccHHHHH-HHHHHHH
Confidence            7777776543 22      24677888999999999999988322221        1   112455555555 4445555


Q ss_pred             hcC---------------ChHHHHHHHH
Q 044988          459 AAK---------------RWQDVAAVRQ  471 (538)
Q Consensus       459 ~~g---------------~~~~A~~~~~  471 (538)
                      ..+               +.+++.++++
T Consensus      1413 ~~~P~~lndLl~~l~~rlD~~R~V~l~~ 1440 (1630)
T 1xi4_A         1413 EFKPLLLNDLLMVLSPRLDHTRAVNYFS 1440 (1630)
T ss_pred             hhChHHHHHHHHHhhhcCChHHHHHHHH
Confidence            555               6666666665

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.74  E-value=3.3e-15  Score=149.90  Aligned_cols=380  Identities=10%  Similarity=0.035  Sum_probs=251.8

Q ss_pred             ccccCCCCCCCCccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHH-HccCChhHHHH----HHhcC
Q 044988            4 EEIIPANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFY-VTSGYLINAHK----VFEKT   78 (538)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~g~~~~a~~----~~~~~   78 (538)
                      ++.+...|.   +...+...+..+.+.++++.|..+|+..++..  |+...|...+... ...|+.++|.+    +|++.
T Consensus        36 e~al~~~P~---~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~~--p~~~lw~~~~~~~~~~~~~~~~a~~~~~~~~~~a  110 (530)
T 2ooe_A           36 ERLVAQFPS---SGRFWKLYIEAEIKAKNYDKVEKLFQRCLMKV--LHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFA  110 (530)
T ss_dssp             HHHHTTCTT---CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTC--CCHHHHHHHHHHHHHHTTTSTTHHHHHHHHHHHH
T ss_pred             HHHHHHCCC---CHHHHHHHHHHHHhcCCHHHHHHHHHHHHhcC--CChHHHHHHHHHHHHHccchhhHHHHHHHHHHHH
Confidence            344444443   34577788888999999999999999998875  5777787777533 45677777665    66653


Q ss_pred             C------CCCcchHHHHHHHHhc---------CCCchHHHHHHHHhHhCCCCCCc---chHHHHHHHHHcc---------
Q 044988           79 E------NPSTAIWNQMIRGHAR---------SETPEKSVYLYKQMIDKETEPDE---YTYSFLLSVCARC---------  131 (538)
Q Consensus        79 ~------~~~~~~~~~li~~~~~---------~~~~~~a~~~~~~m~~~~~~p~~---~~~~~li~~~~~~---------  131 (538)
                      .      .++...|...+....+         .|+++.|..+|++..+   .|+.   ..|..........         
T Consensus       111 l~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~---~P~~~~~~~~~~~~~~e~~~~~~~~~~~l  187 (530)
T 2ooe_A          111 LDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCV---NPMINIEQLWRDYNKYEEGINIHLAKKMI  187 (530)
T ss_dssp             HHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTT---SCCTTHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred             HHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHh---chhhhHHHHHHHHHHHHHhhchhHHHHHH
Confidence            2      2456678887776654         6889999999999987   2432   2333322211111         


Q ss_pred             ----CCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCC---CCC--------chhHHHHHHH
Q 044988          132 ----GLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMP---ARS--------VVSWNSLLKG  196 (538)
Q Consensus       132 ----~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~---~~~--------~~~~~~li~~  196 (538)
                          +++..|..++...                            +.....++...   .|+        ...|...+..
T Consensus       188 ~~~~~~~~~A~~~~~~~----------------------------~~~~~~l~~~~~~~~p~~~~~~~~~~~~w~~~~~~  239 (530)
T 2ooe_A          188 EDRSRDYMNARRVAKEY----------------------------ETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQW  239 (530)
T ss_dssp             HTTHHHHHHHHHHHHHH----------------------------HHHHHHCCSSSCCCCCC--CCHHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHHH----------------------------HHHHHHhccccccCCCCCChhHHHHHHHHHHHHHH
Confidence                1122222222221                            11111222211   111        1344444433


Q ss_pred             HHhc----CCH----HHHHHHHccCCC---CChHHHHHHHHHHHH-------cCCHH-------HHHHHHHHHHHCCCCC
Q 044988          197 YVKR----GDI----DGAWKIFDEMPH---RNVVSWTTMISGCAQ-------NGKSR-------QALSLFNEMRRARVGL  251 (538)
Q Consensus       197 ~~~~----g~~----~~A~~~~~~m~~---~~~~~~~~li~~~~~-------~~~~~-------~a~~~~~~m~~~g~~p  251 (538)
                      ....    ++.    ..+..+|++...   .+...|..++..+.+       .|+++       +|..+|++..+.-.+-
T Consensus       240 e~~~~~~~~~~~~~~~~a~~~y~~al~~~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~~~Al~~~~p~  319 (530)
T 2ooe_A          240 EKSNPLRTEDQTLITKRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKK  319 (530)
T ss_dssp             HHHCSSCCSCSHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHTTTTCSS
T ss_pred             HHcCCccCCcchhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHHHHHHHHhCcc
Confidence            2221    222    356667766543   356678888777765       68876       8999999987632233


Q ss_pred             CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc-hhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHH
Q 044988          252 DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL-VSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMI  330 (538)
Q Consensus       252 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li  330 (538)
                      +...+..++..+.+.|+++.|..+|+.+.+.     .|.+ ..+|..++..+.+.|++++|.++|++..+.....+...+
T Consensus       320 ~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~-----~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~~~~~~~~~~  394 (530)
T 2ooe_A          320 NMLLYFAYADYEESRMKYEKVHSIYNRLLAI-----EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYV  394 (530)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS-----SSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCTTCCTHHHH
T ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc-----cccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhccCCchHHHH
Confidence            5777888888888999999999999999886     4444 357888888899999999999999988763222211111


Q ss_pred             HHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC---
Q 044988          331 TGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP---  406 (538)
Q Consensus       331 ~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---  406 (538)
                      .               ...+ .+...|+.+.|..+|+...+.   .| +...|..++..+.+.|+.++|..+|++..   
T Consensus       395 ~---------------~a~~-~~~~~~~~~~A~~~~e~al~~---~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~  455 (530)
T 2ooe_A          395 T---------------AALM-EYYCSKDKSVAFKIFELGLKK---YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG  455 (530)
T ss_dssp             H---------------HHHH-HHHHTCCHHHHHHHHHHHHHH---HTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSC
T ss_pred             H---------------HHHH-HHHHcCChhHHHHHHHHHHHH---CCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhcc
Confidence            0               0001 112356889999999998876   35 57889999999999999999999999874   


Q ss_pred             -CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCC
Q 044988          407 -MKPN--DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPE  444 (538)
Q Consensus       407 -~~p~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~  444 (538)
                       ..|+  ...|...+......|+.+.+..+.+++ .+..|+
T Consensus       456 ~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~-~~~~p~  495 (530)
T 2ooe_A          456 SLPPEKSGEIWARFLAFESNIGDLASILKVEKRR-FTAFRE  495 (530)
T ss_dssp             CSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHH-HHHTHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHHCch
Confidence             1232  458888888889999999999999999 777774

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.74  E-value=1.6e-16  Score=151.71  Aligned_cols=270  Identities=12%  Similarity=0.037  Sum_probs=204.2

Q ss_pred             hhHHHH-HhhcCCC--C-----CchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHH
Q 044988          172 VGCARL-LFDDMPA--R-----SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSL  240 (538)
Q Consensus       172 ~~~a~~-~~~~~~~--~-----~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~  240 (538)
                      +++|.. .|++...  +     +...+..+...+.+.|++++|...|+++.+   .+..+|..+...+...|++++|...
T Consensus        41 ~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~  120 (368)
T 1fch_A           41 YDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISA  120 (368)
T ss_dssp             -----CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHHHHHH
Confidence            677776 6665443  1     345677788888888888888888888653   3556788888888899999999999


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHH---------------HHHHHHhC
Q 044988          241 FNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNA---------------LIHMYASC  305 (538)
Q Consensus       241 ~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~---------------l~~~~~~~  305 (538)
                      |+++.+.. +.+..++..+...+...|+++.|...++.+.+.     .|.+...+..               .+..+...
T Consensus       121 ~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (368)
T 1fch_A          121 LRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRY-----TPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSD  194 (368)
T ss_dssp             HHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT-----STTTGGGCC---------------CTTHHHHHH
T ss_pred             HHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhc
Confidence            99888753 346778888888888899999999999888876     3333332221               13333488


Q ss_pred             CCHHHHHHHHHhcCC--CC---cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cH
Q 044988          306 GEIEEAYGVFRKMQR--RN---TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RI  379 (538)
Q Consensus       306 g~~~~a~~~~~~m~~--~~---~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~  379 (538)
                      |++++|...|+++.+  |+   ..++..+...+...|                    ++++|...|+++.+.   .| +.
T Consensus       195 ~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g--------------------~~~~A~~~~~~al~~---~~~~~  251 (368)
T 1fch_A          195 SLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSG--------------------EYDKAVDCFTAALSV---RPNDY  251 (368)
T ss_dssp             HHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTT--------------------CHHHHHHHHHHHHHH---CTTCH
T ss_pred             ccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcC--------------------CHHHHHHHHHHHHHh---CcCCH
Confidence            999999999998764  32   445555555555554                    777788888888765   34 57


Q ss_pred             HHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC-----------c
Q 044988          380 EHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ-----------A  446 (538)
Q Consensus       380 ~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~-----------~  446 (538)
                      .++..+...|...|++++|.+.|+++. . +.+...+..+...+...|++++|...++++ ....|++           .
T Consensus       252 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a-l~~~~~~~~~~~~~~~~~~  330 (368)
T 1fch_A          252 LLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEA-LNMQRKSRGPRGEGGAMSE  330 (368)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHHHHTC------CCCCCH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHH-HHhCCCCCCccccccchhh
Confidence            899999999999999999999999874 2 345788999999999999999999999999 7777776           6


Q ss_pred             ccHHHHHHHHHHhcCChHHHHHHHHH
Q 044988          447 AGYLALVANVYAAAKRWQDVAAVRQK  472 (538)
Q Consensus       447 ~~~~~~l~~~~~~~g~~~~A~~~~~~  472 (538)
                      ..+. .++.+|...|++++|..++++
T Consensus       331 ~~~~-~l~~~~~~~g~~~~A~~~~~~  355 (368)
T 1fch_A          331 NIWS-TLRLALSMLGQSDAYGAADAR  355 (368)
T ss_dssp             HHHH-HHHHHHHHHTCGGGHHHHHTT
T ss_pred             HHHH-HHHHHHHHhCChHhHHHhHHH
Confidence            6678 999999999999999988764

>1fch_A Peroxisomal targeting signal 1 receptor; protein-peptide complex, tetratricopeptide repeat, TPR, helical repeat, signaling protein; 2.20A {Homo sapiens} SCOP: a.118.8.1 PDB: 2j9q_A 3imz_B* 3r9a_B* 2c0m_A 2c0l_A

Probab=99.73  E-value=2.4e-16  Score=150.45  Aligned_cols=271  Identities=11%  Similarity=-0.018  Sum_probs=213.7

Q ss_pred             HHccCChhHHHH-HHhcCCC-----C--CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCC
Q 044988           62 YVTSGYLINAHK-VFEKTEN-----P--STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGL  133 (538)
Q Consensus        62 ~~~~g~~~~a~~-~~~~~~~-----~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~  133 (538)
                      +...|++++|.. .|++...     |  +...+..+...+.+.|++++|+..|+++.+.. +.+..++..+...+...|+
T Consensus        35 ~~~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~  113 (368)
T 1fch_A           35 HPWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQ  113 (368)
T ss_dssp             -----------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcC
Confidence            344578888988 8875542     2  35678889999999999999999999999864 4466788999999999999


Q ss_pred             cHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC---CchhHHH---------------HHH
Q 044988          134 FREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPAR---SVVSWNS---------------LLK  195 (538)
Q Consensus       134 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~---~~~~~~~---------------li~  195 (538)
                      +++|...++++.+.. +.+..++..+..+|...|+   .++|...|+++.+.   +...+..               .+.
T Consensus       114 ~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  189 (368)
T 1fch_A          114 ELLAISALRRCLELK-PDNQTALMALAVSFTNESL---QRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILG  189 (368)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHTSTTTGGGCC---------------CTTH
T ss_pred             HHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCC---HHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHH
Confidence            999999999999886 5678899999999999999   99999999886642   2222221               233


Q ss_pred             HHHhcCCHHHHHHHHccCCC--C---ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChH
Q 044988          196 GYVKRGDIDGAWKIFDEMPH--R---NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLK  270 (538)
Q Consensus       196 ~~~~~g~~~~A~~~~~~m~~--~---~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~  270 (538)
                      .+...|++++|...|+++.+  |   +..++..+...|...|++++|...|+++.+.. +.+...+..+...+...|+++
T Consensus       190 ~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~  268 (368)
T 1fch_A          190 SLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSE  268 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHhhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHH
Confidence            34489999999999998753  3   46789999999999999999999999998752 335788999999999999999


Q ss_pred             HHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C-C-----------cchHHHHHHHHHhc
Q 044988          271 LGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--R-N-----------TVSWTSMITGFAKQ  336 (538)
Q Consensus       271 ~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~-~-----------~~~~~~li~~~~~~  336 (538)
                      .|...++.+.+.     .|.+..++..+..+|.+.|++++|...|+++.+  | +           ..+|..+..+|...
T Consensus       269 ~A~~~~~~al~~-----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  343 (368)
T 1fch_A          269 EAVAAYRRALEL-----QPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSML  343 (368)
T ss_dssp             HHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh-----CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHh
Confidence            999999999987     677788889999999999999999999998764  2 2           46777777788877


Q ss_pred             CCccHHH
Q 044988          337 GYAQEAL  343 (538)
Q Consensus       337 ~~~~~a~  343 (538)
                      |+.++|.
T Consensus       344 g~~~~A~  350 (368)
T 1fch_A          344 GQSDAYG  350 (368)
T ss_dssp             TCGGGHH
T ss_pred             CChHhHH
Confidence            7777665

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.73  E-value=2.2e-14  Score=142.39  Aligned_cols=357  Identities=11%  Similarity=0.024  Sum_probs=285.4

Q ss_pred             CCCcchHHHHHHHHhc----CCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHc----cCCcHHHHHHHHHHHHhCCCC
Q 044988           80 NPSTAIWNQMIRGHAR----SETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCAR----CGLFREGEQVHGRVLASGYCS  151 (538)
Q Consensus        80 ~~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~  151 (538)
                      ..+...+..+...|..    .+++++|+..|++..+.|   +...+..|...|..    .+++++|...|++..+.|   
T Consensus        36 ~g~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---  109 (490)
T 2xm6_A           36 SGEAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---  109 (490)
T ss_dssp             TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---
T ss_pred             CCCHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---
Confidence            4567777778888877    899999999999998864   56688888888888    899999999999999876   


Q ss_pred             chhHHhHHHHHHHh----cCCCCChhHHHHHhhcCCCC-CchhHHHHHHHHHh----cCCHHHHHHHHccCCC-CChHHH
Q 044988          152 NVFIRTNLMNLYLM----SGGECGVGCARLLFDDMPAR-SVVSWNSLLKGYVK----RGDIDGAWKIFDEMPH-RNVVSW  221 (538)
Q Consensus       152 ~~~~~~~l~~~~~~----~g~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~-~~~~~~  221 (538)
                      +...+..|...|..    .++   .++|...|++..+. +...+..+...|..    .+++++|...|++..+ .+...+
T Consensus       110 ~~~a~~~Lg~~y~~g~g~~~~---~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~~~~a~  186 (490)
T 2xm6_A          110 LPQAQQNLGVMYHEGNGVKVD---KAESVKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQGNVWSC  186 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCC---HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCCCC---HHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHH
Confidence            56677788888888    677   99999999887654 66778888888887    8899999999988653 567788


Q ss_pred             HHHHHHHHH----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----cCChHHHHHHHHHHHHhccCCCCCcchh
Q 044988          222 TTMISGCAQ----NGKSRQALSLFNEMRRARVGLDQVALVAALSACAE----IGDLKLGKWIHSYVEENFSVGREPVLVS  293 (538)
Q Consensus       222 ~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~  293 (538)
                      ..+...|..    .+++++|..+|++..+.|   +...+..+...+..    .++++.|...++...+.    +.   ..
T Consensus       187 ~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~----~~---~~  256 (490)
T 2xm6_A          187 NQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQ----GN---SI  256 (490)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTT----TC---HH
T ss_pred             HHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHC----CC---HH
Confidence            888888888    899999999999998865   55667777777775    78999999999988775    32   34


Q ss_pred             HHHHHHHHHHh----CCCHHHHHHHHHhcCCC-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHH
Q 044988          294 LNNALIHMYAS----CGEIEEAYGVFRKMQRR-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFEC  368 (538)
Q Consensus       294 ~~~~l~~~~~~----~g~~~~a~~~~~~m~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~  368 (538)
                      .+..+...|..    .++.++|...|++..+. +...+..+...|....               ....+++++|...|++
T Consensus       257 a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~~~---------------~g~~~~~~~A~~~~~~  321 (490)
T 2xm6_A          257 AQFRLGYILEQGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHLYDKGA---------------EGVAKNREQAISWYTK  321 (490)
T ss_dssp             HHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHCB---------------TTBCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCC---------------CCCcCCHHHHHHHHHH
Confidence            55567788887    89999999999987653 4445555555554430               0112588899999998


Q ss_pred             hhhhcCCCccHHHHHHHHHHhhhcC---ChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHchhcc
Q 044988          369 MNQNWGIKPRIEHYGCMVDLFSRAG---LMDEAFSLVQNMPMKPNDAVLGSLLLGCRI----HNNAELASQVAQKLVAEI  441 (538)
Q Consensus       369 ~~~~~~~~p~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~~~  441 (538)
                      ..+. +   +...+..|...|...|   +.++|.+.|++.....+...+..+...+..    .+++++|...+++. .+.
T Consensus       322 a~~~-~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A-~~~  396 (490)
T 2xm6_A          322 SAEQ-G---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKGEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKA-AEQ  396 (490)
T ss_dssp             HHHT-T---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHH-HHT
T ss_pred             HHhc-C---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH-HhC
Confidence            8765 3   4567778888887766   789999999988645678889999999988    89999999999999 553


Q ss_pred             CCCCcccHHHHHHHHHHh----cCChHHHHHHHHHHHhCCC
Q 044988          442 DPEQAAGYLALVANVYAA----AKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       442 ~p~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~~~  478 (538)
                        .++..+. .|+.+|.+    .++.++|...|++..+.+.
T Consensus       397 --~~~~a~~-~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~  434 (490)
T 2xm6_A          397 --GLSAAQV-QLGEIYYYGLGVERDYVQAWAWFDTASTNDM  434 (490)
T ss_dssp             --TCHHHHH-HHHHHHHHTSSSCCCHHHHHHHHHHHHHHHC
T ss_pred             --CCHHHHH-HHHHHHHcCCCCCCCHHHHHHHHHHHHHCCC
Confidence              3455577 89999998    8999999999999998764

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.73  E-value=2.6e-16  Score=150.00  Aligned_cols=242  Identities=10%  Similarity=-0.029  Sum_probs=191.9

Q ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          217 NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       217 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                      +...|..+...+.+.|++++|...|+++.+.. +.+...+..+...+...|+++.|...++.+.+.     .|.+..++.
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~-----~p~~~~~~~  137 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLEL-----QPNNLKALM  137 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc-----CCCCHHHHH
Confidence            44568888889999999999999999998753 346788888999999999999999999999887     677788888


Q ss_pred             HHHHHHHhCCCHHHHHHHHHhcCCCCc---chHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc
Q 044988          297 ALIHMYASCGEIEEAYGVFRKMQRRNT---VSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       297 ~l~~~~~~~g~~~~a~~~~~~m~~~~~---~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  373 (538)
                      .+...|...|++++|...|+++.+.++   ..+..+.          .....+..+...+...|++++|..+|+++.+..
T Consensus       138 ~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~----------~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  207 (365)
T 4eqf_A          138 ALAVSYTNTSHQQDACEALKNWIKQNPKYKYLVKNKK----------GSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQN  207 (365)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCHHHHCC-----------------------------CCHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHccccHHHHHHHHHHHHHhCccchHHHhhhc----------cchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhC
Confidence            999999999999999999998865221   1111110          000234445667778889999999999998773


Q ss_pred             CCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHH
Q 044988          374 GIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLA  451 (538)
Q Consensus       374 ~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~  451 (538)
                      .-.++..++..+...|...|++++|.+.|+++.  .+.+..+|..+..++...|++++|+..++++ ....|++...+. 
T Consensus       208 p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~-  285 (365)
T 4eqf_A          208 GDMIDPDLQTGLGVLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRA-LEIQPGFIRSRY-  285 (365)
T ss_dssp             CSSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-
T ss_pred             cCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhcCCCchHHHH-
Confidence            222258899999999999999999999999874  3445889999999999999999999999999 899999999888 


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          452 LVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       452 ~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      .++.+|.+.|++++|...+++..+.
T Consensus       286 ~l~~~~~~~g~~~~A~~~~~~al~~  310 (365)
T 4eqf_A          286 NLGISCINLGAYREAVSNFLTALSL  310 (365)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            9999999999999999999999753

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.73  E-value=1.7e-16  Score=151.26  Aligned_cols=257  Identities=9%  Similarity=-0.010  Sum_probs=202.3

Q ss_pred             CchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 044988          186 SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSA  262 (538)
Q Consensus       186 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~  262 (538)
                      +...|..+...+.+.|++++|...|+++.+   .+..+|..+...|...|++++|+..|+++.+.. +.+..++..+...
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~  142 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQDPGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAVS  142 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            456688889999999999999999998763   466789999999999999999999999998753 3357888999999


Q ss_pred             HHccCChHHHHHHHHHHHHhccCCCCCcchhHH----------HHHHHHHHhCCCHHHHHHHHHhcCC--C---CcchHH
Q 044988          263 CAEIGDLKLGKWIHSYVEENFSVGREPVLVSLN----------NALIHMYASCGEIEEAYGVFRKMQR--R---NTVSWT  327 (538)
Q Consensus       263 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~----------~~l~~~~~~~g~~~~a~~~~~~m~~--~---~~~~~~  327 (538)
                      +...|+++.|...++.+.+.     .|.+...+          ..+...+...|++++|...|+++.+  |   +...+.
T Consensus       143 ~~~~g~~~~A~~~~~~al~~-----~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~  217 (365)
T 4eqf_A          143 YTNTSHQQDACEALKNWIKQ-----NPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQT  217 (365)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH-----CHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHH
T ss_pred             HHccccHHHHHHHHHHHHHh-----CccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHH
Confidence            99999999999999999886     33333322          3458889999999999999998875  3   345555


Q ss_pred             HHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-
Q 044988          328 SMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-  406 (538)
Q Consensus       328 ~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-  406 (538)
                      .+...|...|                    ++++|...|+++.+..  +.+..+|..+..+|...|++++|.+.|+++. 
T Consensus       218 ~l~~~~~~~g--------------------~~~~A~~~~~~al~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  275 (365)
T 4eqf_A          218 GLGVLFHLSG--------------------EFNRAIDAFNAALTVR--PEDYSLWNRLGATLANGDRSEEAVEAYTRALE  275 (365)
T ss_dssp             HHHHHHHHHT--------------------CHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCC--------------------CHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            5555555555                    7778888888887651  3358899999999999999999999999874 


Q ss_pred             CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCC------------CcccHHHHHHHHHHhcCChHHHHHHHHH
Q 044988          407 MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPE------------QAAGYLALVANVYAAAKRWQDVAAVRQK  472 (538)
Q Consensus       407 ~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~------------~~~~~~~~l~~~~~~~g~~~~A~~~~~~  472 (538)
                      ..| +..++..+...+...|++++|...++++ ..+.|+            ....+. .++.++...|+.+.+.++.++
T Consensus       276 ~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a-l~~~~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          276 IQPGFIRSRYNLGISCINLGAYREAVSNFLTA-LSLQRKSRNQQQVPHPAISGNIWA-ALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHH-HHHHHCC------------CHHHH-HHHHHHHHHTCHHHHHHHHTT
T ss_pred             cCCCchHHHHHHHHHHHHCCCHHHHHHHHHHH-HHhCcccCCCcccchhhhHHHHHH-HHHHHHHHcCcHHHHHHHHHh
Confidence            344 4888999999999999999999999999 666665            244567 899999999999988887655

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.73  E-value=2.5e-15  Score=137.54  Aligned_cols=269  Identities=10%  Similarity=0.050  Sum_probs=197.6

Q ss_pred             HhcCCCCChhHHHHHhhcCCCCCc----hhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHH
Q 044988          164 LMSGGECGVGCARLLFDDMPARSV----VSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALS  239 (538)
Q Consensus       164 ~~~g~~~~~~~a~~~~~~~~~~~~----~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~  239 (538)
                      ...|+   +..|+..++.....++    .....+.++|...|+++.|+..++....|+..++..+...+...++.++|++
T Consensus        10 ~~~g~---y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~~~~~~~~a~~~la~~~~~~~~~~~A~~   86 (291)
T 3mkr_A           10 FYIGS---YQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKPSSAPELQAVRMFAEYLASHSRRDAIVA   86 (291)
T ss_dssp             HHTTC---HHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCTTSCHHHHHHHHHHHHHHCSTTHHHHHH
T ss_pred             HHHHH---HHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcccCChhHHHHHHHHHHHcCCCcHHHHHH
Confidence            34566   7777777666554322    2334566788888888888888877555666778888888888899999999


Q ss_pred             HHHHHHHCCCCCC-HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          240 LFNEMRRARVGLD-QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       240 ~~~~m~~~g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                      .++++...+..|+ ...+..+...+...|++++|...++.          |.+...+..++..|.+.|++++|.+.|+++
T Consensus        87 ~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~----------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~  156 (291)
T 3mkr_A           87 ELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ----------GDSLECMAMTVQILLKLDRLDLARKELKKM  156 (291)
T ss_dssp             HHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT----------CCSHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC----------CCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            9999888776564 44555566778888999999887754          566677788888999999999999999888


Q ss_pred             CC--CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChH
Q 044988          319 QR--RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMD  396 (538)
Q Consensus       319 ~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  396 (538)
                      .+  |+. +...+..++.                ..+...|++++|..+|+++.+..  +.+...++.+..++.+.|+++
T Consensus       157 ~~~~p~~-~~~~l~~a~~----------------~l~~~~~~~~eA~~~~~~~l~~~--p~~~~~~~~la~~~~~~g~~~  217 (291)
T 3mkr_A          157 QDQDEDA-TLTQLATAWV----------------SLAAGGEKLQDAYYIFQEMADKC--SPTLLLLNGQAACHMAQGRWE  217 (291)
T ss_dssp             HHHCTTC-HHHHHHHHHH----------------HHHHCTTHHHHHHHHHHHHHHHS--CCCHHHHHHHHHHHHHTTCHH
T ss_pred             HhhCcCc-HHHHHHHHHH----------------HHHhCchHHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHH
Confidence            65  332 1222222221                11223468899999999998762  446888999999999999999


Q ss_pred             HHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHH-HHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHH
Q 044988          397 EAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAEL-ASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVR  470 (538)
Q Consensus       397 ~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~-A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~  470 (538)
                      +|.+.|+++. ..| +..++..++..+...|+.++ +.++++++ ....|+++. ..    +...+.+.++++..-|
T Consensus       218 eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~-~~~~P~~~~-~~----d~~~~~~~fd~~~~~~  288 (291)
T 3mkr_A          218 AAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQL-KDAHRSHPF-IK----EYRAKENDFDRLVLQY  288 (291)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHH-HHHCTTCHH-HH----HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHH-HHhCCCChH-HH----HHHHHHHHHHHHHHHc
Confidence            9999999863 344 57788899989888998865 67899999 999999877 33    4566666677666544

>1xi4_A Clathrin heavy chain; alpha-ZIG-ZAG, beta-propeller, endocytosis-exocyto complex; 7.90A {Bos taurus} SCOP: i.23.1.1 PDB: 1xi5_A 3iyv_A

Probab=99.72  E-value=5.4e-14  Score=146.76  Aligned_cols=403  Identities=11%  Similarity=0.114  Sum_probs=276.9

Q ss_pred             ccHHHHHHHHhccCChHHHHH-----------HHHHHHHhCC--CCChhHHHHHHHHHHccCChhHHHHHHhcCC-CCC-
Q 044988           18 LTTRQIFSLLQIRNTTKTLFQ-----------IHSQIIINGF--SQKNYILAKLLAFYVTSGYLINAHKVFEKTE-NPS-   82 (538)
Q Consensus        18 ~~~~~ll~~~~~~~~~~~a~~-----------~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-~~~-   82 (538)
                      ..|....+.+.+..+++.-..           +.++.....+  ..++.-....+..|...|.+.+|+++++++. .|+ 
T Consensus       938 ~l~k~~arylv~r~d~~lW~~vl~~~n~~RR~Lidqv~a~aL~e~~~PeeVs~~vKaf~~aglp~EaieLLEKivl~~s~ 1017 (1630)
T 1xi4_A          938 SLFKSLSRYLVRRKDPELWGSVLLESNPYRRPLIDQVVQTALSETQDPEEVSVTVKAFMTADLPNELIELLEKIVLDNSV 1017 (1630)
T ss_pred             hhHHHHHHHHHHhcCHHHHHHHhcCCcHHHHHHHHHHHHhhcccccCHHHhHHHHHHHHhCCCHHHHHHHHHHHHcCCCc
Confidence            345555555665555544333           2233222221  2345555667788888888888888888776 332 


Q ss_pred             ----cchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhH
Q 044988           83 ----TAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTN  158 (538)
Q Consensus        83 ----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  158 (538)
                          ...-+.++.+..+. +..+..+..++....       ...-+...+...|.+++|..+|++..     -.....+.
T Consensus      1018 fs~n~~LqnlLi~tAIka-D~~Rv~eyI~kLd~~-------d~~eIA~Iai~lglyEEAf~IYkKa~-----~~~~A~~V 1084 (1630)
T 1xi4_A         1018 FSEHRNLQNLLILTAIKA-DRTRVMEYINRLDNY-------DAPDIANIAISNELFEEAFAIFRKFD-----VNTSAVQV 1084 (1630)
T ss_pred             ccccHHHHHHHHHHHHHh-ChhhHHHHHHHhhhc-------cHHHHHHHHHhCCCHHHHHHHHHHcC-----CHHHHHHH
Confidence                24456666666666 556666665554421       13346677888899999999988852     11111222


Q ss_pred             HHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHH
Q 044988          159 LMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQAL  238 (538)
Q Consensus       159 l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~  238 (538)
                      +   +-..++   +++|.++.++..  +..+|..+..++...|++++|+..|.+.  .|...|..++.++.+.|++++|.
T Consensus      1085 L---ie~i~n---ldrAiE~Aervn--~p~vWsqLAKAql~~G~~kEAIdsYiKA--dD~say~eVa~~~~~lGkyEEAI 1154 (1630)
T 1xi4_A         1085 L---IEHIGN---LDRAYEFAERCN--EPAVWSQLAKAQLQKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELV 1154 (1630)
T ss_pred             H---HHHHhh---HHHHHHHHHhcC--CHHHHHHHHHHHHhCCCHHHHHHHHHhc--CChHHHHHHHHHHHHcCCHHHHH
Confidence            2   226677   888888888764  4677889999999999999999999764  56777888999999999999999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          239 SLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       239 ~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                      ++|....+..  ++....+.++.+|++.++++....+.    +      .+ +...+..+...|...|++++|...|...
T Consensus      1155 eyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI----~------~~-n~ad~~~iGd~le~eg~YeeA~~~Y~kA 1221 (1630)
T 1xi4_A         1155 KYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI----N------GP-NNAHIQQVGDRCYDEKMYDAAKLLYNNV 1221 (1630)
T ss_pred             HHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH----h------CC-CHHHHHHHHHHHHhcCCHHHHHHHHHhh
Confidence            9998877644  34333445888888888887544332    2      12 2334456888999999999999999885


Q ss_pred             CCCCcchHHHHHHHHHhcCCccHHH---------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHh
Q 044988          319 QRRNTVSWTSMITGFAKQGYAQEAL---------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLF  389 (538)
Q Consensus       319 ~~~~~~~~~~li~~~~~~~~~~~a~---------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~  389 (538)
                           ..|..+...|.+.|++++|+         .+|..+-.+|...|++..|..+...+      ..+...+..++..|
T Consensus      1222 -----~ny~rLA~tLvkLge~q~AIEaarKA~n~~aWkev~~acve~~Ef~LA~~cgl~I------iv~~deLeeli~yY 1290 (1630)
T 1xi4_A         1222 -----SNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHI------VVHADELEELINYY 1290 (1630)
T ss_pred             -----hHHHHHHHHHHHhCCHHHHHHHHHHhCCHHHHHHHHHHHhhhhHHHHHHHHHHhh------hcCHHHHHHHHHHH
Confidence                 48888999999999999988         66677777888888888888876542      23455677899999


Q ss_pred             hhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHh--cCCHHHHHHHHHHchhccCC-----CCcccHHHHHHHHHHhc
Q 044988          390 SRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRI--HNNAELASQVAQKLVAEIDP-----EQAAGYLALVANVYAAA  460 (538)
Q Consensus       390 ~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~--~~~~~~A~~~~~~~~~~~~p-----~~~~~~~~~l~~~~~~~  460 (538)
                      .+.|.+++|+.+++... ..|. ...|.-+...+++  .++..++.++|..- ..+.|     .+...|. -++-.|.+.
T Consensus      1291 e~~G~feEAI~LlE~aL~LeraH~gmftELaiLyaKy~peklmEhlk~f~~r-ini~k~~r~~e~~~lW~-elv~LY~~~ 1368 (1630)
T 1xi4_A         1291 QDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSR-VNIPKVLRAAEQAHLWA-ELVFLYDKY 1368 (1630)
T ss_pred             HHcCCHHHHHHHHHHHhccChhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHh-cccchHhHHHHHHHHHH-HHHHHHHhc
Confidence            99999999999997763 3333 3455555555544  34566666666654 45544     4555577 777889999


Q ss_pred             CChHHHHHH
Q 044988          461 KRWQDVAAV  469 (538)
Q Consensus       461 g~~~~A~~~  469 (538)
                      |+++.|...
T Consensus      1369 ~e~dnA~~t 1377 (1630)
T 1xi4_A         1369 EEYDNAIIT 1377 (1630)
T ss_pred             ccHHHHHHH
Confidence            999999843

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.72  E-value=6.2e-15  Score=134.96  Aligned_cols=248  Identities=10%  Similarity=-0.008  Sum_probs=200.8

Q ss_pred             HHHHHhcCCHHHHHHHHccCCCCCh----HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCh
Q 044988          194 LKGYVKRGDIDGAWKIFDEMPHRNV----VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDL  269 (538)
Q Consensus       194 i~~~~~~g~~~~A~~~~~~m~~~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~  269 (538)
                      ++-....|++..|+..+++....++    .....+..+|...|+++.|+..++.    .-+|+..++..+...+...++.
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~~~   81 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHSRR   81 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCSTTH
T ss_pred             HHHHHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCCcH
Confidence            3445668999999999988765332    3456678999999999999987754    2467788889999999999999


Q ss_pred             HHHHHHHHHHHHhccCCC-CCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHH
Q 044988          270 KLGKWIHSYVEENFSVGR-EPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLG  348 (538)
Q Consensus       270 ~~a~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~  348 (538)
                      +.|...++.+...    + .|.+..++..+...|...|++++|.+.+++  ..+...+..++..+.+.|           
T Consensus        82 ~~A~~~l~~ll~~----~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~--~~~~~~~~~l~~~~~~~g-----------  144 (291)
T 3mkr_A           82 DAIVAELDREMSR----SVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ--GDSLECMAMTVQILLKLD-----------  144 (291)
T ss_dssp             HHHHHHHHHHHHS----CCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT--CCSHHHHHHHHHHHHHTT-----------
T ss_pred             HHHHHHHHHHHhc----ccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC--CCCHHHHHHHHHHHHHCC-----------
Confidence            9999999998875    4 577888888899999999999999999998  445566666666666666           


Q ss_pred             HHHHhcccCcHHHHHHHHHHhhhhcCCCccHHH---HHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHh
Q 044988          349 VLSACSHGGFVDEGRQFFECMNQNWGIKPRIEH---YGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRI  423 (538)
Q Consensus       349 ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~---~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~  423 (538)
                               ++++|...|+++.+.   .|+...   ...++..+...|++++|..+|+++.  .+.+...++.+..++.+
T Consensus       145 ---------~~~~A~~~l~~~~~~---~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~  212 (291)
T 3mkr_A          145 ---------RLDLARKELKKMQDQ---DEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMA  212 (291)
T ss_dssp             ---------CHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHH
T ss_pred             ---------CHHHHHHHHHHHHhh---CcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence                     777888999998876   465321   1233444556699999999999984  45678899999999999


Q ss_pred             cCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHH-HHHHHHHHHhC
Q 044988          424 HNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQD-VAAVRQKMIKM  476 (538)
Q Consensus       424 ~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~-A~~~~~~m~~~  476 (538)
                      .|++++|...++++ ....|+++.++. .++.++...|+.++ +.++++++.+.
T Consensus       213 ~g~~~eA~~~l~~a-l~~~p~~~~~l~-~l~~~~~~~g~~~eaa~~~~~~~~~~  264 (291)
T 3mkr_A          213 QGRWEAAEGVLQEA-LDKDSGHPETLI-NLVVLSQHLGKPPEVTNRYLSQLKDA  264 (291)
T ss_dssp             TTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            99999999999999 999999999888 88899999999976 57899988863

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.70  E-value=5.2e-15  Score=146.30  Aligned_cols=381  Identities=9%  Similarity=-0.056  Sum_probs=192.8

Q ss_pred             ChhHHHHHHHHHHccCChhHHHHHHhcCC-----------CC-CcchHHHHHHHHhcCCCchHHHHHHHHhHhC----C-
Q 044988           51 KNYILAKLLAFYVTSGYLINAHKVFEKTE-----------NP-STAIWNQMIRGHARSETPEKSVYLYKQMIDK----E-  113 (538)
Q Consensus        51 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-----------~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----~-  113 (538)
                      ....|+.|..++...|++++|++.|++..           .| ...+|+.+..+|...|++++|...+++..+-    . 
T Consensus        50 ~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~  129 (472)
T 4g1t_A           50 KATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSS  129 (472)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhccc
Confidence            45678888888888888888888876532           12 3356788888888888888888888776531    1 


Q ss_pred             -CCC-CcchHHHHHHHHHc--cCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC--C-C
Q 044988          114 -TEP-DEYTYSFLLSVCAR--CGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA--R-S  186 (538)
Q Consensus       114 -~~p-~~~~~~~li~~~~~--~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~--~-~  186 (538)
                       ..+ ...++.....++..  .+++++|...|++.++.. +.+...+..+..++.+.++....++|...+++..+  | +
T Consensus       130 ~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~-p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~p~~  208 (472)
T 4g1t_A          130 PYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKK-PKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLNPDN  208 (472)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHCSSC
T ss_pred             ccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcCCcc
Confidence             011 22345544444443  346788888888887764 33455555555554333221115555555544332  1 2


Q ss_pred             chhHHHHHHHHHh----cCCHHHHHHHHccCC---CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC-HHHHHH
Q 044988          187 VVSWNSLLKGYVK----RGDIDGAWKIFDEMP---HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD-QVALVA  258 (538)
Q Consensus       187 ~~~~~~li~~~~~----~g~~~~A~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~  258 (538)
                      ...+..+...+..    .|++++|.+.+++..   ..+..++..+...|...|++++|...|++..+.  .|+ ..++..
T Consensus       209 ~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~  286 (472)
T 4g1t_A          209 QYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIELLKKALEY--IPNNAYLHCQ  286 (472)
T ss_dssp             HHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCChHHHHHH
Confidence            3333333333322    234455555554432   123344555555555555555555555555542  222 223333


Q ss_pred             HHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHh
Q 044988          259 ALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAK  335 (538)
Q Consensus       259 li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~  335 (538)
                      +..++...+...         ...     ...      .........+..+.|...|++..+   .+..++..+...+..
T Consensus       287 lg~~y~~~~~~~---------~~~-----~~~------~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~  346 (472)
T 4g1t_A          287 IGCCYRAKVFQV---------MNL-----REN------GMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHAL  346 (472)
T ss_dssp             HHHHHHHHHHHH---------HHC-----------------CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh---------hhH-----HHH------HHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHH
Confidence            322221110000         000     000      000000111234566666665443   344556666666655


Q ss_pred             cCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccH--HHHHHHHH-HhhhcCChHHHHHHHHhC-CCCCCH
Q 044988          336 QGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRI--EHYGCMVD-LFSRAGLMDEAFSLVQNM-PMKPND  411 (538)
Q Consensus       336 ~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~--~~~~~l~~-~~~~~g~~~~A~~~~~~~-~~~p~~  411 (538)
                      .|                    ++++|...|++..+. ...|..  ..+..+.. .+...|+.++|++.|++. ...|+.
T Consensus       347 ~~--------------------~~~~A~~~~~kaL~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~  405 (472)
T 4g1t_A          347 AD--------------------QYEEAEYYFQKEFSK-ELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKS  405 (472)
T ss_dssp             TT--------------------CHHHHHHHHHHHHHS-CCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCC
T ss_pred             hc--------------------cHHHHHHHHHHHHhc-CCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCccc
Confidence            55                    667777888877654 222221  12333332 234678999999998876 355664


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeE
Q 044988          412 AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSW  486 (538)
Q Consensus       412 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~  486 (538)
                      ......         ...+.+++++. ....|+++.++. .|+.+|...|++++|++.|++..+.|-..+...+|
T Consensus       406 ~~~~~~---------~~~l~~~~~~~-l~~~p~~~~~~~-~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~  469 (472)
T 4g1t_A          406 REKEKM---------KDKLQKIAKMR-LSKNGADSEALH-VLAFLQELNEKMQQADEDSERGLESGSLIPSASSW  469 (472)
T ss_dssp             HHHHHH---------HHHHHHHHHHH-HHHCC-CTTHHH-HHHHHHHHHHHCC----------------------
T ss_pred             HHHHHH---------HHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhc
Confidence            433222         34455667777 788999999888 99999999999999999999999876654445555

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.70  E-value=1.2e-17  Score=168.58  Aligned_cols=147  Identities=16%  Similarity=0.137  Sum_probs=124.0

Q ss_pred             hhHHHHHHHHHHccCChhHHHHHHhcCC-------CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHH
Q 044988           52 NYILAKLLAFYVTSGYLINAHKVFEKTE-------NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFL  124 (538)
Q Consensus        52 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~-------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l  124 (538)
                      ..+|++||++|++.|++++|.++|+.|.       .||+.+||+||.+||+.|++++|.++|++|.+.|+.||..||+++
T Consensus       127 ~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntL  206 (1134)
T 3spa_A          127 QQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAA  206 (1134)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHH
Confidence            4589999999999999999999997653       699999999999999999999999999999999999999999999


Q ss_pred             HHHHHccCCc-HHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC-----CchhHHHHHHHHH
Q 044988          125 LSVCARCGLF-REGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPAR-----SVVSWNSLLKGYV  198 (538)
Q Consensus       125 i~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~-----~~~~~~~li~~~~  198 (538)
                      |.++++.|+. +.|.++|++|.+.|+.||..+|++++..+.+.+-   ++.+.++...+..+     .+.+...|.+.|.
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~v---L~~Vrkv~P~f~p~~~~~~~~~t~~LL~dl~s  283 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATV---LKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYA  283 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHH---HHHHGGGCCCCCCCCCCCCCCCCCTTTHHHHC
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHH---HHHHHHhCcccCCCCCCcccccchHHHHHHHc
Confidence            9999999985 7899999999999999999999999988877765   55555554444321     1334444555565


Q ss_pred             hcC
Q 044988          199 KRG  201 (538)
Q Consensus       199 ~~g  201 (538)
                      +.+
T Consensus       284 ~d~  286 (1134)
T 3spa_A          284 KDG  286 (1134)
T ss_dssp             CCS
T ss_pred             cCC
Confidence            544

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.69  E-value=1.4e-15  Score=142.44  Aligned_cols=257  Identities=10%  Similarity=0.006  Sum_probs=193.4

Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 044988          187 VVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSAC  263 (538)
Q Consensus       187 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  263 (538)
                      ...|..+...+...|++++|..+|+++.+   .+..+|..+...+...|++++|...|+++.+.. +.+..++..+...+
T Consensus        21 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~   99 (327)
T 3cv0_A           21 HENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSH   99 (327)
T ss_dssp             SSCHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHHH
Confidence            34556666777777888888887777642   355677788888888888888888888887752 33567777888888


Q ss_pred             HccCChHHHHHHHHHHHHhccCCCCCcchhHHHHH--------------HH-HHHhCCCHHHHHHHHHhcCC---CCcch
Q 044988          264 AEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNAL--------------IH-MYASCGEIEEAYGVFRKMQR---RNTVS  325 (538)
Q Consensus       264 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l--------------~~-~~~~~g~~~~a~~~~~~m~~---~~~~~  325 (538)
                      ...|+++.|...++.+.+.     .|.+...+..+              .. .+...|++++|...++++.+   .+...
T Consensus       100 ~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  174 (327)
T 3cv0_A          100 TNEHNANAALASLRAWLLS-----QPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQL  174 (327)
T ss_dssp             HHTTCHHHHHHHHHHHHHT-----STTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHSTTCHHH
T ss_pred             HHcCCHHHHHHHHHHHHHh-----CCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhCCCCHHH
Confidence            8888888888888888875     34333333333              22 36777889999999988764   23444


Q ss_pred             HHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhC
Q 044988          326 WTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNM  405 (538)
Q Consensus       326 ~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~  405 (538)
                      +..+...+...                    |++++|...++++.+..  +.+..++..+...+...|++++|.+.++++
T Consensus       175 ~~~la~~~~~~--------------------~~~~~A~~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a  232 (327)
T 3cv0_A          175 HASLGVLYNLS--------------------NNYDSAAANLRRAVELR--PDDAQLWNKLGATLANGNRPQEALDAYNRA  232 (327)
T ss_dssp             HHHHHHHHHHT--------------------TCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh--------------------ccHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            55555555444                    47777788888887651  335788999999999999999999999987


Q ss_pred             C-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCC------------CcccHHHHHHHHHHhcCChHHHHHHHH
Q 044988          406 P-M-KPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPE------------QAAGYLALVANVYAAAKRWQDVAAVRQ  471 (538)
Q Consensus       406 ~-~-~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~------------~~~~~~~~l~~~~~~~g~~~~A~~~~~  471 (538)
                      . . +.+...+..+...+...|++++|.+.++++ ....|+            ....+. .++.++.+.|++++|..+++
T Consensus       233 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a-~~~~~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~~A~~~~~  310 (327)
T 3cv0_A          233 LDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRA-IYMQVGGTTPTGEASREATRSMWD-FFRMLLNVMNRPDLVELTYA  310 (327)
T ss_dssp             HHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHTTSCC-----CCTHHHHHHH-HHHHHHHHTTCHHHHHHHTT
T ss_pred             HHcCCCCHHHHHHHHHHHHHhccHHHHHHHHHHH-HHhCCccccccccchhhcCHHHHH-HHHHHHHhcCCHHHHHHHHH
Confidence            3 2 345788999999999999999999999999 888888            566677 89999999999999999886


Q ss_pred             HH
Q 044988          472 KM  473 (538)
Q Consensus       472 ~m  473 (538)
                      +.
T Consensus       311 ~~  312 (327)
T 3cv0_A          311 QN  312 (327)
T ss_dssp             CC
T ss_pred             HH
Confidence            54

>3cv0_A Peroxisome targeting signal 1 receptor PEX5; TPR motifs, TPR protein, peroxin 5, PEX5, PTS1 binding domain, protein-peptide complex, receptor; 2.00A {Trypanosoma brucei} PDB: 3cvl_A 3cvn_A 3cvp_A 3cvq_A

Probab=99.67  E-value=2.6e-14  Score=133.70  Aligned_cols=271  Identities=9%  Similarity=-0.020  Sum_probs=193.9

Q ss_pred             CccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHH
Q 044988           15 SKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIR   91 (538)
Q Consensus        15 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~   91 (538)
                      .+...+..+...+...++++.|..+++.+.+.... +...+..+...+...|++++|...|++..   +.+...|..+..
T Consensus        19 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~   97 (327)
T 3cv0_A           19 MYHENPMEEGLSMLKLANLAEAALAFEAVCQAAPE-REEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAV   97 (327)
T ss_dssp             GGSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHH
Confidence            35566778888888999999999999999887533 67788888889999999999999998765   345667888888


Q ss_pred             HHhcCCCchHHHHHHHHhHhCCCCCCcchHHHH--------------HH-HHHccCCcHHHHHHHHHHHHhCCCCchhHH
Q 044988           92 GHARSETPEKSVYLYKQMIDKETEPDEYTYSFL--------------LS-VCARCGLFREGEQVHGRVLASGYCSNVFIR  156 (538)
Q Consensus        92 ~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~l--------------i~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  156 (538)
                      .+...|++++|...|+++.+.. +.+...+..+              .. .+...|++++|...++++.+.. +.+..++
T Consensus        98 ~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~  175 (327)
T 3cv0_A           98 SHTNEHNANAALASLRAWLLSQ-PQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQLH  175 (327)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTS-TTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHHH
Confidence            8999999999999999988753 2233333333              22 2566677777877777777664 3345566


Q ss_pred             hHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHH
Q 044988          157 TNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQ  236 (538)
Q Consensus       157 ~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~  236 (538)
                      ..+...|...|+   +++|...+++..+                            ....+..+|..+...+...|++++
T Consensus       176 ~~la~~~~~~~~---~~~A~~~~~~~~~----------------------------~~~~~~~~~~~l~~~~~~~~~~~~  224 (327)
T 3cv0_A          176 ASLGVLYNLSNN---YDSAAANLRRAVE----------------------------LRPDDAQLWNKLGATLANGNRPQE  224 (327)
T ss_dssp             HHHHHHHHHTTC---HHHHHHHHHHHHH----------------------------HCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHhcc---HHHHHHHHHHHHH----------------------------hCCCcHHHHHHHHHHHHHcCCHHH
Confidence            666666666666   5555555443221                            012345677888888888888888


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCc-------chhHHHHHHHHHHhCCCHH
Q 044988          237 ALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPV-------LVSLNNALIHMYASCGEIE  309 (538)
Q Consensus       237 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-------~~~~~~~l~~~~~~~g~~~  309 (538)
                      |...|+++.+.. +.+...+..+...+...|+++.|...++.+.+.......+.       +...+..+..++.+.|+++
T Consensus       225 A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  303 (327)
T 3cv0_A          225 ALDAYNRALDIN-PGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPD  303 (327)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHcC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHH
Confidence            888888887643 33567788888888888899998888888877621100000       6778888999999999999


Q ss_pred             HHHHHHHhcCC
Q 044988          310 EAYGVFRKMQR  320 (538)
Q Consensus       310 ~a~~~~~~m~~  320 (538)
                      +|..++++..+
T Consensus       304 ~A~~~~~~~l~  314 (327)
T 3cv0_A          304 LVELTYAQNVE  314 (327)
T ss_dssp             HHHHHTTCCSH
T ss_pred             HHHHHHHHHHH
Confidence            99999987653

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.65  E-value=2e-16  Score=159.75  Aligned_cols=119  Identities=9%  Similarity=0.061  Sum_probs=99.6

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHccCC-------CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 044988          188 VSWNSLLKGYVKRGDIDGAWKIFDEMP-------HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAAL  260 (538)
Q Consensus       188 ~~~~~li~~~~~~g~~~~A~~~~~~m~-------~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li  260 (538)
                      .+||++|++||+.|++++|.++|++|.       .||++|||+||.+||+.|++++|.++|++|.+.|+.||..||+++|
T Consensus       128 ~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYntLI  207 (1134)
T 3spa_A          128 QRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAAL  207 (1134)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHHHHH
Confidence            578888888888888888888886653       4899999999999999999999999999999999999999999999


Q ss_pred             HHHHccCCh-HHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHH
Q 044988          261 SACAEIGDL-KLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEE  310 (538)
Q Consensus       261 ~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  310 (538)
                      .++++.|+. +.|.++++.|.+.    |..++..+|++++..+.+.+-++.
T Consensus       208 ~glcK~G~~~e~A~~Ll~EM~~k----G~~PD~vtY~~ll~~~eR~~vL~~  254 (1134)
T 3spa_A          208 QCMGRQDQDAGTIERCLEQMSQE----GLKLQALFTAVLLSEEDRATVLKA  254 (1134)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHH----TCCSHHHHHHSCCCHHHHHHHHHH
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHc----CCCCChhhcccccChhhHHHHHHH
Confidence            999998874 7788899999988    899999998888876665433333

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.63  E-value=7.5e-14  Score=137.96  Aligned_cols=382  Identities=11%  Similarity=0.006  Sum_probs=235.8

Q ss_pred             ccccHHHHHHHHhccCChHHHHHHHHHHHHh-----C--CCC-ChhHHHHHHHHHHccCChhHHHHHHhcCC-------C
Q 044988           16 KALTTRQIFSLLQIRNTTKTLFQIHSQIIIN-----G--FSQ-KNYILAKLLAFYVTSGYLINAHKVFEKTE-------N   80 (538)
Q Consensus        16 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-----~--~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-------~   80 (538)
                      ....|+.+..++...|+.++|.+.++...+.     +  ..| ...+|+.+..+|...|++++|...+++..       .
T Consensus        50 ~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~  129 (472)
T 4g1t_A           50 KATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSS  129 (472)
T ss_dssp             CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhccc
Confidence            3567888999999999999999999887642     1  122 35688999999999999999999887653       1


Q ss_pred             ---C-CcchHHHHHHHHhc--CCCchHHHHHHHHhHhCCCCCCc-chHHHHHHH---HHccCCcHHHHHHHHHHHHhCCC
Q 044988           81 ---P-STAIWNQMIRGHAR--SETPEKSVYLYKQMIDKETEPDE-YTYSFLLSV---CARCGLFREGEQVHGRVLASGYC  150 (538)
Q Consensus        81 ---~-~~~~~~~li~~~~~--~~~~~~a~~~~~~m~~~~~~p~~-~~~~~li~~---~~~~~~~~~a~~~~~~~~~~~~~  150 (538)
                         + ...+++.+..++..  .+++++|++.|++..+.  .|+. ..+..+..+   +...++.++|.+.+++.++.. +
T Consensus       130 ~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~--~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p  206 (472)
T 4g1t_A          130 PYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEK--KPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-P  206 (472)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-S
T ss_pred             ccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-C
Confidence               1 23456655555544  45799999999999874  4654 344444444   445678889999999998875 4


Q ss_pred             CchhHHhHHHHHHHhcCC-CCChhHHHHHhhcCCC---CCchhHHHHHHHHHhcCCHHHHHHHHccCCC--C-ChHHHHH
Q 044988          151 SNVFIRTNLMNLYLMSGG-ECGVGCARLLFDDMPA---RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--R-NVVSWTT  223 (538)
Q Consensus       151 ~~~~~~~~l~~~~~~~g~-~~~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~  223 (538)
                      .+..++..+...+...+. ....++|.+.+++...   .+...+..+...|...|++++|...|++..+  | +..++..
T Consensus       207 ~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~  286 (472)
T 4g1t_A          207 DNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYIPNNAYLHCQ  286 (472)
T ss_dssp             SCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCChHHHHHH
Confidence            566677777666665543 1127889999887653   3667888999999999999999999998753  4 4556777


Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHH
Q 044988          224 MISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYA  303 (538)
Q Consensus       224 li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  303 (538)
                      +...|...+....+...          .      .........+..+.|...+....+.     .|.....+..+...|.
T Consensus       287 lg~~y~~~~~~~~~~~~----------~------~~~~~~~~~~~~~~A~~~~~~a~~~-----~~~~~~~~~~lg~~~~  345 (472)
T 4g1t_A          287 IGCCYRAKVFQVMNLRE----------N------GMYGKRKLLELIGHAVAHLKKADEA-----NDNLFRVCSILASLHA  345 (472)
T ss_dssp             HHHHHHHHHHHHHHC----------------------CHHHHHHHHHHHHHHHHHHHHH-----CTTTCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHH----------H------HHHHHHHHHhhHHHHHHHHHHHhhc-----CCchhhhhhhHHHHHH
Confidence            76666432211111000          0      0000111123456778888888776     5666677788999999


Q ss_pred             hCCCHHHHHHHHHhcCC--CCcchHHHHHHHHHhcCCccHHHHHHHHHHH-HhcccCcHHHHHHHHHHhhhhcCCCccHH
Q 044988          304 SCGEIEEAYGVFRKMQR--RNTVSWTSMITGFAKQGYAQEALLTFLGVLS-ACSHGGFVDEGRQFFECMNQNWGIKPRIE  380 (538)
Q Consensus       304 ~~g~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~-~~~~~~~~~~a~~~~~~~~~~~~~~p~~~  380 (538)
                      ..|++++|...|++..+  ++......+                +..+.. .....|+.++|...|++..+.   .|+..
T Consensus       346 ~~~~~~~A~~~~~kaL~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~Ai~~y~kal~i---~~~~~  406 (472)
T 4g1t_A          346 LADQYEEAEYYFQKEFSKELTPVAKQLL----------------HLRYGNFQLYQMKCEDKAIHHFIEGVKI---NQKSR  406 (472)
T ss_dssp             HTTCHHHHHHHHHHHHHSCCCHHHHHHH----------------HHHHHHHHHHTSSCHHHHHHHHHHHHHS---CCCCH
T ss_pred             HhccHHHHHHHHHHHHhcCCCChHHHHH----------------HHHHHHHHHHHCCCHHHHHHHHHHHHhc---CcccH
Confidence            99999999999998754  222111111                111111 123456888888888887754   55543


Q ss_pred             HHHHHHHHhhhcCChHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          381 HYGCMVDLFSRAGLMDEAFSLVQNM-P-MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       381 ~~~~l~~~~~~~g~~~~A~~~~~~~-~-~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                      .....+         ..+.++++.. . .+.+..+|..+...+...|++++|++.|+++ .++.|..+.+..
T Consensus       407 ~~~~~~---------~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kA-Le~~~~~p~a~~  468 (472)
T 4g1t_A          407 EKEKMK---------DKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQADEDSERG-LESGSLIPSASS  468 (472)
T ss_dssp             HHHHHH---------HHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC----------------------
T ss_pred             HHHHHH---------HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhcCCCCCcHhh
Confidence            222222         2223333332 1 2345678889999999999999999999999 888888777544

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.62  E-value=6.2e-14  Score=126.20  Aligned_cols=227  Identities=12%  Similarity=0.005  Sum_probs=183.7

Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCC--CCcchhHH
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGR--EPVLVSLN  295 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~~  295 (538)
                      ...|..+...+...|++++|+..|+++.+..  .+...+..+..++...|+++.|...+..+.+......  .+....++
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~   82 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSF   82 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHH
Confidence            3467788888899999999999999988876  7788888888899999999999999988887621100  00115777


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCC
Q 044988          296 NALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGI  375 (538)
Q Consensus       296 ~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  375 (538)
                      ..+...|...|++++|...|+++.+-+..     .                    ..+...|++++|...++.+...   
T Consensus        83 ~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-----~--------------------~~~~~~~~~~~a~~~~~~~~~~---  134 (258)
T 3uq3_A           83 ARIGNAYHKLGDLKKTIEYYQKSLTEHRT-----A--------------------DILTKLRNAEKELKKAEAEAYV---  134 (258)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCC-----H--------------------HHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhcCch-----h--------------------HHHHHHhHHHHHHHHHHHHHHc---
Confidence            88999999999999999999887652111     1                    1223345788888999988764   


Q ss_pred             Cc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHH
Q 044988          376 KP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLAL  452 (538)
Q Consensus       376 ~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~  452 (538)
                      .| +...+..+...+...|++++|.+.++++.  .+.+...+..+...+...|++++|...++++ ....|+++..+. .
T Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a-l~~~~~~~~~~~-~  212 (258)
T 3uq3_A          135 NPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKA-IEKDPNFVRAYI-R  212 (258)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-H
T ss_pred             CcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHH-HHhCHHHHHHHH-H
Confidence            45 47788999999999999999999999874  3445788999999999999999999999999 889999998888 9


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhC
Q 044988          453 VANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       453 l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      ++.+|.+.|++++|.+.+++..+.
T Consensus       213 l~~~~~~~g~~~~A~~~~~~a~~~  236 (258)
T 3uq3_A          213 KATAQIAVKEYASALETLDAARTK  236 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHh
Confidence            999999999999999999998753

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.58  E-value=6.5e-14  Score=122.40  Aligned_cols=206  Identities=12%  Similarity=0.011  Sum_probs=128.6

Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHH
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNA  297 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  297 (538)
                      ...+..+...+.+.|++++|...|++..+.. +.+...+..+...+.+.|++++|...++.+.+.     .|.+...+..
T Consensus         5 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~-----~P~~~~a~~~   78 (217)
T 2pl2_A            5 EQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVAR-----TPRYLGGYMV   78 (217)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCcHHHHHH
Confidence            3445555555555555555555555555421 123444444444555555555555555555554     3444444444


Q ss_pred             HHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc
Q 044988          298 LIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP  377 (538)
Q Consensus       298 l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p  377 (538)
                      +..++...+.         .  ...                             .....|++++|...|++..+.   .|
T Consensus        79 lg~~~~~~~~---------~--~~~-----------------------------~~~~~g~~~~A~~~~~~al~~---~P  115 (217)
T 2pl2_A           79 LSEAYVALYR---------Q--AED-----------------------------RERGKGYLEQALSVLKDAERV---NP  115 (217)
T ss_dssp             HHHHHHHHHH---------T--CSS-----------------------------HHHHHHHHHHHHHHHHHHHHH---CT
T ss_pred             HHHHHHHhhh---------h--hhh-----------------------------hcccccCHHHHHHHHHHHHHh---Cc
Confidence            4444332210         0  000                             001125888999999998875   56


Q ss_pred             -cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHH
Q 044988          378 -RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVAN  455 (538)
Q Consensus       378 -~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~  455 (538)
                       +...+..+..+|...|++++|+..|++.. ...+...+..+..++...|++++|+..++++ ....|+++..+. .++.
T Consensus       116 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a-l~~~P~~~~~~~-~la~  193 (217)
T 2pl2_A          116 RYAPLHLQRGLVYALLGERDKAEASLKQALALEDTPEIRSALAELYLSMGRLDEALAQYAKA-LEQAPKDLDLRV-RYAS  193 (217)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHHSTTCHHHHH-HHHH
T ss_pred             ccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcccchHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCCCChHHHH-HHHH
Confidence             47889999999999999999999999873 1277889999999999999999999999999 999999999888 9999


Q ss_pred             HHHhcCChHHHHHHHHHHH
Q 044988          456 VYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       456 ~~~~~g~~~~A~~~~~~m~  474 (538)
                      ++.+.|++++|++.+++..
T Consensus       194 ~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          194 ALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHTC---------------
T ss_pred             HHHHccCHHHHHHHHHHHh
Confidence            9999999999999988754

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.56  E-value=6.4e-13  Score=120.69  Aligned_cols=241  Identities=8%  Similarity=-0.040  Sum_probs=183.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHH
Q 044988          189 SWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD--QVALVAALSAC  263 (538)
Q Consensus       189 ~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~  263 (538)
                      .+......+...|++++|+..|++..+   .+...|..+...|...|++++|+..|++..+.+..|+  ...|..+...+
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~~   84 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKIL   84 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHHH
Confidence            445566677788888888888887643   3455888889999999999999999999988432222  34478888899


Q ss_pred             HccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC---CcchHHHHHHHHHhcCCcc
Q 044988          264 AEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR---NTVSWTSMITGFAKQGYAQ  340 (538)
Q Consensus       264 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~  340 (538)
                      ...|+++.|...++.+.+.     .|.+..++..+...|...|++++|...|++..+.   +...|..+...+...    
T Consensus        85 ~~~~~~~~A~~~~~~a~~~-----~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~----  155 (272)
T 3u4t_A           85 MKKGQDSLAIQQYQAAVDR-----DTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRPTTTDPKVFYELGQAYYYN----  155 (272)
T ss_dssp             HHTTCHHHHHHHHHHHHHH-----STTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCSSCCCHHHHHHHHHHHHHT----
T ss_pred             HHcccHHHHHHHHHHHHhc-----CcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhcCCCcHHHHHHHHHHHHHH----
Confidence            9999999999999999987     6677788899999999999999999999998873   333444444122222    


Q ss_pred             HHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCC---hHHHHHHHHhCC----CCCC--
Q 044988          341 EALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGL---MDEAFSLVQNMP----MKPN--  410 (538)
Q Consensus       341 ~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~---~~~A~~~~~~~~----~~p~--  410 (538)
                                      +++++|...|+++.+.   .|+ ...+..+..++...|+   +++|...+++..    ..|+  
T Consensus       156 ----------------~~~~~A~~~~~~a~~~---~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~  216 (272)
T 3u4t_A          156 ----------------KEYVKADSSFVKVLEL---KPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKY  216 (272)
T ss_dssp             ----------------TCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGG
T ss_pred             ----------------HHHHHHHHHHHHHHHh---CccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccc
Confidence                            2788888999998876   454 6778888888888887   777777777653    2244  


Q ss_pred             ----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHh
Q 044988          411 ----DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAA  459 (538)
Q Consensus       411 ----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~  459 (538)
                          ...|..+...+...|++++|.+.++++ ..+.|+++.+.. .+......
T Consensus       217 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a-l~~~p~~~~a~~-~l~~~~~~  267 (272)
T 3u4t_A          217 KDELIEANEYIAYYYTINRDKVKADAAWKNI-LALDPTNKKAID-GLKMKLEH  267 (272)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHC-----
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhcCccHHHHHH-Hhhhhhcc
Confidence                257777888899999999999999999 999999988666 65544433

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.55  E-value=2.5e-13  Score=123.60  Aligned_cols=238  Identities=6%  Similarity=-0.154  Sum_probs=181.5

Q ss_pred             hcCCHHHHHHHHccCCCC-------ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHH
Q 044988          199 KRGDIDGAWKIFDEMPHR-------NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKL  271 (538)
Q Consensus       199 ~~g~~~~A~~~~~~m~~~-------~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~  271 (538)
                      ..|++++|+..|+++.+.       +..+|..+...+...|++++|...|+++.+.. +.+...+..+...+...|+++.
T Consensus        17 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~   95 (275)
T 1xnf_A           17 PTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDA   95 (275)
T ss_dssp             CCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHH
T ss_pred             ccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHH
Confidence            346778888888776541       34578888999999999999999999998753 3367888899999999999999


Q ss_pred             HHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CCcchHHHHHHHHHhcCCccHHHHHHHHH
Q 044988          272 GKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RNTVSWTSMITGFAKQGYAQEALLTFLGV  349 (538)
Q Consensus       272 a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~l  349 (538)
                      |...++.+.+.     .|.+..++..+...|...|++++|...|+++.+  |+.......+..+                
T Consensus        96 A~~~~~~al~~-----~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~----------------  154 (275)
T 1xnf_A           96 AYEAFDSVLEL-----DPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLA----------------  154 (275)
T ss_dssp             HHHHHHHHHHH-----CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH----------------
T ss_pred             HHHHHHHHHhc-----CccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCChHHHHHHHHH----------------
Confidence            99999999987     666778888999999999999999999998865  3332222222222                


Q ss_pred             HHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-----HHHHHHHHHHHHh
Q 044988          350 LSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-----DAVLGSLLLGCRI  423 (538)
Q Consensus       350 l~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-----~~~~~~l~~~~~~  423 (538)
                          ...|++++|...++......  +++...+. ++..+...++.++|.+.+++.. ..|+     ...+..+...+..
T Consensus       155 ----~~~~~~~~A~~~~~~~~~~~--~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~  227 (275)
T 1xnf_A          155 ----EQKLDEKQAKEVLKQHFEKS--DKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLS  227 (275)
T ss_dssp             ----HHHHCHHHHHHHHHHHHHHS--CCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----HHhcCHHHHHHHHHHHHhcC--CcchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHH
Confidence                22358888889998777652  33444444 7777888888999999998875 2232     5778888899999


Q ss_pred             cCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHH
Q 044988          424 HNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVR  470 (538)
Q Consensus       424 ~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~  470 (538)
                      .|++++|...++++ ....|++..    ....++...|++++|++.+
T Consensus       228 ~g~~~~A~~~~~~a-l~~~p~~~~----~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          228 LGDLDSATALFKLA-VANNVHNFV----EHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             TTCHHHHHHHHHHH-HTTCCTTCH----HHHHHHHHHHHHHHC----
T ss_pred             cCCHHHHHHHHHHH-HhCCchhHH----HHHHHHHHHHHHHhhHHHH
Confidence            99999999999999 888898755    4456788889999998876

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.53  E-value=2.7e-13  Score=118.50  Aligned_cols=207  Identities=11%  Similarity=-0.015  Sum_probs=140.6

Q ss_pred             CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHH
Q 044988           81 PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLM  160 (538)
Q Consensus        81 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  160 (538)
                      ++...+..+...+.+.|++++|+..|++..+.. +.+...+..+...+.+.|++++|...+++.++.. +.+...+..+.
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg   80 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLS   80 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHH
Confidence            455667777777778888888888888777643 3355677777777778888888888888777764 44455666666


Q ss_pred             HHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCC--C-ChHHHHHHHHHHHHcCCHHHH
Q 044988          161 NLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--R-NVVSWTTMISGCAQNGKSRQA  237 (538)
Q Consensus       161 ~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a  237 (538)
                      .++...+.   ..           .+         .....|++++|+..|++..+  | +...|..+...+...|++++|
T Consensus        81 ~~~~~~~~---~~-----------~~---------~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A  137 (217)
T 2pl2_A           81 EAYVALYR---QA-----------ED---------RERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLGERDKA  137 (217)
T ss_dssp             HHHHHHHH---TC-----------SS---------HHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHhhh---hh-----------hh---------hcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChHHH
Confidence            66655511   00           00         01122667777777766542  3 456788888899999999999


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHh
Q 044988          238 LSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRK  317 (538)
Q Consensus       238 ~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  317 (538)
                      +..|++..+..  .+...+..+..++...|++++|...++.+.+.     .|.+...+..+...+...|++++|...|++
T Consensus       138 ~~~~~~al~~~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~-----~P~~~~~~~~la~~~~~~g~~~~A~~~~~~  210 (217)
T 2pl2_A          138 EASLKQALALE--DTPEIRSALAELYLSMGRLDEALAQYAKALEQ-----APKDLDLRVRYASALLLKGKAEEAARAAAL  210 (217)
T ss_dssp             HHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-----STTCHHHHHHHHHHHTC-------------
T ss_pred             HHHHHHHHhcc--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCChHHHHHHHHHHHHccCHHHHHHHHHH
Confidence            99999998876  77888888999999999999999999999887     777888888899999999999999998887


Q ss_pred             cC
Q 044988          318 MQ  319 (538)
Q Consensus       318 m~  319 (538)
                      ..
T Consensus       211 ~~  212 (217)
T 2pl2_A          211 EH  212 (217)
T ss_dssp             --
T ss_pred             Hh
Confidence            64

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.52  E-value=8e-13  Score=118.87  Aligned_cols=219  Identities=9%  Similarity=-0.023  Sum_probs=136.0

Q ss_pred             hHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCC--Cc----hhHHhH
Q 044988           85 IWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYC--SN----VFIRTN  158 (538)
Q Consensus        85 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~--~~----~~~~~~  158 (538)
                      .|..+...+...|++++|+..|++..+..  .+...+..+...+...|++++|...+++..+....  ++    ..++..
T Consensus         7 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   84 (258)
T 3uq3_A            7 KEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFAR   84 (258)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHH
Confidence            45566666677777777777777776654  56666777777777777777777777766654211  11    355666


Q ss_pred             HHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHH
Q 044988          159 LMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSR  235 (538)
Q Consensus       159 l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~  235 (538)
                      +...+...|+   +++|...|++..+.+..     ...+.+.|++++|...+++...   .+...|..+...+...|+++
T Consensus        85 l~~~~~~~~~---~~~A~~~~~~a~~~~~~-----~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (258)
T 3uq3_A           85 IGNAYHKLGD---LKKTIEYYQKSLTEHRT-----ADILTKLRNAEKELKKAEAEAYVNPEKAEEARLEGKEYFTKSDWP  156 (258)
T ss_dssp             HHHHHHHTTC---HHHHHHHHHHHHHHCCC-----HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHccc---HHHHHHHHHHHHhcCch-----hHHHHHHhHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHhcCHH
Confidence            6666666666   66666666554431111     1234445556666666665432   23345666666777777777


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHH
Q 044988          236 QALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVF  315 (538)
Q Consensus       236 ~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  315 (538)
                      +|...|++..+.. +.+...+..+...+...|+++.|...++.+.+.     .|.+...+..+...|...|++++|...|
T Consensus       157 ~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-----~~~~~~~~~~l~~~~~~~g~~~~A~~~~  230 (258)
T 3uq3_A          157 NAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEK-----DPNFVRAYIRKATAQIAVKEYASALETL  230 (258)
T ss_dssp             HHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHhcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHh-----CHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence            7777777766542 224566666666677777777777777777665     4555666666777777777777777766


Q ss_pred             HhcC
Q 044988          316 RKMQ  319 (538)
Q Consensus       316 ~~m~  319 (538)
                      ++..
T Consensus       231 ~~a~  234 (258)
T 3uq3_A          231 DAAR  234 (258)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6653

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.51  E-value=8.5e-12  Score=121.83  Aligned_cols=218  Identities=12%  Similarity=0.032  Sum_probs=109.6

Q ss_pred             HHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCCh---hHHHHHHhcCCCCCcchHHHHHHHHhcCC-
Q 044988           22 QIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYL---INAHKVFEKTENPSTAIWNQMIRGHARSE-   97 (538)
Q Consensus        22 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~---~~a~~~~~~~~~~~~~~~~~li~~~~~~~-   97 (538)
                      .+...+.+.|+++.|...++...+.|   ++..+..|..+|...|+.   ++|...|++..+.++..+..|...+...+ 
T Consensus         8 ~la~~~~~~g~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~   84 (452)
T 3e4b_A            8 RLANEALKRGDTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKPG   84 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHT---CCTGGGTCC----------------------------CHHHHHHHHHTC--
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCC
Confidence            35566667788888888888887776   333444555666666766   78888887776556666777766555544 


Q ss_pred             ----CchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHH---HHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCC
Q 044988           98 ----TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFRE---GEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGEC  170 (538)
Q Consensus        98 ----~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~---a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  170 (538)
                          ++++|+..|++..+.|   +...+..|...|...+..+.   +.+.+......|   +......|...|...+.  
T Consensus        85 ~~~~~~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g---~~~a~~~Lg~~y~~~~~--  156 (452)
T 3e4b_A           85 ATEAEHHEAESLLKKAFANG---EGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAG---YPEAGLAQVLLYRTQGT--  156 (452)
T ss_dssp             CCHHHHHHHHHHHHHHHHTT---CSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHT---CTTHHHHHHHHHHHHTC--
T ss_pred             CCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCC--
Confidence                5677888888777754   22356666666655544332   333333333333   23344445555555554  


Q ss_pred             ChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcC---CHHHHHHHHHHHHHC
Q 044988          171 GVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNG---KSRQALSLFNEMRRA  247 (538)
Q Consensus       171 ~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~---~~~~a~~~~~~m~~~  247 (538)
                       ++.                           ..+.+..+++.....++..+..+...|...|   +.++|+..|++..+.
T Consensus       157 -~~~---------------------------~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~  208 (452)
T 3e4b_A          157 -YDQ---------------------------HLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSR  208 (452)
T ss_dssp             -GGG---------------------------GHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHT
T ss_pred             -ccc---------------------------CHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHC
Confidence             322                           2333444555555555557777777777777   777888888777776


Q ss_pred             CCCCCHHHHHHHHHHHHcc----CChHHHHHHHHHH
Q 044988          248 RVGLDQVALVAALSACAEI----GDLKLGKWIHSYV  279 (538)
Q Consensus       248 g~~p~~~~~~~li~~~~~~----~~~~~a~~~~~~~  279 (538)
                      | .++...+..+...|...    +++++|...|+..
T Consensus       209 g-~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~a  243 (452)
T 3e4b_A          209 G-TVTAQRVDSVARVLGDATLGTPDEKTAQALLEKI  243 (452)
T ss_dssp             T-CSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHH
T ss_pred             C-CHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHH
Confidence            5 33333333444444332    4555555555444

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.50  E-value=2.4e-12  Score=116.90  Aligned_cols=125  Identities=11%  Similarity=0.056  Sum_probs=73.0

Q ss_pred             HHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcc----hHHHHHH
Q 044988           54 ILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEY----TYSFLLS  126 (538)
Q Consensus        54 ~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~----~~~~li~  126 (538)
                      .+......+...|++++|+..|++..   +.+...|..+...+.+.|++++|+..|++..+.+  ++..    +|..+..
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~lg~   82 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKKYNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKV--NATKAKSADFEYYGK   82 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTTCCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTS--CTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcc--CchhHHHHHHHHHHH
Confidence            34445556666666666666666543   2234466666666666666777776666666532  2222    2566666


Q ss_pred             HHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC
Q 044988          127 VCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA  184 (538)
Q Consensus       127 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~  184 (538)
                      .+...|++++|...+++..+.. +.+..++..+..+|...|+   +++|...|++..+
T Consensus        83 ~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~---~~~A~~~~~~al~  136 (272)
T 3u4t_A           83 ILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGN---FPLAIQYMEKQIR  136 (272)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTC---HHHHHHHHGGGCC
T ss_pred             HHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccC---HHHHHHHHHHHhh
Confidence            6666666666666666666653 3344555556666666665   5555555555443

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.48  E-value=3.6e-12  Score=123.00  Aligned_cols=304  Identities=11%  Similarity=-0.025  Sum_probs=180.6

Q ss_pred             hHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCc----hhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHH
Q 044988          120 TYSFLLSVCARCGLFREGEQVHGRVLASGYCSN----VFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLK  195 (538)
Q Consensus       120 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~  195 (538)
                      .+......+...|++++|...+++..+.+ +.+    ..++..+...|...|+   +++|...+++              
T Consensus        11 ~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~---~~~A~~~~~~--------------   72 (406)
T 3sf4_A           11 ELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHD---YAKALEYHHH--------------   72 (406)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTC---HHHHHHHHHH--------------
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHHHHHhcC---HHHHHHHHHH--------------
Confidence            44455555666666777776666666653 222    2345555566666666   6665554432              


Q ss_pred             HHHhcCCHHHHHHHHccCCCC--ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC-CCC----HHHHHHHHHHHHccCC
Q 044988          196 GYVKRGDIDGAWKIFDEMPHR--NVVSWTTMISGCAQNGKSRQALSLFNEMRRARV-GLD----QVALVAALSACAEIGD  268 (538)
Q Consensus       196 ~~~~~g~~~~A~~~~~~m~~~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~-~p~----~~~~~~li~~~~~~~~  268 (538)
                                |..+......+  ...++..+...|...|++++|...+++..+... .++    ..++..+...+...|+
T Consensus        73 ----------al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~  142 (406)
T 3sf4_A           73 ----------DLTLARTIGDQLGEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGK  142 (406)
T ss_dssp             ----------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----------HHHHHHhccccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCC
Confidence                      22222222211  123455566666666677666666666554200 011    3355566666666677


Q ss_pred             --------------------hHHHHHHHHHHHHhccCCC-CCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHH
Q 044988          269 --------------------LKLGKWIHSYVEENFSVGR-EPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWT  327 (538)
Q Consensus       269 --------------------~~~a~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~  327 (538)
                                          ++.|...+....+.....+ .+....++..+...|...|++++|...+++..+       
T Consensus       143 ~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~-------  215 (406)
T 3sf4_A          143 SFGCPGPQDVGEFPEEVRDALQAAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLL-------  215 (406)
T ss_dssp             TCC-------CCCCHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHH-------
T ss_pred             cccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHH-------
Confidence                                7777776666554322111 233345677888889999999999998887643       


Q ss_pred             HHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc---CCCc-cHHHHHHHHHHhhhcCChHHHHHHHH
Q 044988          328 SMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW---GIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQ  403 (538)
Q Consensus       328 ~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~---~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~  403 (538)
                          .....+........+..+...+...|++++|...+++..+..   +..+ ...++..+...|...|++++|.+.++
T Consensus       216 ----~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  291 (406)
T 3sf4_A          216 ----IAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHL  291 (406)
T ss_dssp             ----HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             ----HHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHH
Confidence                111112111112344445555555566777777776655431   1111 15678889999999999999999998


Q ss_pred             hCC----CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccC------CCCcccHHHHHHHHHHhcCChH
Q 044988          404 NMP----MKPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEID------PEQAAGYLALVANVYAAAKRWQ  464 (538)
Q Consensus       404 ~~~----~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~------p~~~~~~~~~l~~~~~~~g~~~  464 (538)
                      +..    ..++    ..++..+...+...|++++|...+++.. .+.      +....++. .++.++...|+..
T Consensus       292 ~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al-~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~  364 (406)
T 3sf4_A          292 KHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHL-EISREVGDKSGELTARL-NLSDLQMVLGLSY  364 (406)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH-HHHHHTTCHHHHHHHHH-HHHHHHHHHHTTS
T ss_pred             HHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH-HHHHHhcCCcchhHHHH-HHHHHHHHhhHhH
Confidence            763    1122    5577788888999999999999999984 332      22233455 6777777777653

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.48  E-value=2.1e-11  Score=110.75  Aligned_cols=228  Identities=10%  Similarity=-0.020  Sum_probs=159.3

Q ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----cCChHHHHHHHHHHHHhccCCCCCcch
Q 044988          217 NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAE----IGDLKLGKWIHSYVEENFSVGREPVLV  292 (538)
Q Consensus       217 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  292 (538)
                      +..++..+...|...|++++|...|++..+.   -+...+..+...+..    .+++++|...++...+.    +   +.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~----~---~~   74 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDL----N---YS   74 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT----T---CH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHC----C---CH
Confidence            4456666777777777888888888777762   244566666667777    77788888777777765    3   45


Q ss_pred             hHHHHHHHHHHh----CCCHHHHHHHHHhcCCC-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHH
Q 044988          293 SLNNALIHMYAS----CGEIEEAYGVFRKMQRR-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFE  367 (538)
Q Consensus       293 ~~~~~l~~~~~~----~g~~~~a~~~~~~m~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~  367 (538)
                      ..+..+...|..    .+++++|...|++..+. +...+..+...|....                ...+++++|...|+
T Consensus        75 ~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~----------------~~~~~~~~A~~~~~  138 (273)
T 1ouv_A           75 NGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGK----------------VVTRDFKKAVEYFT  138 (273)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCS----------------SSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCcccCHHHHHHHHHHHHHcCCccHHHHHHHHHHcCC----------------CcccCHHHHHHHHH
Confidence            556677777777    78888888888776542 3344444444444300                01447777777777


Q ss_pred             HhhhhcCCCccHHHHHHHHHHhhh----cCChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHchh
Q 044988          368 CMNQNWGIKPRIEHYGCMVDLFSR----AGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRI----HNNAELASQVAQKLVA  439 (538)
Q Consensus       368 ~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~  439 (538)
                      +..+. +   +...+..+...|..    .+++++|.+.|++.....+...+..+...+..    .+++++|+..+++. .
T Consensus       139 ~a~~~-~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a-~  213 (273)
T 1ouv_A          139 KACDL-N---DGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKA-C  213 (273)
T ss_dssp             HHHHT-T---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHH-H
T ss_pred             HHHhc-C---cHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHH-H
Confidence            77764 3   45566777777777    88888888888876433466777778888888    88999999999888 6


Q ss_pred             ccCCCCcccHHHHHHHHHHh----cCChHHHHHHHHHHHhCCC
Q 044988          440 EIDPEQAAGYLALVANVYAA----AKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       440 ~~~p~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~~~  478 (538)
                      +..|  +..+. .++.+|.+    .+++++|.+.+++..+.|.
T Consensus       214 ~~~~--~~a~~-~l~~~~~~g~~~~~~~~~A~~~~~~a~~~~~  253 (273)
T 1ouv_A          214 ELEN--GGGCF-NLGAMQYNGEGVTRNEKQAIENFKKGCKLGA  253 (273)
T ss_dssp             HTTC--HHHHH-HHHHHHHTTSSSSCCSTTHHHHHHHHHHHTC
T ss_pred             hCCC--HHHHH-HHHHHHHcCCCcccCHHHHHHHHHHHHHcCC
Confidence            6554  44466 78888888    8889999999888876543

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.48  E-value=3.5e-12  Score=120.69  Aligned_cols=247  Identities=9%  Similarity=0.044  Sum_probs=199.1

Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHccCCC--C-ChHHHHHHHHHHHHcCC-HHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 044988          187 VVSWNSLLKGYVKRGDIDGAWKIFDEMPH--R-NVVSWTTMISGCAQNGK-SRQALSLFNEMRRARVGLDQVALVAALSA  262 (538)
Q Consensus       187 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~g~~p~~~~~~~li~~  262 (538)
                      ...|..+...+.+.|++++|+..|++...  | +..+|+.+...+...|+ +++|+..|+++.+.. +-+...|..+..+
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-P~~~~a~~~~g~~  175 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVL  175 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence            35677778888888999999999988653  3 56688999999999996 999999999998843 2257788888888


Q ss_pred             HHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHh-cCC
Q 044988          263 CAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAK-QGY  338 (538)
Q Consensus       263 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~-~~~  338 (538)
                      +...|++++|...++.+.+.     .|.+...|..+..++...|++++|...|+++.+   .+...|+.+..++.. .|.
T Consensus       176 ~~~~g~~~eAl~~~~kal~l-----dP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~P~~~~a~~~lg~~l~~l~~~  250 (382)
T 2h6f_A          176 VEWLRDPSQELEFIADILNQ-----DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGY  250 (382)
T ss_dssp             HHHHTCCTTHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCS
T ss_pred             HHHccCHHHHHHHHHHHHHh-----CccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCc
Confidence            99999999999999999997     788899999999999999999999999998875   466788888888888 555


Q ss_pred             ccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcC--ChHHHHHHHHhCCCCCC-HHHH
Q 044988          339 AQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAG--LMDEAFSLVQNMPMKPN-DAVL  414 (538)
Q Consensus       339 ~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g--~~~~A~~~~~~~~~~p~-~~~~  414 (538)
                      .++|+               .+.+...|++..+.   .| +...|+.+..++...|  ++++|++.++++...|+ ...+
T Consensus       251 ~~eA~---------------~~~el~~~~~Al~l---~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~~~~p~~~~al  312 (382)
T 2h6f_A          251 NDRAV---------------LEREVQYTLEMIKL---VPHNESAWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPYLI  312 (382)
T ss_dssp             CSHHH---------------HHHHHHHHHHHHHH---STTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHHTTTCCCHHHH
T ss_pred             chHHH---------------HHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHccCccchHHHHHHHHHhccCCCCHHHH
Confidence            46552               44556778887765   56 5778999999999988  68999999988854454 6778


Q ss_pred             HHHHHHHHhcC---------CHHHHHHHHHHchhccCCCCcccHHHHHHHHHH
Q 044988          415 GSLLLGCRIHN---------NAELASQVAQKLVAEIDPEQAAGYLALVANVYA  458 (538)
Q Consensus       415 ~~l~~~~~~~~---------~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~  458 (538)
                      ..+...+.+.|         ..++|+++++++..++.|.....|. .++..+.
T Consensus       313 ~~La~~~~~~~~~~~~~~~~~~~~A~~~~~~l~~~~DP~r~~~w~-~~~~~l~  364 (382)
T 2h6f_A          313 AFLVDIYEDMLENQCDNKEDILNKALELCEILAKEKDTIRKEYWR-YIGRSLQ  364 (382)
T ss_dssp             HHHHHHHHHHHHTTCSSHHHHHHHHHHHHHHHHHTTCGGGHHHHH-HHHHHHH
T ss_pred             HHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHhCchhHHHHH-HHHHHHH
Confidence            88888888764         3589999999974578899888676 6655544

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.48  E-value=1.3e-11  Score=110.55  Aligned_cols=204  Identities=13%  Similarity=-0.005  Sum_probs=148.3

Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHH
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNA  297 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  297 (538)
                      ...|..+...+...|++++|...|+++.+.. +.+...+..+...+...|+++.|...++.+.+.     .|.+...+..
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~-----~~~~~~~~~~  110 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALAS-----DSRNARVLNN  110 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-----CcCcHHHHHH
Confidence            4567778888888899999999998887753 335677888888888889999999998888886     5666777788


Q ss_pred             HHHHHHhCCCHHHHHHHHHhcCC--CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCC
Q 044988          298 LIHMYASCGEIEEAYGVFRKMQR--RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGI  375 (538)
Q Consensus       298 l~~~~~~~g~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~  375 (538)
                      +...|...|++++|.+.|+++.+  .++..                 ...+..+...+...|++++|...++++.+..  
T Consensus       111 la~~~~~~g~~~~A~~~~~~~~~~~~~~~~-----------------~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~--  171 (252)
T 2ho1_A          111 YGGFLYEQKRYEEAYQRLLEASQDTLYPER-----------------SRVFENLGLVSLQMKKPAQAKEYFEKSLRLN--  171 (252)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHTTCTTCTTH-----------------HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHhCccCccc-----------------HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--
Confidence            88889999999999999988765  21110                 0122233334444457777777777776551  


Q ss_pred             CccHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          376 KPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       376 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      +.+...+..+...|...|++++|...++++.  ...+...+..+...+...|++++|.+.++++ ....|+++.
T Consensus       172 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~-~~~~p~~~~  244 (252)
T 2ho1_A          172 RNQPSVALEMADLLYKEREYVPARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQL-KRLYPGSLE  244 (252)
T ss_dssp             SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTSHH
T ss_pred             cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHH-HHHCCCCHH
Confidence            2246677788888888888888888887763  2344666777777778888888888888888 777777766

>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis, TPR, superhelix, protein binding; HET: MSE; 2.00A {Pseudomonas aeruginosa} PDB: 2fi7_A

Probab=99.47  E-value=7.1e-12  Score=112.28  Aligned_cols=197  Identities=14%  Similarity=-0.000  Sum_probs=164.1

Q ss_pred             HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHH
Q 044988          253 QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSM  329 (538)
Q Consensus       253 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~l  329 (538)
                      ...+..+...+...|+++.|...++.+.+.     .|.+...+..+...|...|++++|.+.|+++.+   .+...+..+
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~-----~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l  111 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEI-----DPSSADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNY  111 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhc-----CCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHH
Confidence            455677778889999999999999999987     567788888999999999999999999998764   234444444


Q ss_pred             HHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--
Q 044988          330 ITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--  406 (538)
Q Consensus       330 i~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--  406 (538)
                      ...+.                    ..|++++|..+++++.+. +..| +...+..+...|...|++++|.+.++++.  
T Consensus       112 a~~~~--------------------~~g~~~~A~~~~~~~~~~-~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~  170 (252)
T 2ho1_A          112 GGFLY--------------------EQKRYEEAYQRLLEASQD-TLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRL  170 (252)
T ss_dssp             HHHHH--------------------HTTCHHHHHHHHHHHTTC-TTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHH--------------------HHhHHHHHHHHHHHHHhC-ccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            44444                    445788888999988762 3456 57788999999999999999999999874  


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 044988          407 MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       407 ~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                      .+.+...+..+...+...|++++|...++++ ....|++...+. .++.++.+.|++++|.++++++.+..
T Consensus       171 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~-~~~~~~~~~~~~-~~~~~~~~~g~~~~A~~~~~~~~~~~  239 (252)
T 2ho1_A          171 NRNQPSVALEMADLLYKEREYVPARQYYDLF-AQGGGQNARSLL-LGIRLAKVFEDRDTAASYGLQLKRLY  239 (252)
T ss_dssp             CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HTTSCCCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             CcccHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCcCcHHHHH-HHHHHHHHccCHHHHHHHHHHHHHHC
Confidence            2345788889999999999999999999999 889999988777 89999999999999999999998743

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.47  E-value=1.4e-12  Score=116.18  Aligned_cols=205  Identities=13%  Similarity=0.075  Sum_probs=128.4

Q ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          217 NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       217 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                      ....|..+...+...|++++|...|+++.+.. +.+...+..+...+...|+++.|...++.+.+.     .|.+..++.
T Consensus        22 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~   95 (243)
T 2q7f_A           22 ASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALEL-----DSSAATAYY   95 (243)
T ss_dssp             --------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc-----CCcchHHHH
Confidence            34456667777777788888888888777632 335666777777777788888888888877776     455666777


Q ss_pred             HHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc
Q 044988          297 ALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       297 ~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  373 (538)
                      .+...|...|++++|.+.++++.+   .+...+..+...+..                    .|++++|...++++.+..
T Consensus        96 ~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~--------------------~~~~~~A~~~~~~~~~~~  155 (243)
T 2q7f_A           96 GAGNVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVK--------------------LEQPKLALPYLQRAVELN  155 (243)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHH--------------------TSCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH--------------------hccHHHHHHHHHHHHHhC
Confidence            777888888888888888776643   233333333333433                    346666667777766541


Q ss_pred             CCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          374 GIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       374 ~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                        +.+...+..+...+.+.|++++|.+.++++.  ...+..++..+...+...|++++|...++++ ....|++...+.
T Consensus       156 --~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~-~~~~p~~~~~~~  231 (243)
T 2q7f_A          156 --ENDTEARFQFGMCLANEGMLDEALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKA-IDIQPDHMLALH  231 (243)
T ss_dssp             --TTCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHH-HHHCTTCHHHHH
T ss_pred             --CccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHH-HccCcchHHHHH
Confidence              2356677778888888888888888887763  2334667777788888888888888888888 778888776554

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.46  E-value=2.2e-11  Score=106.79  Aligned_cols=201  Identities=11%  Similarity=-0.002  Sum_probs=138.1

Q ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          217 NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       217 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                      +...|..+...+...|++++|...|+++.+.. +.+...+..+...+...|+++.|...++.+.+.     .|.+..++.
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~-----~~~~~~~~~   80 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSI-----KPDSAEINN   80 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHh-----CCCChHHHH
Confidence            34567777788888888888888888877643 334667777777888888888888888888776     556666777


Q ss_pred             HHHHHHHhC-CCHHHHHHHHHhcCC--CC---cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhh
Q 044988          297 ALIHMYASC-GEIEEAYGVFRKMQR--RN---TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMN  370 (538)
Q Consensus       297 ~l~~~~~~~-g~~~~a~~~~~~m~~--~~---~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~  370 (538)
                      .+...|... |++++|...++++.+  .+   ...+..+                    ..++...|++++|...++++.
T Consensus        81 ~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l--------------------~~~~~~~~~~~~A~~~~~~~~  140 (225)
T 2vq2_A           81 NYGWFLCGRLNRPAESMAYFDKALADPTYPTPYIANLNK--------------------GICSAKQGQFGLAEAYLKRSL  140 (225)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHH--------------------HHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHH--------------------HHHHHHcCCHHHHHHHHHHHH
Confidence            788888888 888888888877655  11   1223333                    333334446666667777666


Q ss_pred             hhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-C-C-CCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCc
Q 044988          371 QNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-K-PNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQA  446 (538)
Q Consensus       371 ~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~-p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~  446 (538)
                      +.   .| +...+..+...+...|++++|.+.++++. . + .+...+..+...+...|+.+.|..+++.+ ....|+++
T Consensus       141 ~~---~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~-~~~~p~~~  216 (225)
T 2vq2_A          141 AA---QPQFPPAFKELARTKMLAGQLGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQL-QANFPYSE  216 (225)
T ss_dssp             HH---STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCH
T ss_pred             Hh---CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHH-HHhCCCCH
Confidence            54   33 36667777777777777777777777653 2 2 34556666666677777777777777777 66677766


Q ss_pred             c
Q 044988          447 A  447 (538)
Q Consensus       447 ~  447 (538)
                      .
T Consensus       217 ~  217 (225)
T 2vq2_A          217 E  217 (225)
T ss_dssp             H
T ss_pred             H
Confidence            6

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.45  E-value=3.5e-10  Score=114.32  Aligned_cols=424  Identities=9%  Similarity=0.047  Sum_probs=252.3

Q ss_pred             HHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCC---chHHHHHHHHh
Q 044988           36 LFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSET---PEKSVYLYKQM  109 (538)
Q Consensus        36 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~---~~~a~~~~~~m  109 (538)
                      ....++..+... +-|...|..++..+.+.+.++.+..+|+++.   +.+...|...+..-.+.++   ++.+..+|++.
T Consensus        51 ~i~~lE~~l~~n-p~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRa  129 (679)
T 4e6h_A           51 VIGKLNDMIEEQ-PTDIFLYVKLLKHHVSLKQWKQVYETFDKLHDRFPLMANIWCMRLSLEFDKMEELDAAVIEPVLARC  129 (679)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHC-cCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHH
Confidence            344456655554 3488899999999988899999999998876   3455678888888888888   99999999998


Q ss_pred             HhCC-CCCCcchHHHHHHHHHccCCc--------HHHHHHHHHHHHh-CC-CCc-hhHHhHHHHHHHh---------cCC
Q 044988          110 IDKE-TEPDEYTYSFLLSVCARCGLF--------REGEQVHGRVLAS-GY-CSN-VFIRTNLMNLYLM---------SGG  168 (538)
Q Consensus       110 ~~~~-~~p~~~~~~~li~~~~~~~~~--------~~a~~~~~~~~~~-~~-~~~-~~~~~~l~~~~~~---------~g~  168 (538)
                      .... ..|+...|...+....+.++.        +...++|+..+.. |. .++ ..+|...+.....         .++
T Consensus       130 l~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~~  209 (679)
T 4e6h_A          130 LSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQQR  209 (679)
T ss_dssp             TCSSSCCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHHHHH
T ss_pred             HHhcCCCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHHHhH
Confidence            8753 137888888877766655543        3344677776653 55 444 4677777765543         234


Q ss_pred             CCChhHHHHHhhcCCCCCc----hhHH---HHHHHH----------HhcCCHHHHHHHHcc-------CCC---------
Q 044988          169 ECGVGCARLLFDDMPARSV----VSWN---SLLKGY----------VKRGDIDGAWKIFDE-------MPH---------  215 (538)
Q Consensus       169 ~~~~~~a~~~~~~~~~~~~----~~~~---~li~~~----------~~~g~~~~A~~~~~~-------m~~---------  215 (538)
                         ++.+.++|++...-..    ..|.   .+....          -...+++.|...+.+       +..         
T Consensus       210 ---~~~~R~iy~raL~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~  286 (679)
T 4e6h_A          210 ---VQYIRKLYKTLLCQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQA  286 (679)
T ss_dssp             ---HHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTC
T ss_pred             ---HHHHHHHHHHHHhCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccc
Confidence               6778888888775211    2222   221111          011223444454433       111         


Q ss_pred             -----C--C------hHHHHHHHHHHHHcC-------CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHH-H
Q 044988          216 -----R--N------VVSWTTMISGCAQNG-------KSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGK-W  274 (538)
Q Consensus       216 -----~--~------~~~~~~li~~~~~~~-------~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~-~  274 (538)
                           |  +      ...|...+..--..+       ..+.+..+|++.... ++-+...|...+.-+...|+.+.|. .
T Consensus       287 ~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~~~a~r~  365 (679)
T 4e6h_A          287 TESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTDSTVITK  365 (679)
T ss_dssp             CTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCCTTHHHH
T ss_pred             hhccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcHHHHHHH
Confidence                 1  0      134555555433332       134566788888764 3446777777777778889999996 9


Q ss_pred             HHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCcc--------HHHHHH
Q 044988          275 IHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQ--------EALLTF  346 (538)
Q Consensus       275 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~--------~a~~~~  346 (538)
                      +++.....     .|.+...|-.++....+.|+++.|.++|+++...-...+..+-.   .....+        ....+|
T Consensus       366 il~rAi~~-----~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~---~~p~~~~~~~~~~~~~~~vW  437 (679)
T 4e6h_A          366 YLKLGQQC-----IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALME---DDPTNESAINQLKSKLTYVY  437 (679)
T ss_dssp             HHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHH---HSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHh-----CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhh---ccCcchhhhhhhccchHHHH
Confidence            99999886     67788888889999999999999999999875310000000000   000000        000234


Q ss_pred             HHHHHHhcccCcHHHHHHHHHHhhhh-cCCCccHHHHHHHHHHhhhc-CChHHHHHHHHhCC--CCCCHHHHHHHHHHHH
Q 044988          347 LGVLSACSHGGFVDEGRQFFECMNQN-WGIKPRIEHYGCMVDLFSRA-GLMDEAFSLVQNMP--MKPNDAVLGSLLLGCR  422 (538)
Q Consensus       347 ~~ll~~~~~~~~~~~a~~~~~~~~~~-~~~~p~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~  422 (538)
                      ...+....+.|.++.|+.+|....+. ...  ....|...+..-.+. ++.+.|.++|+...  ..-+...|...+....
T Consensus       438 i~y~~~erR~~~l~~AR~vf~~A~~~~~~~--~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~  515 (679)
T 4e6h_A          438 CVYMNTMKRIQGLAASRKIFGKCRRLKKLV--TPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLI  515 (679)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHHHHHTGGGS--CTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhcCCC--ChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHH
Confidence            44444444555667777777776653 111  122232222222233 34677777776553  2224455556666666


Q ss_pred             hcCCHHHHHHHHHHchhccCCC---CcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          423 IHNNAELASQVAQKLVAEIDPE---QAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       423 ~~~~~~~A~~~~~~~~~~~~p~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      ..|+.+.|..+|+++ ....|+   ....|. ..+..-.+.|+.+.+.++.+++.+.
T Consensus       516 ~~~~~~~AR~lfera-l~~~~~~~~~~~lw~-~~~~fE~~~G~~~~~~~v~~R~~~~  570 (679)
T 4e6h_A          516 YVNEESQVKSLFESS-IDKISDSHLLKMIFQ-KVIFFESKVGSLNSVRTLEKRFFEK  570 (679)
T ss_dssp             HHTCHHHHHHHHHHH-TTTSSSTTHHHHHHH-HHHHHHHHTCCSHHHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHHHH-HHhcCCHHHHHHHHH-HHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            667777777777776 444442   223344 4445555667777777777777654

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.45  E-value=1.4e-12  Score=126.30  Aligned_cols=271  Identities=9%  Similarity=-0.043  Sum_probs=185.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHccCCC--CC-h----HHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCC-CHHHHHHH
Q 044988          192 SLLKGYVKRGDIDGAWKIFDEMPH--RN-V----VSWTTMISGCAQNGKSRQALSLFNEMRRA----RVGL-DQVALVAA  259 (538)
Q Consensus       192 ~li~~~~~~g~~~~A~~~~~~m~~--~~-~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~~~~~l  259 (538)
                      .+...+...|++++|+..|++..+  |+ .    ..|..+...|...|++++|...|++..+.    +-.| ....+..+
T Consensus        53 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l  132 (411)
T 4a1s_A           53 LEGERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNL  132 (411)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHH
Confidence            344556666777777777766542  32 2    36777788888888888888888877652    1122 34566677


Q ss_pred             HHHHHccCChHHHHHHHHHHHHhccC-CCCCcchhHHHHHHHHHHhCCC-----------------HHHHHHHHHhcCCC
Q 044988          260 LSACAEIGDLKLGKWIHSYVEENFSV-GREPVLVSLNNALIHMYASCGE-----------------IEEAYGVFRKMQRR  321 (538)
Q Consensus       260 i~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~g~-----------------~~~a~~~~~~m~~~  321 (538)
                      ...+...|+++.|...+..+.+.... +..+....++..+...|...|+                 +++|...+++..+ 
T Consensus       133 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~-  211 (411)
T 4a1s_A          133 GNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLK-  211 (411)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHH-
Confidence            77788888998888888877665221 1134445677788999999999                 8888888876532 


Q ss_pred             CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc----HHHHHHHHHHhhhcCChHH
Q 044988          322 NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR----IEHYGCMVDLFSRAGLMDE  397 (538)
Q Consensus       322 ~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~l~~~~~~~g~~~~  397 (538)
                                .....++.......+..+...+...|++++|...+++..+...-.++    ..++..+...|...|++++
T Consensus       212 ----------~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  281 (411)
T 4a1s_A          212 ----------LMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFED  281 (411)
T ss_dssp             ----------HHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHH
T ss_pred             ----------HHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHH
Confidence                      11111222222234555555666666777777777776543110111    3478889999999999999


Q ss_pred             HHHHHHhCC----CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC------cccHHHHHHHHHHhcCCh
Q 044988          398 AFSLVQNMP----MKPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ------AAGYLALVANVYAAAKRW  463 (538)
Q Consensus       398 A~~~~~~~~----~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~------~~~~~~~l~~~~~~~g~~  463 (538)
                      |.+.+++..    ...+    ..++..+...+...|++++|...++++ ....+..      ...+. .++.+|.+.|++
T Consensus       282 A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a-l~~~~~~~~~~~~~~~~~-~la~~~~~~g~~  359 (411)
T 4a1s_A          282 AAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRH-LAIAQELGDRIGEARACW-SLGNAHSAIGGH  359 (411)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHHHHTCHHHHHHHHH-HHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHHHHHCCChHHHHHHHH-HHHHHHHHhccH
Confidence            999998763    1112    467788888899999999999999999 4443322      33566 889999999999


Q ss_pred             HHHHHHHHHHHh
Q 044988          464 QDVAAVRQKMIK  475 (538)
Q Consensus       464 ~~A~~~~~~m~~  475 (538)
                      ++|.+.+++..+
T Consensus       360 ~~A~~~~~~al~  371 (411)
T 4a1s_A          360 ERALKYAEQHLQ  371 (411)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999999875

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.45  E-value=1.2e-11  Score=108.61  Aligned_cols=197  Identities=11%  Similarity=-0.079  Sum_probs=162.8

Q ss_pred             CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHH
Q 044988          252 DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTS  328 (538)
Q Consensus       252 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~  328 (538)
                      +...+..+...+...|+++.|...++.+.+.     .|.+...+..+...|...|++++|...++++.+  | +...+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~   81 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKS-----DPKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNN   81 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHh-----CccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHH
Confidence            4566778888899999999999999999987     567778888999999999999999999998764  2 3334444


Q ss_pred             HHHHHHhcCCccHHHHHHHHHHHHhccc-CcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          329 MITGFAKQGYAQEALLTFLGVLSACSHG-GFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       329 li~~~~~~~~~~~a~~~~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      +.                    ..+... |++++|...++.+.+. +..| +...+..+..++...|++++|.+.++++.
T Consensus        82 l~--------------------~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  140 (225)
T 2vq2_A           82 YG--------------------WFLCGRLNRPAESMAYFDKALAD-PTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSL  140 (225)
T ss_dssp             HH--------------------HHHHTTTCCHHHHHHHHHHHHTS-TTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HH--------------------HHHHHhcCcHHHHHHHHHHHHcC-cCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            44                    444555 5888888999988862 3345 36788999999999999999999998874


Q ss_pred             -CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCC-CCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          407 -MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDP-EQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       407 -~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                       ..| +...+..+...+...|++++|...++++ ....| ++...+. .++..+...|+.++|..+++.+.+.
T Consensus       141 ~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~-~~~~~~~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~  211 (225)
T 2vq2_A          141 AAQPQFPPAFKELARTKMLAGQLGDADYYFKKY-QSRVEVLQADDLL-LGWKIAKALGNAQAAYEYEAQLQAN  211 (225)
T ss_dssp             HHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHHHCSCCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HhCCCCchHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCCCCCHHHHH-HHHHHHHhcCcHHHHHHHHHHHHHh
Confidence             234 4788889999999999999999999999 88888 8888676 8888999999999999999998754

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.45  E-value=6.3e-13  Score=120.86  Aligned_cols=241  Identities=11%  Similarity=-0.055  Sum_probs=142.1

Q ss_pred             cCCCchHHHHHHHHhHhCCCC--C-CcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCC
Q 044988           95 RSETPEKSVYLYKQMIDKETE--P-DEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECG  171 (538)
Q Consensus        95 ~~~~~~~a~~~~~~m~~~~~~--p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  171 (538)
                      ..|++++|+..|+++.+....  | +..++..+...+...|++++|...+++..+.. +.+..++..+..+|...|+   
T Consensus        17 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~---   92 (275)
T 1xnf_A           17 PTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGN---   92 (275)
T ss_dssp             CCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTC---
T ss_pred             ccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccC---
Confidence            345566666666666654211  1 23455566666666666666666666666653 3445566666666666666   


Q ss_pred             hhHHHHHhhcCCC---CCchhHHHHHHHHHhcCCHHHHHHHHccCCC--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Q 044988          172 VGCARLLFDDMPA---RSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--RNVVSWTTMISGCAQNGKSRQALSLFNEMRR  246 (538)
Q Consensus       172 ~~~a~~~~~~~~~---~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~  246 (538)
                      +++|...|++..+   .+...|..+...+...|++++|...|+++.+  |+.......+..+...|++++|...+++...
T Consensus        93 ~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  172 (275)
T 1xnf_A           93 FDAAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFE  172 (275)
T ss_dssp             HHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            6666666665543   2455666666666777777777777766542  4444444444445566788888888876665


Q ss_pred             CCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchH
Q 044988          247 ARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSW  326 (538)
Q Consensus       247 ~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~  326 (538)
                      .. +++...+ .++..+...++.+.|...+....+.... ..+.+...+..+...|...|++++|...|++..+.++..+
T Consensus       173 ~~-~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~  249 (275)
T 1xnf_A          173 KS-DKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTS-LAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNF  249 (275)
T ss_dssp             HS-CCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHH-HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTTC
T ss_pred             cC-CcchHHH-HHHHHHHHhcCHHHHHHHHHHHhccccc-ccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCchhH
Confidence            42 2232233 3555666667777777776665443000 0112246667788888888888888888888776444444


Q ss_pred             HHHHHHHHhcCCccHH
Q 044988          327 TSMITGFAKQGYAQEA  342 (538)
Q Consensus       327 ~~li~~~~~~~~~~~a  342 (538)
                      .....++...|++++|
T Consensus       250 ~~~~~~~~~l~~~~~a  265 (275)
T 1xnf_A          250 VEHRYALLELSLLGQD  265 (275)
T ss_dssp             HHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHhh
Confidence            4444455555544443

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.44  E-value=9.4e-12  Score=120.06  Aligned_cols=277  Identities=12%  Similarity=-0.017  Sum_probs=199.0

Q ss_pred             CchhHHHHHHHHHhcCCHHHHHHHHccCCC--CC-----hHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCCC-H
Q 044988          186 SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--RN-----VVSWTTMISGCAQNGKSRQALSLFNEMRRA----RVGLD-Q  253 (538)
Q Consensus       186 ~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~-----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~-~  253 (538)
                      ....+......+...|++++|...|++..+  |+     ..+|..+...|...|++++|...+++....    +-.|. .
T Consensus         8 ~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~   87 (406)
T 3sf4_A            8 SCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEA   87 (406)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHHH
Confidence            344566777888999999999999988653  32     246788888999999999999999987642    22232 4


Q ss_pred             HHHHHHHHHHHccCChHHHHHHHHHHHHhccCCC-CCcchhHHHHHHHHHHhCCC--------------------HHHHH
Q 044988          254 VALVAALSACAEIGDLKLGKWIHSYVEENFSVGR-EPVLVSLNNALIHMYASCGE--------------------IEEAY  312 (538)
Q Consensus       254 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~--------------------~~~a~  312 (538)
                      ..+..+...+...|+++.|...+....+.....+ .+....++..+...|...|+                    +++|.
T Consensus        88 ~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A~  167 (406)
T 3sf4_A           88 KASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAAV  167 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHHH
Confidence            4677788888899999999999999988632111 11224477788888999999                    88888


Q ss_pred             HHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc----HHHHHHHHHH
Q 044988          313 GVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR----IEHYGCMVDL  388 (538)
Q Consensus       313 ~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~l~~~  388 (538)
                      ..+++..+           .+...++......++..+...+...|++++|...+++..+...-.++    ..++..+...
T Consensus       168 ~~~~~al~-----------~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~  236 (406)
T 3sf4_A          168 DFYEENLS-----------LVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNA  236 (406)
T ss_dssp             HHHHHHHH-----------HHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHH-----------HHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHH
Confidence            88776532           11222222222245555566666667777887877776643211122    3478889999


Q ss_pred             hhhcCChHHHHHHHHhCC----CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC------cccHHHHHH
Q 044988          389 FSRAGLMDEAFSLVQNMP----MKPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ------AAGYLALVA  454 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~----~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~------~~~~~~~l~  454 (538)
                      |...|++++|...+++..    ..++    ..++..+...+...|++++|...++++ ....+..      ...+. .++
T Consensus       237 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a-~~~~~~~~~~~~~~~~~~-~la  314 (406)
T 3sf4_A          237 YIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKH-LAIAQELNDRIGEGRACW-SLG  314 (406)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHHHTTCHHHHHHHHH-HHH
T ss_pred             HHHcCChHHHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHH-HHHHHhcCCcHHHHHHHH-HHH
Confidence            999999999999998763    1122    457788888899999999999999999 4443332      34466 889


Q ss_pred             HHHHhcCChHHHHHHHHHHHh
Q 044988          455 NVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       455 ~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .+|.+.|++++|.+.+++..+
T Consensus       315 ~~~~~~g~~~~A~~~~~~al~  335 (406)
T 3sf4_A          315 NAYTALGNHDQAMHFAEKHLE  335 (406)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHH
Confidence            999999999999999998764

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.44  E-value=2.6e-12  Score=114.41  Aligned_cols=197  Identities=12%  Similarity=0.087  Sum_probs=148.1

Q ss_pred             CCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHH
Q 044988          251 LDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWT  327 (538)
Q Consensus       251 p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~  327 (538)
                      .....+..+...+...|+++.|...++.+.+.     .|.+...+..+...|...|++++|...|+++.+   .+...+.
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~-----~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~   95 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEE-----NKEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYY   95 (243)
T ss_dssp             ---------------------CCTTHHHHHTT-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHh-----CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHH
Confidence            34556777778888999999999999999886     677788888999999999999999999998764   2344444


Q ss_pred             HHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-
Q 044988          328 SMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-  406 (538)
Q Consensus       328 ~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-  406 (538)
                      .+...+..                    .|++++|...++++.+..  +.+...+..+...+...|++++|.+.++++. 
T Consensus        96 ~la~~~~~--------------------~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~  153 (243)
T 2q7f_A           96 GAGNVYVV--------------------KEMYKEAKDMFEKALRAG--MENGDLFYMLGTVLVKLEQPKLALPYLQRAVE  153 (243)
T ss_dssp             HHHHHHHH--------------------TTCHHHHHHHHHHHHHHT--CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH--------------------hccHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            44444444                    457888888888888752  3367789999999999999999999999874 


Q ss_pred             -CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          407 -MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       407 -~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                       .+.+...+..+...+...|++++|...++++ ....|++...+. .++.+|.+.|++++|.+.++++.+.
T Consensus       154 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~-~~~~~~~~~~~~-~la~~~~~~~~~~~A~~~~~~~~~~  222 (243)
T 2q7f_A          154 LNENDTEARFQFGMCLANEGMLDEALSQFAAV-TEQDPGHADAFY-NAGVTYAYKENREKALEMLDKAIDI  222 (243)
T ss_dssp             HCTTCHHHHHHHHHHHHHHTCCHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHTTCTTHHHHHHHHHHHH
T ss_pred             hCCccHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCcccHHHHH-HHHHHHHHccCHHHHHHHHHHHHcc
Confidence             3346788889999999999999999999999 888999988788 9999999999999999999999874

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.43  E-value=7.3e-12  Score=117.28  Aligned_cols=272  Identities=12%  Similarity=0.006  Sum_probs=185.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHccCCC--CC-----hHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCC-CHHHHHHH
Q 044988          192 SLLKGYVKRGDIDGAWKIFDEMPH--RN-----VVSWTTMISGCAQNGKSRQALSLFNEMRRA----RVGL-DQVALVAA  259 (538)
Q Consensus       192 ~li~~~~~~g~~~~A~~~~~~m~~--~~-----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~~~~~l  259 (538)
                      .....+...|++++|...|++..+  |+     ...|..+...|...|++++|...+++..+.    +-.| ....+..+
T Consensus        10 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l   89 (338)
T 3ro2_A           10 LEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNL   89 (338)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHHHH
Confidence            344556667777777777776542  22     246777888888889999888888876542    2122 24566777


Q ss_pred             HHHHHccCChHHHHHHHHHHHHhccCCC-CCcchhHHHHHHHHHHhCCC--------------------HHHHHHHHHhc
Q 044988          260 LSACAEIGDLKLGKWIHSYVEENFSVGR-EPVLVSLNNALIHMYASCGE--------------------IEEAYGVFRKM  318 (538)
Q Consensus       260 i~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~--------------------~~~a~~~~~~m  318 (538)
                      ...+...|+++.|...+....+.....+ .+....++..+...|...|+                    +++|...+++.
T Consensus        90 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a  169 (338)
T 3ro2_A           90 GNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLYEEN  169 (338)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHHHHH
Confidence            7788888999999888888776532111 12224467788888889999                    88888888765


Q ss_pred             CCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc---CCCc-cHHHHHHHHHHhhhcCC
Q 044988          319 QRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW---GIKP-RIEHYGCMVDLFSRAGL  394 (538)
Q Consensus       319 ~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~---~~~p-~~~~~~~l~~~~~~~g~  394 (538)
                      ..           .+...++.......+..+...+...|++++|...+++..+..   +..+ ...++..+...|...|+
T Consensus       170 ~~-----------~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  238 (338)
T 3ro2_A          170 LS-----------LVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGE  238 (338)
T ss_dssp             HH-----------HHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTC
T ss_pred             HH-----------HHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCC
Confidence            32           111112222222344555555666667777777777665431   1111 14478889999999999


Q ss_pred             hHHHHHHHHhCC----CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC------cccHHHHHHHHHHhc
Q 044988          395 MDEAFSLVQNMP----MKPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ------AAGYLALVANVYAAA  460 (538)
Q Consensus       395 ~~~A~~~~~~~~----~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~------~~~~~~~l~~~~~~~  460 (538)
                      +++|.+.+++..    ..++    ..++..+...+...|++++|...++++ ....|..      ...+. .++.+|.+.
T Consensus       239 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a-~~~~~~~~~~~~~~~~~~-~la~~~~~~  316 (338)
T 3ro2_A          239 FETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKH-LAIAQELKDRIGEGRACW-SLGNAYTAL  316 (338)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHHHHTCHHHHHHHHH-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHH-HHHHHhcCCcHHHHHHHH-HHHHHHHHc
Confidence            999999998763    1122    457778888899999999999999998 4433322      23466 889999999


Q ss_pred             CChHHHHHHHHHHHhC
Q 044988          461 KRWQDVAAVRQKMIKM  476 (538)
Q Consensus       461 g~~~~A~~~~~~m~~~  476 (538)
                      |++++|...+++..+.
T Consensus       317 g~~~~A~~~~~~a~~~  332 (338)
T 3ro2_A          317 GNHDQAMHFAEKHLEI  332 (338)
T ss_dssp             TCHHHHHHHHHHHHHC
T ss_pred             CChHHHHHHHHHHHHH
Confidence            9999999999998763

>2h6f_A Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit; ftase, farnesyltransferase, farnesyl transferase, prenyltransferase, CAAX, RAS, lipid modification, prenylation; HET: SUC FAR; 1.50A {Homo sapiens} SCOP: a.118.6.1 PDB: 1jcq_A* 1ld7_A* 1mzc_A* 1s63_A* 1sa4_A* 1tn6_A* 1ld8_A* 2h6g_A* 2h6h_A* 2h6i_A* 2iej_A* 3e37_A* 2f0y_A* 3ksl_A* 2zir_A* 2zis_A* 1o5m_A* 3ksq_A* 1o1t_A* 1o1s_A* ...

Probab=99.42  E-value=6.5e-12  Score=118.84  Aligned_cols=125  Identities=6%  Similarity=-0.040  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCC-chHHHHHHHHhHhCCCCCCcchHHHHHHHHH
Q 044988           54 ILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSET-PEKSVYLYKQMIDKETEPDEYTYSFLLSVCA  129 (538)
Q Consensus        54 ~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~-~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  129 (538)
                      +|..+..++.+.|++++|+..|++..   +.+...|+.+..++...|+ +++|+..|++..+.. +-+...|..+..++.
T Consensus        99 a~~~lg~~~~~~g~~~~Al~~~~~al~l~P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-P~~~~a~~~~g~~~~  177 (382)
T 2h6f_A           99 VYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVLVE  177 (382)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCChHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHH
Confidence            34444444445555555555554433   1233344445555555553 555555555554432 123334444555555


Q ss_pred             ccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCC
Q 044988          130 RCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMP  183 (538)
Q Consensus       130 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~  183 (538)
                      ..|++++|...++++++.. +.+...|..+..++.+.|+   +++|+..|+++.
T Consensus       178 ~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~---~~eAl~~~~~al  227 (382)
T 2h6f_A          178 WLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKL---WDNELQYVDQLL  227 (382)
T ss_dssp             HHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC---CTTHHHHHHHHH
T ss_pred             HccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCC---hHHHHHHHHHHH
Confidence            5555555555555555443 3334444444444444444   444444444433

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.41  E-value=2.1e-11  Score=117.92  Aligned_cols=280  Identities=12%  Similarity=0.019  Sum_probs=147.9

Q ss_pred             HHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCc-----chHHHHHHHHHccCCcHHHHHHHHHHHHhC-----CCCchhH
Q 044988           86 WNQMIRGHARSETPEKSVYLYKQMIDKETEPDE-----YTYSFLLSVCARCGLFREGEQVHGRVLASG-----YCSNVFI  155 (538)
Q Consensus        86 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-----~~~~~li~~~~~~~~~~~a~~~~~~~~~~~-----~~~~~~~  155 (538)
                      +..+...+...|++++|+..|++..+.  .|+.     ..|..+...+...|++++|...+++..+..     .+....+
T Consensus        51 l~~~g~~~~~~g~~~~A~~~~~~al~~--~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  128 (411)
T 4a1s_A           51 LALEGERLCNAGDCRAGVAFFQAAIQA--GTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKS  128 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhCcHHHHHHHHHHHHHh--cccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHH
Confidence            444566677788888888888888775  3432     356777777888888888888877776531     0122345


Q ss_pred             HhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCC--CChHHHHHHHHHHHHcCC
Q 044988          156 RTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH--RNVVSWTTMISGCAQNGK  233 (538)
Q Consensus       156 ~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--~~~~~~~~li~~~~~~~~  233 (538)
                      +..+...|...|+   +++|...+++.                        ++++.....  ....++..+...|...|+
T Consensus       129 ~~~l~~~~~~~g~---~~~A~~~~~~a------------------------l~~~~~~~~~~~~~~~~~~l~~~~~~~g~  181 (411)
T 4a1s_A          129 SGNLGNTLKVMGR---FDEAAICCERH------------------------LTLARQLGDRLSEGRALYNLGNVYHAKGK  181 (411)
T ss_dssp             HHHHHHHHHHTTC---HHHHHHHHHHH------------------------HHHHHHHTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCC---HHHHHHHHHHH------------------------HHHHHHhhchHHHHHHHHHHHHHHHHcCc
Confidence            5556666666666   66665554322                        222222111  123366777777777788


Q ss_pred             -----------------HHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCC-CCc
Q 044988          234 -----------------SRQALSLFNEMRRA----RVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGR-EPV  290 (538)
Q Consensus       234 -----------------~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~  290 (538)
                                       +++|+..+++..+.    +-.| ...++..+...+...|+++.|...++...+.....+ ...
T Consensus       182 ~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  261 (411)
T 4a1s_A          182 HLGQRNPGKFGDDVKEALTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAA  261 (411)
T ss_dssp             HHHHHSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHH
T ss_pred             ccccccchhhhhhhhHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHH
Confidence                             77777777665431    1111 122444444555555555555555555544311000 001


Q ss_pred             chhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhh
Q 044988          291 LVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMN  370 (538)
Q Consensus       291 ~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~  370 (538)
                      ....+..+...|...|++++|...|++..+                                            +.... 
T Consensus       262 ~~~~~~~la~~~~~~g~~~~A~~~~~~al~--------------------------------------------~~~~~-  296 (411)
T 4a1s_A          262 ERRANSNLGNSHIFLGQFEDAAEHYKRTLA--------------------------------------------LAVEL-  296 (411)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHH--------------------------------------------HHHHT-
T ss_pred             HHHHHHHHHHHHHHCcCHHHHHHHHHHHHH--------------------------------------------HHHHc-
Confidence            111334445555555555555555544321                                            11110 


Q ss_pred             hhcCCC-ccHHHHHHHHHHhhhcCChHHHHHHHHhCC----CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhcc
Q 044988          371 QNWGIK-PRIEHYGCMVDLFSRAGLMDEAFSLVQNMP----MKPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEI  441 (538)
Q Consensus       371 ~~~~~~-p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  441 (538)
                         +.. ....++..+...|...|++++|.+.+++..    ..++    ..++..+...+...|++++|...++++ ..+
T Consensus       297 ---~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a-l~~  372 (411)
T 4a1s_A          297 ---GEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQH-LQL  372 (411)
T ss_dssp             ---TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHH
T ss_pred             ---CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHH-HHH
Confidence               111 123455556666666666666666665542    0011    235555666667777777777777776 444


Q ss_pred             CC
Q 044988          442 DP  443 (538)
Q Consensus       442 ~p  443 (538)
                      .+
T Consensus       373 ~~  374 (411)
T 4a1s_A          373 AX  374 (411)
T ss_dssp             CC
T ss_pred             Hh
Confidence            33

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.40  E-value=5.1e-11  Score=108.15  Aligned_cols=218  Identities=11%  Similarity=-0.063  Sum_probs=110.1

Q ss_pred             hHHHHHHHHHHccCChhHHHHHHhcCCCC-CcchHHHHHHHHhc----CCCchHHHHHHHHhHhCCCCCCcchHHHHHHH
Q 044988           53 YILAKLLAFYVTSGYLINAHKVFEKTENP-STAIWNQMIRGHAR----SETPEKSVYLYKQMIDKETEPDEYTYSFLLSV  127 (538)
Q Consensus        53 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  127 (538)
                      .++..+...|...|++++|...|++..+| +...+..+...|..    .+++++|+..|++..+.+   +...+..+...
T Consensus         7 ~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~   83 (273)
T 1ouv_A            7 KELVGLGAKSYKEKDFTQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHLLGNL   83 (273)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHHHHHHH
Confidence            34444444455555555555555443322 23344444444555    555555555555555433   34444555555


Q ss_pred             HHc----cCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHh----cCCCCChhHHHHHhhcCCCC-CchhHHHHHHHHH
Q 044988          128 CAR----CGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLM----SGGECGVGCARLLFDDMPAR-SVVSWNSLLKGYV  198 (538)
Q Consensus       128 ~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~~~~a~~~~~~~~~~-~~~~~~~li~~~~  198 (538)
                      +..    .+++++|...+++..+.+   +...+..+...|..    .++   .++|...|++..+. +...+..+...|.
T Consensus        84 ~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~---~~~A~~~~~~a~~~~~~~a~~~lg~~~~  157 (273)
T 1ouv_A           84 YYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRD---FKKAVEYFTKACDLNDGDGCTILGSLYD  157 (273)
T ss_dssp             HHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCC---HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccC---HHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            555    555555555555555443   34444445555554    444   55555444443321 2333333444444


Q ss_pred             h----cCCHHHHHHHHccCCC-CChHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----
Q 044988          199 K----RGDIDGAWKIFDEMPH-RNVVSWTTMISGCAQ----NGKSRQALSLFNEMRRARVGLDQVALVAALSACAE----  265 (538)
Q Consensus       199 ~----~g~~~~A~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----  265 (538)
                      .    .+++++|...|++..+ .+...+..+...|..    .+++++|+..|++..+.+.   ...+..+...+.+    
T Consensus       158 ~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~---~~a~~~l~~~~~~g~~~  234 (273)
T 1ouv_A          158 AGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN---GGGCFNLGAMQYNGEGV  234 (273)
T ss_dssp             HTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHTTSSS
T ss_pred             cCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC---HHHHHHHHHHHHcCCCc
Confidence            4    4555555555544322 234455556666666    6666666666666665432   4445555555555    


Q ss_pred             cCChHHHHHHHHHHHHh
Q 044988          266 IGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       266 ~~~~~~a~~~~~~~~~~  282 (538)
                      .+++++|...++...+.
T Consensus       235 ~~~~~~A~~~~~~a~~~  251 (273)
T 1ouv_A          235 TRNEKQAIENFKKGCKL  251 (273)
T ss_dssp             SCCSTTHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHc
Confidence            66666666666666555

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.38  E-value=3.3e-11  Score=115.35  Aligned_cols=238  Identities=11%  Similarity=-0.009  Sum_probs=167.2

Q ss_pred             HHHHHHHcCCHHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCC--CCcchhHHH
Q 044988          224 MISGCAQNGKSRQALSLFNEMRRA----RVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGR--EPVLVSLNN  296 (538)
Q Consensus       224 li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~  296 (538)
                      ....+...|++++|...|++..+.    +-.+ ...++..+...+...|+++.|...+....+.....+  .+....+++
T Consensus       109 ~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  188 (383)
T 3ulq_A          109 RGMYELDQREYLSAIKFFKKAESKLIFVKDRIEKAEFFFKMSESYYYMKQTYFSMDYARQAYEIYKEHEAYNIRLLQCHS  188 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTCSTTHHHHHHHHH
T ss_pred             HHHHHHHhcCHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCccchHHHHHHHH
Confidence            556677889999999999988763    1111 235677788888889999999998888877643322  223355778


Q ss_pred             HHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh---c
Q 044988          297 ALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQN---W  373 (538)
Q Consensus       297 ~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~---~  373 (538)
                      .+...|...|++++|...|++..+           ...+.++......++..+...+...|++++|...+++..+.   .
T Consensus       189 ~lg~~~~~~g~~~~A~~~~~~al~-----------~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~  257 (383)
T 3ulq_A          189 LFATNFLDLKQYEDAISHFQKAYS-----------MAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEES  257 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH-----------HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHH-----------HHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            899999999999999999988653           11111222222234444555555566777777777766541   0


Q ss_pred             CCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC----C--CCC-HHHHHHHHHHHHhcCC---HHHHHHHHHHchhccC
Q 044988          374 GIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP----M--KPN-DAVLGSLLLGCRIHNN---AELASQVAQKLVAEID  442 (538)
Q Consensus       374 ~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~--~p~-~~~~~~l~~~~~~~~~---~~~A~~~~~~~~~~~~  442 (538)
                      +..| ...++..+...|.+.|++++|.+.+++..    .  .|. ...+..+...+...|+   +++|+.++++.  +..
T Consensus       258 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~--~~~  335 (383)
T 3ulq_A          258 NILPSLPQAYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK--MLY  335 (383)
T ss_dssp             TCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT--TCH
T ss_pred             ccchhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC--cCH
Confidence            2224 36788999999999999999999998763    1  122 2234566677888888   88888888886  444


Q ss_pred             CCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          443 PEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       443 p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      |.....+. .++.+|.+.|++++|.+.+++..+
T Consensus       336 ~~~~~~~~-~la~~y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          336 ADLEDFAI-DVAKYYHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHHHHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHH-HHHHHHHHCCCHHHHHHHHHHHHH
Confidence            55555566 899999999999999999999864

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.38  E-value=8e-11  Score=110.10  Aligned_cols=204  Identities=15%  Similarity=0.053  Sum_probs=110.6

Q ss_pred             HHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCc-----chHHHHHHHHHccCCcHHHHHHHHHHHHh----CCCC-chhH
Q 044988           86 WNQMIRGHARSETPEKSVYLYKQMIDKETEPDE-----YTYSFLLSVCARCGLFREGEQVHGRVLAS----GYCS-NVFI  155 (538)
Q Consensus        86 ~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~-----~~~~~li~~~~~~~~~~~a~~~~~~~~~~----~~~~-~~~~  155 (538)
                      +......+...|++++|+..|+++.+.  .|+.     ..+..+...+...|+++.|...+++..+.    +..+ ...+
T Consensus         8 l~~~g~~~~~~g~~~~A~~~~~~al~~--~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~   85 (338)
T 3ro2_A            8 LALEGERLCKSGDCRAGVSFFEAAVQV--GTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKA   85 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--CCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhh--CcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHH
Confidence            344456667778888888888887764  2332     45667777777888888888877776543    1111 1334


Q ss_pred             HhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCC--ChHHHHHHHHHHHHcCC
Q 044988          156 RTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR--NVVSWTTMISGCAQNGK  233 (538)
Q Consensus       156 ~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--~~~~~~~li~~~~~~~~  233 (538)
                      +..+...|...|+   +++|...+++                        |.++......+  ...++..+...|...|+
T Consensus        86 ~~~l~~~~~~~g~---~~~A~~~~~~------------------------al~~~~~~~~~~~~~~~~~~l~~~~~~~~~  138 (338)
T 3ro2_A           86 SGNLGNTLKVLGN---FDEAIVCCQR------------------------HLDISRELNDKVGEARALYNLGNVYHAKGK  138 (338)
T ss_dssp             HHHHHHHHHHTTC---HHHHHHHHHH------------------------HHHHHHHTTCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccC---HHHHHHHHHH------------------------HHHHHHHhcCchHHHHHHHHHHHHHHHcCc
Confidence            5555555555555   5555554432                        12222222211  12356677777777777


Q ss_pred             --------------------HHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCC-
Q 044988          234 --------------------SRQALSLFNEMRRA----RVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGR-  287 (538)
Q Consensus       234 --------------------~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-  287 (538)
                                          +++|...+++....    +..| ....+..+...+...|+++.|...++...+.....+ 
T Consensus       139 ~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~  218 (338)
T 3ro2_A          139 SFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGD  218 (338)
T ss_dssp             TSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTC
T ss_pred             ccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCC
Confidence                                77777777665431    1111 123445555555666666666666665554311101 


Q ss_pred             CCcchhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          288 EPVLVSLNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       288 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                      .+....++..+...+...|++++|...+++.
T Consensus       219 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a  249 (338)
T 3ro2_A          219 KAAERRAYSNLGNAYIFLGEFETASEYYKKT  249 (338)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            1111224445555555566666665555543

>4e6h_A MRNA 3'-END-processing protein RNA14; HAT domain, heat repeat, CLP1, PCF11, structural protein; 2.30A {Kluyveromyces lactis} PDB: 4e85_A 4eba_A

Probab=99.36  E-value=3.6e-09  Score=106.98  Aligned_cols=420  Identities=9%  Similarity=0.037  Sum_probs=279.2

Q ss_pred             CccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCC---hhHHHHHHhcCC--C---CCcchH
Q 044988           15 SKALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGY---LINAHKVFEKTE--N---PSTAIW   86 (538)
Q Consensus        15 ~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~--~---~~~~~~   86 (538)
                      .+......++..+.+.+.+..+..+++.++.. ++.+...|...+..-.+.|.   ++.+..+|++..  .   |++..|
T Consensus        64 ~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~E~~~~~~~~~~~v~~lfeRal~~~~~~~sv~LW  142 (679)
T 4e6h_A           64 TDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSLEFDKMEELDAAVIEPVLARCLSKELGNNDLSLW  142 (679)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHTC--CCCHHHHHHHHHHHTCSSSCCCCHHHH
T ss_pred             CCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHHhcCCCCCHHHH
Confidence            35567888899998899999999999999988 45577889999999889998   999999999866  2   777788


Q ss_pred             HHHHHHHhcCCCc--------hHHHHHHHHhHh-CCC-CCCc-chHHHHHHHHHc---------cCCcHHHHHHHHHHHH
Q 044988           87 NQMIRGHARSETP--------EKSVYLYKQMID-KET-EPDE-YTYSFLLSVCAR---------CGLFREGEQVHGRVLA  146 (538)
Q Consensus        87 ~~li~~~~~~~~~--------~~a~~~~~~m~~-~~~-~p~~-~~~~~li~~~~~---------~~~~~~a~~~~~~~~~  146 (538)
                      ..-+.-..+.++.        +...++|+.... -|. .|+. ..|...+.....         .++++.+..+|++.+.
T Consensus       143 ~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~eeq~~~~~~R~iy~raL~  222 (679)
T 4e6h_A          143 LSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEEQQRVQYIRKLYKTLLC  222 (679)
T ss_dssp             HHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHHHhHHHHHHHHHHHHHh
Confidence            8877765555443        334578887765 365 5543 577777765442         3456788899999885


Q ss_pred             hCCCCchhHHhHHHHHHHhcCCCC----------ChhHHHHHhhc-------CCC--------------C--C------c
Q 044988          147 SGYCSNVFIRTNLMNLYLMSGGEC----------GVGCARLLFDD-------MPA--------------R--S------V  187 (538)
Q Consensus       147 ~~~~~~~~~~~~l~~~~~~~g~~~----------~~~~a~~~~~~-------~~~--------------~--~------~  187 (538)
                      .....-..+|......-...+...          .++.|...+.+       +..              |  +      .
T Consensus       223 iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~~~~~~p~~~~~~~~ql  302 (679)
T 4e6h_A          223 QPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQATESNLPKPNEYDVQQL  302 (679)
T ss_dssp             SCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTCCTTTSCCTTCCCHHHH
T ss_pred             CccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccchhccCCCCchhHHHHH
Confidence            322212233322222111111100          02333333322       111              0  0      1


Q ss_pred             hhHHHHHHHHHhcC-------CHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHH-HHHHHHHHCCCCCCHHHH
Q 044988          188 VSWNSLLKGYVKRG-------DIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQAL-SLFNEMRRARVGLDQVAL  256 (538)
Q Consensus       188 ~~~~~li~~~~~~g-------~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~-~~~~~m~~~g~~p~~~~~  256 (538)
                      ..|...+.---..+       ..+.+..+|++...   .....|-..+..+...|+.++|. .+|++.... ++.+...+
T Consensus       303 ~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s~~Lw  381 (679)
T 4e6h_A          303 LIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQHVCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQC-IPNSAVLA  381 (679)
T ss_dssp             HHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTCHHHH
T ss_pred             HHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCCHHHH
Confidence            34555554333322       12344556666542   35567888888888889999997 999999863 44456566


Q ss_pred             HHHHHHHHccCChHHHHHHHHHHHHhccC------CCCCc-----------chhHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 044988          257 VAALSACAEIGDLKLGKWIHSYVEENFSV------GREPV-----------LVSLNNALIHMYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       257 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~------~~~~~-----------~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  319 (538)
                      ...+....+.|+++.|..+|+.+.+....      ...|.           ...+|...+....+.|..+.|..+|.+..
T Consensus       382 l~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~  461 (679)
T 4e6h_A          382 FSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCR  461 (679)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            67777788899999999999998875100      00131           23478888888888999999999999876


Q ss_pred             CC-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHH
Q 044988          320 RR-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEA  398 (538)
Q Consensus       320 ~~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A  398 (538)
                      +. ...++...+.               ...+.- ...++.+.|..+|+...+.+  +-+...|...++.....|+.+.|
T Consensus       462 ~~~~~~~~~lyi~---------------~A~lE~-~~~~d~e~Ar~ife~~Lk~~--p~~~~~w~~y~~fe~~~~~~~~A  523 (679)
T 4e6h_A          462 RLKKLVTPDIYLE---------------NAYIEY-HISKDTKTACKVLELGLKYF--ATDGEYINKYLDFLIYVNEESQV  523 (679)
T ss_dssp             HTGGGSCTHHHHH---------------HHHHHH-TTTSCCHHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HhcCCCChHHHHH---------------HHHHHH-HhCCCHHHHHHHHHHHHHHC--CCchHHHHHHHHHHHhCCCHHHH
Confidence            43 2222222111               011111 11245899999999998874  23466677888888889999999


Q ss_pred             HHHHHhCC-CCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHH
Q 044988          399 FSLVQNMP-MKP----NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVY  457 (538)
Q Consensus       399 ~~~~~~~~-~~p----~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~  457 (538)
                      ..+|++.. ..|    ....|...+..-.+.|+.+.+.++.+++ .+..|+++. .. .+++-|
T Consensus       524 R~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~-~~~~P~~~~-~~-~f~~ry  584 (679)
T 4e6h_A          524 KSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRF-FEKFPEVNK-LE-EFTNKY  584 (679)
T ss_dssp             HHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHH-HHHSTTCCH-HH-HHHHHT
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCCCCcH-HH-HHHHHh
Confidence            99999875 234    2468888899999999999999999999 999999876 44 444433

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.36  E-value=1.1e-11  Score=121.85  Aligned_cols=218  Identities=15%  Similarity=0.076  Sum_probs=171.6

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCh-HHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHH
Q 044988          233 KSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDL-KLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEA  311 (538)
Q Consensus       233 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  311 (538)
                      .+++++..+++.... .+.+...+..+...+...|++ ++|...++.+.+.     .|.+...+..+..+|...|++++|
T Consensus        83 ~~~~al~~l~~~~~~-~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~-----~p~~~~a~~~lg~~~~~~g~~~~A  156 (474)
T 4abn_A           83 EMEKTLQQMEEVLGS-AQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKL-----EPELVEAWNQLGEVYWKKGDVTSA  156 (474)
T ss_dssp             HHHHHHHHHHHHHTT-CCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhcc-CchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhh-----CCCCHHHHHHHHHHHHHcCCHHHH
Confidence            356666777665543 234677788888888888999 9999999988887     677788888999999999999999


Q ss_pred             HHHHHhcCC--CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHH
Q 044988          312 YGVFRKMQR--RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDL  388 (538)
Q Consensus       312 ~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~  388 (538)
                      ...|++..+  |+...+..+...|...+....           ....|++++|...|++..+.   .| +...|..+..+
T Consensus       157 ~~~~~~al~~~p~~~~~~~lg~~~~~~~~~~~-----------~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~lg~~  222 (474)
T 4abn_A          157 HTCFSGALTHCKNKVSLQNLSMVLRQLQTDSG-----------DEHSRHVMDSVRQAKLAVQM---DVLDGRSWYILGNA  222 (474)
T ss_dssp             HHHHHHHHTTCCCHHHHHHHHHHHTTCCCSCH-----------HHHHHHHHHHHHHHHHHHHH---CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHhhCCCHHHHHHHHHHHHHhccCCh-----------hhhhhhHHHHHHHHHHHHHh---CCCCHHHHHHHHHH
Confidence            999998765  444444444444444300000           00116889999999998876   45 58899999999


Q ss_pred             hhhc--------CChHHHHHHHHhCC-CCC----CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHH
Q 044988          389 FSRA--------GLMDEAFSLVQNMP-MKP----NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVAN  455 (538)
Q Consensus       389 ~~~~--------g~~~~A~~~~~~~~-~~p----~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~  455 (538)
                      |...        |++++|++.|++.. ..|    +...|..+..++...|++++|.+.|+++ ..+.|++...+. .++.
T Consensus       223 ~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~a-l~l~p~~~~a~~-~l~~  300 (474)
T 4abn_A          223 YLSLYFNTGQNPKISQQALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQA-AALDPAWPEPQQ-REQQ  300 (474)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHH
T ss_pred             HHHHHHhhccccchHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCCCCHHHHH-HHHH
Confidence            9998        99999999999874 355    7889999999999999999999999999 999999998788 9999


Q ss_pred             HHHhcCChHHHHHHHHH
Q 044988          456 VYAAAKRWQDVAAVRQK  472 (538)
Q Consensus       456 ~~~~~g~~~~A~~~~~~  472 (538)
                      ++...|++++|++.+.+
T Consensus       301 ~~~~lg~~~eAi~~~~~  317 (474)
T 4abn_A          301 LLEFLSRLTSLLESKGK  317 (474)
T ss_dssp             HHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHhcc
Confidence            99999999999975443

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.34  E-value=6.6e-11  Score=100.27  Aligned_cols=159  Identities=11%  Similarity=0.079  Sum_probs=100.5

Q ss_pred             hhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHH
Q 044988          292 VSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFEC  368 (538)
Q Consensus       292 ~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~  368 (538)
                      ..+|..+...|.+.|++++|.+.|++..+   .+..+|..+...|.+.|                    ++++|...+..
T Consensus         5 ~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~--------------------~~~~a~~~~~~   64 (184)
T 3vtx_A            5 TTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIG--------------------LPNDAIESLKK   64 (184)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT--------------------CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCC--------------------CHHHHHHHHHH
Confidence            34445555555555555555555555443   12333333333333333                    44444555555


Q ss_pred             hhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC
Q 044988          369 MNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ  445 (538)
Q Consensus       369 ~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~  445 (538)
                      ....   .| +...+..+...+...++++.|.+.+++..  .+.+...+..+...+...|++++|++.++++ .+..|++
T Consensus        65 ~~~~---~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~-l~~~p~~  140 (184)
T 3vtx_A           65 FVVL---DTTSAEAYYILGSANFMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKT-ISIKPGF  140 (184)
T ss_dssp             HHHH---CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTC
T ss_pred             HHhc---CchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHH-HHhcchh
Confidence            5443   23 35566666677777777777777776653  2334666777777788888888888888888 7778888


Q ss_pred             cccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          446 AAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       446 ~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +.++. .++.+|.+.|++++|++.|++..+
T Consensus       141 ~~~~~-~lg~~~~~~g~~~~A~~~~~~al~  169 (184)
T 3vtx_A          141 IRAYQ-SIGLAYEGKGLRDEAVKYFKKALE  169 (184)
T ss_dssp             HHHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhHHH-HHHHHHHHCCCHHHHHHHHHHHHh
Confidence            77777 788888888888888888887765

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.33  E-value=1.7e-10  Score=110.38  Aligned_cols=57  Identities=11%  Similarity=0.088  Sum_probs=38.5

Q ss_pred             HHHHHHHhhhcCC---hHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHch
Q 044988          382 YGCMVDLFSRAGL---MDEAFSLVQNMPMKPN-DAVLGSLLLGCRIHNNAELASQVAQKLV  438 (538)
Q Consensus       382 ~~~l~~~~~~~g~---~~~A~~~~~~~~~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~  438 (538)
                      +..+...|...|+   +++|+.++++....|+ ...+..+...+...|++++|...++++.
T Consensus       306 ~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~~~g~~~~A~~~~~~al  366 (383)
T 3ulq_A          306 FEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAIDVAKYYHERKNFQKASAYFLKVE  366 (383)
T ss_dssp             HHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4556667777777   7777777777653333 3355566667777788888887777773

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.33  E-value=1e-11  Score=114.96  Aligned_cols=245  Identities=9%  Similarity=0.066  Sum_probs=158.9

Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHC-------CCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccC---CC
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRA-------RVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSV---GR  287 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~-------g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~---~~  287 (538)
                      ..++..+...+...|++++|..+|+++.+.       ........+..+...+...|+++.|...++.+.+....   +.
T Consensus        27 ~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  106 (311)
T 3nf1_A           27 LRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKD  106 (311)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCC
Confidence            346777778888888888888888887662       22234556677777788888888888888877665211   12


Q ss_pred             CCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhc--CCccHHHHHHHHHHHHhcccCcHHHHHHH
Q 044988          288 EPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQ--GYAQEALLTFLGVLSACSHGGFVDEGRQF  365 (538)
Q Consensus       288 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~--~~~~~a~~~~~~ll~~~~~~~~~~~a~~~  365 (538)
                      .+....++..+...|...|++++|...|+++.+-           +.+.  ++.......+..+...+...|++++|..+
T Consensus       107 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~-----------~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~  175 (311)
T 3nf1_A          107 HPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEI-----------REKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYY  175 (311)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH-----------HHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHH-----------HHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            4556778889999999999999999999886431           1000  11112224455566666677777788888


Q ss_pred             HHHhhhhc-----CCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC----------CCCC-------HHHHHHHHHHHH
Q 044988          366 FECMNQNW-----GIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP----------MKPN-------DAVLGSLLLGCR  422 (538)
Q Consensus       366 ~~~~~~~~-----~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----------~~p~-------~~~~~~l~~~~~  422 (538)
                      ++++.+..     +..| ...++..+..+|...|++++|.+.++++.          ..+.       ...+..+...+.
T Consensus       176 ~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  255 (311)
T 3nf1_A          176 YQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQK  255 (311)
T ss_dssp             HHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-----
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchh
Confidence            77766531     1133 35678899999999999999999998764          1111       112222233345


Q ss_pred             hcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          423 IHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       423 ~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ..+.+.++...++.. ....|.....+. .++.+|.+.|++++|.+++++..+
T Consensus       256 ~~~~~~~a~~~~~~~-~~~~~~~~~~~~-~la~~~~~~g~~~~A~~~~~~al~  306 (311)
T 3nf1_A          256 DGTSFGEYGGWYKAC-KVDSPTVTTTLK-NLGALYRRQGKFEAAETLEEAAMR  306 (311)
T ss_dssp             --CCSCCCC----------CHHHHHHHH-HHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhhc-CCCCchHHHHHH-HHHHHHHHCCCHHHHHHHHHHHHH
Confidence            555666677777777 667788888778 999999999999999999998764

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.32  E-value=4e-11  Score=117.09  Aligned_cols=336  Identities=10%  Similarity=-0.047  Sum_probs=218.3

Q ss_pred             HHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcC-
Q 044988          123 FLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRG-  201 (538)
Q Consensus       123 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g-  201 (538)
                      .+...+.+.|++++|.++|++..+.|   +...+..|...|...|+....++|...|++..+.+...+..+...+...| 
T Consensus         8 ~la~~~~~~g~~~~A~~~~~~aa~~g---~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~   84 (452)
T 3e4b_A            8 RLANEALKRGDTVTAQQNYQQLAELG---YSEAQVGLADIQVGTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKPG   84 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHT---CCTGGGTCC----------------------------CHHHHHHHHHTC--
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCC
Confidence            35667788899999999999999887   34456667778888888222389999999988777778888887666655 


Q ss_pred             ----CHHHHHHHHccCCC-CChHHHHHHHHHHHHcCCHH---HHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHH
Q 044988          202 ----DIDGAWKIFDEMPH-RNVVSWTTMISGCAQNGKSR---QALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGK  273 (538)
Q Consensus       202 ----~~~~A~~~~~~m~~-~~~~~~~~li~~~~~~~~~~---~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~  273 (538)
                          ++++|...|++..+ .+...+..|...|...+..+   ++.+.+......|.   ......+...|...+.++.+.
T Consensus        85 ~~~~~~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~---~~a~~~Lg~~y~~~~~~~~~~  161 (452)
T 3e4b_A           85 ATEAEHHEAESLLKKAFANGEGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGY---PEAGLAQVLLYRTQGTYDQHL  161 (452)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTC---TTHHHHHHHHHHHHTCGGGGH
T ss_pred             CCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCC---HHHHHHHHHHHHcCCCcccCH
Confidence                78899999988654 34457888888888776543   45555555555453   334556666777777665554


Q ss_pred             HHHHHHHHhccCCCCCcchhHHHHHHHHHHhCC---CHHHHHHHHHhcCCC---CcchHHHHHHHHHhc----CCccHHH
Q 044988          274 WIHSYVEENFSVGREPVLVSLNNALIHMYASCG---EIEEAYGVFRKMQRR---NTVSWTSMITGFAKQ----GYAQEAL  343 (538)
Q Consensus       274 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~----~~~~~a~  343 (538)
                      .....+.+.    ....++..+..|...|...|   +.++|.+.|++..+.   +...+..+...|...    ++.++|+
T Consensus       162 ~~a~~~~~~----a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~  237 (452)
T 3e4b_A          162 DDVERICKA----ALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQ  237 (452)
T ss_dssp             HHHHHHHHH----HTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHH
T ss_pred             HHHHHHHHH----HHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHH
Confidence            443333333    12233336778999999999   899999999987653   333335666666544    5777777


Q ss_pred             HHHHH-----------HHHH-h--cccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcC-----ChHHHHHHHHh
Q 044988          344 LTFLG-----------VLSA-C--SHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAG-----LMDEAFSLVQN  404 (538)
Q Consensus       344 ~~~~~-----------ll~~-~--~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g-----~~~~A~~~~~~  404 (538)
                      ..|..           +... +  ...+++++|...|++..+. |   +...+..|...|. .|     ++++|.+.|++
T Consensus       238 ~~~~~aa~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~-g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~  312 (452)
T 3e4b_A          238 ALLEKIAPGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAA-D---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEK  312 (452)
T ss_dssp             HHHHHHGGGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHT
T ss_pred             HHHHHHcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHH
Confidence            44333           3333 3  4578999999999998865 4   5667777777777 45     89999999999


Q ss_pred             CCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHh----cCChHHHHHHHHHHHhC
Q 044988          405 MPMKPNDAVLGSLLLGCRI----HNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAA----AKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       405 ~~~~p~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~  476 (538)
                      .. ..+...+..|...|..    ..++++|...|++. .+  +.++.... .|+.+|..    .++.++|..+++...+.
T Consensus       313 Aa-~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A-a~--~g~~~A~~-~Lg~~y~~G~g~~~d~~~A~~~~~~A~~~  387 (452)
T 3e4b_A          313 AV-GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTA-AR--NGQNSADF-AIAQLFSQGKGTKPDPLNAYVFSQLAKAQ  387 (452)
T ss_dssp             TT-TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHH-HT--TTCTTHHH-HHHHHHHSCTTBCCCHHHHHHHHHHHHTT
T ss_pred             Hh-CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHH-Hh--hChHHHHH-HHHHHHHhCCCCCCCHHHHHHHHHHHHHC
Confidence            88 6677888888777766    34899999999988 44  44455566 78888875    45899999999999887


Q ss_pred             CC
Q 044988          477 GV  478 (538)
Q Consensus       477 ~~  478 (538)
                      |.
T Consensus       388 g~  389 (452)
T 3e4b_A          388 DT  389 (452)
T ss_dssp             CC
T ss_pred             CC
Confidence            76

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.29  E-value=1.7e-10  Score=97.66  Aligned_cols=166  Identities=13%  Similarity=0.014  Sum_probs=105.0

Q ss_pred             HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHH
Q 044988          253 QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSM  329 (538)
Q Consensus       253 ~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~l  329 (538)
                      ...|..+...+...|++++|...|+.+.+.     .|.+..++..+..+|.+.|++++|...+.+...   .+...+..+
T Consensus         5 ~~iy~~lG~~~~~~g~~~~A~~~~~~al~~-----~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~   79 (184)
T 3vtx_A            5 TTIYMDIGDKKRTKGDFDGAIRAYKKVLKA-----DPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYIL   79 (184)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHH
Confidence            344555555555555555555555555554     455556666666666666666666666665543   122233333


Q ss_pred             HHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-C
Q 044988          330 ITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M  407 (538)
Q Consensus       330 i~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~  407 (538)
                      ...+...                    ++++.|...+.+..+.   .| +...+..+..+|.+.|++++|++.|++.. .
T Consensus        80 ~~~~~~~--------------------~~~~~a~~~~~~a~~~---~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~  136 (184)
T 3vtx_A           80 GSANFMI--------------------DEKQAAIDALQRAIAL---NTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISI  136 (184)
T ss_dssp             HHHHHHT--------------------TCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHc--------------------CCHHHHHHHHHHHHHh---CccchHHHHHHHHHHHHhCCchhHHHHHHHHHHh
Confidence            3333333                    3555666666666554   33 46677788888888888888888887763 2


Q ss_pred             C-CCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          408 K-PNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       408 ~-p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      . .+..+|..+..++.+.|++++|++.|+++ .++.|+++.
T Consensus       137 ~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a-l~~~p~~a~  176 (184)
T 3vtx_A          137 KPGFIRAYQSIGLAYEGKGLRDEAVKYFKKA-LEKEEKKAK  176 (184)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHTTHHHHH
T ss_pred             cchhhhHHHHHHHHHHHCCCHHHHHHHHHHH-HhCCccCHH
Confidence            3 34677888888888888888888888888 777776543

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.29  E-value=5.8e-10  Score=103.06  Aligned_cols=218  Identities=9%  Similarity=0.007  Sum_probs=152.0

Q ss_pred             HHHHHHHccCCC---CChHHHHHHHHHHH-------HcCCH-------HHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHc
Q 044988          204 DGAWKIFDEMPH---RNVVSWTTMISGCA-------QNGKS-------RQALSLFNEMRRARVGL-DQVALVAALSACAE  265 (538)
Q Consensus       204 ~~A~~~~~~m~~---~~~~~~~~li~~~~-------~~~~~-------~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~  265 (538)
                      ++|..+|++...   .+...|..++..+.       +.|++       ++|..+|++..+. +.| +...+..+...+.+
T Consensus        33 ~~a~~~~~~al~~~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~-~~p~~~~~~~~~~~~~~~  111 (308)
T 2ond_A           33 KRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIST-LLKKNMLLYFAYADYEES  111 (308)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTT-TTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHH-hCcccHHHHHHHHHHHHh
Confidence            566666666553   35556777666654       34775       7888888888763 234 45577777888888


Q ss_pred             cCChHHHHHHHHHHHHhccCCCCCcchh-HHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHH
Q 044988          266 IGDLKLGKWIHSYVEENFSVGREPVLVS-LNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALL  344 (538)
Q Consensus       266 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~-~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~  344 (538)
                      .|+++.|..+|+.+.+.     .|.+.. +|..++..+.+.|++++|..+|++..+.++..+...+              
T Consensus       112 ~~~~~~A~~~~~~al~~-----~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~--------------  172 (308)
T 2ond_A          112 RMKYEKVHSIYNRLLAI-----EDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYV--------------  172 (308)
T ss_dssp             TTCHHHHHHHHHHHHTS-----SSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHH--------------
T ss_pred             cCCHHHHHHHHHHHHhc-----cccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCCCHHHHH--------------
Confidence            88888888888888875     444444 7778888888888888888888887653222211111              


Q ss_pred             HHHHHHHH-hcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCC----CC--CHHHHHHH
Q 044988          345 TFLGVLSA-CSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPM----KP--NDAVLGSL  417 (538)
Q Consensus       345 ~~~~ll~~-~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~p--~~~~~~~l  417 (538)
                         ..... +...|+++.|..+|+...+..  +-+...|..++..+.+.|++++|..+|++...    .|  ....|..+
T Consensus       173 ---~~a~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~  247 (308)
T 2ond_A          173 ---TAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARF  247 (308)
T ss_dssp             ---HHHHHHHHTSCCHHHHHHHHHHHHHHH--TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHH
T ss_pred             ---HHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHH
Confidence               00111 112468888888888887652  22577888888888888999999888887742    34  35678888


Q ss_pred             HHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          418 LLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       418 ~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      +....+.|+.+.|..+++++ .+..|++..
T Consensus       248 ~~~~~~~g~~~~a~~~~~~a-~~~~p~~~~  276 (308)
T 2ond_A          248 LAFESNIGDLASILKVEKRR-FTAFREEYE  276 (308)
T ss_dssp             HHHHHHHSCHHHHHHHHHHH-HHHTTTTTS
T ss_pred             HHHHHHcCCHHHHHHHHHHH-HHHcccccc
Confidence            88888888989998888888 788887654

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.29  E-value=6.7e-11  Score=116.22  Aligned_cols=210  Identities=11%  Similarity=0.021  Sum_probs=141.9

Q ss_pred             chHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCc-HHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHH
Q 044988           99 PEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLF-REGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARL  177 (538)
Q Consensus        99 ~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~  177 (538)
                      +++++..++...... +.+...+..+...+...|++ ++|...|++.++.. +.+...+..+..+|...|+   +++|..
T Consensus        84 ~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~---~~~A~~  158 (474)
T 4abn_A           84 MEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGD---VTSAHT  158 (474)
T ss_dssp             HHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC---HHHHHH
T ss_pred             HHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCC---HHHHHH
Confidence            445555555544321 23455666666666777777 77777777776654 3445666666666766666   666666


Q ss_pred             HhhcCCC--CCchhHHHHHHHHHhc---------CCHHHHHHHHccCCC---CChHHHHHHHHHHHHc--------CCHH
Q 044988          178 LFDDMPA--RSVVSWNSLLKGYVKR---------GDIDGAWKIFDEMPH---RNVVSWTTMISGCAQN--------GKSR  235 (538)
Q Consensus       178 ~~~~~~~--~~~~~~~~li~~~~~~---------g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~--------~~~~  235 (538)
                      .|++..+  |+...+..+...+...         |++++|+..|++..+   .+...|..+..+|...        |+++
T Consensus       159 ~~~~al~~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~  238 (474)
T 4abn_A          159 CFSGALTHCKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYFNTGQNPKISQ  238 (474)
T ss_dssp             HHHHHHTTCCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHhhCCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhhccccchHH
Confidence            6666543  3445555555666666         777777777776542   3456777777777777        7888


Q ss_pred             HHHHHHHHHHHCCCC--CCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHH
Q 044988          236 QALSLFNEMRRARVG--LDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYG  313 (538)
Q Consensus       236 ~a~~~~~~m~~~g~~--p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~  313 (538)
                      +|+..|++..+....  -+...+..+..++...|++++|...++...+.     .|.+...+..+..++...|++++|.+
T Consensus       239 ~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l-----~p~~~~a~~~l~~~~~~lg~~~eAi~  313 (474)
T 4abn_A          239 QALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAAL-----DPAWPEPQQREQQLLEFLSRLTSLLE  313 (474)
T ss_dssp             HHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            888888888774210  36777778888888888888888888888876     56667777778888888888888887


Q ss_pred             HHHhc
Q 044988          314 VFRKM  318 (538)
Q Consensus       314 ~~~~m  318 (538)
                      .+.++
T Consensus       314 ~~~~~  318 (474)
T 4abn_A          314 SKGKT  318 (474)
T ss_dssp             HTTTC
T ss_pred             Hhccc
Confidence            77665

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.28  E-value=6.2e-11  Score=121.21  Aligned_cols=165  Identities=17%  Similarity=0.222  Sum_probs=136.1

Q ss_pred             CCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHH
Q 044988          286 GREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEG  362 (538)
Q Consensus       286 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a  362 (538)
                      +..|.+...++.|...|.+.|++++|.+.|++..+  | +..+|..+...|.+.|                    ++++|
T Consensus         3 gs~P~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g--------------------~~~eA   62 (723)
T 4gyw_A            3 GSCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQG--------------------KLQEA   62 (723)
T ss_dssp             ---CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTT--------------------CHHHH
T ss_pred             CCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC--------------------CHHHH
Confidence            35677888888999999999999999999988764  3 4556666666666555                    66777


Q ss_pred             HHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchh
Q 044988          363 RQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVA  439 (538)
Q Consensus       363 ~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  439 (538)
                      ...|++..+.   .|+ ...|..+..+|...|++++|++.|++.. ..|+ ...|..+..++...|++++|++.|+++ .
T Consensus        63 ~~~~~~Al~l---~P~~~~a~~nLg~~l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~A-l  138 (723)
T 4gyw_A           63 LMHYKEAIRI---SPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTA-L  138 (723)
T ss_dssp             HHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-H
T ss_pred             HHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-H
Confidence            7888887765   564 7899999999999999999999998873 4454 788999999999999999999999999 9


Q ss_pred             ccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          440 EIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       440 ~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ++.|++...+. .++.+|...|++++|.+.+++..+
T Consensus       139 ~l~P~~~~a~~-~L~~~l~~~g~~~~A~~~~~kal~  173 (723)
T 4gyw_A          139 KLKPDFPDAYC-NLAHCLQIVCDWTDYDERMKKLVS  173 (723)
T ss_dssp             HHCSCCHHHHH-HHHHHHHHTTCCTTHHHHHHHHHH
T ss_pred             HhCCCChHHHh-hhhhHHHhcccHHHHHHHHHHHHH
Confidence            99999999888 999999999999999998888753

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.27  E-value=7.1e-10  Score=102.48  Aligned_cols=208  Identities=13%  Similarity=0.064  Sum_probs=109.1

Q ss_pred             hHHHHHHhcCC---CCCcchHHHHHHHHh-------cCCCc-------hHHHHHHHHhHhCCCCCC-cchHHHHHHHHHc
Q 044988           69 INAHKVFEKTE---NPSTAIWNQMIRGHA-------RSETP-------EKSVYLYKQMIDKETEPD-EYTYSFLLSVCAR  130 (538)
Q Consensus        69 ~~a~~~~~~~~---~~~~~~~~~li~~~~-------~~~~~-------~~a~~~~~~m~~~~~~p~-~~~~~~li~~~~~  130 (538)
                      +.|...|++..   +.++..|..++..+.       +.|++       ++|..+|++..+. +.|+ ...|..++..+.+
T Consensus        33 ~~a~~~~~~al~~~p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~-~~p~~~~~~~~~~~~~~~  111 (308)
T 2ond_A           33 KRVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIST-LLKKNMLLYFAYADYEES  111 (308)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTT-TTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHH-hCcccHHHHHHHHHHHHh
Confidence            34455555443   234445555555443       24554       6666666666652 1343 3356666666666


Q ss_pred             cCCcHHHHHHHHHHHHhCCCCc-hh-HHhHHHHHHHhcCCCCChhHHHHHhhcCCCC---CchhHHHHHHHH-HhcCCHH
Q 044988          131 CGLFREGEQVHGRVLASGYCSN-VF-IRTNLMNLYLMSGGECGVGCARLLFDDMPAR---SVVSWNSLLKGY-VKRGDID  204 (538)
Q Consensus       131 ~~~~~~a~~~~~~~~~~~~~~~-~~-~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~-~~~g~~~  204 (538)
                      .|+++.|..+|++.++.  .|+ .. +|..++..+.+.|+   +++|..+|++..+.   +...|....... ...|+++
T Consensus       112 ~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~---~~~A~~~~~~a~~~~p~~~~~~~~~a~~~~~~~~~~~  186 (308)
T 2ond_A          112 RMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARRAEG---IKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKS  186 (308)
T ss_dssp             TTCHHHHHHHHHHHHTS--SSSCTHHHHHHHHHHHHHHHC---HHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHH
T ss_pred             cCCHHHHHHHHHHHHhc--cccCccHHHHHHHHHHHHhcC---HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCHH
Confidence            66666666666666653  232 22 56666666666666   66666666554432   122222211111 1145555


Q ss_pred             HHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-CCC--CHHHHHHHHHHHHccCChHHHHHHHHH
Q 044988          205 GAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR-VGL--DQVALVAALSACAEIGDLKLGKWIHSY  278 (538)
Q Consensus       205 ~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p--~~~~~~~li~~~~~~~~~~~a~~~~~~  278 (538)
                      +|..+|++..+   .+...|..++..+.+.|++++|..+|++..... +.|  ....+...+....+.|+.+.|..+++.
T Consensus       187 ~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~  266 (308)
T 2ond_A          187 VAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKR  266 (308)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            55555555432   234455666666666666666666666666542 333  234455555555555666666666665


Q ss_pred             HHHh
Q 044988          279 VEEN  282 (538)
Q Consensus       279 ~~~~  282 (538)
                      +.+.
T Consensus       267 a~~~  270 (308)
T 2ond_A          267 RFTA  270 (308)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5554

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.27  E-value=5.5e-10  Score=106.59  Aligned_cols=239  Identities=9%  Similarity=-0.008  Sum_probs=167.4

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHCC-CCCC----HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCC--CcchhHH
Q 044988          223 TMISGCAQNGKSRQALSLFNEMRRAR-VGLD----QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGRE--PVLVSLN  295 (538)
Q Consensus       223 ~li~~~~~~~~~~~a~~~~~~m~~~g-~~p~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~~~  295 (538)
                      .....+...|++++|+..|++..+.. -.++    ..++..+...+...|+++.|...+....+.....+.  +....++
T Consensus       106 ~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  185 (378)
T 3q15_A          106 FRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSL  185 (378)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHH
Confidence            34556778899999999999887631 1122    446777888888999999999999888776433222  2345677


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcC-
Q 044988          296 NALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWG-  374 (538)
Q Consensus       296 ~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~-  374 (538)
                      +.+...|...|++++|.+.|++..+           ...+.++......++..+..++...|++++|...+++..+... 
T Consensus       186 ~~lg~~y~~~~~~~~A~~~~~~al~-----------~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~  254 (378)
T 3q15_A          186 FVIAGNYDDFKHYDKALPHLEAALE-----------LAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSRE  254 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH-----------HHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHH-----------HHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            8899999999999999999987643           1122222222224455555566666677777777777665110 


Q ss_pred             -CCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC----C--CCC-HHHHHHHHHHHHhcCC---HHHHHHHHHHchhccC
Q 044988          375 -IKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP----M--KPN-DAVLGSLLLGCRIHNN---AELASQVAQKLVAEID  442 (538)
Q Consensus       375 -~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~--~p~-~~~~~~l~~~~~~~~~---~~~A~~~~~~~~~~~~  442 (538)
                       ..| ...++..+...|.+.|++++|...+++..    .  .|. ...+..+...+...++   +++|+..+++.  +..
T Consensus       255 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~--~~~  332 (378)
T 3q15_A          255 KVPDLLPKVLFGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKK--NLH  332 (378)
T ss_dssp             HCGGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHT--TCH
T ss_pred             hCChhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhC--CCh
Confidence             133 36788899999999999999999998763    1  233 3345555556777778   88888888875  334


Q ss_pred             CCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          443 PEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       443 p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      |.....+. .++..|.+.|++++|...+++..+
T Consensus       333 ~~~~~~~~-~la~~y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          333 AYIEACAR-SAAAVFESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHHHHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hHHHHHHH-HHHHHHHHCCCHHHHHHHHHHHHH
Confidence            44455466 899999999999999999998763

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.24  E-value=7.1e-10  Score=93.67  Aligned_cols=163  Identities=13%  Similarity=0.042  Sum_probs=131.7

Q ss_pred             cchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC---CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHH
Q 044988          290 VLVSLNNALIHMYASCGEIEEAYGVFRKMQRR---NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFF  366 (538)
Q Consensus       290 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~  366 (538)
                      .....+..+...+...|++++|...|+++.+.   +...+..+...+..                    .|++++|...+
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------~~~~~~A~~~~   65 (186)
T 3as5_A            6 IRQVYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVK--------------------TGAVDRGTELL   65 (186)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHH--------------------TTCHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHH--------------------cCCHHHHHHHH
Confidence            33456667888899999999999999998763   33444444444444                    44777788888


Q ss_pred             HHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCC
Q 044988          367 ECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPE  444 (538)
Q Consensus       367 ~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~  444 (538)
                      +++.+..  +.+...+..+...+...|++++|.+.++++.  .+.+...+..+...+...|++++|...++++ ....|+
T Consensus        66 ~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~-~~~~~~  142 (186)
T 3as5_A           66 ERSLADA--PDNVKVATVLGLTYVQVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIA-LGLRPN  142 (186)
T ss_dssp             HHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTT
T ss_pred             HHHHhcC--CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHH-HhcCcc
Confidence            8887651  3357788899999999999999999998874  3456788888889999999999999999999 888899


Q ss_pred             CcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          445 QAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       445 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      +...+. .++.++...|++++|.+.+++..+.
T Consensus       143 ~~~~~~-~la~~~~~~~~~~~A~~~~~~~~~~  173 (186)
T 3as5_A          143 EGKVHR-AIAFSYEQMGRHEEALPHFKKANEL  173 (186)
T ss_dssp             CHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             chHHHH-HHHHHHHHcCCHHHHHHHHHHHHHc
Confidence            888788 9999999999999999999998753

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.23  E-value=1.8e-11  Score=113.28  Aligned_cols=172  Identities=15%  Similarity=0.148  Sum_probs=130.4

Q ss_pred             CCCCCCCccccHHHHHHHHhccCChHHHHHHHHHHHHh-------CCCCChhHHHHHHHHHHccCChhHHHHHHhcCCC-
Q 044988            9 ANPATSSKALTTRQIFSLLQIRNTTKTLFQIHSQIIIN-------GFSQKNYILAKLLAFYVTSGYLINAHKVFEKTEN-   80 (538)
Q Consensus         9 ~~~~~~~~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~-------~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-   80 (538)
                      ..+..|....++..+...+...|+++.|..+++...+.       ..+....++..+...|...|++++|...|++... 
T Consensus        19 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~   98 (311)
T 3nf1_A           19 GGYEIPARLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAI   98 (311)
T ss_dssp             SCTTSCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            34455556677888888899999999999999998874       2333456788888999999999999998876541 


Q ss_pred             ----------CCcchHHHHHHHHhcCCCchHHHHHHHHhHhC------CCCC-CcchHHHHHHHHHccCCcHHHHHHHHH
Q 044988           81 ----------PSTAIWNQMIRGHARSETPEKSVYLYKQMIDK------ETEP-DEYTYSFLLSVCARCGLFREGEQVHGR  143 (538)
Q Consensus        81 ----------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~------~~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~  143 (538)
                                .....+..+...+...|++++|...|++..+.      +-.| ....+..+...+...|++++|..++++
T Consensus        99 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~  178 (311)
T 3nf1_A           99 REKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQR  178 (311)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHhCCCChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence                      12346788888899999999999999988753      2122 344677888888999999999999988


Q ss_pred             HHHh------CCCC-chhHHhHHHHHHHhcCCCCChhHHHHHhhcCC
Q 044988          144 VLAS------GYCS-NVFIRTNLMNLYLMSGGECGVGCARLLFDDMP  183 (538)
Q Consensus       144 ~~~~------~~~~-~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~  183 (538)
                      ..+.      +..| ...++..+..+|...|+   +++|...+++..
T Consensus       179 a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~---~~~A~~~~~~al  222 (311)
T 3nf1_A          179 ALEIYQTKLGPDDPNVAKTKNNLASCYLKQGK---FKQAETLYKEIL  222 (311)
T ss_dssp             HHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTC---HHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCC---HHHHHHHHHHHH
Confidence            8775      2122 34567788888888888   888888877654

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.20  E-value=2.1e-08  Score=95.30  Aligned_cols=99  Identities=10%  Similarity=-0.041  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCC--CC-HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcch
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRA----RVG--LD-QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLV  292 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~--p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  292 (538)
                      ++..+...+...|++++|...+++..+.    +..  |. ...+..+...+...|+++.|...+....+.....+.+...
T Consensus        95 ~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  174 (373)
T 1hz4_A           95 SLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQL  174 (373)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHH
Confidence            3556667778888888888888877642    221  22 2344556666677777777777777776653222222233


Q ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          293 SLNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       293 ~~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                      ..+..+...+...|++++|...+++.
T Consensus       175 ~~~~~la~~~~~~g~~~~A~~~l~~a  200 (373)
T 1hz4_A          175 QCLAMLIQCSLARGDLDNARSQLNRL  200 (373)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            45556666677777777777766654

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.19  E-value=1.3e-09  Score=99.71  Aligned_cols=201  Identities=10%  Similarity=-0.007  Sum_probs=136.7

Q ss_pred             HHHccCChHHHHHHHHHHHHhccCCCCCc-chhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCcc
Q 044988          262 ACAEIGDLKLGKWIHSYVEENFSVGREPV-LVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQ  340 (538)
Q Consensus       262 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~  340 (538)
                      .+...|++++|...+....+.....+.+. ...+++.+..+|...|++++|...|++..           ..+...|+..
T Consensus        46 ~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al-----------~l~~~~g~~~  114 (292)
T 1qqe_A           46 IYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAI-----------QIFTHRGQFR  114 (292)
T ss_dssp             HHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-----------HHHHHTTCHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH-----------HHHHHcCCHH
Confidence            35556777777776666655422112222 25677888899999999999998888753           3445566666


Q ss_pred             HHHHHHHHHHHHhccc-CcHHHHHHHHHHhhhhcCCCcc----HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC---H
Q 044988          341 EALLTFLGVLSACSHG-GFVDEGRQFFECMNQNWGIKPR----IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN---D  411 (538)
Q Consensus       341 ~a~~~~~~ll~~~~~~-~~~~~a~~~~~~~~~~~~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~---~  411 (538)
                      .+..++..+...|... |++++|...|++..+...-..+    ..++..+...|.+.|++++|+..|++.. ..|+   .
T Consensus       115 ~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~  194 (292)
T 1qqe_A          115 RGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLS  194 (292)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTT
T ss_pred             HHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcc
Confidence            6667777778888885 8899999988887754210111    3578889999999999999999999873 2222   1


Q ss_pred             -----HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccH----HHHHHHHHH--hcCChHHHHHHHHHHH
Q 044988          412 -----AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGY----LALVANVYA--AAKRWQDVAAVRQKMI  474 (538)
Q Consensus       412 -----~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~----~~~l~~~~~--~~g~~~~A~~~~~~m~  474 (538)
                           ..|..+..++...|++++|...+++. ..+.|+.....    ...++.++.  ..+++++|+..|+++.
T Consensus       195 ~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~a-l~l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~  267 (292)
T 1qqe_A          195 QWSLKDYFLKKGLCQLAATDAVAAARTLQEG-QSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFM  267 (292)
T ss_dssp             GGGHHHHHHHHHHHHHHTTCHHHHHHHHHGG-GCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             cHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhhCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCC
Confidence                 25677788899999999999999999 88888865532    113455554  4567888888876654

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.19  E-value=2.7e-09  Score=93.75  Aligned_cols=211  Identities=9%  Similarity=0.037  Sum_probs=156.8

Q ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHH
Q 044988          216 RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLN  295 (538)
Q Consensus       216 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  295 (538)
                      .|+..|......+...|++++|+..|++..+...+++...+..+..++...|++++|...++...+.     .|.+..++
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~-----~p~~~~~~   79 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK-----NYNLANAY   79 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT-----TCSHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh-----CcchHHHH
Confidence            3567788888899999999999999999988664477788888888899999999999999999986     77788888


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          296 NALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       296 ~~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                      ..+..+|...|++++|...|++..+  | +...+..+...             |..+...+...|++++|...|++..+.
T Consensus        80 ~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~-------------~~~~g~~~~~~~~~~~A~~~~~~al~~  146 (228)
T 4i17_A           80 IGKSAAYRDMKNNQEYIATLTEGIKAVPGNATIEKLYAIY-------------YLKEGQKFQQAGNIEKAEENYKHATDV  146 (228)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHH-------------HHHHHHHHHHTTCHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHH-------------HHHHhHHHHHhccHHHHHHHHHHHHhc
Confidence            9999999999999999999998765  3 33232333322             333445556677999999999999854


Q ss_pred             cCCCcc---HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          373 WGIKPR---IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       373 ~~~~p~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                         .|+   ...+..+..+|...|+.     .++++.  ...+...+....  ....+.+++|+..++++ .++.|+++.
T Consensus       147 ---~p~~~~~~~~~~l~~~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~a-~~l~p~~~~  215 (228)
T 4i17_A          147 ---TSKKWKTDALYSLGVLFYNNGAD-----VLRKATPLASSNKEKYASEK--AKADAAFKKAVDYLGEA-VTLSPNRTE  215 (228)
T ss_dssp             ---SCHHHHHHHHHHHHHHHHHHHHH-----HHHHHGGGTTTCHHHHHHHH--HHHHHHHHHHHHHHHHH-HHHCTTCHH
T ss_pred             ---CCCcccHHHHHHHHHHHHHHHHH-----HHHHHHhcccCCHHHHHHHH--HHHHHHHHHHHHHHHHH-hhcCCCCHH
Confidence               665   56788888888766643     222221  123344444333  34456789999999999 999999988


Q ss_pred             cHHHHHHHH
Q 044988          448 GYLALVANV  456 (538)
Q Consensus       448 ~~~~~l~~~  456 (538)
                      ... .+..+
T Consensus       216 ~~~-~l~~i  223 (228)
T 4i17_A          216 IKQ-MQDQV  223 (228)
T ss_dssp             HHH-HHHHH
T ss_pred             HHH-HHHHH
Confidence            555 55544

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.19  E-value=4.9e-08  Score=92.80  Aligned_cols=275  Identities=12%  Similarity=0.045  Sum_probs=162.5

Q ss_pred             HHHHHhcCCCchHHHHHHHHhHhCCCCCCcc-----hHHHHHHHHHccCCcHHHHHHHHHHHHhCCC-Cc----hhHHhH
Q 044988           89 MIRGHARSETPEKSVYLYKQMIDKETEPDEY-----TYSFLLSVCARCGLFREGEQVHGRVLASGYC-SN----VFIRTN  158 (538)
Q Consensus        89 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~-----~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~----~~~~~~  158 (538)
                      ....+...|++++|...+++..... +++..     ++..+...+...|+++.|...+++....... ++    ..++..
T Consensus        20 ~a~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~   98 (373)
T 1hz4_A           20 RAQVAINDGNPDEAERLAKLALEEL-PPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQ   98 (373)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTC-CTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHcC-CCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            3445567888888888888877643 22221     3555666777788888888888777653210 11    122445


Q ss_pred             HHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCC----ChHHHHHHHHHHHHcCCH
Q 044988          159 LMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR----NVVSWTTMISGCAQNGKS  234 (538)
Q Consensus       159 l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~----~~~~~~~li~~~~~~~~~  234 (538)
                      +...+...|+   +++|...++                        +++.+......+    ....+..+...+...|++
T Consensus        99 la~~~~~~G~---~~~A~~~~~------------------------~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~  151 (373)
T 1hz4_A           99 QSEILFAQGF---LQTAWETQE------------------------KAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARL  151 (373)
T ss_dssp             HHHHHHHTTC---HHHHHHHHH------------------------HHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHCCC---HHHHHHHHH------------------------HHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCH
Confidence            5555666666   666655443                        223333333322    123566677888899999


Q ss_pred             HHHHHHHHHHHHCCCC--C--CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHH--HHHHHHHHhCCCH
Q 044988          235 RQALSLFNEMRRARVG--L--DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLN--NALIHMYASCGEI  308 (538)
Q Consensus       235 ~~a~~~~~~m~~~g~~--p--~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~~~~g~~  308 (538)
                      ++|...+++.......  +  ...++..+...+...|+++.|...++.........+.+......  ...+..+...|++
T Consensus       152 ~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  231 (373)
T 1hz4_A          152 DEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDK  231 (373)
T ss_dssp             HHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHhhccCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCH
Confidence            9999999988763221  1  23567777888889999999999999887763222222111111  1234557799999


Q ss_pred             HHHHHHHHhcCCCCcch-HHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc---CCCccH-HHHH
Q 044988          309 EEAYGVFRKMQRRNTVS-WTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW---GIKPRI-EHYG  383 (538)
Q Consensus       309 ~~a~~~~~~m~~~~~~~-~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~---~~~p~~-~~~~  383 (538)
                      ++|...+++...++... +.            .  ...+..+...+...|++++|...++......   +..++. ..+.
T Consensus       232 ~~A~~~~~~a~~~~~~~~~~------------~--~~~~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~  297 (373)
T 1hz4_A          232 AAAANWLRHTAKPEFANNHF------------L--QGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLL  297 (373)
T ss_dssp             HHHHHHHHHSCCCCCTTCGG------------G--HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCCcchh------------h--HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHH
Confidence            99999999987643210 00            0  0011222333344445566666665544321   211222 2555


Q ss_pred             HHHHHhhhcCChHHHHHHHHhC
Q 044988          384 CMVDLFSRAGLMDEAFSLVQNM  405 (538)
Q Consensus       384 ~l~~~~~~~g~~~~A~~~~~~~  405 (538)
                      .+..++...|+.++|...+++.
T Consensus       298 ~la~~~~~~g~~~~A~~~l~~a  319 (373)
T 1hz4_A          298 LLNQLYWQAGRKSDAQRVLLDA  319 (373)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH
Confidence            6666777777777777777654

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.17  E-value=8.2e-10  Score=105.39  Aligned_cols=213  Identities=11%  Similarity=0.024  Sum_probs=131.6

Q ss_pred             HHccCCcHHHHHHHHHHHHhCC-CC----chhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC-----C-----CchhHHH
Q 044988          128 CARCGLFREGEQVHGRVLASGY-CS----NVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA-----R-----SVVSWNS  192 (538)
Q Consensus       128 ~~~~~~~~~a~~~~~~~~~~~~-~~----~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~-----~-----~~~~~~~  192 (538)
                      +...|++++|...+++..+... .+    ...++..+..+|...|+   .+.|...+++..+     +     ...+++.
T Consensus       111 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~---~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~  187 (378)
T 3q15_A          111 EFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQ---THVSMYHILQALDIYQNHPLYSIRTIQSLFV  187 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHHHHTSTTCHHHHHHHHHH
T ss_pred             HHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCC---cHHHHHHHHHHHHHHHhCCCchhhHHHHHHH
Confidence            4455666666666665554310 01    13345555566666666   5555555444321     1     1234555


Q ss_pred             HHHHHHhcCCHHHHHHHHccCCC-----CC----hHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCCCHHHHHHH
Q 044988          193 LLKGYVKRGDIDGAWKIFDEMPH-----RN----VVSWTTMISGCAQNGKSRQALSLFNEMRRA----RVGLDQVALVAA  259 (538)
Q Consensus       193 li~~~~~~g~~~~A~~~~~~m~~-----~~----~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~~~~~~~l  259 (538)
                      +...|...|++++|...|++..+     ++    ..++..+...|...|++++|...|++..+.    +.+....++..+
T Consensus       188 lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l  267 (378)
T 3q15_A          188 IAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGL  267 (378)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHH
Confidence            66666666776666666655432     11    246778888899999999999999988761    222236778888


Q ss_pred             HHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCC---HHHHHHHHHhcCCC--CcchHHHHHHHHH
Q 044988          260 LSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGE---IEEAYGVFRKMQRR--NTVSWTSMITGFA  334 (538)
Q Consensus       260 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---~~~a~~~~~~m~~~--~~~~~~~li~~~~  334 (538)
                      ...+.+.|+++.|...++...+.....+.+.....+..+...|...|+   +++|...+++....  ....+..+...|.
T Consensus       268 a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~y~  347 (378)
T 3q15_A          268 SWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAVFE  347 (378)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence            888999999999999999988875544455555566677777777888   78888888774331  1123334444455


Q ss_pred             hcCCccHHH
Q 044988          335 KQGYAQEAL  343 (538)
Q Consensus       335 ~~~~~~~a~  343 (538)
                      ..|++++|.
T Consensus       348 ~~g~~~~A~  356 (378)
T 3q15_A          348 SSCHFEQAA  356 (378)
T ss_dssp             HTTCHHHHH
T ss_pred             HCCCHHHHH
Confidence            555444333

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.06  E-value=4.2e-09  Score=92.53  Aligned_cols=190  Identities=12%  Similarity=-0.026  Sum_probs=127.4

Q ss_pred             CCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCC---cchHH
Q 044988          251 LDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRN---TVSWT  327 (538)
Q Consensus       251 p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~---~~~~~  327 (538)
                      .|...+......+...|++++|...|+...+.    ..+.+...+..+..++...|++++|...|++..+.+   ...|.
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~----~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~   80 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKL----TNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYI   80 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH----TTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhc----cCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHH
Confidence            46677777888888888888888888888887    332555666668888888888888888888776422   22333


Q ss_pred             HHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-H-------HHHHHHHHHhhhcCChHHHH
Q 044988          328 SMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-I-------EHYGCMVDLFSRAGLMDEAF  399 (538)
Q Consensus       328 ~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~-------~~~~~l~~~~~~~g~~~~A~  399 (538)
                      .+.                    .++...|++++|...+++..+.   .|+ .       ..|..+...+...|++++|+
T Consensus        81 ~l~--------------------~~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~  137 (228)
T 4i17_A           81 GKS--------------------AAYRDMKNNQEYIATLTEGIKA---VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAE  137 (228)
T ss_dssp             HHH--------------------HHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHH--------------------HHHHHcccHHHHHHHHHHHHHH---CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHH
Confidence            333                    3444445777788888888765   343 3       45777777788888888888


Q ss_pred             HHHHhCC-CCCC---HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          400 SLVQNMP-MKPN---DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       400 ~~~~~~~-~~p~---~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +.|++.. ..|+   ...|..+...+..     .+..+++++ ..+.+.....|. .  ......+.+++|+..+++..+
T Consensus       138 ~~~~~al~~~p~~~~~~~~~~l~~~~~~-----~~~~~~~~a-~~~~~~~~~~~~-~--~~~~~~~~~~~A~~~~~~a~~  208 (228)
T 4i17_A          138 ENYKHATDVTSKKWKTDALYSLGVLFYN-----NGADVLRKA-TPLASSNKEKYA-S--EKAKADAAFKKAVDYLGEAVT  208 (228)
T ss_dssp             HHHHHHTTSSCHHHHHHHHHHHHHHHHH-----HHHHHHHHH-GGGTTTCHHHHH-H--HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCcccHHHHHHHHHHHHH-----HHHHHHHHH-HhcccCCHHHHH-H--HHHHHHHHHHHHHHHHHHHhh
Confidence            8887764 4565   3455566566543     344455666 555555544333 2  223445667999999999886


Q ss_pred             C
Q 044988          476 M  476 (538)
Q Consensus       476 ~  476 (538)
                      .
T Consensus       209 l  209 (228)
T 4i17_A          209 L  209 (228)
T ss_dssp             H
T ss_pred             c
Confidence            3

>3as5_A MAMA; tetratricopeptide repeats (TPR) containing protein, TPR PROT protein-protein interactions, protein binding; 2.00A {Magnetospirillum magnetotacticum} PDB: 3as4_A 3asd_A 3asg_A 3ash_A 3as8_A 3asf_A

Probab=99.06  E-value=1.3e-08  Score=85.83  Aligned_cols=157  Identities=18%  Similarity=0.106  Sum_probs=97.5

Q ss_pred             hHHhHHHHHHHhcCCCCChhHHHHHhhcCCCC---CchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHH
Q 044988          154 FIRTNLMNLYLMSGGECGVGCARLLFDDMPAR---SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISG  227 (538)
Q Consensus       154 ~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~  227 (538)
                      ..+..+...+...|+   +++|...++++.+.   +...+..+...+...|++++|...+++..+   .+...|..+...
T Consensus         9 ~~~~~~~~~~~~~~~---~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~   85 (186)
T 3as5_A            9 VYYRDKGISHAKAGR---YSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLT   85 (186)
T ss_dssp             HHHHHHHHHHHHHTC---HHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcC---HHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            345555566666666   66666666665542   344555566666666666666666665432   344566666666


Q ss_pred             HHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCC
Q 044988          228 CAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGE  307 (538)
Q Consensus       228 ~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  307 (538)
                      +...|++++|...++++.+.. +.+...+..+...+...|+++.|...++.+.+.     .|.+...+..+...+...|+
T Consensus        86 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~la~~~~~~~~  159 (186)
T 3as5_A           86 YVQVQKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGL-----RPNEGKVHRAIAFSYEQMGR  159 (186)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHhcCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhc-----CccchHHHHHHHHHHHHcCC
Confidence            667777777777777666542 234556666666666777777777777766665     34555566666677777777


Q ss_pred             HHHHHHHHHhcC
Q 044988          308 IEEAYGVFRKMQ  319 (538)
Q Consensus       308 ~~~a~~~~~~m~  319 (538)
                      +++|...+++..
T Consensus       160 ~~~A~~~~~~~~  171 (186)
T 3as5_A          160 HEEALPHFKKAN  171 (186)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            777777666553

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=99.05  E-value=5.8e-09  Score=94.72  Aligned_cols=232  Identities=9%  Similarity=0.050  Sum_probs=138.9

Q ss_pred             cCCHHHHHHHHHHHHHC-------CCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccC---CCCCcchhHHHHHHH
Q 044988          231 NGKSRQALSLFNEMRRA-------RVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSV---GREPVLVSLNNALIH  300 (538)
Q Consensus       231 ~~~~~~a~~~~~~m~~~-------g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~~~~~l~~  300 (538)
                      .|++++|+.+|++..+.       ..+....++..+...+...|+++.|...+..+.+....   +..+....++..+..
T Consensus        14 ~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~   93 (283)
T 3edt_B           14 LVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAV   93 (283)
T ss_dssp             CSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHH
Confidence            44555555555544431       11223445566666666777777777777666554210   124556677888999


Q ss_pred             HHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhc--CCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc-----
Q 044988          301 MYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQ--GYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW-----  373 (538)
Q Consensus       301 ~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~--~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-----  373 (538)
                      .|...|++++|...|++..+.           +.+.  .+.......+..+...+...|++++|..++++..+..     
T Consensus        94 ~~~~~g~~~~A~~~~~~al~~-----------~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~  162 (283)
T 3edt_B           94 LYGKRGKYKEAEPLCKRALEI-----------REKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLG  162 (283)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHH-----------HHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSC
T ss_pred             HHHHhccHHHHHHHHHHHHHH-----------HHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcC
Confidence            999999999999999886431           0000  0001112445555566666667777777777765431     


Q ss_pred             CCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC----------CCCC-HHHHHHHHHHHHhcC------CHHHHHHHHH
Q 044988          374 GIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP----------MKPN-DAVLGSLLLGCRIHN------NAELASQVAQ  435 (538)
Q Consensus       374 ~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----------~~p~-~~~~~~l~~~~~~~~------~~~~A~~~~~  435 (538)
                      +..| ...++..+..+|...|++++|.+.+++..          ..+. ...|..+.......+      .+..+...++
T Consensus       163 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  242 (283)
T 3edt_B          163 PDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYK  242 (283)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHH
Confidence            1133 36688899999999999999999998763          1222 223333333333222      2444444555


Q ss_pred             HchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          436 KLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       436 ~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .. ....|.....+. .++.+|.+.|++++|..++++..+
T Consensus       243 ~~-~~~~~~~~~~~~-~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          243 AC-KVDSPTVNTTLR-SLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             CC-CCCCHHHHHHHH-HHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             hc-CCCCHHHHHHHH-HHHHHHHHcCCHHHHHHHHHHHHH
Confidence            44 445566666677 899999999999999999998775

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.05  E-value=2e-08  Score=91.78  Aligned_cols=222  Identities=10%  Similarity=-0.061  Sum_probs=151.9

Q ss_pred             HHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCCC-HHHHHHHHHHHHccCChHHHHHHHH
Q 044988          203 IDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRA----RVGLD-QVALVAALSACAEIGDLKLGKWIHS  277 (538)
Q Consensus       203 ~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~  277 (538)
                      +++|...|++.           ...|...|++++|...|++..+.    |-.++ ..+|..+..+|.+.|++++|...++
T Consensus        33 ~~~A~~~~~~a-----------~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~  101 (292)
T 1qqe_A           33 FEEAADLCVQA-----------ATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLE  101 (292)
T ss_dssp             HHHHHHHHHHH-----------HHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHH-----------HHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            66666665543           55677888999998888877652    32222 4578888888889999999998888


Q ss_pred             HHHHhccCCCCC-cchhHHHHHHHHHHhC-CCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcc
Q 044988          278 YVEENFSVGREP-VLVSLNNALIHMYASC-GEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSH  355 (538)
Q Consensus       278 ~~~~~~~~~~~~-~~~~~~~~l~~~~~~~-g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~  355 (538)
                      ...+.....+.+ ....+++.+...|... |++++|...|++..+           .+-..+....+..++..+...+..
T Consensus       102 ~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~-----------~~~~~~~~~~~~~~~~~lg~~~~~  170 (292)
T 1qqe_A          102 NAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGE-----------WYAQDQSVALSNKCFIKCADLKAL  170 (292)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH-----------HHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHH-----------HHHhCCChHHHHHHHHHHHHHHHH
Confidence            887763221221 1245778899999996 999999999988643           112222222223456666677777


Q ss_pred             cCcHHHHHHHHHHhhhhcCCCccH-----HHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHH------HHHHHHHHHH-
Q 044988          356 GGFVDEGRQFFECMNQNWGIKPRI-----EHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDA------VLGSLLLGCR-  422 (538)
Q Consensus       356 ~~~~~~a~~~~~~~~~~~~~~p~~-----~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~------~~~~l~~~~~-  422 (538)
                      .|++++|...|++..+...-.+..     ..|..+..++...|++++|...|++.. ..|+..      .+..++.++. 
T Consensus       171 ~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~~l~~l~~~~~~  250 (292)
T 1qqe_A          171 DGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNE  250 (292)
T ss_dssp             TTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHT
T ss_pred             hCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHc
Confidence            778999999999988652111111     257788889999999999999999874 345422      3444555554 


Q ss_pred             -hcCCHHHHHHHHHHchhccCCCCcc
Q 044988          423 -IHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       423 -~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                       ..+++++|+..|+++ ..+.|....
T Consensus       251 ~~~~~~~~A~~~~~~~-~~l~~~~~~  275 (292)
T 1qqe_A          251 GDSEQLSEHCKEFDNF-MRLDKWKIT  275 (292)
T ss_dssp             TCTTTHHHHHHHHTTS-SCCCHHHHH
T ss_pred             CCHHHHHHHHHHhccC-CccHHHHHH
Confidence             456799999999988 778777655

>4gyw_A UDP-N-acetylglucosamine--peptide N- acetylglucosaminyltransferase 110 kDa subunit...; GT-B, glycosyltransferase, glcnacylation, transferase-peptid; HET: UDP NAG; 1.70A {Homo sapiens} PDB: 3pe3_A* 3pe4_A* 4ay5_A* 4ay6_A* 3tax_A* 4gyy_A* 4gz3_A* 4gz5_A* 4gz6_A*

Probab=99.01  E-value=1e-08  Score=105.02  Aligned_cols=158  Identities=9%  Similarity=0.058  Sum_probs=100.3

Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                      ..+|+.+...|.+.|++++|++.|++..+.  .| +...+..+..++.+.|++++|...|+.+.+.     .|.+...+.
T Consensus         9 a~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l-----~P~~~~a~~   81 (723)
T 4gyw_A            9 ADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI-----SPTFADAYS   81 (723)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCCHHHHH
Confidence            345667777777777777777777776663  34 3556666666777777777777777777765     566666667


Q ss_pred             HHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc
Q 044988          297 ALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       297 ~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  373 (538)
                      .+..+|...|++++|.+.|++..+   .+...|+.+...|...|                    ++++|...|++..+. 
T Consensus        82 nLg~~l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g--------------------~~~eAi~~~~~Al~l-  140 (723)
T 4gyw_A           82 NMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSG--------------------NIPEAIASYRTALKL-  140 (723)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT--------------------CHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC--------------------CHHHHHHHHHHHHHh-
Confidence            777777777777777777766543   23344444444444444                    555555666666544 


Q ss_pred             CCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhC
Q 044988          374 GIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNM  405 (538)
Q Consensus       374 ~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~  405 (538)
                        .|+ ...+..+..+|...|++++|.+.++++
T Consensus       141 --~P~~~~a~~~L~~~l~~~g~~~~A~~~~~ka  171 (723)
T 4gyw_A          141 --KPDFPDAYCNLAHCLQIVCDWTDYDERMKKL  171 (723)
T ss_dssp             --CSCCHHHHHHHHHHHHHTTCCTTHHHHHHHH
T ss_pred             --CCCChHHHhhhhhHHHhcccHHHHHHHHHHH
Confidence              453 566677777777777777776666543

>3edt_B KLC 2, kinesin light chain 2; superhelical, structural genomics, structural genomics conso SGC, microtubule, motor protein, phosphoprotein; 2.70A {Homo sapiens} PDB: 3ceq_A

Probab=98.97  E-value=7e-09  Score=94.16  Aligned_cols=101  Identities=14%  Similarity=0.186  Sum_probs=70.2

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHC------CCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhcc---CCCC
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRA------RVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFS---VGRE  288 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~------g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~---~~~~  288 (538)
                      .+|..+...|...|++++|...|++..+.      .-.| ...++..+...+...|++++|...++.+.+...   .+..
T Consensus        86 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  165 (283)
T 3edt_B           86 ATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDD  165 (283)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTC
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCC
Confidence            45677777777778888877777777653      1112 355666777777788888888888777766421   1124


Q ss_pred             CcchhHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 044988          289 PVLVSLNNALIHMYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       289 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  319 (538)
                      +....++..+...|...|++++|...+++..
T Consensus       166 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l  196 (283)
T 3edt_B          166 PNVAKTKNNLASCYLKQGKYQDAETLYKEIL  196 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4456677788888889999999988888765

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.96  E-value=1.6e-08  Score=80.03  Aligned_cols=127  Identities=17%  Similarity=0.191  Sum_probs=108.0

Q ss_pred             HHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHh
Q 044988          346 FLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRI  423 (538)
Q Consensus       346 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~  423 (538)
                      +..+...+...|++++|..+++.+.+. . +.+...+..+...+...|++++|...++++.  .+.+...+..+...+..
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~~-~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALEL-D-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHc-C-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHH
Confidence            445566667777999999999998865 2 3357788889999999999999999999874  34457788889999999


Q ss_pred             cCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          424 HNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       424 ~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      .|++++|.+.++++ ....|++...+. .++.++.+.|++++|...++++.+.
T Consensus        82 ~~~~~~A~~~~~~~-~~~~~~~~~~~~-~la~~~~~~~~~~~A~~~~~~~~~~  132 (136)
T 2fo7_A           82 QGDYDEAIEYYQKA-LELDPRSAEAWY-NLGNAYYKQGDYDEAIEYYQKALEL  132 (136)
T ss_dssp             TTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHH-HHhCCCChHHHH-HHHHHHHHHccHHHHHHHHHHHHcc
Confidence            99999999999999 888898888778 8999999999999999999998764

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.94  E-value=1.1e-07  Score=85.31  Aligned_cols=184  Identities=14%  Similarity=0.104  Sum_probs=131.4

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCC-CcchhHHHHHHHHHHhCCCHHHHHHHH
Q 044988          237 ALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGRE-PVLVSLNNALIHMYASCGEIEEAYGVF  315 (538)
Q Consensus       237 a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~a~~~~  315 (538)
                      |+..|++....+ .++..++..+..++...|++++|.+.+......    +. +.+...+..++..+.+.|+.+.|.+.+
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~----~~~~~~lea~~l~vqi~L~~~r~d~A~k~l  159 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDN----DEAEGTTELLLLAIEVALLNNNVSTASTIF  159 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTS----SCSTTHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhcc----CCCcCcHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            677777776654 556666667777788888888888888777554    22 367777778899999999999999999


Q ss_pred             HhcCCCC-------cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHH
Q 044988          316 RKMQRRN-------TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDL  388 (538)
Q Consensus       316 ~~m~~~~-------~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~  388 (538)
                      ++|.+.+       ..+...+..++...                ....+++..|..+|+++.+.   .|+..+-..++.+
T Consensus       160 ~~~~~~~~d~~~~~d~~l~~Laea~v~l----------------~~g~~~~q~A~~~f~El~~~---~p~~~~~~lLln~  220 (310)
T 3mv2_B          160 DNYTNAIEDTVSGDNEMILNLAESYIKF----------------ATNKETATSNFYYYEELSQT---FPTWKTQLGLLNL  220 (310)
T ss_dssp             HHHHHHSCHHHHHHHHHHHHHHHHHHHH----------------HHTCSTTTHHHHHHHHHHTT---SCSHHHHHHHHHH
T ss_pred             HHHHhcCccccccchHHHHHHHHHHHHH----------------HhCCccHHHHHHHHHHHHHh---CCCcccHHHHHHH
Confidence            9886522       33444444442221                11123778889999999765   4653343445558


Q ss_pred             hhhcCChHHHHHHHHhCCC-----------CC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          389 FSRAGLMDEAFSLVQNMPM-----------KP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~~-----------~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      +.+.|++++|.+.++.+..           .| |..++..+|......|+  .|.++++++ ....|+++.
T Consensus       221 ~~~~g~~~eAe~~L~~l~~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL-~~~~P~hp~  288 (310)
T 3mv2_B          221 HLQQRNIAEAQGIVELLLSDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQL-VKLDHEHAF  288 (310)
T ss_dssp             HHHHTCHHHHHHHHHHHHSHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHH-HHTTCCCHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHH-HHhCCCChH
Confidence            9999999999999986532           24 45666566666666787  899999999 999999987

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.91  E-value=5e-08  Score=87.59  Aligned_cols=84  Identities=7%  Similarity=0.020  Sum_probs=66.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHchhccCCCCc---ccHHHHHHHHHHhc----------CChHHHHHHHHHHHhCCCCCC
Q 044988          415 GSLLLGCRIHNNAELASQVAQKLVAEIDPEQA---AGYLALVANVYAAA----------KRWQDVAAVRQKMIKMGVRKP  481 (538)
Q Consensus       415 ~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~---~~~~~~l~~~~~~~----------g~~~~A~~~~~~m~~~~~~~~  481 (538)
                      ..+...+...|++++|+..|+++ ....|+++   ..+. .++.+|...          |++++|...++++.+..    
T Consensus       152 ~~la~~~~~~g~~~~A~~~~~~~-l~~~p~~~~~~~a~~-~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~----  225 (261)
T 3qky_A          152 YEAARLYERRELYEAAAVTYEAV-FDAYPDTPWADDALV-GAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIF----  225 (261)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHH-HHHCTTSTTHHHHHH-HHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHHccCHHHHHHHHHHH-HHHCCCCchHHHHHH-HHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHC----
Confidence            55677799999999999999999 88888854   3566 788888866          89999999999998642    


Q ss_pred             CceeEEEECCEEEEEEeCCCCCcchHHHHHHHHHHHHHHHHc
Q 044988          482 PGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQE  523 (538)
Q Consensus       482 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~m~~~  523 (538)
                                         +.++....+...+.++...+.+.
T Consensus       226 -------------------p~~~~~~~a~~~l~~~~~~~~~~  248 (261)
T 3qky_A          226 -------------------PDSPLLRTAEELYTRARQRLTEL  248 (261)
T ss_dssp             -------------------TTCTHHHHHHHHHHHHHHHHHHH
T ss_pred             -------------------CCChHHHHHHHHHHHHHHHHHHh
Confidence                               23566677777777777776653

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.91  E-value=1.7e-07  Score=86.37  Aligned_cols=232  Identities=13%  Similarity=0.001  Sum_probs=155.4

Q ss_pred             cCCHHHHHHHHccCCCCChHHHHHHHHHHHH-cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHH
Q 044988          200 RGDIDGAWKIFDEMPHRNVVSWTTMISGCAQ-NGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSY  278 (538)
Q Consensus       200 ~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~-~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~  278 (538)
                      .|++++|.+++++..+.....       +.. .++++.|...|.+.               ...+...|+++.|...+..
T Consensus         4 ~~~~~eA~~~~~~a~k~~~~~-------~~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~~~~   61 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLKTS-------FMKWKPDYDSAASEYAKA---------------AVAFKNAKQLEQAKDAYLQ   61 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCC-------SSSCSCCHHHHHHHHHHH---------------HHHHHHTTCHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHcccc-------ccCCCCCHHHHHHHHHHH---------------HHHHHHcCCHHHHHHHHHH
Confidence            456666766666543200000       111 36666666666654               3456778899999888887


Q ss_pred             HHHhccCCCCC-cchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccC
Q 044988          279 VEENFSVGREP-VLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGG  357 (538)
Q Consensus       279 ~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~  357 (538)
                      ..+.....+.+ .....++.+...|...|++++|...|++..           ..+...|+...+..++..+...|.. |
T Consensus        62 al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al-----------~l~~~~g~~~~~a~~~~~lg~~~~~-g  129 (307)
T 2ifu_A           62 EAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKAS-----------VMYVENGTPDTAAMALDRAGKLMEP-L  129 (307)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHH-----------HHHHTTTCHHHHHHHHHHHHHHHTT-T
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH-----------HHHHHcCCHHHHHHHHHHHHHHHHc-C
Confidence            76653211221 234577788889999999999999888753           3344556666666777778888877 8


Q ss_pred             cHHHHHHHHHHhhhhc---CCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC----CCCC----HHHHHHHHHHHHhcC
Q 044988          358 FVDEGRQFFECMNQNW---GIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP----MKPN----DAVLGSLLLGCRIHN  425 (538)
Q Consensus       358 ~~~~a~~~~~~~~~~~---~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~p~----~~~~~~l~~~~~~~~  425 (538)
                      ++++|...|++..+.+   +..+ ...+++.+...|.+.|++++|++.|++..    ..++    ...+..+...+...|
T Consensus       130 ~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g  209 (307)
T 2ifu_A          130 DLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRA  209 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcC
Confidence            9999999988876542   1111 14678889999999999999999998874    1122    235666667788889


Q ss_pred             CHHHHHHHHHHchhccCCCCcccHH----HHHHHHHHhcCChHHHHH
Q 044988          426 NAELASQVAQKLVAEIDPEQAAGYL----ALVANVYAAAKRWQDVAA  468 (538)
Q Consensus       426 ~~~~A~~~~~~~~~~~~p~~~~~~~----~~l~~~~~~~g~~~~A~~  468 (538)
                      ++++|...+++. . ..|+......    ..++.++ ..|+.+.+.+
T Consensus       210 ~~~~A~~~~~~a-l-~~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~  253 (307)
T 2ifu_A          210 DYVAAQKCVRES-Y-SIPGFSGSEDCAALEDLLQAY-DEQDEEQLLR  253 (307)
T ss_dssp             CHHHHHHHHHHH-T-TSTTSTTSHHHHHHHHHHHHH-HTTCHHHHHH
T ss_pred             CHHHHHHHHHHH-h-CCCCCCCCHHHHHHHHHHHHH-HhcCHHHHHH
Confidence            999999999999 7 8887654321    1344444 5677665555

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.89  E-value=3.7e-08  Score=88.42  Aligned_cols=189  Identities=14%  Similarity=0.077  Sum_probs=116.4

Q ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc
Q 044988          216 RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD----QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL  291 (538)
Q Consensus       216 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  291 (538)
                      .+...+-.+...+.+.|++++|...|+++.+..  |+    ...+..+..++.+.|+++.|...++.+.+...  ..+..
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~--p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p--~~~~~   88 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG--RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQ--IDPRV   88 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC--SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT--TCTTH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCC--CCchh
Confidence            455566667777777888888888888877643  43    45566666777777777777777777777510  11223


Q ss_pred             hhHHHHHHHHHHh--------CCCHHHHHHHHHhcCC--CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHH
Q 044988          292 VSLNNALIHMYAS--------CGEIEEAYGVFRKMQR--RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDE  361 (538)
Q Consensus       292 ~~~~~~l~~~~~~--------~g~~~~a~~~~~~m~~--~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~  361 (538)
                      ...+..+..++..        .|++++|...|+++.+  |+..                                 ....
T Consensus        89 ~~a~~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~p~~~---------------------------------~~~~  135 (261)
T 3qky_A           89 PQAEYERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDRYPNHE---------------------------------LVDD  135 (261)
T ss_dssp             HHHHHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHHCTTCT---------------------------------THHH
T ss_pred             HHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHCcCch---------------------------------hHHH
Confidence            3444556666666        6666666666666543  2211                                 1111


Q ss_pred             HHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC----HHHHHHHHHHHHhc----------CC
Q 044988          362 GRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN----DAVLGSLLLGCRIH----------NN  426 (538)
Q Consensus       362 a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~----~~~~~~l~~~~~~~----------~~  426 (538)
                      +...+..+...     -...+..+...|.+.|++++|+..|+++. ..|+    ...+..+..++...          |+
T Consensus       136 a~~~~~~~~~~-----~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~  210 (261)
T 3qky_A          136 ATQKIRELRAK-----LARKQYEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPER  210 (261)
T ss_dssp             HHHHHHHHHHH-----HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHH
T ss_pred             HHHHHHHHHHH-----HHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccch
Confidence            11111111110     01124566777888888888888887763 2343    34566666666655          88


Q ss_pred             HHHHHHHHHHchhccCCCCcc
Q 044988          427 AELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       427 ~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      +++|...++++ ....|+++.
T Consensus       211 ~~~A~~~~~~~-~~~~p~~~~  230 (261)
T 3qky_A          211 YRRAVELYERL-LQIFPDSPL  230 (261)
T ss_dssp             HHHHHHHHHHH-HHHCTTCTH
T ss_pred             HHHHHHHHHHH-HHHCCCChH
Confidence            89999999999 888898864

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.87  E-value=1.5e-07  Score=82.30  Aligned_cols=108  Identities=8%  Similarity=-0.010  Sum_probs=73.0

Q ss_pred             HHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHH
Q 044988          351 SACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAEL  429 (538)
Q Consensus       351 ~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~~~~~  429 (538)
                      ......|+.++|...|+++.+.   .|+ ...+..+....    ......           ......+...+.+.|++++
T Consensus       104 ~~~~~~~~~~~A~~~~~~~l~~---~P~~~~a~~a~~~l~----~~~~~~-----------~~~~~~~a~~~~~~~~~~~  165 (225)
T 2yhc_A          104 RSDRDPQQARAAFSDFSKLVRG---YPNSQYTTDATKRLV----FLKDRL-----------AKYEYSVAEYYTERGAWVA  165 (225)
T ss_dssp             ----CCHHHHHHHHHHHHHHTT---CTTCTTHHHHHHHHH----HHHHHH-----------HHHHHHHHHHHHHHTCHHH
T ss_pred             hhhcCcHHHHHHHHHHHHHHHH---CcCChhHHHHHHHHH----HHHHHH-----------HHHHHHHHHHHHHcCcHHH
Confidence            3344567889999999999865   454 33332221110    000000           0112345667889999999


Q ss_pred             HHHHHHHchhccCCCCc---ccHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          430 ASQVAQKLVAEIDPEQA---AGYLALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       430 A~~~~~~~~~~~~p~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      |+..|+++ .+..|+++   .++. .++.+|.+.|++++|.+.++.+...+.
T Consensus       166 A~~~~~~~-l~~~p~~~~~~~a~~-~l~~~~~~~g~~~~A~~~~~~l~~~~~  215 (225)
T 2yhc_A          166 VVNRVEGM-LRDYPDTQATRDALP-LMENAYRQMQMNAQAEKVAKIIAANSS  215 (225)
T ss_dssp             HHHHHHHH-HHHSTTSHHHHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHCCS
T ss_pred             HHHHHHHH-HHHCcCCCccHHHHH-HHHHHHHHcCCcHHHHHHHHHHHhhCC
Confidence            99999999 88888876   3466 889999999999999999999887544

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.83  E-value=1.5e-07  Score=84.40  Aligned_cols=90  Identities=8%  Similarity=0.048  Sum_probs=38.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHccCCC--C-----ChHHHHHHHHHHH--HcC--CHHHHHHHHHHHHHCCCCCCHHHHH
Q 044988          189 SWNSLLKGYVKRGDIDGAWKIFDEMPH--R-----NVVSWTTMISGCA--QNG--KSRQALSLFNEMRRARVGLDQVALV  257 (538)
Q Consensus       189 ~~~~li~~~~~~g~~~~A~~~~~~m~~--~-----~~~~~~~li~~~~--~~~--~~~~a~~~~~~m~~~g~~p~~~~~~  257 (538)
                      .+..++..+.+.|+.+.|.+.+++|.+  |     +..+...+..+++  ..|  ++.+|..+|+++.+.  .|+..+-.
T Consensus       138 a~~l~vqi~L~~~r~d~A~k~l~~~~~~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~--~p~~~~~~  215 (310)
T 3mv2_B          138 LLLLAIEVALLNNNVSTASTIFDNYTNAIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT--FPTWKTQL  215 (310)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT--SCSHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh--CCCcccHH
Confidence            344444445555555555555554432  2     1223333333311  112  455555555555432  23322222


Q ss_pred             HHHHHHHccCChHHHHHHHHHHH
Q 044988          258 AALSACAEIGDLKLGKWIHSYVE  280 (538)
Q Consensus       258 ~li~~~~~~~~~~~a~~~~~~~~  280 (538)
                      .++.++.+.|++++|+..++.+.
T Consensus       216 lLln~~~~~g~~~eAe~~L~~l~  238 (310)
T 3mv2_B          216 GLLNLHLQQRNIAEAQGIVELLL  238 (310)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHH
Confidence            33334455555555555555443

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.82  E-value=1.9e-08  Score=103.36  Aligned_cols=188  Identities=12%  Similarity=0.061  Sum_probs=126.0

Q ss_pred             HHcCCHHHHHHHHHHHH--------HCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHH
Q 044988          229 AQNGKSRQALSLFNEMR--------RARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIH  300 (538)
Q Consensus       229 ~~~~~~~~a~~~~~~m~--------~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~  300 (538)
                      ...|++++|++.|++..        +. -+.+...+..+..++...|++++|...++.+.+.     .|.+...+..+..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~-~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~-----~p~~~~a~~~lg~  475 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVD-FSESVELPLMEVRALLDLGDVAKATRKLDDLAER-----VGWRWRLVWYRAV  475 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------C-CTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-----HCCCHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccc-cccchhHHHHHHHHHHhcCCHHHHHHHHHHHhcc-----CcchHHHHHHHHH
Confidence            66788888888888877        32 2334566777777888888888888888888876     6667777778888


Q ss_pred             HHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc
Q 044988          301 MYASCGEIEEAYGVFRKMQR--R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP  377 (538)
Q Consensus       301 ~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p  377 (538)
                      +|...|++++|.+.|++..+  | +...|..+...+.+.|                    ++++ ...|++..+.   .|
T Consensus       476 ~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g--------------------~~~~-~~~~~~al~~---~P  531 (681)
T 2pzi_A          476 AELLTGDYDSATKHFTEVLDTFPGELAPKLALAATAELAG--------------------NTDE-HKFYQTVWST---ND  531 (681)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHT--------------------CCCT-TCHHHHHHHH---CT
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcC--------------------ChHH-HHHHHHHHHh---CC
Confidence            88888888888888887664  3 4555666666666555                    4445 5777777654   44


Q ss_pred             -cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCC-----HHHHHHHHHHchhccCCCCcc
Q 044988          378 -RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNN-----AELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       378 -~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~-----~~~A~~~~~~~~~~~~p~~~~  447 (538)
                       +...|..+..+|.+.|++++|++.|++.. ..|+ ...+..+..++...++     .+...+..+.. ..+.++.+.
T Consensus       532 ~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l-~~~~~~~~~  608 (681)
T 2pzi_A          532 GVISAAFGLARARSAEGDRVGAVRTLDEVPPTSRHFTTARLTSAVTLLSGRSTSEVTEEQIRDAARRV-EALPPTEPR  608 (681)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHTSCTTSTTHHHHHHHHHHHTC-------CCHHHHHHHHHHH-HTSCTTSTT
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHhhcccCcccHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHH-hhCCCCcHH
Confidence             46678888888888888888888888774 4565 4556666666555444     23333333333 445555555

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.82  E-value=1.2e-08  Score=82.78  Aligned_cols=140  Identities=10%  Similarity=0.050  Sum_probs=94.5

Q ss_pred             HHHHHHhCCCHHHHHHHHHhcCCCC---cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcC
Q 044988          298 LIHMYASCGEIEEAYGVFRKMQRRN---TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWG  374 (538)
Q Consensus       298 l~~~~~~~g~~~~a~~~~~~m~~~~---~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~  374 (538)
                      |...+...|++++|...+......+   ...+-.+...|.+.|                    ++++|...|++..+.  
T Consensus         3 LG~~~~~~~~~e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~--------------------~~~~A~~~~~~al~~--   60 (150)
T 4ga2_A            3 LGSMRRSKADVERYIASVQGSTPSPRQKSIKGFYFAKLYYEAK--------------------EYDLAKKYICTYINV--   60 (150)
T ss_dssp             ----CCCHHHHHHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTT--------------------CHHHHHHHHHHHHHH--
T ss_pred             hHHHHHHcChHHHHHHHHHHhcccCcccHHHHHHHHHHHHHcC--------------------CHHHHHHHHHHHHHh--
Confidence            3445556677777777777766532   233444444444444                    666677777777754  


Q ss_pred             CCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHH-HHHchhccCCCCcccHH
Q 044988          375 IKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQV-AQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       375 ~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~-~~~~~~~~~p~~~~~~~  450 (538)
                       .| +..+|..+..+|.+.|++++|+..|++.. ..|+ ...|..+...+.+.|++++|.+. ++++ .++.|+++.+|.
T Consensus        61 -~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~a-l~l~P~~~~~~~  138 (150)
T 4ga2_A           61 -QERDPKAHRFLGLLYELEENTDKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERA-AKLFPGSPAVYK  138 (150)
T ss_dssp             -CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHH-HHHSTTCHHHHH
T ss_pred             -CCCCHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHH-HHhCcCCHHHHH
Confidence             45 47788888888888888888888887763 3444 67777888888888887765554 5777 888888888777


Q ss_pred             HHHHHHHHhcCC
Q 044988          451 ALVANVYAAAKR  462 (538)
Q Consensus       451 ~~l~~~~~~~g~  462 (538)
                       +...++.+.|+
T Consensus       139 -l~~~ll~~~G~  149 (150)
T 4ga2_A          139 -LKEQLLDCEGE  149 (150)
T ss_dssp             -HHHHHHHTCCC
T ss_pred             -HHHHHHHHhCc
Confidence             77777777664

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.79  E-value=7.8e-08  Score=77.62  Aligned_cols=101  Identities=11%  Similarity=0.016  Sum_probs=91.1

Q ss_pred             CCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          374 GIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       374 ~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                      .+.|+ ...+..+...+.+.|++++|...|++.. ..| +...|..+..++...|++++|+..|+++ ..+.|+++..+.
T Consensus        30 ~l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~a-l~l~P~~~~~~~  108 (151)
T 3gyz_A           30 AIPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVA-FALGKNDYTPVF  108 (151)
T ss_dssp             CSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHSSSCCHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHH-HhhCCCCcHHHH
Confidence            45674 6788899999999999999999999884 344 5888999999999999999999999999 999999999889


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          451 ALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       451 ~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                       .++.+|.+.|++++|+..|++..+.
T Consensus       109 -~lg~~~~~lg~~~eA~~~~~~al~l  133 (151)
T 3gyz_A          109 -HTGQCQLRLKAPLKAKECFELVIQH  133 (151)
T ss_dssp             -HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -HHHHHHHHcCCHHHHHHHHHHHHHh
Confidence             9999999999999999999999874

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.78  E-value=9.5e-08  Score=87.99  Aligned_cols=200  Identities=11%  Similarity=0.004  Sum_probs=135.8

Q ss_pred             cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc-cCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHH
Q 044988          231 NGKSRQALSLFNEMRRARVGLDQVALVAALSACAE-IGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIE  309 (538)
Q Consensus       231 ~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  309 (538)
                      .|++++|.+++++..+..- ..          +.+ .++++.|...|..                   ....|...|+++
T Consensus         4 ~~~~~eA~~~~~~a~k~~~-~~----------~~~~~~~~~~A~~~~~~-------------------a~~~~~~~g~~~   53 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLK-TS----------FMKWKPDYDSAASEYAK-------------------AAVAFKNAKQLE   53 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-CC----------SSSCSCCHHHHHHHHHH-------------------HHHHHHHTTCHH
T ss_pred             cchHHHHHHHHHHHHHHcc-cc----------ccCCCCCHHHHHHHHHH-------------------HHHHHHHcCCHH
Confidence            4667778888777665311 10          111 3566666655543                   455677889999


Q ss_pred             HHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc---CCCc-cHHHHHHH
Q 044988          310 EAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW---GIKP-RIEHYGCM  385 (538)
Q Consensus       310 ~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~---~~~p-~~~~~~~l  385 (538)
                      +|...|.+..           ..+.+.++...+...|..+...|...|++++|...|++..+.+   |-.. -..++..+
T Consensus        54 ~A~~~~~~al-----------~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~l  122 (307)
T 2ifu_A           54 QAKDAYLQEA-----------EAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRA  122 (307)
T ss_dssp             HHHHHHHHHH-----------HHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-----------HHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            9998887753           3334445555555566666666666666666666666654431   1111 14577888


Q ss_pred             HHHhhhcCChHHHHHHHHhCC-C---CCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc------cHHH
Q 044988          386 VDLFSRAGLMDEAFSLVQNMP-M---KPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA------GYLA  451 (538)
Q Consensus       386 ~~~~~~~g~~~~A~~~~~~~~-~---~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~------~~~~  451 (538)
                      ..+|.. |++++|++.|++.. .   ..+    ..++..+...+...|++++|+..++++ ..+.|....      .+. 
T Consensus       123 g~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~a-l~~~~~~~~~~~~~~~~~-  199 (307)
T 2ifu_A          123 GKLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKE-KSMYKEMENYPTCYKKCI-  199 (307)
T ss_dssp             HHHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHHHTTCHHHHHHHHH-
T ss_pred             HHHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHHHHHcCChhHHHHHHH-
Confidence            899988 99999999998763 1   111    457788888999999999999999999 665554431      344 


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHH
Q 044988          452 LVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       452 ~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      .++.++...|++++|...+++..
T Consensus       200 ~~g~~~~~~g~~~~A~~~~~~al  222 (307)
T 2ifu_A          200 AQVLVQLHRADYVAAQKCVRESY  222 (307)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHh
Confidence            66777888899999999999987

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.78  E-value=1.9e-07  Score=73.72  Aligned_cols=125  Identities=19%  Similarity=0.242  Sum_probs=86.1

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 044988          189 SWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAE  265 (538)
Q Consensus       189 ~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  265 (538)
                      .|..+...+...|++++|..+|+++.+   .+...|..+...+...|++++|...|+++.+.+ +.+...+..+...+..
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~   81 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYK   81 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcCCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHHHH
Confidence            355556666666677777766666432   345567777777777788888888887776643 3345666677777777


Q ss_pred             cCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 044988          266 IGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       266 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  319 (538)
                      .|+++.|...++.+.+.     .|.+...+..+...+...|++++|...++++.
T Consensus        82 ~~~~~~A~~~~~~~~~~-----~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  130 (136)
T 2fo7_A           82 QGDYDEAIEYYQKALEL-----DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKAL  130 (136)
T ss_dssp             TTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHh-----CCCChHHHHHHHHHHHHHccHHHHHHHHHHHH
Confidence            78888888877777776     45555666677777778888888877777654

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.76  E-value=2e-07  Score=80.30  Aligned_cols=126  Identities=13%  Similarity=0.073  Sum_probs=83.3

Q ss_pred             HHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc
Q 044988          297 ALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       297 ~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  373 (538)
                      .+..+|.+.|++++|...|++..+  | +...+..+...+...|                    ++++|...|++..+. 
T Consensus        59 ~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g--------------------~~~~A~~~~~~al~~-  117 (208)
T 3urz_A           59 ELALAYKKNRNYDKAYLFYKELLQKAPNNVDCLEACAEMQVCRG--------------------QEKDALRMYEKILQL-  117 (208)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT--------------------CHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcC--------------------CHHHHHHHHHHHHHc-
Confidence            477788888888888888887664  2 4445555555555554                    666777777777765 


Q ss_pred             CCCc-cHHHHHHHHHHhhhcCC--hHHHHHHHHhCCCCCCHH--HHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          374 GIKP-RIEHYGCMVDLFSRAGL--MDEAFSLVQNMPMKPNDA--VLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       374 ~~~p-~~~~~~~l~~~~~~~g~--~~~A~~~~~~~~~~p~~~--~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                        .| +..++..+..+|...|.  .+.+...++... .|+..  .+.....++...|++++|+..|+++ ..+.|+...
T Consensus       118 --~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~a-l~l~P~~~~  192 (208)
T 3urz_A          118 --EADNLAANIFLGNYYYLTAEQEKKKLETDYKKLS-SPTKMQYARYRDGLSKLFTTRYEKARNSLQKV-ILRFPSTEA  192 (208)
T ss_dssp             --CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHH-TTTSCCHHH
T ss_pred             --CCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh-CCCchhHHHHHHHHHHHHccCHHHHHHHHHHH-HHhCCCHHH
Confidence              45 47778888887766553  445566666654 44433  3444555667788999999999999 888887543

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.76  E-value=1.8e-07  Score=78.10  Aligned_cols=154  Identities=8%  Similarity=0.047  Sum_probs=99.6

Q ss_pred             HHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          296 NALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       296 ~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                      ..+...+.+.|++++|...|++..+   .+...+..+...+...|                    ++++|...++...+.
T Consensus        10 ~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g--------------------~~~~A~~~~~~a~~~   69 (176)
T 2r5s_A           10 LKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETK--------------------QFELAQELLATIPLE   69 (176)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTT--------------------CHHHHHHHHTTCCGG
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCC--------------------CHHHHHHHHHHhhhc
Confidence            3566667777778888877777765   23445555555555554                    566666777766544


Q ss_pred             cCCCccHHHHHHHHHH-hhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC--cc
Q 044988          373 WGIKPRIEHYGCMVDL-FSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ--AA  447 (538)
Q Consensus       373 ~~~~p~~~~~~~l~~~-~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~--~~  447 (538)
                         .|+...+..+... +...+...+|...+++.. ..| +...+..+...+...|++++|...++++ ....|+.  ..
T Consensus        70 ---~p~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~-l~~~p~~~~~~  145 (176)
T 2r5s_A           70 ---YQDNSYKSLIAKLELHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNI-LKVNLGAQDGE  145 (176)
T ss_dssp             ---GCCHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HTTCTTTTTTH
T ss_pred             ---cCChHHHHHHHHHHHHhhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHH-HHhCcccChHH
Confidence               3333322222211 112222334566666552 344 4777888888888999999999999988 7888764  33


Q ss_pred             cHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          448 GYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       448 ~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      .+. .++.++...|+.++|...|++..
T Consensus       146 a~~-~l~~~~~~~g~~~~A~~~y~~al  171 (176)
T 2r5s_A          146 VKK-TFMDILSALGQGNAIASKYRRQL  171 (176)
T ss_dssp             HHH-HHHHHHHHHCSSCHHHHHHHHHH
T ss_pred             HHH-HHHHHHHHhCCCCcHHHHHHHHH
Confidence            567 88888999999999998888765

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.74  E-value=2.3e-07  Score=79.91  Aligned_cols=165  Identities=12%  Similarity=0.006  Sum_probs=94.4

Q ss_pred             HHHHHHcCCHHHHHHHHHHHHHCCCCCC-HHHHHH----------------HHHHHHccCChHHHHHHHHHHHHhccCCC
Q 044988          225 ISGCAQNGKSRQALSLFNEMRRARVGLD-QVALVA----------------ALSACAEIGDLKLGKWIHSYVEENFSVGR  287 (538)
Q Consensus       225 i~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~----------------li~~~~~~~~~~~a~~~~~~~~~~~~~~~  287 (538)
                      ...+...|++++|+..|++..+.  .|+ ...+..                +..++.+.|++++|...++...+.     
T Consensus        11 g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~-----   83 (208)
T 3urz_A           11 VSAAIEAGQNGQAVSYFRQTIAL--NIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQK-----   83 (208)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH--CHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-----
Confidence            34445556666666666665542  232 223333                566667777777777777777776     


Q ss_pred             CCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHH
Q 044988          288 EPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQ  364 (538)
Q Consensus       288 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~  364 (538)
                      .|.+...+..+..+|...|++++|...|++..+  | +..+|..+...|...|..                  ....+..
T Consensus        84 ~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~------------------~~~~~~~  145 (208)
T 3urz_A           84 APNNVDCLEACAEMQVCRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTAEQ------------------EKKKLET  145 (208)
T ss_dssp             CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH------------------HHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhHH------------------HHHHHHH
Confidence            566667777777777777777777777776654  2 445555555555433311                  1223344


Q ss_pred             HHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHHH
Q 044988          365 FFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGSL  417 (538)
Q Consensus       365 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l  417 (538)
                      .++...   ...|....+..+..++...|++++|...|++.. ..|+......+
T Consensus       146 ~~~~~~---~~~~~~~a~~~~g~~~~~~~~~~~A~~~~~~al~l~P~~~~~~~l  196 (208)
T 3urz_A          146 DYKKLS---SPTKMQYARYRDGLSKLFTTRYEKARNSLQKVILRFPSTEAQKTL  196 (208)
T ss_dssp             HHC------CCCHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTTTSCCHHHHHHH
T ss_pred             HHHHHh---CCCchhHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            444433   223333344445556666777788887777653 56775544433

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.74  E-value=2.4e-07  Score=84.24  Aligned_cols=84  Identities=13%  Similarity=0.062  Sum_probs=56.7

Q ss_pred             hhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC--cccHHHHHHHHHHhcCChH
Q 044988          389 FSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ--AAGYLALVANVYAAAKRWQ  464 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~--~~~~~~~l~~~~~~~g~~~  464 (538)
                      +...++.++|.+.+++.. ..| +...+..+...+...|++++|+..++++ ....|++  ...+. .++.+|...|+.+
T Consensus       195 l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~-l~~~p~~~~~~a~~-~l~~~~~~~g~~~  272 (287)
T 3qou_A          195 LLXQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGH-LRXDLTAADGQTRX-TFQEILAALGTGD  272 (287)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTGGGGHHHH-HHHHHHHHHCTTC
T ss_pred             HHhhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHH-HhcccccccchHHH-HHHHHHHHcCCCC
Confidence            445555566666665542 233 4566677777777777777887777777 7777776  55566 7777778888887


Q ss_pred             HHHHHHHHHH
Q 044988          465 DVAAVRQKMI  474 (538)
Q Consensus       465 ~A~~~~~~m~  474 (538)
                      +|...+++..
T Consensus       273 ~a~~~~r~al  282 (287)
T 3qou_A          273 ALASXYRRQL  282 (287)
T ss_dssp             HHHHHHHHHH
T ss_pred             cHHHHHHHHH
Confidence            7777776643

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.73  E-value=5.3e-07  Score=75.26  Aligned_cols=155  Identities=10%  Similarity=0.003  Sum_probs=95.0

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH-HHc
Q 044988          190 WNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSA-CAE  265 (538)
Q Consensus       190 ~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~-~~~  265 (538)
                      +..+...+...|++++|...|++..+   .+...+..+...+...|++++|+..|++.....  |+.......... +..
T Consensus         9 ~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~~~   86 (176)
T 2r5s_A            9 LLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLELHQ   86 (176)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHHHHh
Confidence            33444556666666777777766653   344566666677777777777777776665432  233222221111 112


Q ss_pred             cCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CC---cchHHHHHHHHHhcCCcc
Q 044988          266 IGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--RN---TVSWTSMITGFAKQGYAQ  340 (538)
Q Consensus       266 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~---~~~~~~li~~~~~~~~~~  340 (538)
                      .+....+...++...+.     .|.+...+..+...+...|++++|...|+++.+  |+   ...+..+...+...|+.+
T Consensus        87 ~~~~~~a~~~~~~al~~-----~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  161 (176)
T 2r5s_A           87 QAAESPELKRLEQELAA-----NPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGN  161 (176)
T ss_dssp             HHTSCHHHHHHHHHHHH-----STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSC
T ss_pred             hcccchHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCC
Confidence            22233456667777765     666777777888888888888888888887765  32   346777777788888777


Q ss_pred             HHHHHHHHHHH
Q 044988          341 EALLTFLGVLS  351 (538)
Q Consensus       341 ~a~~~~~~ll~  351 (538)
                      +|...|...+.
T Consensus       162 ~A~~~y~~al~  172 (176)
T 2r5s_A          162 AIASKYRRQLY  172 (176)
T ss_dssp             HHHHHHHHHHH
T ss_pred             cHHHHHHHHHH
Confidence            77655554443

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.72  E-value=3e-08  Score=80.43  Aligned_cols=121  Identities=14%  Similarity=0.033  Sum_probs=101.5

Q ss_pred             HHHhcccCcHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCC
Q 044988          350 LSACSHGGFVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNN  426 (538)
Q Consensus       350 l~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~  426 (538)
                      ...+...|++++|...++.....   .|+ ...+..+...|.+.|++++|++.|++.. ..| +..+|..+...+...|+
T Consensus         4 G~~~~~~~~~e~ai~~~~~a~~~---~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A            4 GSMRRSKADVERYIASVQGSTPS---PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             ---CCCHHHHHHHHHHHHHHSCS---HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcChHHHHHHHHHHhccc---CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCc
Confidence            34556678999999999988743   564 5567789999999999999999999874 444 57899999999999999


Q ss_pred             HHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHH-HHHHHh
Q 044988          427 AELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAV-RQKMIK  475 (538)
Q Consensus       427 ~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~-~~~m~~  475 (538)
                      +++|+..|+++ .++.|+++.++. .++.+|.+.|++++|.+. +++..+
T Consensus        81 ~~~A~~~~~~a-l~~~p~~~~~~~-~la~~~~~~~~~~~aa~~~~~~al~  128 (150)
T 4ga2_A           81 TDKAVECYRRS-VELNPTQKDLVL-KIAELLCKNDVTDGRAKYWVERAAK  128 (150)
T ss_dssp             HHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHHCSSSSHHHHHHHHHHH
T ss_pred             hHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHHHcCChHHHHHHHHHHHHH
Confidence            99999999999 999999999888 999999999999887765 577765

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.70  E-value=4.6e-07  Score=93.09  Aligned_cols=180  Identities=10%  Similarity=0.036  Sum_probs=109.3

Q ss_pred             hccCChHHHHHHHHHHH--------HhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcC
Q 044988           28 QIRNTTKTLFQIHSQII--------INGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARS   96 (538)
Q Consensus        28 ~~~~~~~~a~~~~~~~~--------~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~   96 (538)
                      ...+++++|...++...        +. .+.+...+..+...|...|++++|+..|++..   +.+...|..+..++.+.
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~-~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVD-FSESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------C-CTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccc-cccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHc
Confidence            55667777777777666        22 12345566666677777777777777776655   23455666666677777


Q ss_pred             CCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHH
Q 044988           97 ETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCAR  176 (538)
Q Consensus        97 ~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~  176 (538)
                      |++++|+..|++..+.. +-+...|..+..++.+.|++++ ...|++.++.+ +.+...+..+..++.+.|+   .++|.
T Consensus       481 g~~~~A~~~~~~al~l~-P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~---~~~A~  554 (681)
T 2pzi_A          481 GDYDSATKHFTEVLDTF-PGELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGD---RVGAV  554 (681)
T ss_dssp             TCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTC---HHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCC---HHHHH
Confidence            77777777777766542 2245566666667777777777 77777776654 4455566667777777777   77777


Q ss_pred             HHhhcCCCCC---chhHHHHHHHHHhcC--------CHHHHHHHHccCC
Q 044988          177 LLFDDMPARS---VVSWNSLLKGYVKRG--------DIDGAWKIFDEMP  214 (538)
Q Consensus       177 ~~~~~~~~~~---~~~~~~li~~~~~~g--------~~~~A~~~~~~m~  214 (538)
                      ..|++..+.+   ...|..+..++...+        ++++|.+.+..+.
T Consensus       555 ~~~~~al~l~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~~~  603 (681)
T 2pzi_A          555 RTLDEVPPTSRHFTTARLTSAVTLLSGRSTSEVTEEQIRDAARRVEALP  603 (681)
T ss_dssp             HHHHTSCTTSTTHHHHHHHHHHHTC-------CCHHHHHHHHHHHHTSC
T ss_pred             HHHHhhcccCcccHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhhCC
Confidence            7776666432   234444444443322        3555555555554

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.70  E-value=1.2e-06  Score=76.48  Aligned_cols=186  Identities=13%  Similarity=0.081  Sum_probs=103.6

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC-CC-HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchh---H
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRARVG-LD-QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVS---L  294 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~---~  294 (538)
                      .+..+...+.+.|++++|+..|+++.+.... |. ...+..+..++.+.|+++.|...++.+.+.     .|.+..   .
T Consensus         6 ~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~-----~P~~~~~~~a   80 (225)
T 2yhc_A            6 EIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL-----NPTHPNIDYV   80 (225)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCTTHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH-----CcCCCcHHHH
Confidence            3444555566667777777777766653211 11 234555666666667777777776666665     232221   2


Q ss_pred             HHHHHHHHH------------------hCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhccc
Q 044988          295 NNALIHMYA------------------SCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHG  356 (538)
Q Consensus       295 ~~~l~~~~~------------------~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~  356 (538)
                      +..+..++.                  ..|++++|...|+++.+.+                               -..
T Consensus        81 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~-------------------------------P~~  129 (225)
T 2yhc_A           81 MYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGY-------------------------------PNS  129 (225)
T ss_dssp             HHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTC-------------------------------TTC
T ss_pred             HHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHC-------------------------------cCC
Confidence            223333333                  3456777777777666522                               111


Q ss_pred             CcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCH----HHHHHHHHHHHhcCCHHHHH
Q 044988          357 GFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPND----AVLGSLLLGCRIHNNAELAS  431 (538)
Q Consensus       357 ~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~----~~~~~l~~~~~~~~~~~~A~  431 (538)
                      .....+......+...     .......+...|.+.|++++|+..|+++. ..|+.    ..+..+..++.+.|+.++|.
T Consensus       130 ~~a~~a~~~l~~~~~~-----~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~  204 (225)
T 2yhc_A          130 QYTTDATKRLVFLKDR-----LAKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAE  204 (225)
T ss_dssp             TTHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             hhHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHH
Confidence            1111222111111110     01122345667778888888888887763 23442    45667777888888888888


Q ss_pred             HHHHHchhccCCCCcc
Q 044988          432 QVAQKLVAEIDPEQAA  447 (538)
Q Consensus       432 ~~~~~~~~~~~p~~~~  447 (538)
                      +.++.+ ....|++..
T Consensus       205 ~~~~~l-~~~~~~~~~  219 (225)
T 2yhc_A          205 KVAKII-AANSSNTLE  219 (225)
T ss_dssp             HHHHHH-HHCCSCCCC
T ss_pred             HHHHHH-HhhCCCchh
Confidence            888887 666666543

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.70  E-value=1.2e-06  Score=85.93  Aligned_cols=205  Identities=11%  Similarity=0.016  Sum_probs=132.2

Q ss_pred             HHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHH
Q 044988          204 DGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVE  280 (538)
Q Consensus       204 ~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~  280 (538)
                      +.+..+|++...   .+...|-..+..+.+.|+.++|..+|++....   |....+..   .+....+.+.   +++.+.
T Consensus       196 ~Rv~~~ye~al~~~p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~---P~~~~l~~---~y~~~~e~~~---~~~~l~  266 (493)
T 2uy1_A          196 SRMHFIHNYILDSFYYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM---SDGMFLSL---YYGLVMDEEA---VYGDLK  266 (493)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CCSSHHHH---HHHHHTTCTH---HHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC---CCcHHHHH---HHHhhcchhH---HHHHHH
Confidence            345667777543   34567888888888999999999999999987   44333222   2222212222   133333


Q ss_pred             HhccCC--------CCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHH
Q 044988          281 ENFSVG--------REPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSA  352 (538)
Q Consensus       281 ~~~~~~--------~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~  352 (538)
                      +.....        ..+....+|...+..+.+.+..+.|..+|++...|. .++...+. +              ..+..
T Consensus       267 ~~~~~~~~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A~~~~-~~~~v~i~-~--------------A~lE~  330 (493)
T 2uy1_A          267 RKYSMGEAESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIELGNEG-VGPHVFIY-C--------------AFIEY  330 (493)
T ss_dssp             HHTC----------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSC-CCHHHHHH-H--------------HHHHH
T ss_pred             HHHHhhccchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHhhCCC-CChHHHHH-H--------------HHHHH
Confidence            221000        011223566677777777888999999999884343 23322211 0              01111


Q ss_pred             hcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCCHHHHHH
Q 044988          353 CSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHNNAELASQ  432 (538)
Q Consensus       353 ~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~~~~~A~~  432 (538)
                      . ..++.+.|..+|+...+.++-  +...+...++...+.|+.+.|..+|+++.  .....|...+..-...|+.+.+..
T Consensus       331 ~-~~~d~~~ar~ife~al~~~~~--~~~~~~~yid~e~~~~~~~~aR~l~er~~--k~~~lw~~~~~fE~~~G~~~~~r~  405 (493)
T 2uy1_A          331 Y-ATGSRATPYNIFSSGLLKHPD--STLLKEEFFLFLLRIGDEENARALFKRLE--KTSRMWDSMIEYEFMVGSMELFRE  405 (493)
T ss_dssp             H-HHCCSHHHHHHHHHHHHHCTT--CHHHHHHHHHHHHHHTCHHHHHHHHHHSC--CBHHHHHHHHHHHHHHSCHHHHHH
T ss_pred             H-HCCChHHHHHHHHHHHHHCCC--CHHHHHHHHHHHHHcCCHHHHHHHHHHHH--HHHHHHHHHHHHHHHCCCHHHHHH
Confidence            1 123688999999998887432  24456667887888999999999999984  357788888888888899999999


Q ss_pred             HHHHch
Q 044988          433 VAQKLV  438 (538)
Q Consensus       433 ~~~~~~  438 (538)
                      +++++.
T Consensus       406 v~~~~~  411 (493)
T 2uy1_A          406 LVDQKM  411 (493)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            888885

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.67  E-value=3.6e-06  Score=82.49  Aligned_cols=360  Identities=10%  Similarity=0.002  Sum_probs=183.3

Q ss_pred             hhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCC-cHHHHHHHHHHHH
Q 044988           68 LINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGL-FREGEQVHGRVLA  146 (538)
Q Consensus        68 ~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~-~~~a~~~~~~~~~  146 (538)
                      ++.|+.+|+...           ..+-. |+++.+..+|++....  .|+...|...+....+.++ .+....+|+..+.
T Consensus        11 i~~aR~vyer~l-----------~~~P~-~~~e~~~~iferal~~--~ps~~LW~~Y~~f~~~~~~~~~~i~~~fe~al~   76 (493)
T 2uy1_A           11 LSSPSAIMEHAR-----------RLYMS-KDYRSLESLFGRCLKK--SYNLDLWMLYIEYVRKVSQKKFKLYEVYEFTLG   76 (493)
T ss_dssp             -CCHHHHHHHHH-----------HHHHT-TCHHHHHHHHHHHSTT--CCCHHHHHHHHHHHHHHC----CTHHHHHHHHH
T ss_pred             hHHHHHHHHHHH-----------HHCCC-CCHHHHHHHHHHHhcc--CCCHHHHHHHHHHHHHhCchHHHHHHHHHHHHH
Confidence            666666665543           22221 8899999999998874  5788888888888777663 4566778887776


Q ss_pred             h-CC-CCchhHHhHHHHHHH----hcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHh---cCCHHHHHHHHccCCCCC
Q 044988          147 S-GY-CSNVFIRTNLMNLYL----MSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVK---RGDIDGAWKIFDEMPHRN  217 (538)
Q Consensus       147 ~-~~-~~~~~~~~~l~~~~~----~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~---~g~~~~A~~~~~~m~~~~  217 (538)
                      . |. ..+..+|...+..+.    ..|+   ++.+.++|++...-....+..+-..|..   ......+..++.+     
T Consensus        77 ~vg~d~~s~~iW~~Yi~f~~~~~~~~~~---~~~vR~iy~rAL~~P~~~~~~lw~~Y~~fE~~~~~~~~~~~~~~-----  148 (493)
T 2uy1_A           77 QFENYWDSYGLYKEYIEEEGKIEDEQTR---IEKIRNGYMRALQTPMGSLSELWKDFENFELELNKITGKKIVGD-----  148 (493)
T ss_dssp             HSTTCTTCHHHHHHHHHHTSSCSSHHHH---HHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCHHHHHHHHHH-----
T ss_pred             HcCCCcccHHHHHHHHHHHHhchhhhHH---HHHHHHHHHHHHhChhhhHHHHHHHHHHHHHHhccccHHHHHHH-----
Confidence            5 43 235567777766543    2345   7778888877654212212222222211   1111111111111     


Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc--CC-----hHHHHHHHHHHHHhccCCCCCc
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEI--GD-----LKLGKWIHSYVEENFSVGREPV  290 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~--~~-----~~~a~~~~~~~~~~~~~~~~~~  290 (538)
                                .  .+.+..|...++.+...--..+...+...+.--...  +-     .+.+..+|+.+...     .|.
T Consensus       149 ----------~--~~~y~~ar~~y~~~~~~~~~~s~~~W~~y~~~E~~~~~~~~~~~~~~Rv~~~ye~al~~-----~p~  211 (493)
T 2uy1_A          149 ----------T--LPIFQSSFQRYQQIQPLIRGWSVKNAARLIDLEMENGMKLGGRPHESRMHFIHNYILDS-----FYY  211 (493)
T ss_dssp             ----------H--HHHHHHHHHHHHHHHHHHHTCSHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-----TTT
T ss_pred             ----------H--hHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHhcCCccCcchhhHHHHHHHHHHHHHc-----CCC
Confidence                      0  011122222222221100000111222211111110  00     12233344444443     333


Q ss_pred             chhHHHHHHHHHHhCCCHHHHHHHHHhcCC-CCcc-hHH-------------HHHHHHHhc-------CCccHHHHHHHH
Q 044988          291 LVSLNNALIHMYASCGEIEEAYGVFRKMQR-RNTV-SWT-------------SMITGFAKQ-------GYAQEALLTFLG  348 (538)
Q Consensus       291 ~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-~~~~-~~~-------------~li~~~~~~-------~~~~~a~~~~~~  348 (538)
                      ...+|...+..+.+.|+.+.|..+|++... |+.. .|.             .+...+...       ........+|..
T Consensus       212 ~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~P~~~~l~~~y~~~~e~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~lw~~  291 (493)
T 2uy1_A          212 AEEVYFFYSEYLIGIGQKEKAKKVVERGIEMSDGMFLSLYYGLVMDEEAVYGDLKRKYSMGEAESAEKVFSKELDLLRIN  291 (493)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHHHHHHTTCTHHHHHHHHHTC----------CHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCcHHHHHHHHhhcchhHHHHHHHHHHHhhccchhhhhcccccHHHHHH
Confidence            444444444444444555555444443322 1111 000             011100000       001111144555


Q ss_pred             HHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcC-ChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcC
Q 044988          349 VLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAG-LMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHN  425 (538)
Q Consensus       349 ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~  425 (538)
                      .+....+.++++.|+.+|+.. +..+  ++...|......-...+ +.+.|..+|+... .-|+ ...|...+....+.|
T Consensus       292 y~~~~~r~~~~~~AR~i~~~A-~~~~--~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~~~~~~~~yid~e~~~~  368 (493)
T 2uy1_A          292 HLNYVLKKRGLELFRKLFIEL-GNEG--VGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLKEEFFLFLLRIG  368 (493)
T ss_dssp             HHHHHHHHHCHHHHHHHHHHH-TTSC--CCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHHh-hCCC--CChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcC
Confidence            566665677899999999998 4312  24444443333333333 6999999998763 1233 455667777788899


Q ss_pred             CHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          426 NAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       426 ~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +.+.|..+|+++ .    .....|. ..+..-...|+.+.+.+++++..+
T Consensus       369 ~~~~aR~l~er~-~----k~~~lw~-~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          369 DEENARALFKRL-E----KTSRMWD-SMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             CHHHHHHHHHHS-C----CBHHHHH-HHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH-H----HHHHHHH-HHHHHHHHCCCHHHHHHHHHHHHH
Confidence            999999999998 3    3445455 555656678999999998888763

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.67  E-value=9.5e-08  Score=77.18  Aligned_cols=108  Identities=11%  Similarity=0.028  Sum_probs=92.5

Q ss_pred             HHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhc
Q 044988          364 QFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGCRIHNNAELASQVAQKLVAE  440 (538)
Q Consensus       364 ~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  440 (538)
                      ..|+++.   .+.| +...+..+...+.+.|++++|...|++.. . +.+...|..+..++...|++++|+..++++ ..
T Consensus         8 ~~~~~al---~~~p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a-l~   83 (148)
T 2vgx_A            8 GTIAMLN---EISSDTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYG-AV   83 (148)
T ss_dssp             CSHHHHT---TCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HH
T ss_pred             hhHHHHH---cCCHhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHH-Hh
Confidence            3455555   3456 46678889999999999999999999874 3 346788889999999999999999999999 99


Q ss_pred             cCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          441 IDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       441 ~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      +.|+++..+. .++.+|...|++++|.+.|++..+.
T Consensus        84 l~p~~~~~~~-~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           84 MDIXEPRFPF-HAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             HSTTCTHHHH-HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cCCCCchHHH-HHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            9999999888 9999999999999999999998763

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.65  E-value=2.2e-07  Score=72.57  Aligned_cols=99  Identities=12%  Similarity=0.133  Sum_probs=78.6

Q ss_pred             CCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHH
Q 044988          375 IKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MK-PNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLA  451 (538)
Q Consensus       375 ~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~-p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~  451 (538)
                      +.|+ ...+......|.+.|++++|++.|++.. .. .+...|..+..++.+.|++++|+..++++ .++.|++...|. 
T Consensus         8 inP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~a-l~~~p~~~~a~~-   85 (126)
T 4gco_A            8 INPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTC-IRLDSKFIKGYI-   85 (126)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-
T ss_pred             HCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHH-HHhhhhhhHHHH-
Confidence            4564 5567778888888888888888887763 33 35677778888888888888888888888 888888888777 


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHh
Q 044988          452 LVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       452 ~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .++.+|...|++++|++.|++..+
T Consensus        86 ~lg~~~~~~~~~~~A~~~~~~al~  109 (126)
T 4gco_A           86 RKAACLVAMREWSKAQRAYEDALQ  109 (126)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHH
Confidence            888888888888888888888776

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.64  E-value=5.8e-07  Score=77.63  Aligned_cols=123  Identities=11%  Similarity=-0.046  Sum_probs=105.3

Q ss_pred             HHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcC
Q 044988          348 GVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHN  425 (538)
Q Consensus       348 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~  425 (538)
                      .+...+...|++++|...|++..     .|+...+..+...|.+.|++++|++.|++..  .+.+...|..+..++...|
T Consensus        11 ~~g~~~~~~~~~~~A~~~~~~a~-----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~lg~~~~~~~   85 (213)
T 1hh8_A           11 NEGVLAADKKDWKGALDAFSAVQ-----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTE   85 (213)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHTSS-----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHc-----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcc
Confidence            44556667789999999998764     5678899999999999999999999998874  3345788899999999999


Q ss_pred             CHHHHHHHHHHchhccCCCCc----------------ccHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 044988          426 NAELASQVAQKLVAEIDPEQA----------------AGYLALVANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       426 ~~~~A~~~~~~~~~~~~p~~~----------------~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                      ++++|...++++ ....|.+.                ..+. .++.+|.+.|++++|.+.+++..+..
T Consensus        86 ~~~~A~~~~~~a-l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~~A~~~~~~al~~~  151 (213)
T 1hh8_A           86 KYDLAIKDLKEA-LIQLRGNQLIDYKILGLQFKLFACEVLY-NIAFMYAKKEEWKKAEEQLALATSMK  151 (213)
T ss_dssp             CHHHHHHHHHHH-HHTTTTCSEEECGGGTBCCEEEHHHHHH-HHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHHHH-HHhCCCccHHHHHHhccccCccchHHHH-HHHHHHHHccCHHHHHHHHHHHHHcC
Confidence            999999999999 88777766                6677 89999999999999999999998743

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.63  E-value=3.7e-07  Score=92.06  Aligned_cols=159  Identities=9%  Similarity=-0.034  Sum_probs=115.7

Q ss_pred             cCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC---CcchHHHHHHHHHhcCCccHH
Q 044988          266 IGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR---NTVSWTSMITGFAKQGYAQEA  342 (538)
Q Consensus       266 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a  342 (538)
                      .|++++|...++.+.+.     .|.+...+..+...|...|++++|.+.|++..+.   +...+..+...|...      
T Consensus         2 ~g~~~~A~~~~~~al~~-----~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~------   70 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRH-----RPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQ------   70 (568)
T ss_dssp             ------------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHT------
T ss_pred             CccHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHC------
Confidence            47889999999998886     6777888899999999999999999999988763   344555555555444      


Q ss_pred             HHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHH
Q 044988          343 LLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLL  419 (538)
Q Consensus       343 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~  419 (538)
                                    |++++|.+.+++..+.   .| +...+..+..+|.+.|++++|.+.|++.. ..| +...+..+..
T Consensus        71 --------------g~~~~A~~~~~~al~~---~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~  133 (568)
T 2vsy_A           71 --------------QRHAEAAVLLQQASDA---APEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLN  133 (568)
T ss_dssp             --------------TCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             --------------CCHHHHHHHHHHHHhc---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence                          5888889999999876   45 57899999999999999999999999874 334 5778888999


Q ss_pred             HHHhc---CCHHHHHHHHHHchhccCCCCcccHHHHHH
Q 044988          420 GCRIH---NNAELASQVAQKLVAEIDPEQAAGYLALVA  454 (538)
Q Consensus       420 ~~~~~---~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~  454 (538)
                      .+...   |+.++|.+.++++ ....|+....+. .++
T Consensus       134 ~~~~~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~-~l~  169 (568)
T 2vsy_A          134 WRRRLCDWRALDVLSAQVRAA-VAQGVGAVEPFA-FLS  169 (568)
T ss_dssp             HHHHTTCCTTHHHHHHHHHHH-HHHTCCCSCHHH-HTT
T ss_pred             HHHHhhccccHHHHHHHHHHH-HhcCCcccChHH-HhC
Confidence            99999   9999999999999 999999888666 554

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.62  E-value=1e-06  Score=80.09  Aligned_cols=154  Identities=10%  Similarity=-0.052  Sum_probs=73.6

Q ss_pred             hhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHH-HH
Q 044988           52 NYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLL-SV  127 (538)
Q Consensus        52 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li-~~  127 (538)
                      ...+..+...+...|++++|+..|++..   +.+...+..+...+.+.|++++|...+++....  .|+........ ..
T Consensus       117 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~~~~~~~  194 (287)
T 3qou_A          117 EELXAQQAMQLMQESNYTDALPLLXDAWQLSNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ--DQDTRYQGLVAQIE  194 (287)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG--GCSHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh--hcchHHHHHHHHHH
Confidence            3444444455555555555555555443   223344555555555555555555555555432  23322211111 12


Q ss_pred             HHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC--CC---chhHHHHHHHHHhcCC
Q 044988          128 CARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA--RS---VVSWNSLLKGYVKRGD  202 (538)
Q Consensus       128 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~--~~---~~~~~~li~~~~~~g~  202 (538)
                      +...++.+.|...+++..... +.+...+..+..++...|+   .++|...|.+..+  |+   ...+..++..+...|+
T Consensus       195 l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~---~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~  270 (287)
T 3qou_A          195 LLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGR---NEEALELLFGHLRXDLTAADGQTRXTFQEILAALGT  270 (287)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC---HHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCT
T ss_pred             HHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHccc---HHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCC
Confidence            334444555555555555543 3344455555555555555   5555555555443  21   3345555555555555


Q ss_pred             HHHHHHHHc
Q 044988          203 IDGAWKIFD  211 (538)
Q Consensus       203 ~~~A~~~~~  211 (538)
                      .++|...|+
T Consensus       271 ~~~a~~~~r  279 (287)
T 3qou_A          271 GDALASXYR  279 (287)
T ss_dssp             TCHHHHHHH
T ss_pred             CCcHHHHHH
Confidence            555555544

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.61  E-value=1e-05  Score=73.36  Aligned_cols=215  Identities=9%  Similarity=0.028  Sum_probs=132.1

Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHH-HHHHHHHHHccC--ChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHH----Hh
Q 044988          232 GKSRQALSLFNEMRRARVGLDQVA-LVAALSACAEIG--DLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMY----AS  304 (538)
Q Consensus       232 ~~~~~a~~~~~~m~~~g~~p~~~~-~~~li~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~----~~  304 (538)
                      ...++|+++++.+..  +.|+..| ++.--..+...+  +++++...++.+...     .|.+..+|+.-...+    ..
T Consensus        47 e~s~~aL~~t~~~L~--~nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~-----nPk~y~aW~~R~~iL~~~~~~  119 (306)
T 3dra_A           47 EYSERALHITELGIN--ELASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALD-----NEKNYQIWNYRQLIIGQIMEL  119 (306)
T ss_dssp             CCSHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHH-----CTTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--HCcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHH-----CcccHHHHHHHHHHHHHHHHh
Confidence            334577777777766  3454333 444444555556  777777777777775     666666666555555    44


Q ss_pred             C---CCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc
Q 044988          305 C---GEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR  378 (538)
Q Consensus       305 ~---g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~  378 (538)
                      .   ++++++..+++++.+   ++..+|+.-...+.+.|.++                  ..++.+.++++.+..  .-|
T Consensus       120 l~~~~~~~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~------------------~~~EL~~~~~~i~~d--~~N  179 (306)
T 3dra_A          120 NNNDFDPYREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHN------------------DAKELSFVDKVIDTD--LKN  179 (306)
T ss_dssp             TTTCCCTHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTT------------------CHHHHHHHHHHHHHC--TTC
T ss_pred             ccccCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccC------------------hHHHHHHHHHHHHhC--CCC
Confidence            4   677777777777765   34445554444444444322                  115556666666541  225


Q ss_pred             HHHHHHHHHHhhhcCC------hHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHH-HHHHHHHchhccC---CCCc
Q 044988          379 IEHYGCMVDLFSRAGL------MDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAEL-ASQVAQKLVAEID---PEQA  446 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~------~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~-A~~~~~~~~~~~~---p~~~  446 (538)
                      ...|+.-...+.+.|+      ++++++.++++.  ..-|...|+.+...+.+.|+... +..+.+++ ..+.   |.++
T Consensus       180 ~sAW~~R~~ll~~l~~~~~~~~~~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~-~~~~~~~~~s~  258 (306)
T 3dra_A          180 NSAWSHRFFLLFSKKHLATDNTIDEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQF-VDLEKDQVTSS  258 (306)
T ss_dssp             HHHHHHHHHHHHSSGGGCCHHHHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTT-EEGGGTEESCH
T ss_pred             HHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHH-HhccCCCCCCH
Confidence            6666665555555555      677777776653  33456777777777777666433 44566666 4443   6666


Q ss_pred             ccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          447 AGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       447 ~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .++. .++++|.+.|+.++|.++++.+.+
T Consensus       259 ~al~-~la~~~~~~~~~~~A~~~~~~l~~  286 (306)
T 3dra_A          259 FALE-TLAKIYTQQKKYNESRTVYDLLKS  286 (306)
T ss_dssp             HHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHH-HHHHHHHccCCHHHHHHHHHHHHh
Confidence            6566 777888888888888888888764

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.60  E-value=5e-07  Score=91.13  Aligned_cols=146  Identities=13%  Similarity=0.013  Sum_probs=104.6

Q ss_pred             cCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHH
Q 044988          231 NGKSRQALSLFNEMRRARVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIE  309 (538)
Q Consensus       231 ~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  309 (538)
                      .|++++|...|++..+.  .| +...+..+...+...|++++|...++...+.     .|.+...+..+...|...|+++
T Consensus         2 ~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~-----~p~~~~~~~~lg~~~~~~g~~~   74 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRH--RPQDFVAWLMLADAELGMGDTTAGEMAVQRGLAL-----HPGHPEAVARLGRVRWTQQRHA   74 (568)
T ss_dssp             ---------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT-----STTCHHHHHHHHHHHHHTTCHH
T ss_pred             CccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHCCCHH
Confidence            47889999999998774  44 5778888999999999999999999999986     6777888889999999999999


Q ss_pred             HHHHHHHhcCC--C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHH
Q 044988          310 EAYGVFRKMQR--R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCM  385 (538)
Q Consensus       310 ~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l  385 (538)
                      +|.+.|++..+  | +...+..+...|...                    |++++|.+.|++..+.   .| +...+..+
T Consensus        75 ~A~~~~~~al~~~p~~~~~~~~la~~~~~~--------------------g~~~~A~~~~~~al~~---~p~~~~~~~~l  131 (568)
T 2vsy_A           75 EAAVLLQQASDAAPEHPGIALWLGHALEDA--------------------GQAEAAAAAYTRAHQL---LPEEPYITAQL  131 (568)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHT--------------------TCHHHHHHHHHHHHHH---CTTCHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHHHHHHc--------------------CCHHHHHHHHHHHHHh---CCCCHHHHHHH
Confidence            99999998764  2 344555555555444                    5888889999998876   45 57788899


Q ss_pred             HHHhhhc---CChHHHHHHHHhCC
Q 044988          386 VDLFSRA---GLMDEAFSLVQNMP  406 (538)
Q Consensus       386 ~~~~~~~---g~~~~A~~~~~~~~  406 (538)
                      ..++...   |+.++|.+.+++..
T Consensus       132 ~~~~~~~~~~g~~~~A~~~~~~al  155 (568)
T 2vsy_A          132 LNWRRRLCDWRALDVLSAQVRAAV  155 (568)
T ss_dssp             HHHHHHTTCCTTHHHHHHHHHHHH
T ss_pred             HHHHHHhhccccHHHHHHHHHHHH
Confidence            9999999   99999999998773

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.59  E-value=5.8e-07  Score=70.18  Aligned_cols=107  Identities=8%  Similarity=-0.052  Sum_probs=89.3

Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHHH
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGC  421 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~  421 (538)
                      .+......+.+.|++++|.+.|++..+.   .| +...|..+..+|.+.|++++|++.+++.. . +.+...|..+..++
T Consensus        15 ~~~~~G~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~   91 (126)
T 4gco_A           15 EEKNKGNEYFKKGDYPTAMRHYNEAVKR---DPENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIRKAACL   91 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHHHHHHH
Confidence            3445556667777999999999998875   45 68899999999999999999999999874 3 34578899999999


Q ss_pred             HhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          422 RIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       422 ~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ...|++++|++.|+++ .++.|++..++. .|..+
T Consensus        92 ~~~~~~~~A~~~~~~a-l~l~P~~~~a~~-~l~~~  124 (126)
T 4gco_A           92 VAMREWSKAQRAYEDA-LQVDPSNEEARE-GVRNC  124 (126)
T ss_dssp             HHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHH
T ss_pred             HHCCCHHHHHHHHHHH-HHHCcCCHHHHH-HHHHh
Confidence            9999999999999999 999999988666 55543

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.56  E-value=4e-07  Score=82.51  Aligned_cols=184  Identities=9%  Similarity=-0.040  Sum_probs=101.7

Q ss_pred             HHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC---CcchHHHHH
Q 044988          254 VALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR---NTVSWTSMI  330 (538)
Q Consensus       254 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~---~~~~~~~li  330 (538)
                      ..+..+...+.+.|+++.|...++.+.+.     .|.+...+..+..+|.+.|++++|...+++..+-   +...+..+.
T Consensus         5 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~-----~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg   79 (281)
T 2c2l_A            5 QELKEQGNRLFVGRKYPEAAACYGRAITR-----NPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLG   79 (281)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            34444555555566666666666666554     4555666666666777777777777777666542   233444444


Q ss_pred             HHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc------HHHHHHHHHHhhhcCChHHHHHHHHh
Q 044988          331 TGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR------IEHYGCMVDLFSRAGLMDEAFSLVQN  404 (538)
Q Consensus       331 ~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~------~~~~~~l~~~~~~~g~~~~A~~~~~~  404 (538)
                      .+|...|                    ++++|...|++..+.   .|+      ...+..+  ...+...+..    ...
T Consensus        80 ~~~~~~g--------------------~~~~A~~~~~~al~l---~p~~~~~~~~~~~~~~--~~~~~~~~~~----~~~  130 (281)
T 2c2l_A           80 QCQLEME--------------------SYDEAIANLQRAYSL---AKEQRLNFGDDIPSAL--RIAKKKRWNS----IEE  130 (281)
T ss_dssp             HHHHHTT--------------------CHHHHHHHHHHHHHH---HHHTTCCCCSHHHHHH--HHHHHHHHHH----HHH
T ss_pred             HHHHHcC--------------------CHHHHHHHHHHHHHh---CccchhhHHHHHHHHH--HHHHHHHHHH----HHH
Confidence            4444444                    444444555444432   121      1111111  1111111111    222


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhc-CChHHHHHHHHHHHh
Q 044988          405 MPMKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAA-KRWQDVAAVRQKMIK  475 (538)
Q Consensus       405 ~~~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~-g~~~~A~~~~~~m~~  475 (538)
                      ....++......+. .+ ..|+.++|++.++++ .+..|++..... .+...+.+. +++++|.++|.+..+
T Consensus       131 ~~~~~~~~i~~~l~-~l-~~~~~~~A~~~~~~a-l~~~p~~~~~~~-~l~~~~~~~~~~~~~a~~~f~~a~~  198 (281)
T 2c2l_A          131 RRIHQESELHSYLT-RL-IAAERERELEECQRN-HEGHEDDGHIRA-QQACIEAKHDKYMADMDELFSQVDE  198 (281)
T ss_dssp             TCCCCCCHHHHHHH-HH-HHHHHHHHHTTTSGG-GTTTSCHHHHTH-HHHHHHHHHHHHHHHHHHHHHHSSC
T ss_pred             HHHhhhHHHHHHHH-HH-HHHHHHHHHHHHHhh-hccccchhhhhh-HHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            23334444433332 22 368889999999998 888898876445 666666665 678899999988765

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.56  E-value=1e-06  Score=72.52  Aligned_cols=126  Identities=10%  Similarity=-0.017  Sum_probs=104.0

Q ss_pred             HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHH
Q 044988          344 LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLG  420 (538)
Q Consensus       344 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~  420 (538)
                      ..+..+...+...|+++.|...|++..+.   .| +..++..+..++...|++++|.+.+++..  .+.+...+..+...
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~---~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~   90 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIEL---NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHH
Confidence            34555666677778999999999998875   34 57889999999999999999999998874  33457888899999


Q ss_pred             HHhcCCHHHHHHHHHHchhccCCCCcccHHHHHH--HHHHhcCChHHHHHHHHHHH
Q 044988          421 CRIHNNAELASQVAQKLVAEIDPEQAAGYLALVA--NVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       421 ~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~--~~~~~~g~~~~A~~~~~~m~  474 (538)
                      +...|++++|...++++ ....|++...+. .+.  ..+.+.|++++|++.+++..
T Consensus        91 ~~~~~~~~~A~~~~~~a-~~~~p~~~~~~~-~~~~~~~~~~~~~~~~A~~~~~~~~  144 (166)
T 1a17_A           91 NMALGKFRAALRDYETV-VKVKPHDKDAKM-KYQECNKIVKQKAFERAIAGDEHKR  144 (166)
T ss_dssp             HHHTTCHHHHHHHHHHH-HHHSTTCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHHHHHHHHHHHHHHcccchH
Confidence            99999999999999999 889999887664 444  44788899999999998775

>1hh8_A P67PHOX, NCF-2, neutrophil cytosol factor 2; cell cycle, phagocyte oxidase factor, SH3 domain, repeat, TPR repeat cell cycle; HET: FLC; 1.8A {Homo sapiens} SCOP: a.118.8.1 PDB: 1wm5_A 1e96_B*

Probab=98.56  E-value=2.8e-06  Score=73.27  Aligned_cols=130  Identities=11%  Similarity=-0.080  Sum_probs=102.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCh
Q 044988          190 WNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDL  269 (538)
Q Consensus       190 ~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~  269 (538)
                      +..+...+...|++++|...|++...++...|..+...|...|++++|+..|++..+.. +.+...+..+..++...|++
T Consensus         9 ~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~   87 (213)
T 1hh8_A            9 LWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKY   87 (213)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcccH
Confidence            44556677788888888888888887888888888899999999999999999888753 34567788888888899999


Q ss_pred             HHHHHHHHHHHHhccCC-----------CCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          270 KLGKWIHSYVEENFSVG-----------REPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       270 ~~a~~~~~~~~~~~~~~-----------~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      +.|...++.+.+.....           ..+.....+..+..+|...|++++|...|++..+
T Consensus        88 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  149 (213)
T 1hh8_A           88 DLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  149 (213)
T ss_dssp             HHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence            99999998888851110           0112336777899999999999999999998776

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.55  E-value=2.4e-06  Score=73.64  Aligned_cols=174  Identities=14%  Similarity=0.016  Sum_probs=101.9

Q ss_pred             HHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhh
Q 044988          101 KSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFD  180 (538)
Q Consensus       101 ~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~  180 (538)
                      +|++.|++..+.   -+...+..+...+...+++++|...|++..+.|   +...+..|...|...|.....++|...|+
T Consensus         4 eA~~~~~~aa~~---g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~   77 (212)
T 3rjv_A            4 EPGSQYQQQAEA---GDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIRNPQQADYPQARQLAE   77 (212)
T ss_dssp             CTTHHHHHHHHT---TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTSSTTSCCHHHHHHHHH
T ss_pred             hHHHHHHHHHHC---CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence            344555555543   244455555555555666666666666665544   34445555555555111111566666655


Q ss_pred             cCCCC-CchhHHHHHHHHHh----cCCHHHHHHHHccCCCC-C----hHHHHHHHHHHHH----cCCHHHHHHHHHHHHH
Q 044988          181 DMPAR-SVVSWNSLLKGYVK----RGDIDGAWKIFDEMPHR-N----VVSWTTMISGCAQ----NGKSRQALSLFNEMRR  246 (538)
Q Consensus       181 ~~~~~-~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~-~----~~~~~~li~~~~~----~~~~~~a~~~~~~m~~  246 (538)
                      +..++ +...+..+...|..    .+++++|..+|++..+. +    +.++..|...|..    .+++++|+.+|++..+
T Consensus        78 ~A~~~g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~  157 (212)
T 3rjv_A           78 KAVEAGSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSS  157 (212)
T ss_dssp             HHHHTTCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHH
Confidence            54433 44455555555554    66777777777776542 2    5677777777777    6778888888888777


Q ss_pred             CCCCCCHHHHHHHHHHHHcc-C-----ChHHHHHHHHHHHHh
Q 044988          247 ARVGLDQVALVAALSACAEI-G-----DLKLGKWIHSYVEEN  282 (538)
Q Consensus       247 ~g~~p~~~~~~~li~~~~~~-~-----~~~~a~~~~~~~~~~  282 (538)
                      .  ..+...+..+...|... |     ++++|...++...+.
T Consensus       158 ~--~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~  197 (212)
T 3rjv_A          158 L--SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLE  197 (212)
T ss_dssp             T--SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHH
T ss_pred             c--CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHc
Confidence            5  22333455555555432 2     778888877777776

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.55  E-value=8.8e-07  Score=70.87  Aligned_cols=101  Identities=14%  Similarity=-0.032  Sum_probs=87.8

Q ss_pred             CCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CC-CCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          374 GIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MK-PNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       374 ~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~-p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                      .+.| +...+..+...+.+.|++++|...|++.. .. .+...|..+..++...|++++|+..++++ ..+.|+++..+.
T Consensus        12 ~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~   90 (142)
T 2xcb_A           12 GLSEDTLEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYG-ALMDINEPRFPF   90 (142)
T ss_dssp             TCCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCTHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHH-HhcCCCCcHHHH
Confidence            3456 45677788889999999999999999874 33 46788888999999999999999999999 999999999888


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          451 ALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       451 ~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                       .++.+|...|++++|.+.+++..+.
T Consensus        91 -~lg~~~~~~g~~~~A~~~~~~al~~  115 (142)
T 2xcb_A           91 -HAAECHLQLGDLDGAESGFYSARAL  115 (142)
T ss_dssp             -HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             -HHHHHHHHcCCHHHHHHHHHHHHHh
Confidence             9999999999999999999998763

>3rjv_A Putative SEL1 repeat protein; alpha-alpha superhelix, structural genomics, joint center FO structural genomics, JCSG; HET: MSE; 1.65A {Klebsiella pneumoniae subsp}

Probab=98.54  E-value=4.5e-06  Score=71.97  Aligned_cols=163  Identities=12%  Similarity=-0.006  Sum_probs=114.9

Q ss_pred             hhHHHHHHHHHHhCCCHHHHHHHHHhcCCC-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhh
Q 044988          292 VSLNNALIHMYASCGEIEEAYGVFRKMQRR-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMN  370 (538)
Q Consensus       292 ~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~  370 (538)
                      ...+..|...|...+++++|...|++..+. ++..+..+...|.. +..                ..++++|...|++..
T Consensus        18 ~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g~~~a~~~lg~~y~~-~g~----------------~~~~~~A~~~~~~A~   80 (212)
T 3rjv_A           18 RRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIR-NPQ----------------QADYPQARQLAEKAV   80 (212)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCHHHHHHHHHHTTS-STT----------------SCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHc-CCC----------------CCCHHHHHHHHHHHH
Confidence            344556777777778888888887776543 33333333333332 100                016788888888876


Q ss_pred             hhcCCCccHHHHHHHHHHhhh----cCChHHHHHHHHhCCCCCC----HHHHHHHHHHHHh----cCCHHHHHHHHHHch
Q 044988          371 QNWGIKPRIEHYGCMVDLFSR----AGLMDEAFSLVQNMPMKPN----DAVLGSLLLGCRI----HNNAELASQVAQKLV  438 (538)
Q Consensus       371 ~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~p~----~~~~~~l~~~~~~----~~~~~~A~~~~~~~~  438 (538)
                      +.    -+...+..|...|..    .+++++|.++|++.....+    ...+..|...|..    .+++++|+..|++. 
T Consensus        81 ~~----g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A-  155 (212)
T 3rjv_A           81 EA----GSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGS-  155 (212)
T ss_dssp             HT----TCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHH-
T ss_pred             HC----CCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH-
Confidence            53    256677778888877    7899999999988753333    7788888888888    78999999999999 


Q ss_pred             hccCCCCcccHHHHHHHHHHhc-C-----ChHHHHHHHHHHHhCCC
Q 044988          439 AEIDPEQAAGYLALVANVYAAA-K-----RWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       439 ~~~~p~~~~~~~~~l~~~~~~~-g-----~~~~A~~~~~~m~~~~~  478 (538)
                      .+. |.++..+. .|+.+|... |     ++++|..++++..+.|.
T Consensus       156 ~~~-~~~~~a~~-~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          156 SSL-SRTGYAEY-WAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HHT-SCTTHHHH-HHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             HHc-CCCHHHHH-HHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            666 55555577 888888764 3     89999999999887654

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.53  E-value=1.7e-06  Score=73.89  Aligned_cols=172  Identities=10%  Similarity=-0.001  Sum_probs=105.8

Q ss_pred             HhcCCHHHHHH---HHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCCh
Q 044988          198 VKRGDIDGAWK---IFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRA----RVGL-DQVALVAALSACAEIGDL  269 (538)
Q Consensus       198 ~~~g~~~~A~~---~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~~~~~~~  269 (538)
                      ...|++++|.+   ++..-+.....++..+...+...|++++|...+++..+.    +..| ....+..+...+...|++
T Consensus         3 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~   82 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNW   82 (203)
T ss_dssp             ----CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             cccccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCH
Confidence            34677777777   554433344557777888888888888888888877651    2222 244566677777888888


Q ss_pred             HHHHHHHHHHHHhccCCC-CC-cchhHHHHHHHHHHhCCCHHHHHHHHHhcCC-----CCc----chHHHHHHHHHhcCC
Q 044988          270 KLGKWIHSYVEENFSVGR-EP-VLVSLNNALIHMYASCGEIEEAYGVFRKMQR-----RNT----VSWTSMITGFAKQGY  338 (538)
Q Consensus       270 ~~a~~~~~~~~~~~~~~~-~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-----~~~----~~~~~li~~~~~~~~  338 (538)
                      +.|...+....+.....+ .+ .....+..+...+...|++++|...+++..+     .+.    .++..+...+...|+
T Consensus        83 ~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~  162 (203)
T 3gw4_A           83 DAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKN  162 (203)
T ss_dssp             HHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcC
Confidence            888888887766533223 22 2345567788888888999988888877642     111    223455556666666


Q ss_pred             ccHHHHHHHHHHHHhcccCcHHHHHHHHHHh
Q 044988          339 AQEALLTFLGVLSACSHGGFVDEGRQFFECM  369 (538)
Q Consensus       339 ~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~  369 (538)
                      +++|...+...+..+...|+......+...+
T Consensus       163 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~  193 (203)
T 3gw4_A          163 LLEAQQHWLRARDIFAELEDSEAVNELMTRL  193 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHhcc
Confidence            6666655555555555555444444443333

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.51  E-value=1.7e-05  Score=72.33  Aligned_cols=165  Identities=9%  Similarity=-0.007  Sum_probs=117.9

Q ss_pred             HHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCC
Q 044988          297 ALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIK  376 (538)
Q Consensus       297 ~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~  376 (538)
                      ..+..+...|++++|...+++..+.....-..-           .....+..+...+...|++++|...|++..+...-.
T Consensus        80 ~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~-----------~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~  148 (293)
T 3u3w_A           80 DQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQ-----------QFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTG  148 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHH-----------HHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCC
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHhccccCChHHH-----------HHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhccc
Confidence            346778899999999999998765221110000           000223345556667778999999999988642112


Q ss_pred             cc----HHHHHHHHHHhhhcCChHHHHHHHHhCC-----CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCC
Q 044988          377 PR----IEHYGCMVDLFSRAGLMDEAFSLVQNMP-----MKPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDP  443 (538)
Q Consensus       377 p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p  443 (538)
                      ++    ..+++.+...|...|++++|...|+++.     ...+    ..++..+...|.+.|++++|...++++. .+.+
T Consensus       149 ~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al-~~~~  227 (293)
T 3u3w_A          149 IDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAI-EISC  227 (293)
T ss_dssp             SCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH-HHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH-HHHH
Confidence            23    3478999999999999999999998764     1112    3477888889999999999999999994 4332


Q ss_pred             CC------cccHHHHHHHHHHhcCC-hHHHHHHHHHHH
Q 044988          444 EQ------AAGYLALVANVYAAAKR-WQDVAAVRQKMI  474 (538)
Q Consensus       444 ~~------~~~~~~~l~~~~~~~g~-~~~A~~~~~~m~  474 (538)
                      ..      ..++. .++.+|.+.|+ +++|.+.+++..
T Consensus       228 ~~~~~~~~~~~~~-~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          228 RINSMALIGQLYY-QRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HTTBCTTHHHHHH-HHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HcCcHHHHHHHHH-HHHHHHHHhCCcHHHHHHHHHHHH
Confidence            22      44566 89999999995 699999998876

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.51  E-value=1.8e-06  Score=66.92  Aligned_cols=112  Identities=18%  Similarity=0.125  Sum_probs=79.1

Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHH
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCR  422 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~  422 (538)
                      .+..+...+...|+++.|...++++.+..  +.+..++..+...+...|++++|...++++.  .+.+..++..+...+.
T Consensus        11 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~   88 (125)
T 1na0_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELD--PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYY   88 (125)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHC--cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHH
Confidence            34444555556667777788888777651  2346677788888888888888888887763  2345677777788888


Q ss_pred             hcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhc
Q 044988          423 IHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAA  460 (538)
Q Consensus       423 ~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~  460 (538)
                      ..|++++|...++++ ....|+++..+. .++.++...
T Consensus        89 ~~~~~~~A~~~~~~~-~~~~~~~~~~~~-~l~~~~~~~  124 (125)
T 1na0_A           89 KQGDYDEAIEYYQKA-LELDPNNAEAKQ-NLGNAKQKQ  124 (125)
T ss_dssp             HTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHH-HHhCCCcHHHHH-HHHHHHHhc
Confidence            888888888888888 777787777555 666665543

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.49  E-value=6.5e-07  Score=79.24  Aligned_cols=198  Identities=7%  Similarity=-0.084  Sum_probs=138.5

Q ss_pred             ccCChHHHHHHHHHHHHhccCCCCCcchhHHHHH-------HHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHh-c
Q 044988          265 EIGDLKLGKWIHSYVEENFSVGREPVLVSLNNAL-------IHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAK-Q  336 (538)
Q Consensus       265 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l-------~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~-~  336 (538)
                      ..++...|...|..+.+.     .|.....|..+       ...+.+.++..++...+.+-..-.+.+....    .. .
T Consensus        18 ~~~d~~~A~~~F~~a~~~-----dP~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~----~~~~   88 (282)
T 4f3v_A           18 LPMSEARSLDLFTEITNY-----DESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNAR----IAIG   88 (282)
T ss_dssp             TTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCE----EECC
T ss_pred             cCCCHHHHHHHHHHHHHh-----ChhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhh----hccC
Confidence            578889999999999887     78888888777       4556555555666656655544111111000    00 1


Q ss_pred             CCc-------cHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCC
Q 044988          337 GYA-------QEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKP  409 (538)
Q Consensus       337 ~~~-------~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p  409 (538)
                      |-+       .............+...|++++|.++|..+...   .|+......+...+.+.+++++|+..|+.....|
T Consensus        89 g~y~~~~~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~---~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~  165 (282)
T 4f3v_A           89 GLYGDITYPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVA---GSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP  165 (282)
T ss_dssp             TTTCCCEEECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCT---TCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS
T ss_pred             CcccccccccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---CCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC
Confidence            111       001123334445566677999999999988754   5654477777778999999999999999775444


Q ss_pred             CH----HHHHHHHHHHHhcCCHHHHHHHHHHchhccC--CC-CcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          410 ND----AVLGSLLLGCRIHNNAELASQVAQKLVAEID--PE-QAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       410 ~~----~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~--p~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      +.    ..+..+..++...|++++|+..|++. ....  |. ...... .++.++.+.|+.++|..+|+++...
T Consensus       166 d~~~~~~a~~~LG~al~~LG~~~eAl~~l~~a-~~g~~~P~~~~da~~-~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          166 DKFLAGAAGVAHGVAAANLALFTEAERRLTEA-NDSPAGEACARAIAW-YLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HTSTTTTTTHHHHHH-HHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CcccHHHHHHHHHHHHHHCCCHHHHHHHHHHH-hcCCCCccccHHHHH-HHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            33    36777888899999999999999998 4332  54 333456 7888999999999999999999874

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.49  E-value=8.3e-07  Score=82.70  Aligned_cols=124  Identities=12%  Similarity=-0.007  Sum_probs=100.7

Q ss_pred             HHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc----------------HHHHHHHHHHhhhcCChHHHHHHHHhCC-C-
Q 044988          346 FLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR----------------IEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-  407 (538)
Q Consensus       346 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~----------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-  407 (538)
                      +..+...+...|++++|...|++..+.   .|+                ..+|..+..+|.+.|++++|+..+++.. . 
T Consensus       150 ~~~~g~~~~~~g~~~~A~~~y~~Al~~---~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  226 (336)
T 1p5q_A          150 VKERGTVYFKEGKYKQALLQYKKIVSW---LEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELD  226 (336)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHH---TTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHH---hhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            334444455555777777777777655   333                4789999999999999999999999874 3 


Q ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHH-HHHHHHHH
Q 044988          408 KPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDV-AAVRQKMI  474 (538)
Q Consensus       408 ~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A-~~~~~~m~  474 (538)
                      +.+...|..+..++...|++++|+..|+++ ..+.|++...+. .++.++.+.|++++| ..++++|.
T Consensus       227 p~~~~a~~~lg~~~~~~g~~~~A~~~~~~a-l~l~P~~~~a~~-~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          227 SNNEKGLSRRGEAHLAVNDFELARADFQKV-LQLYPNNKAAKT-QLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCSSCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHCCCHHHHHHHHHHH-HHHCCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345788999999999999999999999999 999999999788 999999999999998 44666664

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=98.48  E-value=7.7e-06  Score=74.58  Aligned_cols=161  Identities=11%  Similarity=-0.048  Sum_probs=111.8

Q ss_pred             HHHHHHhcCCHHHHHHHHccCCC-----CCh----HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC-CC----HHHHHH
Q 044988          193 LLKGYVKRGDIDGAWKIFDEMPH-----RNV----VSWTTMISGCAQNGKSRQALSLFNEMRRARVG-LD----QVALVA  258 (538)
Q Consensus       193 li~~~~~~g~~~~A~~~~~~m~~-----~~~----~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-p~----~~~~~~  258 (538)
                      .+..+...|++++|...+++..+     ++.    ..+..+...+...+++++|+..|++..+.... ++    ..+++.
T Consensus        81 ~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~  160 (293)
T 3u3w_A           81 QVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENA  160 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHH
Confidence            46677888999999999887543     121    12334666677778999999999999874322 22    336888


Q ss_pred             HHHHHHccCChHHHHHHHHHHHHhccCC--CCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC----C-C----cchHH
Q 044988          259 ALSACAEIGDLKLGKWIHSYVEENFSVG--REPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR----R-N----TVSWT  327 (538)
Q Consensus       259 li~~~~~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~----~-~----~~~~~  327 (538)
                      +...|...|+++.|...++.+.+.....  ..+....++..+...|.+.|++++|...+++..+    . +    ...|.
T Consensus       161 lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~  240 (293)
T 3u3w_A          161 IANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYY  240 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHH
Confidence            8889999999999999999888643211  2233445778899999999999999999987653    1 1    34566


Q ss_pred             HHHHHHHhcCC-ccHHHHHHHHHHHHh
Q 044988          328 SMITGFAKQGY-AQEALLTFLGVLSAC  353 (538)
Q Consensus       328 ~li~~~~~~~~-~~~a~~~~~~ll~~~  353 (538)
                      .+...|.+.|+ .++|...|...+..+
T Consensus       241 ~lg~~~~~~g~~~~~A~~~~~~Al~i~  267 (293)
T 3u3w_A          241 QRGECLRKLEYEEAEIEDAYKKASFFF  267 (293)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCcHHHHHHHHHHHHHHH
Confidence            66777777774 366664444444333

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.48  E-value=5.5e-06  Score=75.53  Aligned_cols=170  Identities=8%  Similarity=-0.028  Sum_probs=98.6

Q ss_pred             hHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCc------chHHHHHHHHHccCCcHHHHHHHHHHHHhCCC---Cc--h
Q 044988           85 IWNQMIRGHARSETPEKSVYLYKQMIDKETEPDE------YTYSFLLSVCARCGLFREGEQVHGRVLASGYC---SN--V  153 (538)
Q Consensus        85 ~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~------~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~---~~--~  153 (538)
                      .+...+..+...|++++|.+.+++..+..- .+.      ..+..+...+...|++++|...+++..+....   +.  .
T Consensus        77 ~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~  155 (293)
T 2qfc_A           77 QFKDQVIMLCKQKRYKEIYNKVWNELKKEE-YHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNL  155 (293)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCC-CCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhcccc-CChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHH
Confidence            444556677778888888888877766421 111      12233444556667777777777777653211   11  2


Q ss_pred             hHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCC---ChHHHHHHHHHHHH
Q 044988          154 FIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR---NVVSWTTMISGCAQ  230 (538)
Q Consensus       154 ~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~li~~~~~  230 (538)
                      .+++.+...|...|+   +++|...|++                        |+++++..+..   ...+|..+...|..
T Consensus       156 ~~~~~lg~~y~~~~~---~~~A~~~~~k------------------------al~~~~~~~~~~~~~~~~~~nlg~~y~~  208 (293)
T 2qfc_A          156 YIENAIANIYAENGY---LKKGIDLFEQ------------------------ILKQLEALHDNEEFDVKVRYNHAKALYL  208 (293)
T ss_dssp             HHHHHHHHHHHHTTC---HHHHHHHHHH------------------------HHHHHHHSCCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCC---HHHHHHHHHH------------------------HHHHHHhcCccccchHHHHHhHHHHHHH
Confidence            355556666666666   5555555432                        22222322221   12467777788888


Q ss_pred             cCCHHHHHHHHHHHHHC----CCCCC-HHHHHHHHHHHHccCChHHH-HHHHHHHHHh
Q 044988          231 NGKSRQALSLFNEMRRA----RVGLD-QVALVAALSACAEIGDLKLG-KWIHSYVEEN  282 (538)
Q Consensus       231 ~~~~~~a~~~~~~m~~~----g~~p~-~~~~~~li~~~~~~~~~~~a-~~~~~~~~~~  282 (538)
                      .|++++|+..+++..+.    +.... ..+|..+..++.+.|+.++| ...++.....
T Consensus       209 ~~~y~~Al~~~~kal~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~~  266 (293)
T 2qfc_A          209 DSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKASFF  266 (293)
T ss_dssp             TTCHHHHHHHHHHHHHHHHHTTBCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence            88888888888877642    11111 45666677777777777777 5556555443

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.47  E-value=6.5e-07  Score=74.79  Aligned_cols=120  Identities=8%  Similarity=0.080  Sum_probs=99.0

Q ss_pred             cccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHH-HHhcCCH--H
Q 044988          354 SHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLG-CRIHNNA--E  428 (538)
Q Consensus       354 ~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~-~~~~~~~--~  428 (538)
                      ...|++++|...++...+..  +.+...|..+...|...|++++|...|++.. . +.+...+..+... +...|++  +
T Consensus        21 ~~~~~~~~A~~~~~~al~~~--p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRAN--PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             C-----CCCCHHHHHHHHHC--CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hhccCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchH
Confidence            44578888899999888652  3367899999999999999999999999874 2 3357778888888 7789998  9


Q ss_pred             HHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 044988          429 LASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       429 ~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                      +|...++++ ....|++...+. .++.+|...|++++|...+++..+..
T Consensus        99 ~A~~~~~~a-l~~~p~~~~~~~-~la~~~~~~g~~~~A~~~~~~al~~~  145 (177)
T 2e2e_A           99 QTRAMIDKA-LALDSNEITALM-LLASDAFMQANYAQAIELWQKVMDLN  145 (177)
T ss_dssp             HHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHH-HHhCCCcHHHHH-HHHHHHHHcccHHHHHHHHHHHHhhC
Confidence            999999999 899999998788 99999999999999999999998743

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.46  E-value=1.9e-05  Score=71.51  Aligned_cols=231  Identities=10%  Similarity=0.073  Sum_probs=110.6

Q ss_pred             ChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccC--ChhHHHHHHhcCC---CCCcchHHHHHHHH----hcC---CCc
Q 044988           32 TTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSG--YLINAHKVFEKTE---NPSTAIWNQMIRGH----ARS---ETP   99 (538)
Q Consensus        32 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~~~a~~~~~~~~---~~~~~~~~~li~~~----~~~---~~~   99 (538)
                      ..++|....+.++...+. ...+|+.--.++...|  ++++++.+++.+.   +.+..+|+.-...+    ...   +++
T Consensus        48 ~s~~aL~~t~~~L~~nP~-~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~~~  126 (306)
T 3dra_A           48 YSERALHITELGINELAS-HYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDFDP  126 (306)
T ss_dssp             CSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCCCT
T ss_pred             CCHHHHHHHHHHHHHCcH-HHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccCCH
Confidence            334566666666655422 3344555555555555  5666666665544   22333444433333    333   455


Q ss_pred             hHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcH--HHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHH
Q 044988          100 EKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFR--EGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARL  177 (538)
Q Consensus       100 ~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~--~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~  177 (538)
                      ++++.+++.+.+.. +-|-.+|+.-.-.+.+.|.++  ++.+.++++++.. +.|...|+....+..+.+.   ..    
T Consensus       127 ~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d-~~N~sAW~~R~~ll~~l~~---~~----  197 (306)
T 3dra_A          127 YREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTD-LKNNSAWSHRFFLLFSKKH---LA----  197 (306)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHSSGG---GC----
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccc---cc----
Confidence            56666666555532 234445555444445555554  5555555555543 3333344333333222221   00    


Q ss_pred             HhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHH-HHHHHHHHHHCC--CCC
Q 044988          178 LFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQ-ALSLFNEMRRAR--VGL  251 (538)
Q Consensus       178 ~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~-a~~~~~~m~~~g--~~p  251 (538)
                                           ....++++++.+++...   .|...|+-+-..+.+.|+... +..+..+..+.+  -..
T Consensus       198 ---------------------~~~~~~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~  256 (306)
T 3dra_A          198 ---------------------TDNTIDEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVT  256 (306)
T ss_dssp             ---------------------CHHHHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEES
T ss_pred             ---------------------hhhhHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCC
Confidence                                 00004455555544331   344556666555555555333 333444443321  123


Q ss_pred             CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHH
Q 044988          252 DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNA  297 (538)
Q Consensus       252 ~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  297 (538)
                      +...+..+...+.+.|+.++|..+++.+.+.    -.|.....|+.
T Consensus       257 s~~al~~la~~~~~~~~~~~A~~~~~~l~~~----~Dpir~~yW~~  298 (306)
T 3dra_A          257 SSFALETLAKIYTQQKKYNESRTVYDLLKSK----YNPIRSNFWDY  298 (306)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT----TCGGGHHHHHH
T ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHHHhc----cChHHHHHHHH
Confidence            4555556666666666666666666666553    35555555543

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.45  E-value=2.7e-06  Score=66.51  Aligned_cols=115  Identities=10%  Similarity=-0.026  Sum_probs=89.7

Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHH
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCR  422 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~  422 (538)
                      .+..+...+...|+++.|...|++.....  +.+...+..+...+...|++++|.+.+++..  .+.+...+..+...+.
T Consensus        14 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (131)
T 2vyi_A           14 RLKTEGNEQMKVENFEAAVHFYGKAIELN--PANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLALS   91 (131)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHHHHH
Confidence            44555566666778888888888887651  2357788888889999999999999988763  2334777888888899


Q ss_pred             hcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCCh
Q 044988          423 IHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRW  463 (538)
Q Consensus       423 ~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~  463 (538)
                      ..|++++|...++++ ....|++...+. .++.++.+.|++
T Consensus        92 ~~~~~~~A~~~~~~~-~~~~p~~~~~~~-~l~~~~~~~~~~  130 (131)
T 2vyi_A           92 SLNKHVEAVAYYKKA-LELDPDNETYKS-NLKIAELKLREA  130 (131)
T ss_dssp             HTTCHHHHHHHHHHH-HHHSTTCHHHHH-HHHHHHHHHTTC
T ss_pred             HhCCHHHHHHHHHHH-HhcCccchHHHH-HHHHHHHHHhcC
Confidence            999999999999998 888888887677 888888877765

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.43  E-value=5.9e-06  Score=75.32  Aligned_cols=170  Identities=8%  Similarity=-0.078  Sum_probs=107.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHccCCC---CCh------HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC---CCC--HHH
Q 044988          190 WNSLLKGYVKRGDIDGAWKIFDEMPH---RNV------VSWTTMISGCAQNGKSRQALSLFNEMRRARV---GLD--QVA  255 (538)
Q Consensus       190 ~~~li~~~~~~g~~~~A~~~~~~m~~---~~~------~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~---~p~--~~~  255 (538)
                      +...+..+...|++++|.+.+.+..+   ...      ..+..+...+...|++++|+..|++..+...   .+.  ..+
T Consensus        78 l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  157 (293)
T 2qfc_A           78 FKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYI  157 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHHHH
Confidence            33455566677777777777654321   111      1234455666777888999988888775321   122  447


Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCc--chhHHHHHHHHHHhCCCHHHHHHHHHhcCC--CC-------cc
Q 044988          256 LVAALSACAEIGDLKLGKWIHSYVEENFSVGREPV--LVSLNNALIHMYASCGEIEEAYGVFRKMQR--RN-------TV  324 (538)
Q Consensus       256 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~~-------~~  324 (538)
                      +..+...|...|+++.|...++.+.+.........  ...++..+...|...|++++|...+++..+  ++       ..
T Consensus       158 ~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~~~  237 (293)
T 2qfc_A          158 ENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQ  237 (293)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHHHH
Confidence            77888888888999999888888774321111111  225777888999999999999998887653  11       34


Q ss_pred             hHHHHHHHHHhcCCccHH-HHHHHHHHHHhcccCcH
Q 044988          325 SWTSMITGFAKQGYAQEA-LLTFLGVLSACSHGGFV  359 (538)
Q Consensus       325 ~~~~li~~~~~~~~~~~a-~~~~~~ll~~~~~~~~~  359 (538)
                      +|..+...|...|+.++| ...|...+..+...++.
T Consensus       238 ~~~~lg~~y~~~g~~~~Ai~~~~~~Al~~~~~~~~~  273 (293)
T 2qfc_A          238 LYYQRGECLRKLEYEEAEIEDAYKKASFFFDILEMH  273 (293)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhCcH
Confidence            667777777788877777 44444444444333433

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.42  E-value=1.9e-06  Score=67.21  Aligned_cols=95  Identities=13%  Similarity=-0.014  Sum_probs=76.8

Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ...+..+...+.+.|++++|+..|++..  .+.+...|..+..++...|++++|+..++++ ..+.|++...+. .++.+
T Consensus         4 a~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~a-l~~~p~~~~~~~-~lg~~   81 (126)
T 3upv_A            4 AEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKA-IEKDPNFVRAYI-RKATA   81 (126)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHH-HHhCCCcHHHHH-HHHHH
Confidence            4566777778888888888888887763  2335677888888888888888888888888 888888888777 88888


Q ss_pred             HHhcCChHHHHHHHHHHHh
Q 044988          457 YAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       457 ~~~~g~~~~A~~~~~~m~~  475 (538)
                      |...|++++|...+++..+
T Consensus        82 ~~~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           82 QIAVKEYASALETLDAART  100 (126)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhCHHHHHHHHHHHHH
Confidence            8888888888888888775

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.41  E-value=2.9e-06  Score=66.58  Aligned_cols=110  Identities=10%  Similarity=-0.016  Sum_probs=73.8

Q ss_pred             HHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHh
Q 044988          347 LGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRI  423 (538)
Q Consensus       347 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~  423 (538)
                      ..+...+...|++++|...|++..+.   .| +...+..+..+|...|++++|.+.+++..  ...+...+..+...+..
T Consensus        20 ~~~~~~~~~~~~~~~A~~~~~~al~~---~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~   96 (133)
T 2lni_A           20 KNKGNECFQKGDYPQAMKHYTEAIKR---NPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRKAAALEA   96 (133)
T ss_dssp             HHHHHHHHHTTCSHHHHHHHHHHHTT---CTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHc---CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCchHHHHHHHHHHHH
Confidence            33344444455666677777776643   34 56677777777777888888877777653  22346677777777777


Q ss_pred             cCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcC
Q 044988          424 HNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAK  461 (538)
Q Consensus       424 ~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g  461 (538)
                      .|++++|.+.++++ ....|.+...+. .++.++.+.|
T Consensus        97 ~~~~~~A~~~~~~~-~~~~p~~~~~~~-~l~~~~~~~~  132 (133)
T 2lni_A           97 MKDYTKAMDVYQKA-LDLDSSCKEAAD-GYQRCMMAQY  132 (133)
T ss_dssp             TTCHHHHHHHHHHH-HHHCGGGTHHHH-HHHHHHHHHT
T ss_pred             HhhHHHHHHHHHHH-HHhCCCchHHHH-HHHHHHHHhc
Confidence            78888888888877 777777766566 6666666554

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.38  E-value=8.2e-06  Score=65.64  Aligned_cols=83  Identities=6%  Similarity=-0.045  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHH
Q 044988          254 VALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMI  330 (538)
Q Consensus       254 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li  330 (538)
                      ..+..+...+.+.|++++|...|+.+.+.     .|.+...|..+..+|...|++++|...|++..+   .++..|..+.
T Consensus        37 ~~~~~lg~~~~~~g~~~eA~~~~~~al~~-----~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~lg  111 (151)
T 3gyz_A           37 DDIYSYAYDFYNKGRIEEAEVFFRFLCIY-----DFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTG  111 (151)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHHHH
Confidence            34555566667777777777777777776     666777777777777777777777777776653   3455666666


Q ss_pred             HHHHhcCCccH
Q 044988          331 TGFAKQGYAQE  341 (538)
Q Consensus       331 ~~~~~~~~~~~  341 (538)
                      .+|...|++++
T Consensus       112 ~~~~~lg~~~e  122 (151)
T 3gyz_A          112 QCQLRLKAPLK  122 (151)
T ss_dssp             HHHHHTTCHHH
T ss_pred             HHHHHcCCHHH
Confidence            66666653333

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.38  E-value=2e-06  Score=65.14  Aligned_cols=99  Identities=10%  Similarity=-0.086  Sum_probs=84.4

Q ss_pred             cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCC--CcccHHHHH
Q 044988          378 RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPE--QAAGYLALV  453 (538)
Q Consensus       378 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~--~~~~~~~~l  453 (538)
                      +...+..+...+...|++++|...+++..  ...+...+..+...+...|++++|...++++ ....|+  +...+. .+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a-~~~~~~~~~~~~~~-~l   82 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYV-INVIEDEYNKDVWA-AK   82 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHTSCCTTCHHHHH-HH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHH-HHhCcccchHHHHH-HH
Confidence            35567778888899999999999998763  2345778888888999999999999999999 888898  888777 89


Q ss_pred             HHHHHhc-CChHHHHHHHHHHHhCCC
Q 044988          454 ANVYAAA-KRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       454 ~~~~~~~-g~~~~A~~~~~~m~~~~~  478 (538)
                      +.++.+. |++++|.+.+++......
T Consensus        83 ~~~~~~~~~~~~~A~~~~~~~~~~~p  108 (112)
T 2kck_A           83 ADALRYIEGKEVEAEIAEARAKLEHH  108 (112)
T ss_dssp             HHHHTTCSSCSHHHHHHHHHHGGGCC
T ss_pred             HHHHHHHhCCHHHHHHHHHHHhhccc
Confidence            9999999 999999999999987544

>2c2l_A CHIP, carboxy terminus of HSP70-interacting protein; chaperone, E3 ligase, ubiquitinylation, TPR, heat-shock protein complex; 3.3A {Mus musculus} SCOP: a.118.8.1 g.44.1.2

Probab=98.37  E-value=1.4e-06  Score=78.81  Aligned_cols=96  Identities=8%  Similarity=0.005  Sum_probs=60.5

Q ss_pred             ChhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHH
Q 044988           51 KNYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSV  127 (538)
Q Consensus        51 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  127 (538)
                      +...+..+...+.+.|++++|+..|++..   +.+...|..+..++.+.|++++|+..+++..+.. +-+...+..+..+
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~   81 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQC   81 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            34455566666666677777777666544   2345566666666777777777777777666532 2234566666666


Q ss_pred             HHccCCcHHHHHHHHHHHHh
Q 044988          128 CARCGLFREGEQVHGRVLAS  147 (538)
Q Consensus       128 ~~~~~~~~~a~~~~~~~~~~  147 (538)
                      +...|++++|...+++..+.
T Consensus        82 ~~~~g~~~~A~~~~~~al~l  101 (281)
T 2c2l_A           82 QLEMESYDEAIANLQRAYSL  101 (281)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh
Confidence            77777777777777666654

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.36  E-value=3e-05  Score=68.58  Aligned_cols=123  Identities=8%  Similarity=-0.062  Sum_probs=70.4

Q ss_pred             hHHHHHHHhcCCCCChhHHHHHhhcCCCC--CchhHHHHHHHHHhcCCHHHHHHHHccCCC-CC----hHHHHHHHHHHH
Q 044988          157 TNLMNLYLMSGGECGVGCARLLFDDMPAR--SVVSWNSLLKGYVKRGDIDGAWKIFDEMPH-RN----VVSWTTMISGCA  229 (538)
Q Consensus       157 ~~l~~~~~~~g~~~~~~~a~~~~~~~~~~--~~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~~----~~~~~~li~~~~  229 (538)
                      ..+..++...|+   +++|.++|+.+...  +......+...+.+.+++++|+..|+.... ++    ...+..+..++.
T Consensus       106 LayA~~L~~~g~---y~eA~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~al~  182 (282)
T 4f3v_A          106 MGFAACEAAQGN---YADAMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVAAA  182 (282)
T ss_dssp             HHHHHHHHHHTC---HHHHHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCC---HHHHHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHHHH
Confidence            345556666666   77777777666542  112344444456666777777777765443 21    224556666677


Q ss_pred             HcCCHHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          230 QNGKSRQALSLFNEMRRARVGLD--QVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       230 ~~~~~~~a~~~~~~m~~~g~~p~--~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      ..|++++|+..|++.......|.  .........++.+.|+.++|..+|+.+...
T Consensus       183 ~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~  237 (282)
T 4f3v_A          183 NLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT  237 (282)
T ss_dssp             HTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            77777777777776653322143  223344444556666666666666666665

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.34  E-value=5.5e-06  Score=64.01  Aligned_cols=111  Identities=14%  Similarity=0.136  Sum_probs=69.8

Q ss_pred             hhHHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHH
Q 044988           52 NYILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVC  128 (538)
Q Consensus        52 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  128 (538)
                      ...+..+...+...|++++|.+.|++..   +.+...+..+...+.+.|++++|...|+++.+.. +.+..++..+...+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~   87 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAY   87 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHH
Confidence            3456666666667777777777766554   2344566666777777777777777777776542 33455666777777


Q ss_pred             HccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHH
Q 044988          129 ARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYL  164 (538)
Q Consensus       129 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  164 (538)
                      ...|++++|...++++.+.. +.+...+..+..++.
T Consensus        88 ~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~  122 (125)
T 1na0_A           88 YKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNAKQ  122 (125)
T ss_dssp             HHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHH
Confidence            77777777777777776654 334444444444443

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=98.33  E-value=5e-06  Score=65.79  Aligned_cols=98  Identities=10%  Similarity=0.020  Sum_probs=85.8

Q ss_pred             ccHHHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHH
Q 044988          377 PRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVA  454 (538)
Q Consensus       377 p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~  454 (538)
                      .+...+..+...+...|++++|...|++.. . +.+...|..+...+...|++++|...++++ ....|++...+. .++
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a-l~~~p~~~~~~~-~l~   84 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRA-LELDGQSVKAHF-FLG   84 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHH-HHhCchhHHHHH-HHH
Confidence            457788899999999999999999998863 2 344788888889999999999999999999 889999998788 999


Q ss_pred             HHHHhcCChHHHHHHHHHHHhC
Q 044988          455 NVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       455 ~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      .+|...|++++|...+++..+.
T Consensus        85 ~~~~~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           85 QCQLEMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHH
Confidence            9999999999999999998753

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.33  E-value=3.5e-06  Score=69.22  Aligned_cols=95  Identities=13%  Similarity=0.098  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ...+..+...+.+.|++++|++.|++.. ..| +...|..+..++...|++++|+..++++ ..+.|++...+. .++.+
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~-~lg~~   88 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSIAPANPIYLSNRAAAYSASGQHEKAAEDAELA-TVVDPKYSKAWS-RLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHccCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHH
Confidence            3444445555555555555555555442 122 3444455555555555555555555555 555555555444 55555


Q ss_pred             HHhcCChHHHHHHHHHHHh
Q 044988          457 YAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       457 ~~~~g~~~~A~~~~~~m~~  475 (538)
                      |...|++++|...|++..+
T Consensus        89 ~~~~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKGIE  107 (164)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHHH
Confidence            5555555555555555543

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.31  E-value=2.3e-06  Score=66.17  Aligned_cols=94  Identities=14%  Similarity=-0.013  Sum_probs=82.2

Q ss_pred             HHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHH
Q 044988          381 HYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYA  458 (538)
Q Consensus       381 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~  458 (538)
                      .+..+...+.+.|++++|...|++.. ..| +...|..+..++...|++++|+..++++ ..+.|++...+. .++.+|.
T Consensus        19 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a-l~l~P~~~~~~~-~la~~~~   96 (121)
T 1hxi_A           19 NPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHA-RMLDPKDIAVHA-ALAVSHT   96 (121)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHH
Confidence            45667778889999999999998874 344 5788888888999999999999999999 999999999888 9999999


Q ss_pred             hcCChHHHHHHHHHHHhC
Q 044988          459 AAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       459 ~~g~~~~A~~~~~~m~~~  476 (538)
                      +.|++++|+..+++..+.
T Consensus        97 ~~g~~~~A~~~~~~al~~  114 (121)
T 1hxi_A           97 NEHNANAALASLRAWLLS  114 (121)
T ss_dssp             HHHHHHHHHHHHHHHHC-
T ss_pred             HcCCHHHHHHHHHHHHHh
Confidence            999999999999998864

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=98.30  E-value=2.3e-06  Score=72.96  Aligned_cols=128  Identities=12%  Similarity=-0.043  Sum_probs=91.1

Q ss_pred             HHHHHhcccCcHHHHHHHHHHhhhhcCCCcc--------------HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCH
Q 044988          348 GVLSACSHGGFVDEGRQFFECMNQNWGIKPR--------------IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPND  411 (538)
Q Consensus       348 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~--------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~  411 (538)
                      .+...+...|++++|...|++..+...-.|+              ..+|..+..+|.+.|++++|+..+++..  .+.+.
T Consensus        43 ~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~  122 (198)
T 2fbn_A           43 EEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNV  122 (198)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccH
Confidence            3344445556777777777777654211221              2788889999999999999999998874  33457


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHH-HHHHHHHhCC
Q 044988          412 AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVA-AVRQKMIKMG  477 (538)
Q Consensus       412 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~-~~~~~m~~~~  477 (538)
                      ..+..+..++...|++++|...|+++ ..+.|++...+. .+..++...|+.+++. ..++.|...+
T Consensus       123 ~~~~~lg~~~~~~~~~~~A~~~~~~a-l~~~p~~~~~~~-~l~~~~~~~~~~~~~~~~~~~~~f~~~  187 (198)
T 2fbn_A          123 KALYKLGVANMYFGFLEEAKENLYKA-ASLNPNNLDIRN-SYELCVNKLKEARKKDKLTFGGMFDKG  187 (198)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHH-HHHSTTCHHHHH-HHHHHHHHHHHHHC-------------
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHH-HHHCCCcHHHHH-HHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            88888999999999999999999999 999999998777 8888888888777776 5566665443

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.30  E-value=4e-06  Score=71.57  Aligned_cols=163  Identities=13%  Similarity=-0.003  Sum_probs=100.2

Q ss_pred             HccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHH
Q 044988          129 ARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWK  208 (538)
Q Consensus       129 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~  208 (538)
                      ...|++++|.++++.+.. .......++..+...+...|+   +++|...++                        +|+.
T Consensus         3 ~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~---~~~A~~~~~------------------------~al~   54 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLA-HPATASGARFMLGYVYAFMDR---FDEARASFQ------------------------ALQQ   54 (203)
T ss_dssp             ----CHHHHHHHHHHHHT-STTTHHHHHHHHHHHHHHTTC---HHHHHHHHH------------------------HHHH
T ss_pred             cccccHHHHHHHHHHhcC-ChHHHHHHHHHHHHHHHHhCc---HHHHHHHHH------------------------HHHH
Confidence            356777777775444432 112345566666666666666   666666543                        2333


Q ss_pred             HHccCCCC--ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCC--CHHHHHHHHHHHHccCChHHHHHHHHHHH
Q 044988          209 IFDEMPHR--NVVSWTTMISGCAQNGKSRQALSLFNEMRRA----RVGL--DQVALVAALSACAEIGDLKLGKWIHSYVE  280 (538)
Q Consensus       209 ~~~~m~~~--~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p--~~~~~~~li~~~~~~~~~~~a~~~~~~~~  280 (538)
                      +++....+  ...++..+...|...|++++|...+++..+.    +-.|  ....+..+...+...|++++|...++...
T Consensus        55 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al  134 (203)
T 3gw4_A           55 QAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSL  134 (203)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            33333321  2346777788888888888888888877653    2122  23446677777888889998888888776


Q ss_pred             HhccCCCCCc-chhHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 044988          281 ENFSVGREPV-LVSLNNALIHMYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       281 ~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  319 (538)
                      +.....+.+. ...++..+...+...|++++|...+++..
T Consensus       135 ~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al  174 (203)
T 3gw4_A          135 VYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRAR  174 (203)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            5422212222 23345678888889999999988887764

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.29  E-value=7.1e-06  Score=62.64  Aligned_cols=95  Identities=13%  Similarity=0.128  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ...+..+...+...|++++|...+++..  .+.+...+..+...+...|++++|...++++ ....|++...+. .++.+
T Consensus         4 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~-~~~~~~~~~~~~-~~a~~   81 (118)
T 1elw_A            4 VNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKT-VDLKPDWGKGYS-RKAAA   81 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHH-HHhCcccHHHHH-HHHHH
Confidence            3445555555666666666666665542  1224555555556666666666666666666 555666655555 66666


Q ss_pred             HHhcCChHHHHHHHHHHHh
Q 044988          457 YAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       457 ~~~~g~~~~A~~~~~~m~~  475 (538)
                      +...|++++|.+.+++..+
T Consensus        82 ~~~~~~~~~A~~~~~~~~~  100 (118)
T 1elw_A           82 LEFLNRFEEAKRTYEEGLK  100 (118)
T ss_dssp             HHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHhhHHHHHHHHHHHHH
Confidence            6666666666666666554

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.28  E-value=7.6e-06  Score=64.14  Aligned_cols=115  Identities=8%  Similarity=-0.039  Sum_probs=69.1

Q ss_pred             ChhHHHHHHHHHHccCChhHHHHHHhcCCC---CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHH
Q 044988           51 KNYILAKLLAFYVTSGYLINAHKVFEKTEN---PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSV  127 (538)
Q Consensus        51 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~  127 (538)
                      +...+..+...+...|++++|...|++..+   .+...|..+...+...|++++|+..|++..+.. +.+...+..+...
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~   93 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAA   93 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHH
Confidence            344556666666666666666666665432   244556666666667777777777777766542 2344566666666


Q ss_pred             HHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcC
Q 044988          128 CARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSG  167 (538)
Q Consensus       128 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  167 (538)
                      +...|++++|...+++..+.. +.+...+..+..++...|
T Consensus        94 ~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           94 LEAMKDYTKAMDVYQKALDLD-SSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-GGGTHHHHHHHHHHHHHT
T ss_pred             HHHHhhHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHhc
Confidence            777777777777777766653 233445555555554433

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.26  E-value=0.0002  Score=65.61  Aligned_cols=232  Identities=9%  Similarity=-0.008  Sum_probs=152.5

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHccC-ChHHHHHHHHHHHHhccCCCCCcchhHHHHH
Q 044988          221 WTTMISGCAQNGKSRQALSLFNEMRRARVGLDQV-ALVAALSACAEIG-DLKLGKWIHSYVEENFSVGREPVLVSLNNAL  298 (538)
Q Consensus       221 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~-~~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l  298 (538)
                      ++.+-....+.+..++|+++++.+..  +.|+.. .++.--..+...| .++++..+++.+.+.     .|.+..+|+.-
T Consensus        57 ~~~~r~~~~~~e~se~AL~lt~~~L~--~nP~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~-----nPKny~aW~hR  129 (349)
T 3q7a_A           57 MDYFRAIAAKEEKSERALELTEIIVR--MNPAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQ-----NLKSYQVWHHR  129 (349)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHT-----TCCCHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHH--hCchhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHh-----CCCcHHHHHHH
Confidence            33333344445566789999998887  355443 4555555555667 588999999998886     88888889888


Q ss_pred             HHHHHhC-C-CHHHHHHHHHhcCCCCc---chHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc
Q 044988          299 IHMYASC-G-EIEEAYGVFRKMQRRNT---VSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       299 ~~~~~~~-g-~~~~a~~~~~~m~~~~~---~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  373 (538)
                      ..++.+. + +++++.++++++.+.++   .+|+.-...+.+.|..+.+            ....+.++.+.++++.+..
T Consensus       130 ~wlL~~l~~~~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~------------~~~~~~eELe~~~k~I~~d  197 (349)
T 3q7a_A          130 LLLLDRISPQDPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRI------------SEAQWGSELDWCNEMLRVD  197 (349)
T ss_dssp             HHHHHHHCCSCCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCC------------CHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHhcCCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccccc------------chhhHHHHHHHHHHHHHhC
Confidence            7777776 7 88999999999987544   4444433333333322200            0012347788888888761


Q ss_pred             CCCccHHHHHHHHHHhhhcCC-------hHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCH-----------------
Q 044988          374 GIKPRIEHYGCMVDLFSRAGL-------MDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNA-----------------  427 (538)
Q Consensus       374 ~~~p~~~~~~~l~~~~~~~g~-------~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~-----------------  427 (538)
                        .-|...|+.....+.+.++       ++++++.++++.  ..-|...|+.+-..+.+.|+.                 
T Consensus       198 --p~N~SAW~~R~~lL~~l~~~~~~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~  275 (349)
T 3q7a_A          198 --GRNNSAWGWRWYLRVSRPGAETSSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLN  275 (349)
T ss_dssp             --TTCHHHHHHHHHHHTTSTTCCCCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC----
T ss_pred             --CCCHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCCccccccccccccccccc
Confidence              3378888888888888776       688888887763  344577888777777766653                 


Q ss_pred             ---HHHHHHHHHchhccC------CCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          428 ---ELASQVAQKLVAEID------PEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       428 ---~~A~~~~~~~~~~~~------p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                         .........+ ....      +..+.+.. .|+++|...|+.++|.++++.+.+
T Consensus       276 ~~~~~~~~~~~~~-~~~~~~~~~~~~s~~al~-~l~d~~~~~~~~~~a~~~~~~l~~  330 (349)
T 3q7a_A          276 PDIETVEAFGFPM-PSDPLPEDTPLPVPLALE-YLADSFIEQNRVDDAAKVFEKLSS  330 (349)
T ss_dssp             ----------CCC-CC-CCCSSCCSCCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccchhHHHHHHHH-HhcccccccCCCcHHHHH-HHHHHHHhcCCHHHHHHHHHHHHh
Confidence               2333333333 2221      34445455 899999999999999999999874

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.26  E-value=2.3e-05  Score=61.02  Aligned_cols=114  Identities=11%  Similarity=-0.002  Sum_probs=71.5

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHH
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNAL  298 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l  298 (538)
                      ..+..+...+...|++++|...|++..+.. +.+...+..+...+...|+++.|...+....+.     .|.+...+..+
T Consensus        13 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~~   86 (131)
T 2vyi_A           13 ERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICI-----DPAYSKAYGRM   86 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhc-----CccCHHHHHHH
Confidence            355566666667777777777777666532 224556666666666777777777777776665     45555666667


Q ss_pred             HHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCC
Q 044988          299 IHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGY  338 (538)
Q Consensus       299 ~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~  338 (538)
                      ...+...|++++|...|++..+   .+...+..+...+...|+
T Consensus        87 ~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           87 GLALSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhc
Confidence            7777777777777777766543   244455555555555543

>1elw_A TPR1-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, HSP70, protein binding, chaperone; 1.60A {Homo sapiens} SCOP: a.118.8.1

Probab=98.23  E-value=2.2e-05  Score=59.85  Aligned_cols=107  Identities=12%  Similarity=0.043  Sum_probs=87.4

Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHH
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGC  421 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~  421 (538)
                      .+..+...+...|++++|...|+.....   .| +...+..+...+...|++++|...+++.. ..| +...+..+..++
T Consensus         6 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~   82 (118)
T 1elw_A            6 ELKEKGNKALSVGNIDDALQCYSEAIKL---DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHH---CCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            3445556666777999999999998875   34 67888999999999999999999998874 334 578888899999


Q ss_pred             HhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          422 RIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       422 ~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ...|++++|.+.+++. ....|+++..+. .+..+
T Consensus        83 ~~~~~~~~A~~~~~~~-~~~~~~~~~~~~-~l~~~  115 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEG-LKHEANNPQLKE-GLQNM  115 (118)
T ss_dssp             HHTTCHHHHHHHHHHH-HTTCTTCHHHHH-HHHHH
T ss_pred             HHHhhHHHHHHHHHHH-HHcCCCCHHHHH-HHHHh
Confidence            9999999999999999 899999887555 55443

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.23  E-value=5e-06  Score=64.88  Aligned_cols=95  Identities=9%  Similarity=-0.003  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc-------cH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA-------GY  449 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~-------~~  449 (538)
                      ...+..+...+.+.|++++|++.|++.. ..| +...|..+..++...|++++|++.++++ .++.|+...       +|
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~a-l~~~~~~~~~~~~~a~~~   86 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKA-VEVGRETRADYKLIAKAM   86 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHH-HHhCcccchhhHHHHHHH
Confidence            3456677778888888888888887763 333 4667777788888888888888888888 666666543       34


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          450 LALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       450 ~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      . .++.++...|++++|++.|++...
T Consensus        87 ~-~lg~~~~~~~~~~~A~~~~~kal~  111 (127)
T 4gcn_A           87 S-RAGNAFQKQNDLSLAVQWFHRSLS  111 (127)
T ss_dssp             H-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             H-HHHHHHHHcCCHHHHHHHHHHHHh
Confidence            4 567777788888888888887665

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.21  E-value=1e-05  Score=64.55  Aligned_cols=97  Identities=10%  Similarity=-0.027  Sum_probs=80.8

Q ss_pred             HHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhc
Q 044988          348 GVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIH  424 (538)
Q Consensus       348 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~  424 (538)
                      .+...+...|++++|...|+.....   .| +...|..+..+|...|++++|+..|++.. ..| +...+..+..++...
T Consensus        23 ~~a~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~   99 (142)
T 2xcb_A           23 ALGFNQYQAGKWDDAQKIFQALCML---DHYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECHLQL   99 (142)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHccHHHHHHHHHHHHHh---CCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHc
Confidence            3444555667888999999998875   45 67889999999999999999999999874 333 467788888999999


Q ss_pred             CCHHHHHHHHHHchhccCCCCccc
Q 044988          425 NNAELASQVAQKLVAEIDPEQAAG  448 (538)
Q Consensus       425 ~~~~~A~~~~~~~~~~~~p~~~~~  448 (538)
                      |++++|...|+++ ....|+++..
T Consensus       100 g~~~~A~~~~~~a-l~~~p~~~~~  122 (142)
T 2xcb_A          100 GDLDGAESGFYSA-RALAAAQPAH  122 (142)
T ss_dssp             TCHHHHHHHHHHH-HHHHHTCGGG
T ss_pred             CCHHHHHHHHHHH-HHhCCCCcch
Confidence            9999999999999 8888988873

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.20  E-value=1.5e-05  Score=63.77  Aligned_cols=97  Identities=10%  Similarity=0.035  Sum_probs=76.6

Q ss_pred             cHHHHHHHHHHhhhcCChHHHHHHHHhC-CCCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHH
Q 044988          378 RIEHYGCMVDLFSRAGLMDEAFSLVQNM-PMKPN----DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLAL  452 (538)
Q Consensus       378 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~-~~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~  452 (538)
                      +...+..+...+...|++++|.+.|++. ...|+    ...|..+...+...|++++|+..++++ ....|++...+. .
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~-~~~~~~~~~~~~-~  104 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKA-IEKDGGDVKALY-R  104 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHTSCCHHHHH-H
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHH-HhhCccCHHHHH-H
Confidence            4667777888888888888888888776 34566    567777777788888888888888888 777888877677 8


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHhC
Q 044988          453 VANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       453 l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      ++.+|...|++++|...+++..+.
T Consensus       105 ~a~~~~~~~~~~~A~~~~~~al~~  128 (148)
T 2dba_A          105 RSQALEKLGRLDQAVLDLQRCVSL  128 (148)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHc
Confidence            888888888888888888887753

>2vgx_A Chaperone SYCD; alternative dimer assembly, tetratricopeptide repeat, type III secretion; HET: MLY; 1.95A {Yersinia enterocolitica} SCOP: k.38.1.1 PDB: 2vgx_B* 2vgy_A*

Probab=98.19  E-value=2e-05  Score=63.27  Aligned_cols=98  Identities=8%  Similarity=-0.060  Sum_probs=81.5

Q ss_pred             HHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHH
Q 044988          346 FLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCR  422 (538)
Q Consensus       346 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~  422 (538)
                      +..+...+...|++++|...|+.....   .| +...|..+..+|...|++++|++.|++.. ..| +...+..+..++.
T Consensus        24 ~~~~g~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~  100 (148)
T 2vgx_A           24 LYSLAFNQYQSGXYEDAHXVFQALCVL---DHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAECLL  100 (148)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHc---CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHH
Confidence            334445555666888889999998865   45 68889999999999999999999999874 334 5678888999999


Q ss_pred             hcCCHHHHHHHHHHchhccCCCCcc
Q 044988          423 IHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       423 ~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      ..|++++|...|+++ ..+.|+++.
T Consensus       101 ~~g~~~~A~~~~~~a-l~~~p~~~~  124 (148)
T 2vgx_A          101 QXGELAEAESGLFLA-QELIANXPE  124 (148)
T ss_dssp             HTTCHHHHHHHHHHH-HHHHTTCGG
T ss_pred             HcCCHHHHHHHHHHH-HHHCcCCCc
Confidence            999999999999999 888898877

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.18  E-value=3.2e-05  Score=63.28  Aligned_cols=92  Identities=7%  Similarity=-0.052  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHH
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALI  299 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~  299 (538)
                      .|..+...+...|++++|...|++..+.. +.+...+..+...+...|+++.|...+....+.     .|.+...+..+.
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~-----~~~~~~~~~~~a   88 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIEL-----DKKYIKGYYRRA   88 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CcccHHHHHHHH
Confidence            34444455555555555555555554431 123444444444444444444444444444443     233333444444


Q ss_pred             HHHHhCCCHHHHHHHHHh
Q 044988          300 HMYASCGEIEEAYGVFRK  317 (538)
Q Consensus       300 ~~~~~~g~~~~a~~~~~~  317 (538)
                      .++...|++++|...|++
T Consensus        89 ~~~~~~~~~~~A~~~~~~  106 (166)
T 1a17_A           89 ASNMALGKFRAALRDYET  106 (166)
T ss_dssp             HHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHH
Confidence            444444444444444443

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.18  E-value=1.9e-05  Score=61.36  Aligned_cols=107  Identities=8%  Similarity=-0.113  Sum_probs=86.6

Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHH
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGC  421 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~  421 (538)
                      .+......+...|++++|...|++..+.   .| +...|..+..+|.+.|++++|+..+++.. ..| +...|..+..++
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~---~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~   82 (126)
T 3upv_A            6 EARLEGKEYFTKSDWPNAVKAYTEMIKR---APEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHH
Confidence            3445556667778999999999998876   45 58899999999999999999999999874 334 477888999999


Q ss_pred             HhcCCHHHHHHHHHHchhccC------CCCcccHHHHHHHH
Q 044988          422 RIHNNAELASQVAQKLVAEID------PEQAAGYLALVANV  456 (538)
Q Consensus       422 ~~~~~~~~A~~~~~~~~~~~~------p~~~~~~~~~l~~~  456 (538)
                      ...|++++|...++++ ..+.      |++..... .+..+
T Consensus        83 ~~~~~~~~A~~~~~~a-l~~~p~~~~~p~~~~~~~-~l~~~  121 (126)
T 3upv_A           83 IAVKEYASALETLDAA-RTKDAEVNNGSSAREIDQ-LYYKA  121 (126)
T ss_dssp             HHTTCHHHHHHHHHHH-HHHHHHHHTTTTHHHHHH-HHHHH
T ss_pred             HHHhCHHHHHHHHHHH-HHhCcccCCchhHHHHHH-HHHHH
Confidence            9999999999999999 7777      77766444 44443

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.17  E-value=2.9e-05  Score=60.50  Aligned_cols=109  Identities=13%  Similarity=0.021  Sum_probs=67.6

Q ss_pred             HHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHH
Q 044988          255 ALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTSMIT  331 (538)
Q Consensus       255 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~  331 (538)
                      .+..+...+.+.|++++|...|+...+.     .|.+..+|..+..+|...|++++|.+.|++..+  | +...+..+..
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~-----~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~   84 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIEL-----DPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAK   84 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHH
Confidence            3445555666667777777777766665     566777777888888888888888888877654  1 2222222222


Q ss_pred             HHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHH
Q 044988          332 GFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGC  384 (538)
Q Consensus       332 ~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~  384 (538)
                      +             |..+..++...|++++|.+.|++..+.   .||..+...
T Consensus        85 ~-------------~~~lg~~~~~~~~~~~A~~~~~kal~~---~~~~~~~~~  121 (127)
T 4gcn_A           85 A-------------MSRAGNAFQKQNDLSLAVQWFHRSLSE---FRDPELVKK  121 (127)
T ss_dssp             H-------------HHHHHHHHHHTTCHHHHHHHHHHHHHH---SCCHHHHHH
T ss_pred             H-------------HHHHHHHHHHcCCHHHHHHHHHHHHhh---CcCHHHHHH
Confidence            2             333334555566777888888877654   455544433

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.16  E-value=2.8e-05  Score=62.17  Aligned_cols=108  Identities=7%  Similarity=-0.128  Sum_probs=86.6

Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc----HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHH
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR----IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLL  418 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~  418 (538)
                      .+..+...+...|+++.|...|++..+.   .|+    ...+..+..+|...|++++|.+.+++.. ..| +...+..+.
T Consensus        30 ~~~~~a~~~~~~~~~~~A~~~~~~a~~~---~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a  106 (148)
T 2dba_A           30 QLRKEGNELFKCGDYGGALAAYTQALGL---DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKALYRRS  106 (148)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHTS---CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHH---cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHHHHHHH
Confidence            3444455566667888999999998854   565    6788899999999999999999998863 334 577888889


Q ss_pred             HHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHH
Q 044988          419 LGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVY  457 (538)
Q Consensus       419 ~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~  457 (538)
                      .++...|++++|...++++ ....|++...+. .+..+.
T Consensus       107 ~~~~~~~~~~~A~~~~~~a-l~~~p~~~~~~~-~l~~~~  143 (148)
T 2dba_A          107 QALEKLGRLDQAVLDLQRC-VSLEPKNKVFQE-ALRNIS  143 (148)
T ss_dssp             HHHHHHTCHHHHHHHHHHH-HHHCSSCHHHHH-HHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHH-HHcCCCcHHHHH-HHHHHH
Confidence            9999999999999999999 899999887555 555543

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.16  E-value=2.8e-05  Score=63.72  Aligned_cols=103  Identities=11%  Similarity=-0.014  Sum_probs=87.0

Q ss_pred             HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHH
Q 044988          344 LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLG  420 (538)
Q Consensus       344 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~  420 (538)
                      ..+..+...+...|++++|...|++..+.   .| +...|..+..+|.+.|++++|+..|++.. ..| +...|..+..+
T Consensus        12 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~   88 (164)
T 3sz7_A           12 DKLKSEGNAAMARKEYSKAIDLYTQALSI---APANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh---CCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            34555666667777999999999998876   45 68899999999999999999999999874 334 47889999999


Q ss_pred             HHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          421 CRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       421 ~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                      +...|++++|...|+++ ..+.|++...+.
T Consensus        89 ~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~  117 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKG-IEAEGNGGSDAM  117 (164)
T ss_dssp             HHHTTCHHHHHHHHHHH-HHHHSSSCCHHH
T ss_pred             HHHccCHHHHHHHHHHH-HHhCCCchHHHH
Confidence            99999999999999999 999999988554

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.13  E-value=0.0001  Score=71.17  Aligned_cols=168  Identities=9%  Similarity=-0.082  Sum_probs=113.8

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc-
Q 044988          295 NNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW-  373 (538)
Q Consensus       295 ~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-  373 (538)
                      +..++..|...|++++|.+.+..+.+.           ....++...+..+...+-..+...|+.+.|..++....... 
T Consensus        58 l~~l~~~y~~~~~~~~a~~~~~~~~~~-----------~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  126 (434)
T 4b4t_Q           58 ILELGQLYVTMGAKDKLREFIPHSTEY-----------MMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAK  126 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHTHHH-----------HHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHH-----------HHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHH
Confidence            467899999999999999999876431           11111111111223333344455677788877777654321 


Q ss_pred             --CCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-------CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHch--hc
Q 044988          374 --GIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-------MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLV--AE  440 (538)
Q Consensus       374 --~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-------~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~--~~  440 (538)
                        +..+ -..++..|...|...|++++|..+++++.       .+|. ..++..++..|...|++++|..++++..  ..
T Consensus       127 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~  206 (434)
T 4b4t_Q          127 REKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAAN  206 (434)
T ss_dssp             HSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhh
Confidence              2233 35678889999999999999999998763       1222 4577888889999999999999999985  11


Q ss_pred             cCCCC----cccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          441 IDPEQ----AAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       441 ~~p~~----~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      ..++.    ...+. .++..+...|++++|...+.+..
T Consensus       207 ~~~~~~~~~~~~~~-~~g~~~~~~~~y~~A~~~~~~a~  243 (434)
T 4b4t_Q          207 SIYCPTQTVAELDL-MSGILHCEDKDYKTAFSYFFESF  243 (434)
T ss_dssp             HSCCCHHHHHHHHH-HHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             cCCCchHHHHHHHH-HHHHHHHHHHhHHHHHHHHHHHH
Confidence            12222    12234 67777888999999998887765

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=98.11  E-value=1.5e-05  Score=77.69  Aligned_cols=127  Identities=13%  Similarity=0.067  Sum_probs=93.6

Q ss_pred             HHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-------------cHHHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCH
Q 044988          347 LGVLSACSHGGFVDEGRQFFECMNQNWGIKP-------------RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPND  411 (538)
Q Consensus       347 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-------------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~  411 (538)
                      ......+.+.|+++.|...|++..+...-.+             ...+|..+..+|.+.|++++|+..+++.. . ..+.
T Consensus       272 ~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~  351 (457)
T 1kt0_A          272 KEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLDSANE  351 (457)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCH
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccH
Confidence            3334444455566666666666665411111             15788999999999999999999999874 3 3457


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHH-HHHHHHh
Q 044988          412 AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAA-VRQKMIK  475 (538)
Q Consensus       412 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~-~~~~m~~  475 (538)
                      ..|..+..++...|++++|+..|+++ ..+.|++..++. .++.++.+.|++++|.+ .+++|..
T Consensus       352 ~a~~~~g~a~~~~g~~~~A~~~~~~a-l~l~P~~~~a~~-~l~~~~~~~~~~~~a~~~~~~~~f~  414 (457)
T 1kt0_A          352 KGLYRRGEAQLLMNEFESAKGDFEKV-LEVNPQNKAARL-QISMCQKKAKEHNERDRRIYANMFK  414 (457)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHH-HTTC----CHHH-HHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            88999999999999999999999999 999999999888 99999999999988774 5566654

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=98.11  E-value=8.7e-06  Score=79.64  Aligned_cols=116  Identities=9%  Similarity=0.014  Sum_probs=96.2

Q ss_pred             HhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHH
Q 044988          352 ACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAE  428 (538)
Q Consensus       352 ~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~  428 (538)
                      .+...|++++|.+.|++..+.   .| +..+|..+..+|.+.|++++|++.+++.. ..| +...|..+..++...|+++
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~---~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g~~~   91 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIEL---NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFR   91 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHh---CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHH
Confidence            455678999999999999876   45 58899999999999999999999998874 344 4788899999999999999


Q ss_pred             HHHHHHHHchhccCCCCcccHHHHHHHH--HHhcCChHHHHHHHHH
Q 044988          429 LASQVAQKLVAEIDPEQAAGYLALVANV--YAAAKRWQDVAAVRQK  472 (538)
Q Consensus       429 ~A~~~~~~~~~~~~p~~~~~~~~~l~~~--~~~~g~~~~A~~~~~~  472 (538)
                      +|++.++++ .+..|++...+. .++.+  +.+.|++++|++.+++
T Consensus        92 eA~~~~~~a-l~~~p~~~~~~~-~l~~~~~~~~~g~~~~A~~~~~~  135 (477)
T 1wao_1           92 AALRDYETV-VKVKPHDKDAKM-KYQECNKIVKQKAFERAIAGDEH  135 (477)
T ss_dssp             HHHHHHHHH-HHHSTTCTTHHH-HHHHHHHHHHHHHHCCC------
T ss_pred             HHHHHHHHH-HHhCCCCHHHHH-HHHHHHHHHHHHHHHHHhccccc
Confidence            999999999 899999988777 77777  8889999999999884

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.10  E-value=1.4e-05  Score=74.35  Aligned_cols=127  Identities=11%  Similarity=-0.077  Sum_probs=71.9

Q ss_pred             HHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccH------------------HHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          345 TFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRI------------------EHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       345 ~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~------------------~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      .+..+...+...|++++|...|++....   .|+.                  ..|..+..+|.+.|++++|+..+++..
T Consensus       181 ~~~~~g~~~~~~g~~~~A~~~y~~Al~~---~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al  257 (338)
T 2if4_A          181 RRKMDGNSLFKEEKLEEAMQQYEMAIAY---MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVL  257 (338)
T ss_dssp             HHHHHHHHTCSSSCCHHHHHHHHHHHHH---SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHH---hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3445556666777777777777776654   4443                  278888999999999999999998873


Q ss_pred             -CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH-HHhcCChHHHHHHHHHHHhC
Q 044988          407 -MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV-YAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       407 -~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~-~~~~g~~~~A~~~~~~m~~~  476 (538)
                       ..| +...|..+..++...|++++|+..|+++ ..+.|++...+. .|..+ ....+..+++..+|++|...
T Consensus       258 ~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~a-l~l~p~~~~a~~-~L~~l~~~~~~~~~~a~~~~~~~l~~  328 (338)
T 2if4_A          258 TEEEKNPKALFRRGKAKAELGQMDSARDDFRKA-QKYAPDDKAIRR-ELRALAEQEKALYQKQKEMYKGIFKG  328 (338)
T ss_dssp             HHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHT-TC-------------------------------------
T ss_pred             HhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHHCCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence             334 5788888999999999999999999999 889999888676 66666 33456677888888888754

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.09  E-value=2.5e-05  Score=63.46  Aligned_cols=130  Identities=12%  Similarity=-0.017  Sum_probs=94.2

Q ss_pred             HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc----HHHHHHHHHHhhhcCChHHHHHHHHhCC----CCCC----H
Q 044988          344 LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR----IEHYGCMVDLFSRAGLMDEAFSLVQNMP----MKPN----D  411 (538)
Q Consensus       344 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~p~----~  411 (538)
                      .++..+...+...|++++|...+++..+...-.++    ..++..+...|...|++++|.+.+++..    ..++    .
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~   89 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEA   89 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHH
Confidence            44555566666677777888887776643110111    2478889999999999999999998763    1122    4


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHchhccCC------CCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          412 AVLGSLLLGCRIHNNAELASQVAQKLVAEIDP------EQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       412 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ..+..+...+...|++++|...+++.. ...+      .....+. .++.+|...|++++|.+.+++..+
T Consensus        90 ~~~~~l~~~~~~~~~~~~A~~~~~~a~-~~~~~~~~~~~~~~~~~-~la~~~~~~g~~~~A~~~~~~a~~  157 (164)
T 3ro3_A           90 QSCYSLGNTYTLLQDYEKAIDYHLKHL-AIAQELKDRIGEGRACW-SLGNAYTALGNHDQAMHFAEKHLE  157 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHH-HHHHHTTCHHHHHHHHH-HHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHH-HHHHHccchHhHHHHHH-HHHHHHHHccCHHHHHHHHHHHHH
Confidence            567777888999999999999999984 3221      1223455 788999999999999999998764

>1p5q_A FKBP52, FK506-binding protein 4; isomerase; 2.80A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 PDB: 1qz2_A

Probab=98.08  E-value=4.6e-05  Score=70.83  Aligned_cols=120  Identities=10%  Similarity=-0.070  Sum_probs=80.2

Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC--------------HHHHHHHHHHHHccCChHHHHHHHHHHHHhc
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD--------------QVALVAALSACAEIGDLKLGKWIHSYVEENF  283 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--------------~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~  283 (538)
                      ...|..+...|.+.|++++|+..|++..+......              ...|..+..++.+.|++++|...++.+.+. 
T Consensus       147 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~-  225 (336)
T 1p5q_A          147 STIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL-  225 (336)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-
Confidence            34566666777777777777777777766422211              366777777777777777777777777776 


Q ss_pred             cCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHH
Q 044988          284 SVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEA  342 (538)
Q Consensus       284 ~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a  342 (538)
                          .|.+...+..+..+|...|++++|...|++..+   .+...+..+...+...|+.++|
T Consensus       226 ----~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a  283 (336)
T 1p5q_A          226 ----DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAR  283 (336)
T ss_dssp             ----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ----CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Confidence                566667777777777777888877777776654   2445566666666666655544

>2e2e_A Formate-dependent nitrite reductase complex NRFG; TPR, cytochrome C biogenesis, O157:H7 EDL933, formate- nitrite reductase complex, lyase; 2.05A {Escherichia coli}

Probab=98.08  E-value=1.8e-05  Score=65.84  Aligned_cols=116  Identities=8%  Similarity=0.039  Sum_probs=84.5

Q ss_pred             hcCCHHHHHHHHccCC---CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHH-HHccCCh--HHH
Q 044988          199 KRGDIDGAWKIFDEMP---HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSA-CAEIGDL--KLG  272 (538)
Q Consensus       199 ~~g~~~~A~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~-~~~~~~~--~~a  272 (538)
                      ..|++++|...|++..   ..+...|..+...|...|++++|...|++..+.. +.+...+..+..+ +...|++  +.|
T Consensus        22 ~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~~A  100 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRANPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTAQT  100 (177)
T ss_dssp             -----CCCCHHHHHHHHHCCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCHHH
T ss_pred             hccCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchHHH
Confidence            3566666666666543   2355678888888888899999999888887643 2355666677777 6678887  888


Q ss_pred             HHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          273 KWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       273 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      ...++.+.+.     .|.+...+..+...|...|++++|...|+++.+
T Consensus       101 ~~~~~~al~~-----~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  143 (177)
T 2e2e_A          101 RAMIDKALAL-----DSNEITALMLLASDAFMQANYAQAIELWQKVMD  143 (177)
T ss_dssp             HHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHh-----CCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            8888888886     566677777888888889999999988887654

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=98.06  E-value=1.7e-05  Score=61.78  Aligned_cols=96  Identities=13%  Similarity=0.086  Sum_probs=78.2

Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC-------cccH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ-------AAGY  449 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~-------~~~~  449 (538)
                      ...+..+...+...|++++|...|++..  .+.+...+..+...+...|++++|...++++ ....|++       ...+
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~-~~~~~~~~~~~~~~~~~~   82 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKA-IEVGRENREDYRQIAKAY   82 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHHHHHSTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHH-HhhccccchhHHHHHHHH
Confidence            4567778888888899999998888763  2345777888888899999999999999998 6666655       5556


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          450 LALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       450 ~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      . .++.+|.+.|++++|.+.+++..+.
T Consensus        83 ~-~la~~~~~~~~~~~A~~~~~~~~~~  108 (131)
T 1elr_A           83 A-RIGNSYFKEEKYKDAIHFYNKSLAE  108 (131)
T ss_dssp             H-HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             H-HHHHHHHHhccHHHHHHHHHHHHHh
Confidence            7 8889999999999999999998863

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.05  E-value=1.6e-05  Score=62.01  Aligned_cols=89  Identities=19%  Similarity=0.127  Sum_probs=53.1

Q ss_pred             HHHHhhhcCChHHHHHHHHhCC-CCCCH----HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC---cccHHHHHHHH
Q 044988          385 MVDLFSRAGLMDEAFSLVQNMP-MKPND----AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ---AAGYLALVANV  456 (538)
Q Consensus       385 l~~~~~~~g~~~~A~~~~~~~~-~~p~~----~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~---~~~~~~~l~~~  456 (538)
                      +...+...|++++|.+.|+.+. ..|+.    ..+..+..++...|++++|...++++ ....|++   +..+. .++.+
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~-~~~~p~~~~~~~~~~-~la~~   85 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDL-VSRYPTHDKAAGGLL-KLGLS   85 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTSTTHHHHHH-HHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHH-HHHCCCCcccHHHHH-HHHHH
Confidence            4445555666666666665542 12221    34555556666666666666666666 6666666   44455 66666


Q ss_pred             HHhcCChHHHHHHHHHHHh
Q 044988          457 YAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       457 ~~~~g~~~~A~~~~~~m~~  475 (538)
                      |.+.|++++|...++++.+
T Consensus        86 ~~~~g~~~~A~~~~~~~~~  104 (129)
T 2xev_A           86 QYGEGKNTEAQQTLQQVAT  104 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            6666777777776666654

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=98.03  E-value=2e-05  Score=62.85  Aligned_cols=92  Identities=13%  Similarity=-0.015  Sum_probs=68.0

Q ss_pred             HHHHHHHhhhcCChHHHHHHHHhCC-CCCC-------------HHHHHHHHHHHHhcCCHHHHHHHHHHchhcc------
Q 044988          382 YGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-------------DAVLGSLLLGCRIHNNAELASQVAQKLVAEI------  441 (538)
Q Consensus       382 ~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-------------~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~------  441 (538)
                      +......+.+.|++++|++.|++.. ..|+             ...|..+..++.+.|++++|+..+++. .++      
T Consensus        14 ~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kA-L~l~n~~~e   92 (159)
T 2hr2_A           14 ALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKA-LHYFNRRGE   92 (159)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHHHHCC
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHH-HHhhhcccc
Confidence            3444455555666666666665542 2222             237777778888888888888888888 777      


Q ss_pred             -CCCCcccH----HHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          442 -DPEQAAGY----LALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       442 -~p~~~~~~----~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                       .|++...|    . ..+.++...|++++|+..|++..+
T Consensus        93 ~~pd~~~A~~~~~~-~rG~aL~~lgr~eEAl~~y~kAle  130 (159)
T 2hr2_A           93 LNQDEGKLWISAVY-SRALALDGLGRGAEAMPEFKKVVE  130 (159)
T ss_dssp             TTSTHHHHHHHHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHH-hHHHHHHHCCCHHHHHHHHHHHHh
Confidence             99998888    8 889999999999999999999875

>3q7a_A Farnesyltransferase alpha subunit; protein prenyltransferase, transferase-transferase inhibitor; HET: SUC 3FX FPP 778; 2.00A {Cryptococcus neoformans} PDB: 3q73_A* 3q78_A* 3q79_A* 3q75_A* 3q7f_A* 3sfx_A* 3sfy_A*

Probab=98.03  E-value=0.00024  Score=65.13  Aligned_cols=80  Identities=8%  Similarity=0.115  Sum_probs=35.7

Q ss_pred             CChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccC-ChhHHHHHHhcCCC---CCcchHHHHHHHHhcC-C-CchHHHH
Q 044988           31 NTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSG-YLINAHKVFEKTEN---PSTAIWNQMIRGHARS-E-TPEKSVY  104 (538)
Q Consensus        31 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~a~~~~~~~~~---~~~~~~~~li~~~~~~-~-~~~~a~~  104 (538)
                      +..++|..+.+.++..... +..+|+.--.++...| .+++++.+++.+..   .+..+|+.-...+.+. + +++++++
T Consensus        68 e~se~AL~lt~~~L~~nP~-~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~~l~~~~~~~EL~  146 (349)
T 3q7a_A           68 EKSERALELTEIIVRMNPA-HYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLDRISPQDPVSEIE  146 (349)
T ss_dssp             CCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHCCSCCHHHHH
T ss_pred             CCCHHHHHHHHHHHHhCch-hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCCChHHHHH
Confidence            3344555555555554322 3334444444444444 35555555554432   2333344433333332 3 4555555


Q ss_pred             HHHHhHh
Q 044988          105 LYKQMID  111 (538)
Q Consensus       105 ~~~~m~~  111 (538)
                      +++.+.+
T Consensus       147 ~~~k~L~  153 (349)
T 3q7a_A          147 YIHGSLL  153 (349)
T ss_dssp             HHHHHTS
T ss_pred             HHHHHHH
Confidence            5555554

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.02  E-value=4.9e-05  Score=62.11  Aligned_cols=93  Identities=6%  Similarity=-0.024  Sum_probs=63.0

Q ss_pred             HHHHHHHHhhhcCChHHHHHHHHhCC-C------------------CCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhc
Q 044988          381 HYGCMVDLFSRAGLMDEAFSLVQNMP-M------------------KPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAE  440 (538)
Q Consensus       381 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~------------------~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~  440 (538)
                      .+......+.+.|++++|+..|++.. .                  .|. ...|..+..++.+.|++++|+..++++ ..
T Consensus        13 ~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~a-l~   91 (162)
T 3rkv_A           13 ALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEV-LK   91 (162)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHH-HH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHH-Hh
Confidence            44445555555555555555554432 1                  111 346666777777888888888888888 77


Q ss_pred             cCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          441 IDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       441 ~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +.|++..+|. .++.+|...|++++|...|++...
T Consensus        92 ~~p~~~~a~~-~~g~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A           92 REETNEKALF-RRAKARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             HSTTCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cCCcchHHHH-HHHHHHHHHhcHHHHHHHHHHHHh
Confidence            7888877777 788888888888888888877765

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.00  E-value=3.3e-05  Score=59.52  Aligned_cols=93  Identities=17%  Similarity=0.103  Sum_probs=73.9

Q ss_pred             HHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCC
Q 044988          350 LSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNN  426 (538)
Q Consensus       350 l~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~  426 (538)
                      ...+...|++++|...|++..+.   .| +...|..+..++...|++++|+..|++.. ..| +...+..+..++...|+
T Consensus        24 g~~~~~~g~~~~A~~~~~~al~~---~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~~g~  100 (121)
T 1hxi_A           24 GLSMLKLANLAEAALAFEAVCQK---EPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHN  100 (121)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCC
Confidence            34445566888999999999876   56 58889999999999999999999999874 445 47788889999999999


Q ss_pred             HHHHHHHHHHchhccCCCCc
Q 044988          427 AELASQVAQKLVAEIDPEQA  446 (538)
Q Consensus       427 ~~~A~~~~~~~~~~~~p~~~  446 (538)
                      +++|+..++++ ....|++.
T Consensus       101 ~~~A~~~~~~a-l~~~P~~~  119 (121)
T 1hxi_A          101 ANAALASLRAW-LLSQPQYE  119 (121)
T ss_dssp             HHHHHHHHHHH-HC------
T ss_pred             HHHHHHHHHHH-HHhCcCCC
Confidence            99999999999 88888764

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.99  E-value=0.00039  Score=67.09  Aligned_cols=172  Identities=5%  Similarity=-0.082  Sum_probs=80.0

Q ss_pred             HHHHHHHHHccCChHHHHHHHHHHHHhccCCCCC-cchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHH
Q 044988          256 LVAALSACAEIGDLKLGKWIHSYVEENFSVGREP-VLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFA  334 (538)
Q Consensus       256 ~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~  334 (538)
                      +..+...|...|++++|...+..+.+....-+.. ....+.+.+...+...|+.+.|..+++....           ...
T Consensus        58 l~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----------~~~  126 (434)
T 4b4t_Q           58 ILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIE-----------FAK  126 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHH-----------HHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-----------HHH
Confidence            4455555666666666666555554432110000 0111223333344455666776666655421           011


Q ss_pred             hcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcC---CCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC----
Q 044988          335 KQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWG---IKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP----  406 (538)
Q Consensus       335 ~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~---~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----  406 (538)
                      ..++...-..++..+...+...|++++|..+++.+.....   -.| ...++..++..|...|++++|..++++..    
T Consensus       127 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~  206 (434)
T 4b4t_Q          127 REKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAAN  206 (434)
T ss_dssp             HSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred             HhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhh
Confidence            1111111112233333333444455555555554433211   112 24466667777777777777777766542    


Q ss_pred             -C-CCC---HHHHHHHHHHHHhcCCHHHHHHHHHHch
Q 044988          407 -M-KPN---DAVLGSLLLGCRIHNNAELASQVAQKLV  438 (538)
Q Consensus       407 -~-~p~---~~~~~~l~~~~~~~~~~~~A~~~~~~~~  438 (538)
                       . .|.   ...+..+...+...+++++|...+.+..
T Consensus       207 ~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~  243 (434)
T 4b4t_Q          207 SIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESF  243 (434)
T ss_dssp             HSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             cCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence             1 111   2344444555666677777766666553

>2fbn_A 70 kDa peptidylprolyl isomerase, putative; sulfur SAD, PFL2275C, TPR-containing domain, structural genomics; 1.63A {Plasmodium falciparum} SCOP: a.118.8.1

Probab=97.98  E-value=1.3e-05  Score=68.23  Aligned_cols=119  Identities=13%  Similarity=0.024  Sum_probs=75.6

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHccCCC---CCh----------------HHHHHHHHHHHHcCCHHHHHHHHHHHHHCC
Q 044988          188 VSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNV----------------VSWTTMISGCAQNGKSRQALSLFNEMRRAR  248 (538)
Q Consensus       188 ~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~----------------~~~~~li~~~~~~~~~~~a~~~~~~m~~~g  248 (538)
                      ..+..+...+...|++++|...|++...   .+.                ..|..+..+|...|++++|+..+++..+..
T Consensus        39 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~  118 (198)
T 2fbn_A           39 FDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKID  118 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC
Confidence            3455555666666777777766665431   111                566667777777777777777777776642


Q ss_pred             CCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHH
Q 044988          249 VGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAY  312 (538)
Q Consensus       249 ~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  312 (538)
                       +.+...+..+..++...|+++.|...++...+.     .|.+..++..+..++...++.+++.
T Consensus       119 -p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~-----~p~~~~~~~~l~~~~~~~~~~~~~~  176 (198)
T 2fbn_A          119 -KNNVKALYKLGVANMYFGFLEEAKENLYKAASL-----NPNNLDIRNSYELCVNKLKEARKKD  176 (198)
T ss_dssp             -TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-----STTCHHHHHHHHHHHHHHHHHHC--
T ss_pred             -cccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH-----CCCcHHHHHHHHHHHHHHHHHHHHH
Confidence             234566667777777777777777777777776     5556666666666666655555544

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.97  E-value=7e-05  Score=58.25  Aligned_cols=98  Identities=17%  Similarity=0.112  Sum_probs=79.0

Q ss_pred             HHHHhcccCcHHHHHHHHHHhhhhcCCCcc-H---HHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC----HHHHHHHHH
Q 044988          349 VLSACSHGGFVDEGRQFFECMNQNWGIKPR-I---EHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN----DAVLGSLLL  419 (538)
Q Consensus       349 ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-~---~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~----~~~~~~l~~  419 (538)
                      +...+...|++++|...|+.+.+.   .|+ .   ..+..+..++...|++++|...|++.. ..|+    ...+..+..
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~---~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~   84 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLEL---YPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGL   84 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH---CSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHH---CCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHH
Confidence            345556677999999999998876   343 3   578889999999999999999998874 3344    567788888


Q ss_pred             HHHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          420 GCRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       420 ~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                      ++...|++++|...++++ ....|+++....
T Consensus        85 ~~~~~g~~~~A~~~~~~~-~~~~p~~~~~~~  114 (129)
T 2xev_A           85 SQYGEGKNTEAQQTLQQV-ATQYPGSDAARV  114 (129)
T ss_dssp             HHHHTTCHHHHHHHHHHH-HHHSTTSHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHH-HHHCCCChHHHH
Confidence            999999999999999999 888898876333

>3q49_B STIP1 homology and U box-containing protein 1; E3 ubiquitin ligase, ligase-chaperone complex; 1.54A {Mus musculus} PDB: 3q47_B 3q4a_B*

Probab=97.96  E-value=0.0002  Score=56.28  Aligned_cols=99  Identities=9%  Similarity=-0.085  Sum_probs=72.8

Q ss_pred             CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHH
Q 044988          216 RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLN  295 (538)
Q Consensus       216 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  295 (538)
                      .+...|..+...+...|++++|...|++..... +.+...+..+..++...|+++.|...++.+.+.     .|.+...+
T Consensus         7 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-----~p~~~~~~   80 (137)
T 3q49_B            7 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALEL-----DGQSVKAH   80 (137)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHH
T ss_pred             ccHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh-----CchhHHHH
Confidence            355667777777888888888888888777643 234666777777777888888888888877776     56666777


Q ss_pred             HHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          296 NALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       296 ~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      ..+..+|...|++++|...|++..+
T Consensus        81 ~~l~~~~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           81 FFLGQCQLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            7788888888888888888777653

>1elr_A TPR2A-domain of HOP; HOP, TPR-domain, peptide-complex, helical repeat, protein binding, chaperone; 1.90A {Homo sapiens} SCOP: a.118.8.1 PDB: 3esk_A 3fwv_A

Probab=97.94  E-value=7.9e-05  Score=57.86  Aligned_cols=96  Identities=9%  Similarity=0.035  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc-------
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL-------  291 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~-------  291 (538)
                      ..|..+...+...|++++|...|++..+.. +.+...+..+...+...|+++.|...+..+.+.     .|.+       
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~~~~~   78 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEV-----GRENREDYRQI   78 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-----HHHSTTCHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhh-----ccccchhHHHH
Confidence            345566666667777777777777766542 234555666666666777777777777766665     1221       


Q ss_pred             hhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          292 VSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       292 ~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      ..++..+...|...|++++|.+.|++..+
T Consensus        79 ~~~~~~la~~~~~~~~~~~A~~~~~~~~~  107 (131)
T 1elr_A           79 AKAYARIGNSYFKEEKYKDAIHFYNKSLA  107 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            45556667777777777777777766543

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=97.93  E-value=4.9e-05  Score=57.21  Aligned_cols=93  Identities=16%  Similarity=0.098  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCC--CcchHHHHHHHH
Q 044988           54 ILAKLLAFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEP--DEYTYSFLLSVC  128 (538)
Q Consensus        54 ~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p--~~~~~~~li~~~  128 (538)
                      .+..+...+...|++++|...|++..   +.+...|..+...+...|++++|+..|++..+.. +.  +...+..+...+
T Consensus         8 ~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~~~   86 (112)
T 2kck_A            8 EYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKADAL   86 (112)
T ss_dssp             GGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHHHH
Confidence            33334444444444444444444332   1223334444444444455555555554444431 11  233444444444


Q ss_pred             Hcc-CCcHHHHHHHHHHHHh
Q 044988          129 ARC-GLFREGEQVHGRVLAS  147 (538)
Q Consensus       129 ~~~-~~~~~a~~~~~~~~~~  147 (538)
                      ... |++++|.+.++.....
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~  106 (112)
T 2kck_A           87 RYIEGKEVEAEIAEARAKLE  106 (112)
T ss_dssp             TTCSSCSHHHHHHHHHHGGG
T ss_pred             HHHhCCHHHHHHHHHHHhhc
Confidence            445 5555555555444443

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.93  E-value=7.8e-06  Score=62.70  Aligned_cols=90  Identities=14%  Similarity=0.106  Sum_probs=49.6

Q ss_pred             cCcHHHHHHHHHHhhhhcCC-Cc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHH
Q 044988          356 GGFVDEGRQFFECMNQNWGI-KP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELAS  431 (538)
Q Consensus       356 ~~~~~~a~~~~~~~~~~~~~-~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~  431 (538)
                      .|++++|...|++..+. +. .| +...+..+..+|...|++++|++.|++.. ..| +...+..+..++...|++++|+
T Consensus         3 ~g~~~~A~~~~~~al~~-~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIAS-GLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             ----CCCHHHHHHHHSS-CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCcHHHHHHHHHHHHHc-CCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHH
Confidence            45666666666666543 10 13 24556666666666666666666666552 222 3455555666666666666666


Q ss_pred             HHHHHchhccCCCCcc
Q 044988          432 QVAQKLVAEIDPEQAA  447 (538)
Q Consensus       432 ~~~~~~~~~~~p~~~~  447 (538)
                      ..+++. ....|+++.
T Consensus        82 ~~~~~a-l~~~p~~~~   96 (117)
T 3k9i_A           82 ELLLKI-IAETSDDET   96 (117)
T ss_dssp             HHHHHH-HHHHCCCHH
T ss_pred             HHHHHH-HHhCCCcHH
Confidence            666666 555555544

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.93  E-value=0.00017  Score=58.39  Aligned_cols=99  Identities=13%  Similarity=-0.003  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCC-CC----HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCC-Ccchh
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRARVG-LD----QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGRE-PVLVS  293 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~-p~----~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~-~~~~~  293 (538)
                      ++..+...+...|++++|+..+++..+.... ++    ..++..+...+...|+++.|...++...+.....+. +....
T Consensus        11 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~   90 (164)
T 3ro3_A           11 AFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQ   90 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHH
Confidence            4566667777777777777777776542100 11    124555555566666666666666665554211111 11233


Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          294 LNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       294 ~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                      .+..+...+...|++++|...+++.
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a  115 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKH  115 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHH
Confidence            4455666666666666666666554

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=97.92  E-value=5.2e-05  Score=71.33  Aligned_cols=90  Identities=17%  Similarity=0.027  Sum_probs=77.6

Q ss_pred             cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHH
Q 044988          378 RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVAN  455 (538)
Q Consensus       378 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~  455 (538)
                      +..+|..+..+|.+.|++++|++.+++.. ..| +...|..+..++...|++++|+..++++ ..+.|++...+. .+..
T Consensus       272 ~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~A-l~l~P~~~~~~~-~l~~  349 (370)
T 1ihg_A          272 ALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKA-QEIAPEDKAIQA-ELLK  349 (370)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHH
T ss_pred             HHHHHHHHHHHHHhccCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHccCHHHHHHHHHHH-HHhCCCCHHHHH-HHHH
Confidence            46789999999999999999999998873 445 4788889999999999999999999999 999999988677 8888


Q ss_pred             HHHhcCChHHHHHH
Q 044988          456 VYAAAKRWQDVAAV  469 (538)
Q Consensus       456 ~~~~~g~~~~A~~~  469 (538)
                      ++.+.++.+++.+.
T Consensus       350 ~~~~~~~~~~a~k~  363 (370)
T 1ihg_A          350 VKQKIKAQKDKEKA  363 (370)
T ss_dssp             HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHH
Confidence            88888887776543

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=97.90  E-value=0.0025  Score=58.05  Aligned_cols=179  Identities=11%  Similarity=0.005  Sum_probs=109.1

Q ss_pred             hHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCC--CHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHH
Q 044988          269 LKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCG--EIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEAL  343 (538)
Q Consensus       269 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~  343 (538)
                      ++.+..+++.+...     .|.+..+|+.-..++...|  .++++..+++++.+   +|..+|+.-...+...|..    
T Consensus        90 l~~EL~~~~~~L~~-----~PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~----  160 (331)
T 3dss_A           90 VKAELGFLESCLRV-----NPKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVA----  160 (331)
T ss_dssp             HHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCC----
T ss_pred             HHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcC----
Confidence            45666677777665     6777777777777777777  37777777777765   3444444444444443321    


Q ss_pred             HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhc--------------CChHHHHHHHHhCC--C
Q 044988          344 LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRA--------------GLMDEAFSLVQNMP--M  407 (538)
Q Consensus       344 ~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~--------------g~~~~A~~~~~~~~--~  407 (538)
                                     ++++.+.+..+.+..  +-|...|+.....+.+.              +.++++++.+++..  .
T Consensus       161 ---------------~~eel~~~~~~I~~~--p~N~SAW~~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~~  223 (331)
T 3dss_A          161 ---------------PAEELAFTDSLITRN--FSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFTD  223 (331)
T ss_dssp             ---------------HHHHHHHHHHHHHHC--SCCHHHHHHHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHHS
T ss_pred             ---------------HHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHhC
Confidence                           355666667666551  22566666555554443              34667777776653  2


Q ss_pred             CCCHHHHHHHHHHHHhc-----------CCHHHHHHHHHHchhccCCCCcccHHHHHHH---HHHhcCChHHHHHHHHHH
Q 044988          408 KPNDAVLGSLLLGCRIH-----------NNAELASQVAQKLVAEIDPEQAAGYLALVAN---VYAAAKRWQDVAAVRQKM  473 (538)
Q Consensus       408 ~p~~~~~~~l~~~~~~~-----------~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~---~~~~~g~~~~A~~~~~~m  473 (538)
                      +-|...|+-+-..+.+.           +.++++++.++++ .+..|++.-.+. .++.   .....|..+++...+.++
T Consensus       224 P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~el-le~~pd~~w~l~-~~~~~~~~~~~~~~~~~~~~~l~~l  301 (331)
T 3dss_A          224 PNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKEL-QELEPENKWCLL-TIILLMRALDPLLYEKETLQYFSTL  301 (331)
T ss_dssp             TTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHHCTTTTHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHH-HhhCcccchHHH-HHHHHHHhhcccccHHHHHHHHHHH
Confidence            33466666554444444           4578888888888 888898744332 2211   122457778888888888


Q ss_pred             Hh
Q 044988          474 IK  475 (538)
Q Consensus       474 ~~  475 (538)
                      .+
T Consensus       302 ~~  303 (331)
T 3dss_A          302 KA  303 (331)
T ss_dssp             HH
T ss_pred             HH
Confidence            76

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.86  E-value=0.00011  Score=71.43  Aligned_cols=124  Identities=10%  Similarity=0.021  Sum_probs=95.0

Q ss_pred             hcccCcHHHHHHHHHHhhhhc----CC-Ccc-HHHHHHHHHHhhhcCChHHHHHHHHhCC---------CCCC-HHHHHH
Q 044988          353 CSHGGFVDEGRQFFECMNQNW----GI-KPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP---------MKPN-DAVLGS  416 (538)
Q Consensus       353 ~~~~~~~~~a~~~~~~~~~~~----~~-~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~---------~~p~-~~~~~~  416 (538)
                      +...|++++|+.++++..+..    |- .|+ ..+++.|..+|...|++++|..++++..         ..|+ ..+++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            445567777777776655431    21 233 5689999999999999999999998763         3344 468889


Q ss_pred             HHHHHHhcCCHHHHHHHHHHch----hccCCCCcccHH--HHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          417 LLLGCRIHNNAELASQVAQKLV----AEIDPEQAAGYL--ALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       417 l~~~~~~~~~~~~A~~~~~~~~----~~~~p~~~~~~~--~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      |...|...|++++|+.+++++.    .-+.|+++.+-.  ..+..++...|++++|..++.++++.
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999986    445677665322  36778888999999999999999864

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.85  E-value=1.7e-05  Score=60.68  Aligned_cols=84  Identities=17%  Similarity=0.059  Sum_probs=69.3

Q ss_pred             hcCChHHHHHHHHhCC-C---CCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHH
Q 044988          391 RAGLMDEAFSLVQNMP-M---KPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQD  465 (538)
Q Consensus       391 ~~g~~~~A~~~~~~~~-~---~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~  465 (538)
                      ..|++++|+..|++.. .   .|+ ...+..+...+...|++++|+..++++ ....|+++..+. .++.+|.+.|++++
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~a-l~~~p~~~~~~~-~l~~~~~~~g~~~~   79 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANG-VKQFPNHQALRV-FYAMVLYNLGRYEQ   79 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHHTCHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCCCchHHHH-HHHHHHHHcCCHHH
Confidence            4678889999998874 3   244 567788888999999999999999999 999999999888 99999999999999


Q ss_pred             HHHHHHHHHhC
Q 044988          466 VAAVRQKMIKM  476 (538)
Q Consensus       466 A~~~~~~m~~~  476 (538)
                      |+..+++....
T Consensus        80 A~~~~~~al~~   90 (117)
T 3k9i_A           80 GVELLLKIIAE   90 (117)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99999988754

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.83  E-value=7.7e-06  Score=61.83  Aligned_cols=94  Identities=12%  Similarity=-0.029  Sum_probs=73.4

Q ss_pred             ccHHHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC------ccc
Q 044988          377 PRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ------AAG  448 (538)
Q Consensus       377 p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~------~~~  448 (538)
                      ++...+..+...+...|++++|.+.|++.. . +.+...|..+..++...|++++|+..++++ ..+.|++      ...
T Consensus         2 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~~~~~   80 (111)
T 2l6j_A            2 SQFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQG-LRYTSTAEHVAIRSKL   80 (111)
T ss_dssp             THHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HTSCSSTTSHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHH-HHhCCCccHHHHHHHH
Confidence            356677888889999999999999998873 2 345778888888999999999999999999 8899988      554


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHH
Q 044988          449 YLALVANVYAAAKRWQDVAAVRQK  472 (538)
Q Consensus       449 ~~~~l~~~~~~~g~~~~A~~~~~~  472 (538)
                      +. .++.++...|++++|+..+++
T Consensus        81 ~~-~~~~~~~~~~~~~~a~~~~~~  103 (111)
T 2l6j_A           81 QY-RLELAQGAVGSVQIPVVEVDE  103 (111)
T ss_dssp             HH-HHHHHHHHHHCCCCCSSSSSS
T ss_pred             HH-HHHHHHHHHHhHhhhHhHHHH
Confidence            55 667777777776666555443

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.83  E-value=7e-05  Score=61.15  Aligned_cols=69  Identities=17%  Similarity=0.097  Sum_probs=60.7

Q ss_pred             cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          378 RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       378 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      +...|..+..+|.+.|++++|+..+++.. ..| +...|..+..++...|++++|...|+++ ..+.|++..
T Consensus        62 ~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~a-l~l~p~~~~  132 (162)
T 3rkv_A           62 NIPLYANMSQCYLNIGDLHEAEETSSEVLKREETNEKALFRRAKARIAAWKLDEAEEDLKLL-LRNHPAAAS  132 (162)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCGGGHH
T ss_pred             HHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHH-HhcCCCCHH
Confidence            35688999999999999999999998874 334 5788999999999999999999999999 999999883

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.77  E-value=0.00023  Score=69.15  Aligned_cols=121  Identities=12%  Similarity=-0.076  Sum_probs=92.9

Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC--------------HHHHHHHHHHHHccCChHHHHHHHHHHHHhc
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD--------------QVALVAALSACAEIGDLKLGKWIHSYVEENF  283 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~--------------~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~  283 (538)
                      ...|..+...|.+.|++++|+..|++..+......              ...|..+..++.+.|+++.|...++.+.+. 
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~-  346 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGL-  346 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc-
Confidence            34677788888899999999999998877421111              477888888889999999999999999887 


Q ss_pred             cCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHH
Q 044988          284 SVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEAL  343 (538)
Q Consensus       284 ~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~  343 (538)
                          .|.+...+..+..+|...|++++|...|++..+   .+...+..+...+.+.++.+++.
T Consensus       347 ----~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a~  405 (457)
T 1kt0_A          347 ----DSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQKKAKEHNERD  405 (457)
T ss_dssp             ----STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHHHHHHHHHHHH
T ss_pred             ----CCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence                677788888899999999999999999998765   24566777777777666555443

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=97.74  E-value=0.0036  Score=57.03  Aligned_cols=203  Identities=9%  Similarity=-0.020  Sum_probs=129.0

Q ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC--ChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCC-HHH
Q 044988          234 SRQALSLFNEMRRARVGLDQVALVAALSACAEIG--DLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGE-IEE  310 (538)
Q Consensus       234 ~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~--~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~-~~~  310 (538)
                      +++++.+++.+.... +-+..++..-.-.+.+.+  .++.+..+++.+.+.     .|.+..+|+.-..++...|. +++
T Consensus        90 l~~EL~~~~~~L~~~-PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~-----dprNy~AW~~R~~vl~~l~~~~~e  163 (331)
T 3dss_A           90 VKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEA-----DERNFHCWDYRRFVAAQAAVAPAE  163 (331)
T ss_dssp             HHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHHhC-CCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHhCcCHHH
Confidence            567777777777642 235555655555555555  477888888888876     77788888777777777777 578


Q ss_pred             HHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHH
Q 044988          311 AYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMV  386 (538)
Q Consensus       311 a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~  386 (538)
                      +.+.++++.+   .|..+|+.....+...+....+-      ...-...+.++++.+.+......   .| |...|+-+-
T Consensus       164 el~~~~~~I~~~p~N~SAW~~R~~ll~~l~~~~~~~------~~~~~~~~~~~eEle~~~~ai~~---~P~d~SaW~Y~r  234 (331)
T 3dss_A          164 ELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSG------PQGRLPENVLLKELELVQNAFFT---DPNDQSAWFYHR  234 (331)
T ss_dssp             HHHHHHHHHHHCSCCHHHHHHHHHHHHHHSCCC------------CCCHHHHHHHHHHHHHHHHH---STTCHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHhhhccccc------cccccchHHHHHHHHHHHHHHHh---CCCCHHHHHHHH
Confidence            8888877765   35556666555554432111000      00000113577888888888865   56 577777665


Q ss_pred             HHhhhc-----------CChHHHHHHHHhCC-CCCCHHHHHHHHHH-----HHhcCCHHHHHHHHHHchhccCCCCcccH
Q 044988          387 DLFSRA-----------GLMDEAFSLVQNMP-MKPNDAVLGSLLLG-----CRIHNNAELASQVAQKLVAEIDPEQAAGY  449 (538)
Q Consensus       387 ~~~~~~-----------g~~~~A~~~~~~~~-~~p~~~~~~~l~~~-----~~~~~~~~~A~~~~~~~~~~~~p~~~~~~  449 (538)
                      ..+.+.           +.++++++.++++. ..||. .|..+..+     ....+..++....+.++ .+++|....-|
T Consensus       235 ~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~~pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l-~~~Dp~r~~~y  312 (331)
T 3dss_A          235 WLLGAGSGRCELSVEKSTVLQSELESCKELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTL-KAVDPMRAAYL  312 (331)
T ss_dssp             HHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHHCTTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHH-HHHCGGGHHHH
T ss_pred             HHHHhccCccccchHHHHHHHHHHHHHHHHHhhCccc-chHHHHHHHHHHhhcccccHHHHHHHHHHH-HHhCcchhhHH
Confidence            555544           45778888887773 55764 34322222     22467788999999999 99999998866


Q ss_pred             HHHHH
Q 044988          450 LALVA  454 (538)
Q Consensus       450 ~~~l~  454 (538)
                      . -+.
T Consensus       313 ~-d~~  316 (331)
T 3dss_A          313 D-DLR  316 (331)
T ss_dssp             H-HHH
T ss_pred             H-HHH
Confidence            6 443

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.73  E-value=0.00011  Score=58.65  Aligned_cols=100  Identities=13%  Similarity=-0.017  Sum_probs=79.6

Q ss_pred             HHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc-------------HHHHHHHHHHhhhcCChHHHHHHHHhCC-C-----
Q 044988          347 LGVLSACSHGGFVDEGRQFFECMNQNWGIKPR-------------IEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-----  407 (538)
Q Consensus       347 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~-------------~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-----  407 (538)
                      ......+...|++++|...|++..+.   .|+             ...|..+..++.+.|++++|+..+++.. .     
T Consensus        15 ~~~G~~l~~~g~~eeAi~~Y~kAL~l---~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~   91 (159)
T 2hr2_A           15 LSDAQRQLVAGEYDEAAANCRRAMEI---SHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRG   91 (159)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHH---HTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhh---CCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccc
Confidence            34445555667777888888877754   333             3389999999999999999999988763 4     


Q ss_pred             --CCC-HHHH----HHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          408 --KPN-DAVL----GSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       408 --~p~-~~~~----~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                        .|+ ...|    .....++...|++++|+..|++. .++.|++.....
T Consensus        92 e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kA-lel~p~d~~~~~  140 (159)
T 2hr2_A           92 ELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKV-VEMIEERKGETP  140 (159)
T ss_dssp             CTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHHHCCSCCT
T ss_pred             cCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHH-HhcCCCcHHHHH
Confidence              777 4677    88899999999999999999999 999999887544

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.68  E-value=0.00017  Score=53.13  Aligned_cols=64  Identities=22%  Similarity=0.252  Sum_probs=55.7

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          410 NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       410 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +...+..+...+...|++++|+..|+++ .+..|+++..|. .++.+|.+.|++++|++.+++..+
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~a-l~~~p~~~~a~~-~lg~~~~~~g~~~~A~~~~~~al~   69 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEEL-VETDPDYVGTYY-HLGKLYERLDRTDDAIDTYAQGIE   69 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHSTTCTHHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCCCcHHHHH-HHHHHHHHcCCHHHHHHHHHHHHh
Confidence            4677888888889999999999999999 888899888788 899999999999999999988775

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.65  E-value=0.0019  Score=64.26  Aligned_cols=169  Identities=9%  Similarity=0.002  Sum_probs=128.6

Q ss_pred             hHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCC----------HHHHHHHHHhcCCC---CcchHHHHHHHHHh
Q 044988          269 LKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGE----------IEEAYGVFRKMQRR---NTVSWTSMITGFAK  335 (538)
Q Consensus       269 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~----------~~~a~~~~~~m~~~---~~~~~~~li~~~~~  335 (538)
                      .++|...++.+.+.     .|.+..+|+.--.++...|+          ++++.+.++++.+.   +..+|+.-...+.+
T Consensus        45 ~eeal~~~~~~l~~-----nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~pK~y~aW~hR~w~l~~  119 (567)
T 1dce_A           45 DESVLELTSQILGA-----NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSR  119 (567)
T ss_dssp             SHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHH-----CchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            35667778888776     77788888777777777776          89999999988763   44455554444444


Q ss_pred             cCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcC-ChHHHHHHHHhCC-CC-CCH
Q 044988          336 QGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAG-LMDEAFSLVQNMP-MK-PND  411 (538)
Q Consensus       336 ~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~-~~-p~~  411 (538)
                      .++.                  +++++.+.++++.+.   .| |..+|+.-..++.+.| .++++++.++++. .. -|.
T Consensus       120 l~~~------------------~~~~el~~~~k~l~~---d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~  178 (567)
T 1dce_A          120 LPEP------------------NWARELELCARFLEA---DERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNY  178 (567)
T ss_dssp             CSSC------------------CHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCH
T ss_pred             cccc------------------cHHHHHHHHHHHHhh---ccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCc
Confidence            4311                  567888999998876   44 6888888888888888 8999999999885 33 457


Q ss_pred             HHHHHHHHHHHhc--------------CCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHH
Q 044988          412 AVLGSLLLGCRIH--------------NNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQD  465 (538)
Q Consensus       412 ~~~~~l~~~~~~~--------------~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~  465 (538)
                      ..|+.....+.+.              +.++++++.++++ ....|++..+|. .+..++.+.++.++
T Consensus       179 saW~~r~~ll~~l~~~~~~~~~~~~~~~~~~eel~~~~~a-i~~~P~~~saW~-y~~~ll~~~~~~~~  244 (567)
T 1dce_A          179 SSWHYRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNA-FFTDPNDQSAWF-YHRWLLGRAEPHDV  244 (567)
T ss_dssp             HHHHHHHHHHHHHSCCCCSSSCCSSCHHHHHHHHHHHHHH-HHHCSSCSHHHH-HHHHHHSCCCCCSC
T ss_pred             cHHHHHHHHHHhhcccccccccccccHHHHHHHHHHHHHH-HhhCCCCccHHH-HHHHHHhcCCCccc
Confidence            7888777776553              5679999999999 999999999999 89899988888554

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.61  E-value=0.00028  Score=50.64  Aligned_cols=82  Identities=20%  Similarity=0.150  Sum_probs=64.2

Q ss_pred             cHHHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHH
Q 044988          378 RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVAN  455 (538)
Q Consensus       378 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~  455 (538)
                      +...+..+...+...|++++|...+++.. . +.+...+..+...+...|++++|...++++ ....|++...+. .++.
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a-~~~~p~~~~~~~-~l~~   85 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKA-LELDPNNAEAKQ-NLGN   85 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHH-HhcCCCCHHHHH-HHHH
Confidence            35677788888888899999998888763 2 335677888888888999999999999998 888888887676 7777


Q ss_pred             HHHhcC
Q 044988          456 VYAAAK  461 (538)
Q Consensus       456 ~~~~~g  461 (538)
                      ++.+.|
T Consensus        86 ~~~~~g   91 (91)
T 1na3_A           86 AKQKQG   91 (91)
T ss_dssp             HHHHHC
T ss_pred             HHHhcC
Confidence            766543

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=97.59  E-value=4.4e-06  Score=77.67  Aligned_cols=360  Identities=11%  Similarity=0.051  Sum_probs=195.2

Q ss_pred             ChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHc
Q 044988           51 KNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCAR  130 (538)
Q Consensus        51 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~  130 (538)
                      .+.+|+.|..++...+++.+|++-|  ++..|+..|..+|.+..+.|.+++-+..+...++.  .-++..=+.|+-+|++
T Consensus        53 ~p~VWs~LgkAqL~~~~v~eAIdsy--IkA~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~--~ke~~IDteLi~ayAk  128 (624)
T 3lvg_A           53 EPAVWSQLAKAQLQKGMVKEAIDSY--IKADDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFALAK  128 (624)
T ss_dssp             CCCCSSSHHHHTTTSSSCTTTTTSS--CCCSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTT--CCSTTTTHHHHHHHHT
T ss_pred             CccHHHHHHHHHHccCchHHHHHHH--HhCCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--hcccccHHHHHHHHHh
Confidence            4567777888887777777777755  33456667777888888888888888877766654  2344444577777888


Q ss_pred             cCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC------------------------CC
Q 044988          131 CGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA------------------------RS  186 (538)
Q Consensus       131 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~------------------------~~  186 (538)
                      .++..+.++++       -.||..-...+..-|...|.   ++.|.-+|..+..                        .+
T Consensus       129 ~~rL~elEefl-------~~~N~A~iq~VGDrcf~e~l---YeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns  198 (624)
T 3lvg_A          129 TNRLAELEEFI-------NGPNNAHIQQVGDRCYDEKM---YDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANS  198 (624)
T ss_dssp             SCSSSTTTSTT-------SCCSSSCTHHHHHHHHHSCC---STTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCS
T ss_pred             hCcHHHHHHHH-------cCCCcccHHHHHHHHHHccC---HHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            77766544432       13565556666677777777   7777666655442                        25


Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHccC-CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 044988          187 VVSWNSLLKGYVKRGDIDGAWKIFDEM-PHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAE  265 (538)
Q Consensus       187 ~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~  265 (538)
                      +.+|..+-.+|...+.+.-|.-.--.+ ..+|  -...++..|-..|.+++-+.+++.-... -......|+-|.-.|++
T Consensus       199 ~ktWKeV~~ACvd~~EfrLAqicGLniIvhad--eL~elv~~YE~~G~f~ELIsLlEaglgl-ErAHmGmFTELaILYsK  275 (624)
T 3lvg_A          199 TRTWKEVCFACVDGKEFRLAQMCGLHIVVHAD--ELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSK  275 (624)
T ss_dssp             SCSHHHHTHHHHHSCTTTTTTHHHHHHHCCSS--CCSGGGSSSSTTCCCTTSTTTHHHHTTS-TTCCHHHHHHHHHHHHS
T ss_pred             hhHHHHHHHHHhCchHHHHHHHhcchhcccHH--HHHHHHHHHHhCCCHHHHHHHHHHHhCC-CchhHHHHHHHHHHHHh
Confidence            566776666776666665443222111 1111  0112344566667777777766665421 23455566666655555


Q ss_pred             cCChHHHHHHHHHHHHhccCCCCCc------chhHHHHHHHHHHhCCCHHHHHHHHH-------------hcCC--CCcc
Q 044988          266 IGDLKLGKWIHSYVEENFSVGREPV------LVSLNNALIHMYASCGEIEEAYGVFR-------------KMQR--RNTV  324 (538)
Q Consensus       266 ~~~~~~a~~~~~~~~~~~~~~~~~~------~~~~~~~l~~~~~~~g~~~~a~~~~~-------------~m~~--~~~~  324 (538)
                      - ++++..+.++..-..   -.+|.      ....|.-++-.|..-.+++.|....-             ++..  .|..
T Consensus       276 Y-~PeKlmEHlklf~sr---iNipKviracE~ahLW~ElvfLY~~ydE~DnA~ltMi~h~~~Aw~h~~Fkdii~KVaN~E  351 (624)
T 3lvg_A          276 F-KPQKMREHLELFWSR---VNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVE  351 (624)
T ss_dssp             S-CTTHHHHHHTTSSSS---SCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHHHHTTTSCHHHHCCGGGGTTTGGGCSCSH
T ss_pred             c-CHHHHHHHHHHHHHh---ccHHHHHHHHHHHhhHHHHHHHHhcchhHHHHHHHHHhCChhhccHHHHHHHHHHcchHH
Confidence            4 333333332222111   12221      23345555555655555554432110             0000  2444


Q ss_pred             hHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc-------CC-Ccc-HHHHHHHHHHhhhcCCh
Q 044988          325 SWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW-------GI-KPR-IEHYGCMVDLFSRAGLM  395 (538)
Q Consensus       325 ~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~-------~~-~p~-~~~~~~l~~~~~~~g~~  395 (538)
                      .|-..|.-|....-     ...+.++.++...=|..++.++|++.-...       .+ .-| ..+-.++-+.|....++
T Consensus       352 iyYKAi~FYL~e~P-----~lL~DLL~vL~prlDh~RvV~~~~k~~~LpLIkpYL~~Vq~~N~~aVNeAln~L~IEEEDy  426 (624)
T 3lvg_A          352 LYYRAIQFYLEFKP-----LLLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDY  426 (624)
T ss_dssp             HHHHHHHHHTTSCC-----TTSHHHHHHHCTTCCSTTTHHHHHTTTCGGGGTGGGTSCCCSCCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHHhCh-----HHHHHHHHhccccCChHHHHHHHHhcCCchhhHHHHHHHHHhhHHHHHHHHHHHHhhhhhH
Confidence            45544554444331     224556666666666666666666532110       11 112 34445666677777777


Q ss_pred             HHHHHHHHhCC------------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 044988          396 DEAFSLVQNMP------------MKPNDAVLGSLLLGCRIHNNAELASQVAQK  436 (538)
Q Consensus       396 ~~A~~~~~~~~------------~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~  436 (538)
                      +.-....+.-.            ..+-...-..-...|.+++++++++.+.++
T Consensus       427 ~~LR~SId~ydNFD~i~LA~rLEkHeL~eFRrIAA~LYkkn~rw~qsi~l~Kk  479 (624)
T 3lvg_A          427 QALRTSIDAYDNFDNISLAQRLEKHELIEFRRIAAYLFKGNNRWKQSVELCKK  479 (624)
T ss_dssp             HHHHHTTSSCCCSCTTHHHHHHHTCSSHHHHHHHHHHHHTTCHHHHHSSCSST
T ss_pred             HHHHHHHHHhccccHHHHHHHHhhCchHHHHHHHHHHHHhcccHHHHHHHHHh
Confidence            65544443321            223333334444457788888877665443

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.57  E-value=0.00036  Score=64.77  Aligned_cols=94  Identities=13%  Similarity=-0.017  Sum_probs=74.4

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHH------------------HHHHHHHHHHccCChHHHHHHHHHHHH
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQV------------------ALVAALSACAEIGDLKLGKWIHSYVEE  281 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~------------------~~~~li~~~~~~~~~~~a~~~~~~~~~  281 (538)
                      .+..+...+.+.|++++|...|++....  .|+..                  .|..+..++.+.|+++.|...++.+.+
T Consensus       181 ~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~l~~~~~~nla~~~~~~g~~~~A~~~~~~al~  258 (338)
T 2if4_A          181 RRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFMFQLYGKYQDMALAVKNPCHLNIAACLIKLKRYDEAIGHCNIVLT  258 (338)
T ss_dssp             HHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHHHTCCHHHHHHHHHHHTHHHHHHHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchhhhhcccHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3555556666667777777777766552  33332                  678888889999999999999999998


Q ss_pred             hccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          282 NFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       282 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      .     .|.+...+..+..+|...|++++|...|++..+
T Consensus       259 ~-----~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~  292 (338)
T 2if4_A          259 E-----EEKNPKALFRRGKAKAELGQMDSARDDFRKAQK  292 (338)
T ss_dssp             H-----CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC
T ss_pred             h-----CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            7     677888888999999999999999999999876

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=97.56  E-value=0.0012  Score=52.05  Aligned_cols=112  Identities=11%  Similarity=-0.022  Sum_probs=93.7

Q ss_pred             CcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHH
Q 044988          357 GFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRI----HNNAELASQ  432 (538)
Q Consensus       357 ~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~~~~~~A~~  432 (538)
                      +++++|...|++..+. | .|+..    |...|...+.+++|.+.|++.....+...+..|...|..    .+++++|.+
T Consensus         9 ~d~~~A~~~~~~aa~~-g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~   82 (138)
T 1klx_A            9 KDLKKAIQYYVKACEL-N-EMFGC----LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQ   82 (138)
T ss_dssp             HHHHHHHHHHHHHHHT-T-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHH
T ss_pred             cCHHHHHHHHHHHHcC-C-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHH
Confidence            4788999999999876 5 33333    888888889999999999988655788888889888888    899999999


Q ss_pred             HHHHchhccCCCCcccHHHHHHHHHHh----cCChHHHHHHHHHHHhCCC
Q 044988          433 VAQKLVAEIDPEQAAGYLALVANVYAA----AKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       433 ~~~~~~~~~~p~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~~~  478 (538)
                      .|++. .+.  .++..+. .|+.+|..    .++.++|.+++++..+.|.
T Consensus        83 ~~~~A-a~~--g~~~a~~-~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           83 YYSKA-CGL--NDQDGCL-ILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHH-HHT--TCHHHHH-HHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHH-HcC--CCHHHHH-HHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            99999 554  4555577 89999998    8999999999999988765

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.53  E-value=0.00019  Score=54.54  Aligned_cols=64  Identities=9%  Similarity=0.035  Sum_probs=46.3

Q ss_pred             CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          410 NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       410 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +...+..+...+...|++++|+..++++ ....|++...+. .++.+|...|++++|...+++..+
T Consensus        18 ~~~~~~~lg~~~~~~g~~~~A~~~~~~a-l~~~p~~~~~~~-~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A           18 NMLLRFTLGKTYAEHEQFDAALPHLRAA-LDFDPTYSVAWK-WLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHH-HHHCCCcHHHHH-HHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3566666667777777777777777777 677777776666 777777777777777777777664

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=97.52  E-value=0.00067  Score=63.71  Aligned_cols=119  Identities=8%  Similarity=-0.006  Sum_probs=86.4

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHccCCC-------------------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCC
Q 044988          189 SWNSLLKGYVKRGDIDGAWKIFDEMPH-------------------RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARV  249 (538)
Q Consensus       189 ~~~~li~~~~~~g~~~~A~~~~~~m~~-------------------~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~  249 (538)
                      .|..+...+.+.|++++|+..|++..+                   .+..+|..+..+|.+.|++++|+..+++..+.. 
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-  303 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-  303 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-
Confidence            456666677777777777777766542                   133567778888888888888888888887743 


Q ss_pred             CCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHH
Q 044988          250 GLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYG  313 (538)
Q Consensus       250 ~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~  313 (538)
                      +-+...+..+..++...|++++|...++.+.+.     .|.+...+..+..++...++.+++.+
T Consensus       304 p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l-----~P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          304 PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI-----APEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh-----CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            235667777788888888888888888888886     56666777777777777776666554

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.50  E-value=0.00014  Score=54.70  Aligned_cols=96  Identities=15%  Similarity=0.098  Sum_probs=63.5

Q ss_pred             cchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCc------hhHH
Q 044988           83 TAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSN------VFIR  156 (538)
Q Consensus        83 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~  156 (538)
                      ...|..+...+.+.|++++|+..|++..+.. +.+...+..+..++...|++++|...+++.++.. +.+      ...+
T Consensus         4 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~   81 (111)
T 2l6j_A            4 FEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYT-STAEHVAIRSKLQ   81 (111)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC-SSTTSHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCccHHHHHHHHH
Confidence            3456667777777888888888888777642 3355677777777788888888888888877653 222      4455


Q ss_pred             hHHHHHHHhcCCCCChhHHHHHhhcCC
Q 044988          157 TNLMNLYLMSGGECGVGCARLLFDDMP  183 (538)
Q Consensus       157 ~~l~~~~~~~g~~~~~~~a~~~~~~~~  183 (538)
                      ..+..++...|+   .+.|...+++++
T Consensus        82 ~~~~~~~~~~~~---~~~a~~~~~~~~  105 (111)
T 2l6j_A           82 YRLELAQGAVGS---VQIPVVEVDELP  105 (111)
T ss_dssp             HHHHHHHHHHHC---CCCCSSSSSSCS
T ss_pred             HHHHHHHHHHHh---HhhhHhHHHHhH
Confidence            556666666666   655555555443

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=97.48  E-value=0.00017  Score=70.49  Aligned_cols=115  Identities=11%  Similarity=-0.023  Sum_probs=56.5

Q ss_pred             HHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHH
Q 044988           61 FYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREG  137 (538)
Q Consensus        61 ~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a  137 (538)
                      .+.+.|++++|++.|++..   +.+...|..+..+|.+.|++++|+..+++..+.. +-+..+|..+..++...|++++|
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA   93 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAA   93 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHH
Confidence            3344555555555555443   2234455555566666666666666666655532 22344555555566666666666


Q ss_pred             HHHHHHHHHhCCCCchhHHhHHHHH--HHhcCCCCChhHHHHHhh
Q 044988          138 EQVHGRVLASGYCSNVFIRTNLMNL--YLMSGGECGVGCARLLFD  180 (538)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~~l~~~--~~~~g~~~~~~~a~~~~~  180 (538)
                      .+.+++..+.. +.+...+..+..+  +.+.|+   +++|.+.++
T Consensus        94 ~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~g~---~~~A~~~~~  134 (477)
T 1wao_1           94 LRDYETVVKVK-PHDKDAKMKYQECNKIVKQKA---FERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHS-TTCTTHHHHHHHHHHHHHHHH---HCCC-----
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHHH---HHHHhcccc
Confidence            66666655543 2223333333333  444455   555555444

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.37  E-value=0.001  Score=48.01  Aligned_cols=69  Identities=13%  Similarity=0.108  Sum_probs=57.5

Q ss_pred             CCCHHHHHHHHHHHHhcCC---HHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          408 KPNDAVLGSLLLGCRIHNN---AELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       408 ~p~~~~~~~l~~~~~~~~~---~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      .+|...+..+..++...++   .++|..+++++ ....|+++.+.. .++..+.+.|++++|+..|+++.+...
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~A-L~~dp~~~rA~~-~lg~~~~~~g~y~~Ai~~w~~~l~~~p   74 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQA-LQLEPYNEAALS-LIANDHFISFRFQEAIDTWVLLLDSND   74 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHTCCC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHH-HHHCcCCHHHHH-HHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            3456777777777654544   68999999999 999999999888 999999999999999999999987544

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.36  E-value=0.00056  Score=66.47  Aligned_cols=128  Identities=10%  Similarity=-0.037  Sum_probs=86.0

Q ss_pred             HHccCChHHHHHHHHHHHHhccC---CCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC-------CC----cchHHH
Q 044988          263 CAEIGDLKLGKWIHSYVEENFSV---GREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR-------RN----TVSWTS  328 (538)
Q Consensus       263 ~~~~~~~~~a~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-------~~----~~~~~~  328 (538)
                      +...|++++|..+++...+....   ...|....+++.|..+|...|++++|..++++...       ++    ..+++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            45678888888888877665332   12345667888999999999999999998887653       21    235666


Q ss_pred             HHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCC-Ccc-HHHHHHHHHHhhhcCChHHHHHHHHhCC
Q 044988          329 MITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGI-KPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP  406 (538)
Q Consensus       329 li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~-~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~  406 (538)
                      |...|...|++++|...             +++|+.+++...   |- .|+ ..+.+.+..++...+.+++|..+|..++
T Consensus       399 La~~~~~~G~~~eA~~~-------------~~~Al~i~~~~l---G~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~  462 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGM-------------ICKAYAILLVTH---GPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMR  462 (490)
T ss_dssp             HHHHHHHTTCHHHHHHH-------------HHHHHHHHHHHT---CTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHH-------------HHHHHHHHHHHh---CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66677777766666522             233444444433   32 233 4466777778888888888888887763

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=97.36  E-value=0.00062  Score=65.10  Aligned_cols=118  Identities=8%  Similarity=-0.006  Sum_probs=88.9

Q ss_pred             HHHhhhcCChHHHHHHHHhCC------CCCC----HHHHHHHHHHHHhcCCHHHHHHHHHHch----hccCCCCc---cc
Q 044988          386 VDLFSRAGLMDEAFSLVQNMP------MKPN----DAVLGSLLLGCRIHNNAELASQVAQKLV----AEIDPEQA---AG  448 (538)
Q Consensus       386 ~~~~~~~g~~~~A~~~~~~~~------~~p~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~----~~~~p~~~---~~  448 (538)
                      +..+.+.|++++|++++++..      ..|+    ..+++.+..+|...|++++|+.+++++.    .-+.|+++   ..
T Consensus       294 ie~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~  373 (429)
T 3qwp_A          294 IEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQ  373 (429)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHH
T ss_pred             HHHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHH
Confidence            445667889999999987652      2233    4578888889999999999999999886    23445544   34


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHhCCCCCCCceeEEEECCEEEEEEeCCCCCcchHHHHHHHHHHHHHHHH
Q 044988          449 YLALVANVYAAAKRWQDVAAVRQKMIKMGVRKPPGQSWVQINGVLHDFVAGDSTYKQASLIYKTLGEITMQAMQ  522 (538)
Q Consensus       449 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~m~~  522 (538)
                      +. .|+.+|...|++++|..++++..+--.                  ..-...||...+.+..+.+.+.+|+.
T Consensus       374 l~-nLa~~~~~~g~~~eA~~~~~~Al~i~~------------------~~lG~~Hp~~~~~~~~l~~~~~e~~~  428 (429)
T 3qwp_A          374 VM-KVGKLQLHQGMFPQAMKNLRLAFDIMR------------------VTHGREHSLIEDLILLLEECDANIRA  428 (429)
T ss_dssp             HH-HHHHHHHHTTCHHHHHHHHHHHHHHHH------------------HHTCTTSHHHHHHHHHHHHHHHHHHC
T ss_pred             HH-HHHHHHHhcCCHHHHHHHHHHHHHHHH------------------HhcCCCChHHHHHHHHHHHHHHHHhc
Confidence            55 789999999999999999999875100                  12245799999999999988888763

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.16  E-value=0.0057  Score=43.46  Aligned_cols=80  Identities=13%  Similarity=0.068  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHH
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNAL  298 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l  298 (538)
                      ..|..+...+...|++++|+..|++..+.. +.+...+..+...+...|++++|...++...+.     .|.+...+..+
T Consensus        10 ~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~-----~p~~~~~~~~l   83 (91)
T 1na3_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL-----DPNNAEAKQNL   83 (91)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc-----CCCCHHHHHHH
Confidence            456666677777777777777777776642 224556666666777777777777777777765     45555555555


Q ss_pred             HHHHHh
Q 044988          299 IHMYAS  304 (538)
Q Consensus       299 ~~~~~~  304 (538)
                      ..++..
T Consensus        84 ~~~~~~   89 (91)
T 1na3_A           84 GNAKQK   89 (91)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            555543

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.12  E-value=0.00027  Score=56.21  Aligned_cols=48  Identities=15%  Similarity=0.182  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcC-----------ChHHHHHHHHHHHhC
Q 044988          427 AELASQVAQKLVAEIDPEQAAGYLALVANVYAAAK-----------RWQDVAAVRQKMIKM  476 (538)
Q Consensus       427 ~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g-----------~~~~A~~~~~~m~~~  476 (538)
                      +++|+..|+++ .++.|+...+|. .++.+|.+.|           ++++|++.|++..+.
T Consensus        62 ~~eAi~~le~A-L~ldP~~~~A~~-~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~l  120 (158)
T 1zu2_A           62 IQEAITKFEEA-LLIDPKKDEAVW-CIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDE  120 (158)
T ss_dssp             HHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH-HHhCcCcHHHHH-HHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHHh
Confidence            67999999999 999999999899 9999999875           899999999999873

>1zu2_A Mitochondrial import receptor subunit TOM20-3; TPR, tetratricopeptide repeat like, TPR-like, transport protein; NMR {Arabidopsis thaliana} SCOP: a.118.8.1

Probab=97.01  E-value=0.00088  Score=53.25  Aligned_cols=110  Identities=16%  Similarity=0.195  Sum_probs=83.0

Q ss_pred             cCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCCh----------HHHHHHHHhCC-CCCC-HHHHHHHHHHHH
Q 044988          356 GGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLM----------DEAFSLVQNMP-MKPN-DAVLGSLLLGCR  422 (538)
Q Consensus       356 ~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~----------~~A~~~~~~~~-~~p~-~~~~~~l~~~~~  422 (538)
                      .+.+++|.+.++...+.   .| +...|..+..++...+++          ++|+..|++.. +.|+ ...|..+..+|.
T Consensus        15 ~~~feeA~~~~~~Ai~l---~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~   91 (158)
T 1zu2_A           15 ILLFEQIRQDAENTYKS---NPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYT   91 (158)
T ss_dssp             HHHHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHH
Confidence            34788899999998876   56 688888888888888764          58999998874 4555 778999999998


Q ss_pred             hcC-----------CHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 044988          423 IHN-----------NAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       423 ~~~-----------~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                      ..|           ++++|++.|+++ .++.|++.. |...+ ..      .++|-++.-.+...+
T Consensus        92 ~lg~l~P~~~~a~g~~~eA~~~~~kA-l~l~P~~~~-y~~al-~~------~~ka~el~~~~~~~~  148 (158)
T 1zu2_A           92 SFAFLTPDETEAKHNFDLATQFFQQA-VDEQPDNTH-YLKSL-EM------TAKAPQLHAEAYKQG  148 (158)
T ss_dssp             HHHHHCCCHHHHHHHHHHHHHHHHHH-HHHCTTCHH-HHHHH-HH------HHTHHHHHHHHHHSS
T ss_pred             HhcccCcchhhhhccHHHHHHHHHHH-HHhCCCCHH-HHHHH-HH------HHhCHhccCcccccc
Confidence            774           899999999999 999999877 55133 22      244556555555443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.92  E-value=0.005  Score=45.05  Aligned_cols=59  Identities=12%  Similarity=0.118  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHh
Q 044988          254 VALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRK  317 (538)
Q Consensus       254 ~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  317 (538)
                      ..+..+...+...|++++|...++.+.+.     .|.+...|..+..+|...|++++|.+.|++
T Consensus         8 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~-----~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~   66 (100)
T 3ma5_A            8 FTRYALAQEHLKHDNASRALALFEELVET-----DPDYVGTYYHLGKLYERLDRTDDAIDTYAQ   66 (100)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----STTCTHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHh-----CCCcHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            33444444444444444444444444443     333334444444444444444444444443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=96.89  E-value=0.0075  Score=45.36  Aligned_cols=77  Identities=9%  Similarity=-0.075  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHH
Q 044988          236 QALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVF  315 (538)
Q Consensus       236 ~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  315 (538)
                      +|+..|++..+.. +.+...+..+...+...|+++.|...++...+.     .|.+...+..+..+|...|++++|...|
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~-----~p~~~~~~~~la~~~~~~g~~~~A~~~~   76 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDF-----DPTYSVAWKWLGKTLQGQGDRAGARQAW   76 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH-----CCCcHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            3555565555532 224555555666666666666666666666665     4445555556666666666666666666


Q ss_pred             Hhc
Q 044988          316 RKM  318 (538)
Q Consensus       316 ~~m  318 (538)
                      ++.
T Consensus        77 ~~a   79 (115)
T 2kat_A           77 ESG   79 (115)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>1qsa_A Protein (soluble lytic transglycosylase SLT70); alpha-superhelix, transferase; HET: GOL; 1.65A {Escherichia coli} SCOP: a.118.5.1 d.2.1.6 PDB: 1qte_A* 1sly_A*

Probab=96.86  E-value=0.44  Score=47.50  Aligned_cols=257  Identities=9%  Similarity=0.013  Sum_probs=129.3

Q ss_pred             HHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHH
Q 044988          192 SLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKL  271 (538)
Q Consensus       192 ~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~  271 (538)
                      ..+..+.+.+++......+.. ...+...-.....+....|+..+|......+-..|- .....+..++..+.+.|.+..
T Consensus        77 ~~l~~l~~~~~w~~~l~~~~~-~p~~~~~~c~~~~A~~~~G~~~~a~~~~~~lW~~~~-~~p~~c~~l~~~~~~~g~lt~  154 (618)
T 1qsa_A           77 RFVNELARREDWRGLLAFSPE-KPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTGK-SQPNACDKLFSVWRASGKQDP  154 (618)
T ss_dssp             HHHHHHHHTTCHHHHHHHCCS-CCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCSS-CCCTHHHHHHHHHHHTTCSCH
T ss_pred             HHHHHHHhCCCHHHHHHhccC-CCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHhCCC-CCcHHHHHHHHHHHHCCCCCH
Confidence            344556667777777776665 323444444556667777887777776666655442 222334445554444333221


Q ss_pred             HHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcch-HHHHHHHHHhcCCcc----------
Q 044988          272 GKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVS-WTSMITGFAKQGYAQ----------  340 (538)
Q Consensus       272 a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~-~~~li~~~~~~~~~~----------  340 (538)
                                          ...+ .-+......|+...|..+...+.. +... ...++..+..-....          
T Consensus       155 --------------------~~~~-~R~~~al~~~~~~~a~~l~~~l~~-~~~~~a~~~~al~~~p~~~~~~~~~~~~~~  212 (618)
T 1qsa_A          155 --------------------LAYL-ERIRLAMKAGNTGLVTVLAGQMPA-DYQTIASAIISLANNPNTVLTFARTTGATD  212 (618)
T ss_dssp             --------------------HHHH-HHHHHHHHTTCHHHHHHHHHTCCG-GGHHHHHHHHHHHHCGGGHHHHHHHSCCCH
T ss_pred             --------------------HHHH-HHHHHHHHCCCHHHHHHHHHhCCH-HHHHHHHHHHHHHhChHhHHHHHhccCCCh
Confidence                                1122 122333344445555544444421 1111 111111111000000          


Q ss_pred             HHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccH--HHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHHH
Q 044988          341 EALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRI--EHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGSL  417 (538)
Q Consensus       341 ~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~--~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l  417 (538)
                      .....+...+.-..+. +.+.|...+....+...+.+..  ..+..+...+...+...++...+.... ..++.....-.
T Consensus       213 ~~~~~~~~~~~rlar~-d~~~A~~~~~~~~~~~~~~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  291 (618)
T 1qsa_A          213 FTRQMAAVAFASVARQ-DAENARLMIPSLAQAQQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQSTSLIERR  291 (618)
T ss_dssp             HHHHHHHHHHHHHHHH-CHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTCCCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhc-CHHHHHHHHHhhhhccCCCHHHHHHHHHHHHHHHHHcCCChHHHHHHHhccccCCChHHHHHH
Confidence            0001111122222222 6788888888776553333322  233344444555553455555555432 23444334444


Q ss_pred             HHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          418 LLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       418 ~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +....+.|+++.|...|+.+ ....+....... -++.++...|+.++|..+|+.+.+
T Consensus       292 ~r~Alr~~d~~~a~~~~~~l-~~~~~~~~r~~Y-W~~ra~~~~g~~~~a~~~~~~~a~  347 (618)
T 1qsa_A          292 VRMALGTGDRRGLNTWLARL-PMEAKEKDEWRY-WQADLLLERGREAEAKEILHQLMQ  347 (618)
T ss_dssp             HHHHHHHTCHHHHHHHHHHS-CTTGGGSHHHHH-HHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHCCCHHHHHHHHHHc-cccccccHhHHH-HHHHHHHHcCCHHHHHHHHHHHhc
Confidence            45556778999999988888 443333344345 677788888998888888887753

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.84  E-value=0.0021  Score=61.31  Aligned_cols=83  Identities=12%  Similarity=0.055  Sum_probs=51.6

Q ss_pred             cCChHHHHHHHHhCC------CCC---C-HHHHHHHHHHHHhcCCHHHHHHHHHHch----hccCCCCc---ccHHHHHH
Q 044988          392 AGLMDEAFSLVQNMP------MKP---N-DAVLGSLLLGCRIHNNAELASQVAQKLV----AEIDPEQA---AGYLALVA  454 (538)
Q Consensus       392 ~g~~~~A~~~~~~~~------~~p---~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~----~~~~p~~~---~~~~~~l~  454 (538)
                      .|++++|..++++..      ..|   + ..+++.|..+|...|++++|+.+++++.    .-+.|+++   ..+. .|+
T Consensus       311 ~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~-nLa  389 (433)
T 3qww_A          311 YKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWL-KLG  389 (433)
T ss_dssp             TSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHH-HHH
T ss_pred             ccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHH-HHH
Confidence            456666666665431      122   2 3466666777777777777777777665    22334433   3344 677


Q ss_pred             HHHHhcCChHHHHHHHHHHHh
Q 044988          455 NVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       455 ~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .+|..+|++++|..++++..+
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHH
Confidence            788888888888888877764

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.74  E-value=0.057  Score=49.47  Aligned_cols=113  Identities=9%  Similarity=0.127  Sum_probs=71.4

Q ss_pred             cHHHHHHHHHHhhhhcCCCcc-HHHHHHHHHHhhh----cCC-------hHHHHHHHHhCC-CCCCHHHHHHHHHHHHhc
Q 044988          358 FVDEGRQFFECMNQNWGIKPR-IEHYGCMVDLFSR----AGL-------MDEAFSLVQNMP-MKPNDAVLGSLLLGCRIH  424 (538)
Q Consensus       358 ~~~~a~~~~~~~~~~~~~~p~-~~~~~~l~~~~~~----~g~-------~~~A~~~~~~~~-~~p~~~~~~~l~~~~~~~  424 (538)
                      ...+|..+|++..+.   .|+ ...|..+..+|.-    .+.       ...+.+....+. ...+..+|..+...+...
T Consensus       214 ~~~~A~~l~e~Al~l---DP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a~~~~~~~a~~~~alal~~l~~  290 (372)
T 3ly7_A          214 SLNRASELLGEIVQS---SPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVTLPELNNLSIIYQIKAVSALVK  290 (372)
T ss_dssp             HHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHTCGGGTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHhcccCCcCHHHHHHHHHHHHhC
Confidence            467788888887765   665 3444444433321    100       111222222222 245577777777767777


Q ss_pred             CCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          425 NNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       425 ~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      |++++|...++++ ..+.|+. ..|. .++.++.-.|++++|.+.+++....
T Consensus       291 gd~d~A~~~l~rA-l~Ln~s~-~a~~-llG~~~~~~G~~~eA~e~~~~AlrL  339 (372)
T 3ly7_A          291 GKTDESYQAINTG-IDLEMSW-LNYV-LLGKVYEMKGMNREAADAYLTAFNL  339 (372)
T ss_dssp             TCHHHHHHHHHHH-HHHCCCH-HHHH-HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HhcCCCH-HHHH-HHHHHHHHCCCHHHHHHHHHHHHhc
Confidence            8888888888888 7777653 3366 8888888888888888888877763

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.72  E-value=0.0067  Score=57.85  Aligned_cols=93  Identities=10%  Similarity=-0.077  Sum_probs=70.6

Q ss_pred             ccCcHHHHHHHHHHhhhhc----CC-Ccc-HHHHHHHHHHhhhcCChHHHHHHHHhCC---------CCCC-HHHHHHHH
Q 044988          355 HGGFVDEGRQFFECMNQNW----GI-KPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP---------MKPN-DAVLGSLL  418 (538)
Q Consensus       355 ~~~~~~~a~~~~~~~~~~~----~~-~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~---------~~p~-~~~~~~l~  418 (538)
                      ..|++++|+.++++..+..    |- .|+ ..+++.|..+|...|++++|..++++..         ..|+ ..+++.|.
T Consensus       310 ~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa  389 (433)
T 3qww_A          310 HYKSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLG  389 (433)
T ss_dssp             TTSCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHH
Confidence            3456777777777655431    11 233 5689999999999999999999998763         3344 46889999


Q ss_pred             HHHHhcCCHHHHHHHHHHch----hccCCCCcc
Q 044988          419 LGCRIHNNAELASQVAQKLV----AEIDPEQAA  447 (538)
Q Consensus       419 ~~~~~~~~~~~A~~~~~~~~----~~~~p~~~~  447 (538)
                      ..|...|++++|+.+++++.    .-+.|+++.
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~i~~~~lG~~Hp~  422 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIAIMEVAHGKDHPY  422 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHH
T ss_pred             HHHHhccCHHHHHHHHHHHHHHHHHHcCCCChH
Confidence            99999999999999999986    445666665

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.69  E-value=0.067  Score=40.37  Aligned_cols=116  Identities=11%  Similarity=0.139  Sum_probs=83.3

Q ss_pred             cCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHh----------------------hhcCChHHHHHHHHhCCCCCCHHH
Q 044988          356 GGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLF----------------------SRAGLMDEAFSLVQNMPMKPNDAV  413 (538)
Q Consensus       356 ~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~----------------------~~~g~~~~A~~~~~~~~~~p~~~~  413 (538)
                      .|.++++.++..+....    .+..-||-.|--.                      ..+|++.....-+-.+.  .+...
T Consensus        20 dG~v~qGveii~k~~~s----sni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDis~C~NlKrVi~C~~~~n--~~se~   93 (172)
T 1wy6_A           20 DGYIDEGVKIVLEITKS----STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINN--TLNEH   93 (172)
T ss_dssp             TTCHHHHHHHHHHHHHH----SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTT--CCCHH
T ss_pred             hhhHHHHHHHHHHHcCC----CCccccceeeeecchhhchhHHHHHHHHHhhhcCcHhhhcHHHHHHHHHHhc--chHHH
Confidence            46778888888877654    1222233222222                      24556666665555553  45566


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCC
Q 044988          414 LGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVR  479 (538)
Q Consensus       414 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  479 (538)
                      ++..+.....+|+-++-.+++..+ .+..|.++.... -++.+|.+-|+..+|.+++++..++|++
T Consensus        94 vd~ALd~lv~~~KkDqLdki~~~~-l~n~~~~~~~l~-kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           94 VNKALDILVIQGKRDKLEEIGREI-LKNNEVSASILV-AIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHH-C--CCSCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHHhccHhHHHHHHHHH-hccCCCChHHHH-HHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            778888999999999999999997 566677777566 8999999999999999999999999984

>1klx_A Cysteine rich protein B; structural genomics, helix-turn-helix, right handed super helix, modular structure', hydrolase; 1.95A {Helicobacter pylori} SCOP: a.118.18.1

Probab=96.65  E-value=0.017  Score=45.22  Aligned_cols=110  Identities=9%  Similarity=-0.115  Sum_probs=86.3

Q ss_pred             CChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC-CCCcchHHHHHHHHhc----CCCchHHHHH
Q 044988           31 NTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE-NPSTAIWNQMIRGHAR----SETPEKSVYL  105 (538)
Q Consensus        31 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-~~~~~~~~~li~~~~~----~~~~~~a~~~  105 (538)
                      +++++|...+....+.|.   +...  |-..|...+.+++|.+.|++.- ..+...+..|...|..    .+++++|+.+
T Consensus         9 ~d~~~A~~~~~~aa~~g~---~~a~--lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~   83 (138)
T 1klx_A            9 KDLKKAIQYYVKACELNE---MFGC--LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQY   83 (138)
T ss_dssp             HHHHHHHHHHHHHHHTTC---TTHH--HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCC---Hhhh--HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHHH
Confidence            467888889998888872   2233  6777777778888988887755 4567778888888877    7889999999


Q ss_pred             HHHhHhCCCCCCcchHHHHHHHHHc----cCCcHHHHHHHHHHHHhC
Q 044988          106 YKQMIDKETEPDEYTYSFLLSVCAR----CGLFREGEQVHGRVLASG  148 (538)
Q Consensus       106 ~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~  148 (538)
                      |++..+.|   +...+..|...|..    .+++++|...+++..+.|
T Consensus        84 ~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           84 YSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            99988764   56677778888877    788999999999888877

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=96.63  E-value=0.13  Score=51.15  Aligned_cols=181  Identities=8%  Similarity=-0.042  Sum_probs=130.2

Q ss_pred             CHHHHHHHHccCCC--C-ChHHHHHHHHHHHHcCC----------HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC-
Q 044988          202 DIDGAWKIFDEMPH--R-NVVSWTTMISGCAQNGK----------SRQALSLFNEMRRARVGLDQVALVAALSACAEIG-  267 (538)
Q Consensus       202 ~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~~----------~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~-  267 (538)
                      ..++|++.++++..  | +..+|+.--..+...|+          ++++++.++.+.+.. +-+...|..-.-.+.+.+ 
T Consensus        44 ~~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l~~  122 (567)
T 1dce_A           44 LDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPE  122 (567)
T ss_dssp             CSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSS
T ss_pred             CCHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHccc
Confidence            34577888887663  4 34567776666666666          899999999998753 335677777777777888 


Q ss_pred             -ChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCC-CHHHHHHHHHhcCCC---CcchHHHHHHHHHhcCCccHH
Q 044988          268 -DLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCG-EIEEAYGVFRKMQRR---NTVSWTSMITGFAKQGYAQEA  342 (538)
Q Consensus       268 -~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~a~~~~~~m~~~---~~~~~~~li~~~~~~~~~~~a  342 (538)
                       +++++...++.+.+.     .|.+..+|+.-..++.+.| .++++.+.++++.+.   |..+|+.....+.+.+...++
T Consensus       123 ~~~~~el~~~~k~l~~-----d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~~  197 (567)
T 1dce_A          123 PNWARELELCARFLEA-----DERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDS  197 (567)
T ss_dssp             CCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCS
T ss_pred             ccHHHHHHHHHHHHhh-----ccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhhcccccc
Confidence             679999999999997     7889999998888888999 899999999999874   556777766666553222100


Q ss_pred             HHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHH
Q 044988          343 LLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDE  397 (538)
Q Consensus       343 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~  397 (538)
                      ..      .+-...+.++++.+.+......   .| |...|+-+...+.+.++.++
T Consensus       198 ~~------~~~~~~~~~~eel~~~~~ai~~---~P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          198 GP------QGRLPENVLLKELELVQNAFFT---DPNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             SS------CCSSCHHHHHHHHHHHHHHHHH---CSSCSHHHHHHHHHHSCCCCCSC
T ss_pred             cc------cccccHHHHHHHHHHHHHHHhh---CCCCccHHHHHHHHHhcCCCccc
Confidence            00      0000113578888999888865   56 57888888888888777444

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=96.59  E-value=0.0094  Score=46.79  Aligned_cols=87  Identities=11%  Similarity=0.031  Sum_probs=42.6

Q ss_pred             cHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcC---ChHHHHHHHHhCC-CC-C--CHHHHHHHHHHHHhcCCHHHH
Q 044988          358 FVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAG---LMDEAFSLVQNMP-MK-P--NDAVLGSLLLGCRIHNNAELA  430 (538)
Q Consensus       358 ~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~-~~-p--~~~~~~~l~~~~~~~~~~~~A  430 (538)
                      .+..+++-|.+..+. + .++..+...+..++++.+   +.++++.+|+... .. |  +...+-.+.-++.+.|++++|
T Consensus        13 ~l~~~~~~y~~e~~~-~-~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A   90 (152)
T 1pc2_A           13 DLLKFEKKFQSEKAA-G-SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKA   90 (152)
T ss_dssp             HHHHHHHHHHHHHHT-T-CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHH
T ss_pred             HHHHHHHHHHHHHcc-C-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHH
Confidence            344455555544432 2 245555555555555555   3445555555442 11 2  123333344445555555555


Q ss_pred             HHHHHHchhccCCCCcc
Q 044988          431 SQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       431 ~~~~~~~~~~~~p~~~~  447 (538)
                      .+.++.+ .+..|++..
T Consensus        91 ~~y~~~l-L~ieP~n~Q  106 (152)
T 1pc2_A           91 LKYVRGL-LQTEPQNNQ  106 (152)
T ss_dssp             HHHHHHH-HHHCTTCHH
T ss_pred             HHHHHHH-HhcCCCCHH
Confidence            5555555 555555544

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=96.59  E-value=0.002  Score=60.30  Aligned_cols=360  Identities=12%  Similarity=0.083  Sum_probs=202.8

Q ss_pred             ccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhc
Q 044988           16 KALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHAR   95 (538)
Q Consensus        16 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~   95 (538)
                      ++..|..++.++.+.|.++.....+....+.  ..++.+=+.|+-+|++.++..+-.+++.   .||..-...+.+-|..
T Consensus        82 Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~--~ke~~IDteLi~ayAk~~rL~elEefl~---~~N~A~iq~VGDrcf~  156 (624)
T 3lvg_A           82 DPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFALAKTNRLAELEEFIN---GPNNAHIQQVGDRCYD  156 (624)
T ss_dssp             CCCSSSHHHHHTTTSSCCTTHHHHHHTTSTT--CCSTTTTHHHHHHHHTSCSSSTTTSTTS---CCSSSCTHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--hcccccHHHHHHHHHhhCcHHHHHHHHc---CCCcccHHHHHHHHHH
Confidence            4457789999999999999998888776665  3456666789999999988766544332   3555555555555555


Q ss_pred             CCCchHHHHHHHHhHhCC--------------------CCCCcchHHHHHHHHHccCCcHHHH-----------------
Q 044988           96 SETPEKSVYLYKQMIDKE--------------------TEPDEYTYSFLLSVCARCGLFREGE-----------------  138 (538)
Q Consensus        96 ~~~~~~a~~~~~~m~~~~--------------------~~p~~~~~~~li~~~~~~~~~~~a~-----------------  138 (538)
                      .|.++.|.-+|..+....                    -.-++.||..+-.+|...+.+..|.                 
T Consensus       157 e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktWKeV~~ACvd~~EfrLAqicGLniIvhadeL~elv  236 (624)
T 3lvg_A          157 EKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWKEVCFACVDGKEFRLAQMCGLHIVVHADELEELI  236 (624)
T ss_dssp             SCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHHHHTHHHHHSCTTTTTTHHHHHHHCCSSCCSGGG
T ss_pred             ccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHHHHHHHHhCchHHHHHHHhcchhcccHHHHHHHH
Confidence            555555555544432110                    0235567777777777666655543                 


Q ss_pred             -------------HHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCC----C-------CchhHHHHH
Q 044988          139 -------------QVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPA----R-------SVVSWNSLL  194 (538)
Q Consensus       139 -------------~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~----~-------~~~~~~~li  194 (538)
                                   .+++.-+.. -......|+.|.-.|++-.    .++..+.++..-.    |       ....|.-++
T Consensus       237 ~~YE~~G~f~ELIsLlEaglgl-ErAHmGmFTELaILYsKY~----PeKlmEHlklf~sriNipKviracE~ahLW~Elv  311 (624)
T 3lvg_A          237 NYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFK----PQKMREHLELFWSRVNIPKVLRAAEQAHLWAELV  311 (624)
T ss_dssp             SSSSTTCCCTTSTTTHHHHTTS-TTCCHHHHHHHHHHHHSSC----TTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHhCC-CchhHHHHHHHHHHHHhcC----HHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHH
Confidence                         333332211 1234456778888887765    4555555444332    2       456788888


Q ss_pred             HHHHhcCCHHHHHHHHcc-------------CC--CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHH
Q 044988          195 KGYVKRGDIDGAWKIFDE-------------MP--HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAA  259 (538)
Q Consensus       195 ~~~~~~g~~~~A~~~~~~-------------m~--~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~l  259 (538)
                      -.|++-.++|.|....-.             +.  -.|...|-..|+.|.... +..--+++.-+.. .+.++     .+
T Consensus       312 fLY~~ydE~DnA~ltMi~h~~~Aw~h~~Fkdii~KVaN~EiyYKAi~FYL~e~-P~lL~DLL~vL~p-rlDh~-----Rv  384 (624)
T 3lvg_A          312 FLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFK-PLLLNDLLMVLSP-RLDHT-----RA  384 (624)
T ss_dssp             HHHHHHTCHHHHHHTTTSCHHHHCCGGGGTTTGGGCSCSHHHHHHHHHHTTSC-CTTSHHHHHHHCT-TCCST-----TT
T ss_pred             HHHhcchhHHHHHHHHHhCChhhccHHHHHHHHHHcchHHHHHHHHHHHHHhC-hHHHHHHHHhccc-cCChH-----HH
Confidence            888888888866533211             11  145556666666665432 2222233322211 11111     22


Q ss_pred             HHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC------------CCcchHH
Q 044988          260 LSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR------------RNTVSWT  327 (538)
Q Consensus       260 i~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~------------~~~~~~~  327 (538)
                      ++.+.+.|++.....++..+       ....+..+..++-+.|....+++.-+...+.-..            .+..-+.
T Consensus       385 V~~~~k~~~LpLIkpYL~~V-------q~~N~~aVNeAln~L~IEEEDy~~LR~SId~ydNFD~i~LA~rLEkHeL~eFR  457 (624)
T 3lvg_A          385 VNYFSKVKQLPLVKPYLRSV-------QNHNNKSVNESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLEKHELIEFR  457 (624)
T ss_dssp             HHHHHTTTCGGGGTGGGTSC-------CCSCCHHHHHHHHHHHHHTTCCHHHHHTTSSCCCSCTTHHHHHHHTCSSHHHH
T ss_pred             HHHHHhcCCchhhHHHHHHH-------HHhhHHHHHHHHHHHHhhhhhHHHHHHHHHHhccccHHHHHHHHhhCchHHHH
Confidence            33334444444433222211       2334455566777788888887765554433222            1111122


Q ss_pred             H-HHHHHHhcCCccHHH------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHH
Q 044988          328 S-MITGFAKQGYAQEAL------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFS  400 (538)
Q Consensus       328 ~-li~~~~~~~~~~~a~------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~  400 (538)
                      . -...|.+++++.+++      ..|...+.....+|+.+.++++++...+. |   +...|.+.+-.|-..=+++-+++
T Consensus       458 rIAA~LYkkn~rw~qsi~l~KkDklykDAietAa~S~~~elaeeLL~yFv~~-g---~~EcF~a~LytCYdLlrpDvVlE  533 (624)
T 3lvg_A          458 RIAAYLFKGNNRWKQSVELCKKDSLYKDAMQYASESKDTELAEELLQWFLQE-E---KRECFGACLFTCYDLLRPDVVLE  533 (624)
T ss_dssp             HHHHHHHHTTCHHHHHSSCSSTTCCTTGGGTTTTTCCCTTHHHHHHHHHHHH-C---STHHHHHHHHHTSSSSSCHHHHH
T ss_pred             HHHHHHHHhcccHHHHHHHHHhcccHHHHHHHHHHcCCHHHHHHHHHHHHHc-C---chHHHHHHHHHHhhccChHHHHH
Confidence            2 233456677777766      45666666777777777777777777664 2   34455556555656666676666


Q ss_pred             HHH
Q 044988          401 LVQ  403 (538)
Q Consensus       401 ~~~  403 (538)
                      +-.
T Consensus       534 laW  536 (624)
T 3lvg_A          534 TAW  536 (624)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            643

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.58  E-value=0.0051  Score=44.72  Aligned_cols=53  Identities=23%  Similarity=0.329  Sum_probs=24.6

Q ss_pred             HHhcCCHHHHHHHHHHchhccCCCCcc-cHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          421 CRIHNNAELASQVAQKLVAEIDPEQAA-GYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       421 ~~~~~~~~~A~~~~~~~~~~~~p~~~~-~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +...|++++|...++++ ....|++.. .+. .++.+|...|++++|.+.|++..+
T Consensus        10 ~~~~~~~~~A~~~~~~a-l~~~p~~~~~~~~-~lg~~~~~~~~~~~A~~~~~~al~   63 (99)
T 2kc7_A           10 LINQGDIENALQALEEF-LQTEPVGKDEAYY-LMGNAYRKLGDWQKALNNYQSAIE   63 (99)
T ss_dssp             HHHHTCHHHHHHHHHHH-HHHCSSTHHHHHH-HHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHH-HHHCCCcHHHHHH-HHHHHHHHcCCHHHHHHHHHHHHh
Confidence            34444444444444444 444444444 444 444444444444444444444443

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.57  E-value=0.27  Score=51.46  Aligned_cols=153  Identities=14%  Similarity=0.076  Sum_probs=89.8

Q ss_pred             HHccCCcHHHHH-HHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHH
Q 044988          128 CARCGLFREGEQ-VHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGA  206 (538)
Q Consensus       128 ~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A  206 (538)
                      ....++++.|.+ ++..      .++......++..+.+.|.   .+.|.++.+..        ..-.......|+++.|
T Consensus       609 ~~~~~~~~~a~~~~l~~------i~~~~~~~~~~~~l~~~~~---~~~a~~~~~~~--------~~~f~~~l~~~~~~~A  671 (814)
T 3mkq_A          609 LTLRGEIEEAIENVLPN------VEGKDSLTKIARFLEGQEY---YEEALNISPDQ--------DQKFELALKVGQLTLA  671 (814)
T ss_dssp             HHHTTCHHHHHHHTGGG------CCCHHHHHHHHHHHHHTTC---HHHHHHHCCCH--------HHHHHHHHHHTCHHHH
T ss_pred             HHHhCCHHHHHHHHHhc------CCchHHHHHHHHHHHhCCC---hHHheecCCCc--------chheehhhhcCCHHHH
Confidence            345667777655 4311      1101122566677777777   77777665321        1123345667888888


Q ss_pred             HHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCC
Q 044988          207 WKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVG  286 (538)
Q Consensus       207 ~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~  286 (538)
                      .++.+.+.  +...|..+...+.+.++++.|.+.|.++..         |..+...+...++.+....+.+.....    
T Consensus       672 ~~~~~~~~--~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~----  736 (814)
T 3mkq_A          672 RDLLTDES--AEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAETT----  736 (814)
T ss_dssp             HHHHTTCC--CHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHHHT----
T ss_pred             HHHHHhhC--cHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHHHc----
Confidence            88877664  456788888888888888888888887743         334444444466666555444444333    


Q ss_pred             CCCcchhHHHHHHHHHHhCCCHHHHHHHHHhc
Q 044988          287 REPVLVSLNNALIHMYASCGEIEEAYGVFRKM  318 (538)
Q Consensus       287 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  318 (538)
                      +.      ++....+|.+.|++++|.+++.++
T Consensus       737 ~~------~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          737 GK------FNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             TC------HHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             Cc------hHHHHHHHHHcCCHHHHHHHHHHc
Confidence            11      122333455566666666666554

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.53  E-value=0.015  Score=55.54  Aligned_cols=97  Identities=9%  Similarity=-0.015  Sum_probs=74.3

Q ss_pred             HHhcccCcHHHHHHHHHHhhhhcC--CCcc----HHHHHHHHHHhhhcCChHHHHHHHHhCC---------CCCC-HHHH
Q 044988          351 SACSHGGFVDEGRQFFECMNQNWG--IKPR----IEHYGCMVDLFSRAGLMDEAFSLVQNMP---------MKPN-DAVL  414 (538)
Q Consensus       351 ~~~~~~~~~~~a~~~~~~~~~~~~--~~p~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~---------~~p~-~~~~  414 (538)
                      ..+...|++++|+.++++..+...  +.|+    ..+++.|..+|...|++++|+.++++..         ..|+ ..++
T Consensus       295 e~~~~~g~~~~a~~~~~~~L~~~~~~lg~~h~~~~~~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l  374 (429)
T 3qwp_A          295 EELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQV  374 (429)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTCSSCCCCTTSHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHH
T ss_pred             HHHHhhccHHHHHHHHHHHHHhccCcCCccchHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHH
Confidence            334456688888888887765321  2222    5689999999999999999999998763         3344 4688


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHch----hccCCCCcc
Q 044988          415 GSLLLGCRIHNNAELASQVAQKLV----AEIDPEQAA  447 (538)
Q Consensus       415 ~~l~~~~~~~~~~~~A~~~~~~~~----~~~~p~~~~  447 (538)
                      +.|...|...|++++|+.+++++.    .-+.|+++.
T Consensus       375 ~nLa~~~~~~g~~~eA~~~~~~Al~i~~~~lG~~Hp~  411 (429)
T 3qwp_A          375 MKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSL  411 (429)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHHHHHhcCCCChH
Confidence            899999999999999999999986    446677766

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.29  E-value=0.016  Score=41.90  Aligned_cols=64  Identities=14%  Similarity=0.142  Sum_probs=45.5

Q ss_pred             HHHHhhhcCChHHHHHHHHhCC-CCC-CHH-HHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccH
Q 044988          385 MVDLFSRAGLMDEAFSLVQNMP-MKP-NDA-VLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGY  449 (538)
Q Consensus       385 l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~-~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~  449 (538)
                      ....+.+.|++++|.+.|++.. ..| +.. .+..+..++...|++++|...|+++ ....|++...+
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a-l~~~p~~~~~~   72 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSA-IELNPDSPALQ   72 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHHCTTSTHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhcCCCcHHHH
Confidence            3455667778888887777663 234 345 6777777788888888888888888 77788777644

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.15  E-value=0.066  Score=49.07  Aligned_cols=73  Identities=10%  Similarity=-0.052  Sum_probs=62.1

Q ss_pred             CccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          376 KPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       376 ~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                      +.+..+|..+...+...|++++|...++++. ..|+...|..+...+...|++++|.+.++++ ..+.|..++ |.
T Consensus       274 ~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln~s~~a~~llG~~~~~~G~~~eA~e~~~~A-lrL~P~~~t-~~  347 (372)
T 3ly7_A          274 NNLSIIYQIKAVSALVKGKTDESYQAINTGIDLEMSWLNYVLLGKVYEMKGMNREAADAYLTA-FNLRPGANT-LY  347 (372)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHSCSHHH-HH
T ss_pred             CcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH-HhcCCCcCh-HH
Confidence            4467888888887888899999999999874 5688888878888899999999999999999 999998876 55

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=95.92  E-value=0.21  Score=52.31  Aligned_cols=155  Identities=15%  Similarity=0.108  Sum_probs=89.0

Q ss_pred             HHHhccCChHHHHH-HHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchHHH
Q 044988           25 SLLQIRNTTKTLFQ-IHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSV  103 (538)
Q Consensus        25 ~~~~~~~~~~~a~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~  103 (538)
                      ......++++.|.+ ++..     + ++......++..+.+.|..++|.++.+.-        ..-.....+.|+++.|+
T Consensus       607 ~~~~~~~~~~~a~~~~l~~-----i-~~~~~~~~~~~~l~~~~~~~~a~~~~~~~--------~~~f~~~l~~~~~~~A~  672 (814)
T 3mkq_A          607 QTLTLRGEIEEAIENVLPN-----V-EGKDSLTKIARFLEGQEYYEEALNISPDQ--------DQKFELALKVGQLTLAR  672 (814)
T ss_dssp             HHHHHTTCHHHHHHHTGGG-----C-CCHHHHHHHHHHHHHTTCHHHHHHHCCCH--------HHHHHHHHHHTCHHHHH
T ss_pred             hHHHHhCCHHHHHHHHHhc-----C-CchHHHHHHHHHHHhCCChHHheecCCCc--------chheehhhhcCCHHHHH
Confidence            44455778887766 4421     1 11223367777788888888888776321        11133345678888888


Q ss_pred             HHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCC
Q 044988          104 YLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMP  183 (538)
Q Consensus       104 ~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~  183 (538)
                      ++.+.+      .+...|..+...+.+.++++.|.+.|.++..         +..+...|...|+   .+...++-+...
T Consensus       673 ~~~~~~------~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~---~~~~~~~~~~a~  734 (814)
T 3mkq_A          673 DLLTDE------SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNN---KEGLVTLAKDAE  734 (814)
T ss_dssp             HHHTTC------CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTC---HHHHHHHHHHHH
T ss_pred             HHHHhh------CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCC---HHHHHHHHHHHH
Confidence            875433      4567888888888888888888888887643         3345555555665   444333221111


Q ss_pred             CCCchhHHHHHHHHHhcCCHHHHHHHHccC
Q 044988          184 ARSVVSWNSLLKGYVKRGDIDGAWKIFDEM  213 (538)
Q Consensus       184 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  213 (538)
                      ..  .-++....+|.+.|++++|.+++.++
T Consensus       735 ~~--~~~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          735 TT--GKFNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             HT--TCHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             Hc--CchHHHHHHHHHcCCHHHHHHHHHHc
Confidence            10  11233333445556666665555543

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=95.65  E-value=0.11  Score=37.06  Aligned_cols=71  Identities=13%  Similarity=0.029  Sum_probs=54.5

Q ss_pred             CccHHHHHHHHHHhhhcCC---hHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          376 KPRIEHYGCMVDLFSRAGL---MDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       376 ~p~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      +.|...+..+..++...++   .++|..++++.. ..|+ ......+...+.+.|++++|+..|+++ .+..|+++.
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~-l~~~p~~~~   78 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLL-LDSNDPNLD   78 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HTCCCTTCC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HhhCCCCcc
Confidence            3467777788877765554   789999998874 4454 667777777899999999999999999 888888443

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=95.41  E-value=0.68  Score=37.30  Aligned_cols=46  Identities=15%  Similarity=0.235  Sum_probs=24.5

Q ss_pred             HccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchHHHHHHHHhH
Q 044988           63 VTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMI  110 (538)
Q Consensus        63 ~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~  110 (538)
                      ...|+++.|.++.+.+  .+...|..|.....++|+++-|.++|....
T Consensus        16 L~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~   61 (177)
T 3mkq_B           16 LEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQH   61 (177)
T ss_dssp             HHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTT
T ss_pred             HhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhC
Confidence            3455555555555444  234455555555555555555555555543

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=95.40  E-value=0.047  Score=42.85  Aligned_cols=80  Identities=8%  Similarity=-0.071  Sum_probs=60.7

Q ss_pred             hHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHchhccC-C-CCcccHHHHHHHHHHhcCChHHHH
Q 044988          395 MDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHN---NAELASQVAQKLVAEID-P-EQAAGYLALVANVYAAAKRWQDVA  467 (538)
Q Consensus       395 ~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~---~~~~A~~~~~~~~~~~~-p-~~~~~~~~~l~~~~~~~g~~~~A~  467 (538)
                      ...+.+.|.+..  -.++..+.-.+..++.+.+   +.++++.+++.. .+.. | ++...+. .|+-+|.+.|++++|.
T Consensus        14 l~~~~~~y~~e~~~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~l-l~~~~p~~~rd~lY-~LAv~~~kl~~Y~~A~   91 (152)
T 1pc2_A           14 LLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEEL-LPKGSKEEQRDYVF-YLAVGNYRLKEYEKAL   91 (152)
T ss_dssp             HHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHH-HHHSCHHHHHHHHH-HHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHHccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH-HhcCCccchHHHHH-HHHHHHHHccCHHHHH
Confidence            344444454431  2467888888888999988   667999999999 6656 6 4455566 8888999999999999


Q ss_pred             HHHHHHHhC
Q 044988          468 AVRQKMIKM  476 (538)
Q Consensus       468 ~~~~~m~~~  476 (538)
                      +.++.+.+.
T Consensus        92 ~y~~~lL~i  100 (152)
T 1pc2_A           92 KYVRGLLQT  100 (152)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhc
Confidence            999999874

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=95.23  E-value=1.6  Score=39.03  Aligned_cols=171  Identities=10%  Similarity=0.016  Sum_probs=106.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHH----HHHHHHHCCCCCCHHHHHHHHHHHHc
Q 044988          190 WNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALS----LFNEMRRARVGLDQVALVAALSACAE  265 (538)
Q Consensus       190 ~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~----~~~~m~~~g~~p~~~~~~~li~~~~~  265 (538)
                      |.++..-|.+.+++++|++++..           -...+.+.|+...|-+    +++...+.+++++......++..+..
T Consensus        36 ~Rtl~~Ry~~~~~~~eAidlL~~-----------ga~~ll~~~Q~~sa~DLa~llvev~~~~~~~~~~~~~~rl~~l~~~  104 (312)
T 2wpv_A           36 LRTIANRYVRSKSYEHAIELISQ-----------GALSFLKAKQGGSGTDLIFYLLEVYDLAEVKVDDISVARLVRLIAE  104 (312)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHH-----------HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCCSHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHH-----------HHHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence            45666677777788888777653           2233455677655555    45555667888888888888877655


Q ss_pred             cCChH-HHHHHHHHHHHhcc-CCC-CCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhc---CCc
Q 044988          266 IGDLK-LGKWIHSYVEENFS-VGR-EPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQ---GYA  339 (538)
Q Consensus       266 ~~~~~-~a~~~~~~~~~~~~-~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~---~~~  339 (538)
                      ...-+ .-..+.+.+.+.-. .++ ...++.....+...|.+.|++.+|+..|-.-...+...+..++.-+...   |..
T Consensus       105 ~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~~~~~s~~~~a~~l~~w~~~~~~~~~  184 (312)
T 2wpv_A          105 LDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLGTHDSMIKYVDLLWDWLCQVDDIED  184 (312)
T ss_dssp             CCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTCCCH
T ss_pred             CCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHhCCCccHHHHHHHHHHHHHhcCCCCc
Confidence            33211 12334444443321 111 2346677788999999999999999988743333566777777766665   655


Q ss_pred             cHHHHHHHHHHHHhcccCcHHHHHHHHHHhhh
Q 044988          340 QEALLTFLGVLSACSHGGFVDEGRQFFECMNQ  371 (538)
Q Consensus       340 ~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  371 (538)
                      .++-......+--|.-.|++..|..+|+...+
T Consensus       185 ~e~dlf~~RaVL~yL~l~n~~~A~~~~~~f~~  216 (312)
T 2wpv_A          185 STVAEFFSRLVFNYLFISNISFAHESKDIFLE  216 (312)
T ss_dssp             HHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            55543334444444556677777777766543

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=95.12  E-value=0.18  Score=44.35  Aligned_cols=106  Identities=13%  Similarity=0.102  Sum_probs=76.3

Q ss_pred             cHHHHHHHHHHhhhhcCCCcc---HHHHHHHHHHhhhc-----CChHHHHHHHHhCC-CCCC--HHHHHHHHHHHHh-cC
Q 044988          358 FVDEGRQFFECMNQNWGIKPR---IEHYGCMVDLFSRA-----GLMDEAFSLVQNMP-MKPN--DAVLGSLLLGCRI-HN  425 (538)
Q Consensus       358 ~~~~a~~~~~~~~~~~~~~p~---~~~~~~l~~~~~~~-----g~~~~A~~~~~~~~-~~p~--~~~~~~l~~~~~~-~~  425 (538)
                      ....|...+++..+.   .|+   ...|..|...|.+.     |+.++|.+.|++.. +.|+  ..++......++. .|
T Consensus       178 ~l~~A~a~lerAleL---DP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~g  254 (301)
T 3u64_A          178 TVHAAVMMLERACDL---WPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLN  254 (301)
T ss_dssp             HHHHHHHHHHHHHHH---CTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTT
T ss_pred             hHHHHHHHHHHHHHh---CCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcC
Confidence            567778888887765   676   56889999989884     89999999998874 5663  6777777777777 48


Q ss_pred             CHHHHHHHHHHchhccCCCC-cccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          426 NAELASQVAQKLVAEIDPEQ-AAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       426 ~~~~A~~~~~~~~~~~~p~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      +.+.+.+.+++. ....|.. +. +  .+    ...++-++|..+++++.
T Consensus       255 d~~~a~~~L~kA-L~a~p~~~P~-~--~l----an~~~q~eA~~LL~~~~  296 (301)
T 3u64_A          255 NRAGFDEALDRA-LAIDPESVPH-N--KL----LVILSQKRARWLKAHVQ  296 (301)
T ss_dssp             CHHHHHHHHHHH-HHCCGGGCSS-C--HH----HHHHHHHHHHHHHHTHH
T ss_pred             CHHHHHHHHHHH-HcCCCCCCCC-h--hH----HHHHHHHHHHHHHHHhH
Confidence            999999999999 7776664 33 2  22    22334466777766654

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.11  E-value=0.11  Score=39.12  Aligned_cols=88  Identities=14%  Similarity=0.061  Sum_probs=47.9

Q ss_pred             CcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHH---HHHHHHhCCCC--C-C-HHHHHHHHHHHHhcCCHHH
Q 044988          357 GFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDE---AFSLVQNMPMK--P-N-DAVLGSLLLGCRIHNNAEL  429 (538)
Q Consensus       357 ~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~---A~~~~~~~~~~--p-~-~~~~~~l~~~~~~~~~~~~  429 (538)
                      ..+..+++-|...... | .|+..+-..+..++.+..+...   ++.+++.+...  | + ....-.|.-++.+.|++++
T Consensus        15 ~~l~~~~~~y~~e~~~-~-~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~   92 (126)
T 1nzn_A           15 EDLLKFEKKFQSEKAA-G-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEK   92 (126)
T ss_dssp             HHHHHHHHHHHHHHHH-S-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHHHhcc-C-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHH
Confidence            3444555555554443 2 2555555666666666665444   66666655322  2 1 1222334445666666666


Q ss_pred             HHHHHHHchhccCCCCcc
Q 044988          430 ASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       430 A~~~~~~~~~~~~p~~~~  447 (538)
                      |.+.++.+ .+..|++..
T Consensus        93 A~~~~~~l-L~~eP~n~Q  109 (126)
T 1nzn_A           93 ALKYVRGL-LQTEPQNNQ  109 (126)
T ss_dssp             HHHHHHHH-HHHCTTCHH
T ss_pred             HHHHHHHH-HHhCCCCHH
Confidence            66666666 666666655

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=95.03  E-value=0.088  Score=38.57  Aligned_cols=72  Identities=15%  Similarity=0.047  Sum_probs=55.2

Q ss_pred             cHHHHHHHHHHhhhcCChHHHHHHHHhCC---------CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCccc
Q 044988          378 RIEHYGCMVDLFSRAGLMDEAFSLVQNMP---------MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAG  448 (538)
Q Consensus       378 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---------~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~  448 (538)
                      +..-+..|...+.+.|++..|...|+...         -.+....+..+..++.+.|+++.|...++++ ..+.|++..+
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~a-l~l~P~~~~~   82 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKL-LELDPEHQRA   82 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHH-HhcCCCCHHH
Confidence            44455677778888888888888887652         0134677888888999999999999999999 8999998774


Q ss_pred             HH
Q 044988          449 YL  450 (538)
Q Consensus       449 ~~  450 (538)
                      ..
T Consensus        83 ~~   84 (104)
T 2v5f_A           83 NG   84 (104)
T ss_dssp             HH
T ss_pred             Hh
Confidence            33

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=94.99  E-value=1.1  Score=36.01  Aligned_cols=100  Identities=13%  Similarity=0.101  Sum_probs=60.3

Q ss_pred             HHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHH
Q 044988          163 YLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFN  242 (538)
Q Consensus       163 ~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~  242 (538)
                      ....|+   ++.|.++.+++  .+...|..|.......|+++-|.+.|.+..+     +..+.-.|.-.|+.++..++-+
T Consensus        15 AL~lg~---l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D-----~~~L~~Ly~~tg~~e~L~kla~   84 (177)
T 3mkq_B           15 ALEYGN---LDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQHS-----FDKLSFLYLVTGDVNKLSKMQN   84 (177)
T ss_dssp             HHHTTC---HHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC-----HHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHhcCC---HHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC-----HHHHHHHHHHhCCHHHHHHHHH
Confidence            345555   66666665544  2455677777777777777777777777654     3344444555677666655555


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHH
Q 044988          243 EMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSY  278 (538)
Q Consensus       243 ~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~  278 (538)
                      .....|      -++....++.-.|+++++.+++..
T Consensus        85 iA~~~g------~~n~af~~~l~lGdv~~~i~lL~~  114 (177)
T 3mkq_B           85 IAQTRE------DFGSMLLNTFYNNSTKERSSIFAE  114 (177)
T ss_dssp             HHHHTT------CHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHCc------cHHHHHHHHHHcCCHHHHHHHHHH
Confidence            444443      234455556667777777777643

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=94.97  E-value=0.27  Score=35.87  Aligned_cols=65  Identities=11%  Similarity=-0.091  Sum_probs=44.3

Q ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC------CCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          218 VVSWTTMISGCAQNGKSRQALSLFNEMRRAR------VGLDQVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       218 ~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g------~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      ...+..+...+.+.|++..|...|+...+.-      -.+....+..+..++.+.|+++.|...++.+.+.
T Consensus         5 a~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l   75 (104)
T 2v5f_A            5 AEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL   75 (104)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            3445567777778888888888888776521      1234556667777777777777777777777765

>3u64_A Protein TP_0956; tetratrico peptide repeat, protein-prote interaction, syphilis, lipoprotein, transport protein; 2.30A {Treponema pallidum subsp} PDB: 4di3_A 4di4_A*

Probab=94.85  E-value=0.08  Score=46.46  Aligned_cols=83  Identities=11%  Similarity=0.091  Sum_probs=68.2

Q ss_pred             hHHHHHHHHhCC-CCCC---HHHHHHHHHHHHh-----cCCHHHHHHHHHHchhccCCCC-cccHHHHHHHHHHhc-CCh
Q 044988          395 MDEAFSLVQNMP-MKPN---DAVLGSLLLGCRI-----HNNAELASQVAQKLVAEIDPEQ-AAGYLALVANVYAAA-KRW  463 (538)
Q Consensus       395 ~~~A~~~~~~~~-~~p~---~~~~~~l~~~~~~-----~~~~~~A~~~~~~~~~~~~p~~-~~~~~~~l~~~~~~~-g~~  463 (538)
                      ...|...+++.. ..|+   ...|..+...|.+     -|+.++|.+.|+++ ..+.|+. ...+. ..++.++.. |+.
T Consensus       179 l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferA-L~LnP~~~id~~v-~YA~~l~~~~gd~  256 (301)
T 3u64_A          179 VHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHL-TRYCSAHDPDHHI-TYADALCIPLNNR  256 (301)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHH-HHHCCTTCSHHHH-HHHHHTTTTTTCH
T ss_pred             HHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHH-HHhCCCCCchHHH-HHHHHHHHhcCCH
Confidence            456666666653 5677   5688888888888     49999999999999 9999975 77788 889999884 999


Q ss_pred             HHHHHHHHHHHhCCCC
Q 044988          464 QDVAAVRQKMIKMGVR  479 (538)
Q Consensus       464 ~~A~~~~~~m~~~~~~  479 (538)
                      ++|.+.+++.......
T Consensus       257 ~~a~~~L~kAL~a~p~  272 (301)
T 3u64_A          257 AGFDEALDRALAIDPE  272 (301)
T ss_dssp             HHHHHHHHHHHHCCGG
T ss_pred             HHHHHHHHHHHcCCCC
Confidence            9999999999986654

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=94.47  E-value=0.17  Score=51.38  Aligned_cols=119  Identities=11%  Similarity=0.092  Sum_probs=79.9

Q ss_pred             HHhcccCc-HHHHHHHHHHhhhhcCCCccHHH--HHHHHHHhhhcCC-hHHHHHHHHhCC---------CC-CCHH----
Q 044988          351 SACSHGGF-VDEGRQFFECMNQNWGIKPRIEH--YGCMVDLFSRAGL-MDEAFSLVQNMP---------MK-PNDA----  412 (538)
Q Consensus       351 ~~~~~~~~-~~~a~~~~~~~~~~~~~~p~~~~--~~~l~~~~~~~g~-~~~A~~~~~~~~---------~~-p~~~----  412 (538)
                      ..+...++ ++.|..+|+++.+.   .|...+  ...++..+.+.++ --+|.+++.+..         .. .+..    
T Consensus       256 ~~~~~t~~~~~~a~~~le~L~~~---~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~~~~  332 (754)
T 4gns_B          256 SFIAITPSLVDFTIDYLKGLTKK---DPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADSARL  332 (754)
T ss_dssp             HHHHTCGGGHHHHHHHHHHHHHH---CGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHH
T ss_pred             HHHcccccHHHHHHHHHHHHHhh---CCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhcccccccccc
Confidence            33334445 57899999999876   554332  2334444444332 223444443321         11 1111    


Q ss_pred             ------HHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          413 ------VLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       413 ------~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                            ....-...|...|+++.|+++.+++ ....|.+..+|. .|+.+|.+.|+|+.|+-.++.+.
T Consensus       333 ~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~A-V~~aPseF~tW~-~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          333 MNCMSDLLNIQTNFLLNRGDYELALGVSNTS-TELALDSFESWY-NLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCSSCHHHHH-HHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             cCcchHHHHHHHHHHhccCcHHHHHHHHHHH-HhcCchhhHHHH-HHHHHHHHhccHHHHHHHHhcCC
Confidence                  1222233477899999999999999 999999999999 99999999999999999999985

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=94.38  E-value=2.8  Score=37.77  Aligned_cols=171  Identities=15%  Similarity=0.079  Sum_probs=106.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHH----HHHHHHCCCCCCHHHHHHHHHHHHc
Q 044988          190 WNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSL----FNEMRRARVGLDQVALVAALSACAE  265 (538)
Q Consensus       190 ~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~----~~~m~~~g~~p~~~~~~~li~~~~~  265 (538)
                      |.++..-|.+.+++++|++++-.           -...+.+.|+...+-++    ++...+.++++|......++..+..
T Consensus        38 ~RTi~~Ry~~~k~y~eAidLL~~-----------GA~~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~~L~~~  106 (336)
T 3lpz_A           38 TRLVAARYSKQGNWAAAVDILAS-----------VSQTLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLLGCLRL  106 (336)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHH-----------HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhhcCHHHHHHHHHH-----------HHHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Confidence            44566667777888888777543           22334555666554444    3555567888888887777777765


Q ss_pred             cCChH-HHHHHHHHHHHhccC-C-CCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHH
Q 044988          266 IGDLK-LGKWIHSYVEENFSV-G-REPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEA  342 (538)
Q Consensus       266 ~~~~~-~a~~~~~~~~~~~~~-~-~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a  342 (538)
                      ...-+ .-..+.+.+.+.-.. + ...-++.....+...|.+.+++.+|+..|-.-..+.+..+..++.-+...+...++
T Consensus       107 ~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~ilg~~~s~~~~a~mL~ew~~~~~~~e~  186 (336)
T 3lpz_A          107 FQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHLVLGTKESPEVLARMEYEWYKQDESHTA  186 (336)
T ss_dssp             SCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHTTSCTTHHHHHHHHHHHHHHTSCGGGH
T ss_pred             CCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHhcCCchHHHHHHHHHHHHHhcCCccH
Confidence            54321 112333333332111 1 23445667778999999999999999999532233346787777777766665555


Q ss_pred             HHHHHHHHHHhcccCcHHHHHHHHHHhhh
Q 044988          343 LLTFLGVLSACSHGGFVDEGRQFFECMNQ  371 (538)
Q Consensus       343 ~~~~~~ll~~~~~~~~~~~a~~~~~~~~~  371 (538)
                      -......+--|.-.+++..|..+++...+
T Consensus       187 dlfiaRaVL~yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          187 PLYCARAVLPYLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            54455555556667788888887766554

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=94.37  E-value=1.3  Score=33.98  Aligned_cols=66  Identities=5%  Similarity=-0.036  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHhcCCH---HHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          409 PNDAVLGSLLLGCRIHNNA---ELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       409 p~~~~~~~l~~~~~~~~~~---~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      |+..+--.+..++.+..+.   .+++.+++.+ ....|....-+.-.|+-++.+.|++++|.++.+.+.+
T Consensus        37 vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l-~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~  105 (144)
T 1y8m_A           37 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDI-YKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  105 (144)
T ss_dssp             SCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHH-HHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH-HhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            4444444444555554432   3555666665 4444533222222556666666666666666666665

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=94.10  E-value=1.4  Score=33.36  Aligned_cols=60  Identities=15%  Similarity=0.099  Sum_probs=26.4

Q ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          222 TTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       222 ~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      +..+..+...|.-+.-.+++..+.. +.+|++.....+..+|.+.|+..++..++..+.+.
T Consensus        95 d~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~k  154 (172)
T 1wy6_A           95 NKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIEACKK  154 (172)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHh
Confidence            3334444444444444444444322 22344444444444444444444444444444444

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.05  E-value=4.3  Score=38.72  Aligned_cols=232  Identities=9%  Similarity=0.026  Sum_probs=120.3

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHC--CCCCC---HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc--hh
Q 044988          221 WTTMISGCAQNGKSRQALSLFNEMRRA--RVGLD---QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL--VS  293 (538)
Q Consensus       221 ~~~li~~~~~~~~~~~a~~~~~~m~~~--g~~p~---~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~--~~  293 (538)
                      ...|...|...|++.+|.+++..+...  |.-+.   ...+...++.|...+++..|..++..+.........++.  ..
T Consensus       140 ~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~  219 (445)
T 4b4t_P          140 TKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSILKGDYSQATVLSRKILKKTFKNPKYESLKLE  219 (445)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHH
Confidence            345667777888888888888887643  22111   234556677788888888888888776542211122222  34


Q ss_pred             HHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc
Q 044988          294 LNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       294 ~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  373 (538)
                      .+...+..+...+++.+|-+.|.++.+           .+...++..........++.+..-.+....-..+....... 
T Consensus       220 ~~~~~~~~~~~e~~y~~a~~~y~e~~~-----------~~~~~~d~~~~~~~L~~~v~~~iLa~~~~~~~~ll~~~~~~-  287 (445)
T 4b4t_P          220 YYNLLVKISLHKREYLEVAQYLQEIYQ-----------TDAIKSDEAKWKPVLSHIVYFLVLSPYGNLQNDLIHKIQND-  287 (445)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHHHHHH-----------HHHHHSCHHHHHHHHHHHHHHHHHSSCSSTTHHHHHSHHHH-
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHh-----------cccccCCHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHhhc-
Confidence            556677777788888888877766532           22222222211111111111110011111111222222222 


Q ss_pred             CCCccHHHHHHHHHHhhhc--CChHHHHHHHHhCCCC--------CCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCC
Q 044988          374 GIKPRIEHYGCMVDLFSRA--GLMDEAFSLVQNMPMK--------PNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDP  443 (538)
Q Consensus       374 ~~~p~~~~~~~l~~~~~~~--g~~~~A~~~~~~~~~~--------p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p  443 (538)
                      ...++...|..++.+|...  .+++.+.+.|......        .....|..|......++ +-..          ..|
T Consensus       288 ~~~~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~L~~~v~ehn-l~~i----------~k~  356 (445)
T 4b4t_P          288 NNLKKLESQESLVKLFTTNELMRWPIVQKTYEPVLNEDDLAFGGEANKHHWEDLQKRVIEHN-LRVI----------SEY  356 (445)
T ss_dssp             SSCHHHHHHHHHHHHHHHCCSSSHHHHHHHTCSSTTTCCSSCCCSCSSHHHHHHHHHHHHHH-HHHH----------HHH
T ss_pred             ccccccHHHHHHHHHHHhchHhhhHHHHHHHHHHhcccchhhhcchhhHHHHHHHHHHHHHH-HHHH----------HHH
Confidence            2235677888899988764  4677777777654211        11223444433322211 1111          122


Q ss_pred             CCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          444 EQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       444 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      -....+. .++..+.-  ..+++...+.+|...|.
T Consensus       357 Ys~I~l~-~la~lL~l--~~~evE~~ls~mI~~g~  388 (445)
T 4b4t_P          357 YSRITLL-RLNELLDL--TESQTETYISDLVNQGI  388 (445)
T ss_dssp             EEEEEHH-HHHHHHTS--CHHHHHHHHHHHHHHTS
T ss_pred             hceeeHH-HHHHHhCc--CHHHHHHHHHHHHHCCC
Confidence            2222255 66554432  57889999999986554

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=93.34  E-value=0.91  Score=34.15  Aligned_cols=66  Identities=8%  Similarity=-0.047  Sum_probs=45.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCHHH---HHHHHHHchhccC-C-CCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          408 KPNDAVLGSLLLGCRIHNNAEL---ASQVAQKLVAEID-P-EQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       408 ~p~~~~~~~l~~~~~~~~~~~~---A~~~~~~~~~~~~-p-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .|+..+--.+..++.+..+...   ++.+++.+ .... | ....... .|+-++.+.|++++|.+.++.+.+
T Consensus        32 ~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l-~~~~~p~~~Rd~lY-~LAvg~yklg~Y~~A~~~~~~lL~  102 (126)
T 1nzn_A           32 SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEEL-LPKGSKEEQRDYVF-YLAVGNYRLKEYEKALKYVRGLLQ  102 (126)
T ss_dssp             CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHH-TTTSCHHHHHHHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH-HhcCCcchHHHHHH-HHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3666666667777777776555   77788877 4444 4 2333334 677788888888888888888876

>3o48_A Mitochondria fission 1 protein; tetratricopeptide repeat fold, TPR, scaffold, peroxisome, membrane fission, protein binding; 1.75A {Saccharomyces cerevisiae} PDB: 2pqr_A 2pqn_A 3uux_A

Probab=92.40  E-value=1  Score=34.03  Aligned_cols=30  Identities=20%  Similarity=0.333  Sum_probs=14.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          417 LLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       417 l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      |.-++.+.|++++|.+..+.+ .+..|++..
T Consensus        84 LAvg~yklgdY~~Ar~y~d~l-L~~eP~N~Q  113 (134)
T 3o48_A           84 LTIGCYKLGEYSMAKRYVDTL-FEHERNNKQ  113 (134)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHH-HTTCTTCHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHH-HhhCCCCHH
Confidence            333444445555555555544 444444443

>1qsa_A Protein (soluble lytic transglycosylase SLT70); alpha-superhelix, transferase; HET: GOL; 1.65A {Escherichia coli} SCOP: a.118.5.1 d.2.1.6 PDB: 1qte_A* 1sly_A*

Probab=92.35  E-value=9.7  Score=37.94  Aligned_cols=79  Identities=9%  Similarity=-0.030  Sum_probs=48.5

Q ss_pred             HHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCC
Q 044988           54 ILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGL  133 (538)
Q Consensus        54 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~  133 (538)
                      .-+.-+..+.+.+++...+.++.. .+.+...-.....+....|+..+|......+-..| ...+..+..++..+.+.|.
T Consensus        74 Lr~~~l~~l~~~~~w~~~l~~~~~-~p~~~~~~c~~~~A~~~~G~~~~a~~~~~~lW~~~-~~~p~~c~~l~~~~~~~g~  151 (618)
T 1qsa_A           74 LQSRFVNELARREDWRGLLAFSPE-KPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTG-KSQPNACDKLFSVWRASGK  151 (618)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHCCS-CCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCS-SCCCTHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHhCCCHHHHHHhccC-CCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHhCC-CCCcHHHHHHHHHHHHCCC
Confidence            334555666677777777776665 33344444455666677777777777766666554 3455566666666665554


Q ss_pred             c
Q 044988          134 F  134 (538)
Q Consensus       134 ~  134 (538)
                      +
T Consensus       152 l  152 (618)
T 1qsa_A          152 Q  152 (618)
T ss_dssp             S
T ss_pred             C
Confidence            3

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=91.62  E-value=3.8  Score=38.10  Aligned_cols=163  Identities=12%  Similarity=0.003  Sum_probs=85.7

Q ss_pred             HHHHHHHHhCCCHHHHHHHHHhcCC--------CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHH
Q 044988          296 NALIHMYASCGEIEEAYGVFRKMQR--------RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFE  367 (538)
Q Consensus       296 ~~l~~~~~~~g~~~~a~~~~~~m~~--------~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~  367 (538)
                      ..|...|.+.|+.++..+++.....        +.......++..+.......+-               .++-..+.++
T Consensus        23 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~---------------~~~~~~~~~~   87 (394)
T 3txn_A           23 LQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGI---------------EVQLCKDCIE   87 (394)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHH---------------HHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHH---------------HHHHHHHHHH
Confidence            4677888888888888888877654        1112233344444433322111               1233333333


Q ss_pred             HhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC---CCCC-----HHHHHHHHHHHHhcCCHHHHHHHHHHch-
Q 044988          368 CMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP---MKPN-----DAVLGSLLLGCRIHNNAELASQVAQKLV-  438 (538)
Q Consensus       368 ~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---~~p~-----~~~~~~l~~~~~~~~~~~~A~~~~~~~~-  438 (538)
                      ........-.....=.-|+..|...|++.+|.+++.++.   .+.|     ...+-.-+..|...++..++..++..+. 
T Consensus        88 ~a~~~~r~flr~~l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~  167 (394)
T 3txn_A           88 WAKQEKRTFLRQSLEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSART  167 (394)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHh
Confidence            333220000011122357777888888888877777663   1212     1233444556777888888888887775 


Q ss_pred             -hccCCCCcc---cHHHHHHHHHH-hcCChHHHHHHHHHH
Q 044988          439 -AEIDPEQAA---GYLALVANVYA-AAKRWQDVAAVRQKM  473 (538)
Q Consensus       439 -~~~~p~~~~---~~~~~l~~~~~-~~g~~~~A~~~~~~m  473 (538)
                       ....+.++.   .+...-+..+. ..++|.+|...|-+.
T Consensus       168 ~~~ai~~~p~i~a~i~~~~Gi~~l~~~rdyk~A~~~F~ea  207 (394)
T 3txn_A          168 TANAIYCPPKVQGALDLQSGILHAADERDFKTAFSYFYEA  207 (394)
T ss_dssp             HHHHSCCCHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             hhccCCCCHHHHHHHHHHhhHHHHHhccCHHHHHHHHHHH
Confidence             111112221   11113344456 678888887766554

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=90.80  E-value=1  Score=34.97  Aligned_cols=52  Identities=13%  Similarity=-0.022  Sum_probs=29.8

Q ss_pred             cCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 044988          424 HNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       424 ~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                      .+|+++|.++|+.+ ..+.......|. ..+..-.++|+.+.|.+++.+....+
T Consensus        73 i~D~d~aR~vy~~a-~~~hKkFAKiwi-~~AqFEiRqgnl~kARkILg~AiG~~  124 (161)
T 4h7y_A           73 IQEPDDARDYFQMA-RANCKKFAFVHI-SFAQFELSQGNVKKSKQLLQKAVERG  124 (161)
T ss_dssp             HHCGGGCHHHHHHH-HHHCTTBHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             hcCHHHHHHHHHHH-HHHhHHHHHHHH-HHHHHHHHcccHHHHHHHHHHHhccC
Confidence            35666667777766 333333333344 44555556677777777766666543

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=90.40  E-value=9.3  Score=34.10  Aligned_cols=153  Identities=9%  Similarity=-0.011  Sum_probs=98.9

Q ss_pred             HHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHH----HHHhhhhcCC
Q 044988          300 HMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQF----FECMNQNWGI  375 (538)
Q Consensus       300 ~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~----~~~~~~~~~~  375 (538)
                      ..-...|++=+|.+.+           .++..-|.+.+++++|+.....-...+.+.|....|-++    .+-..+. ++
T Consensus        21 ~~~I~~G~yYEAhQ~~-----------Rtl~~Ry~~~~~~~eAidlL~~ga~~ll~~~Q~~sa~DLa~llvev~~~~-~~   88 (312)
T 2wpv_A           21 ENKIKAGDYYEAHQTL-----------RTIANRYVRSKSYEHAIELISQGALSFLKAKQGGSGTDLIFYLLEVYDLA-EV   88 (312)
T ss_dssp             HHHHHHTCHHHHHHHH-----------HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHT-TC
T ss_pred             HHHhhccChHHHHHHH-----------HHHHHHHHHhcCHHHHHHHHHHHHHHHHHCCCcchHHHHHHHHHHHHHHc-CC
Confidence            3444556666666554           456777888999999998877777777777887776665    3333333 78


Q ss_pred             CccHHHHHHHHHHhhhcCC--------hHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC
Q 044988          376 KPRIEHYGCMVDLFSRAGL--------MDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ  445 (538)
Q Consensus       376 ~p~~~~~~~l~~~~~~~g~--------~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~  445 (538)
                      +++......++..+.....        ..+|++.-.+..  ...++..+..+...+.+.|++.+|...|=..    ..++
T Consensus        89 ~~~~~~~~rl~~l~~~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~~----~~~s  164 (312)
T 2wpv_A           89 KVDDISVARLVRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLG----THDS  164 (312)
T ss_dssp             CCSHHHHHHHHHHHTTCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHTS----CHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHhC----CCcc
Confidence            8888888888887765432        233444443332  2357788888888899999999998877533    1223


Q ss_pred             cccHHHHHHHHHHhc--CChHHHHH
Q 044988          446 AAGYLALVANVYAAA--KRWQDVAA  468 (538)
Q Consensus       446 ~~~~~~~l~~~~~~~--g~~~~A~~  468 (538)
                      +..+...+.+-+.+.  |...++--
T Consensus       165 ~~~~a~~l~~w~~~~~~~~~~e~dl  189 (312)
T 2wpv_A          165 MIKYVDLLWDWLCQVDDIEDSTVAE  189 (312)
T ss_dssp             HHHHHHHHHHHHHHTTCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCCcchHHH
Confidence            344654555555443  66555443

>4h7y_A Dual specificity protein kinase TTK; mitotic checkpoint kinase, chromosome instability, cancer, tetratricopeptide repeat (TPR) motif; 1.80A {Homo sapiens} PDB: 4h7x_A

Probab=90.37  E-value=1.8  Score=33.55  Aligned_cols=59  Identities=7%  Similarity=0.095  Sum_probs=44.6

Q ss_pred             CCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhH
Q 044988           96 SETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFI  155 (538)
Q Consensus        96 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  155 (538)
                      .+++++|.++|+.+++.+-+- ...|......-.++|++..|.+++...+..+..|....
T Consensus        73 i~D~d~aR~vy~~a~~~hKkF-AKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~~~l  131 (161)
T 4h7y_A           73 IQEPDDARDYFQMARANCKKF-AFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEML  131 (161)
T ss_dssp             HHCGGGCHHHHHHHHHHCTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCHHHH
T ss_pred             hcCHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcHHHH
Confidence            378999999999997642222 55666666667889999999999999999886655443

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=90.20  E-value=0.68  Score=43.37  Aligned_cols=69  Identities=12%  Similarity=0.082  Sum_probs=56.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH-----hCCCCCCCce
Q 044988          414 LGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI-----KMGVRKPPGQ  484 (538)
Q Consensus       414 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~-----~~~~~~~~~~  484 (538)
                      ...++.++...|++++|...++.+ ....|-+...+. .++.+|.+.|+..+|.+.|++..     +-|+.|.+..
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~-~~~~P~~E~~~~-~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEAL-TFEHPYREPLWT-QLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHH-HHHSTTCHHHHH-HHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            345667778889999999999988 888898888777 88899999999999999888875     3588877643

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=89.85  E-value=0.93  Score=35.88  Aligned_cols=101  Identities=17%  Similarity=0.057  Sum_probs=56.1

Q ss_pred             CCCccHHH--HHHHHHHhhhcCChHHHHHHHHhCC----CCCC-------HHHHHHHHHHHHhcCCHHHHHHHHHHch--
Q 044988          374 GIKPRIEH--YGCMVDLFSRAGLMDEAFSLVQNMP----MKPN-------DAVLGSLLLGCRIHNNAELASQVAQKLV--  438 (538)
Q Consensus       374 ~~~p~~~~--~~~l~~~~~~~g~~~~A~~~~~~~~----~~p~-------~~~~~~l~~~~~~~~~~~~A~~~~~~~~--  438 (538)
                      |+.|....  +-.-++.+...|.++.|+-+.+.+.    ..|+       ..++..+.+++...+++.+|...|+++.  
T Consensus        13 ~~~~~~~~~~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~   92 (167)
T 3ffl_A           13 GLVPRGSHMNVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQ   92 (167)
T ss_dssp             --------CCHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCCCccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHH
Confidence            44454333  2333555666677777766665532    2233       1244555666777777777777777754  


Q ss_pred             hccCCCC----------------------cccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          439 AEIDPEQ----------------------AAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       439 ~~~~p~~----------------------~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .+.-|..                      ...-. .++.+|.+.|++++|+.+++.+..
T Consensus        93 ~k~l~k~~s~~~~~~~~ss~p~s~~~~~e~Elky-kia~C~~~l~~~~~Ai~~Le~Ip~  150 (167)
T 3ffl_A           93 KKALSKTSKVRPSTGNSASTPQSQCLPSEIEVKY-KLAECYTVLKQDKDAIAILDGIPS  150 (167)
T ss_dssp             HHCC--------------------CCCCHHHHHH-HHHHHHHHTTCHHHHHHHHHTSCG
T ss_pred             HHHHhcCCCccccccccCCCcccccccchHHHHH-HHHHHHHHHCCHHHHHHHHhcCCc
Confidence            1111111                      12234 678899999999999999988653

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=88.58  E-value=4.3  Score=44.23  Aligned_cols=53  Identities=6%  Similarity=0.043  Sum_probs=36.0

Q ss_pred             HHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHH
Q 044988          191 NSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEM  244 (538)
Q Consensus       191 ~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m  244 (538)
                      ..++..+.+.+..+.+.++..-.+. +...--.+..+|...|++++|...|++.
T Consensus       816 ~~l~~~l~~~~~~~~~~~l~~~~~~-~~~~~yl~g~~~L~~ge~~~A~~~F~ka  868 (1139)
T 4fhn_B          816 TELVEKLFLFKQYNACMQLIGWLNS-DPIAVYLKALIYLKSKEAVKAVRCFKTT  868 (1139)
T ss_dssp             HHHHHHHHHHSCTTHHHHHHHHSCC-CHHHHHHHHHHHHHTTCHHHHHHHHHTC
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhccC-CcHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            3455666777777777776655544 3333345567788889999999888765

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=88.48  E-value=4  Score=29.02  Aligned_cols=63  Identities=16%  Similarity=0.147  Sum_probs=49.3

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHH
Q 044988          233 KSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIH  300 (538)
Q Consensus       233 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~  300 (538)
                      +.-++.+-++.+....+.|+.....+.+++|-+.+++..|.++++.++..     ......+|..+++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K-----~~~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-----AGPHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----TTTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-----hcCchhhHHHHHH
Confidence            55677788888888889999999999999999999999999999988887     2222445555543

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.33  E-value=18  Score=34.44  Aligned_cols=51  Identities=8%  Similarity=0.030  Sum_probs=39.8

Q ss_pred             CCHHHHHHHHHHHHH-----CCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          232 GKSRQALSLFNEMRR-----ARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       232 ~~~~~a~~~~~~m~~-----~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      |+++.|++.+..+.+     ............++..|...++++...+.+..+.+.
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskk   85 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKK   85 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence            678889888877664     235556778888999999999999988877776654

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=88.01  E-value=15  Score=39.95  Aligned_cols=207  Identities=9%  Similarity=-0.006  Sum_probs=116.0

Q ss_pred             HHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC---C---cchHHHHHH
Q 044988          258 AALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR---N---TVSWTSMIT  331 (538)
Q Consensus       258 ~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~---~---~~~~~~li~  331 (538)
                      .++..+...+..+.+..+..    .     .+.+....-.+..+|..+|++++|...|.+....   +   ......+..
T Consensus       817 ~l~~~l~~~~~~~~~~~l~~----~-----~~~~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~~~~  887 (1139)
T 4fhn_B          817 ELVEKLFLFKQYNACMQLIG----W-----LNSDPIAVYLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLREFQE  887 (1139)
T ss_dssp             HHHHHHHHHSCTTHHHHHHH----H-----SCCCHHHHHHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhh----h-----ccCCcHHHHHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhccccc
Confidence            34455556666666554332    2     2223222236788899999999999999987541   1   111111111


Q ss_pred             HHHhcCCccHH-HHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCC-cc--HHHHHHHHHHhhhcCChHHHHHHHHhCC-
Q 044988          332 GFAKQGYAQEA-LLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIK-PR--IEHYGCMVDLFSRAGLMDEAFSLVQNMP-  406 (538)
Q Consensus       332 ~~~~~~~~~~a-~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~-p~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~-  406 (538)
                      . ......... ...|..++..+.+.+.++.+.++-+...+.-+-. ++  ...|..+...+...|++++|...+-.++ 
T Consensus       888 ~-~~~~~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd  966 (1139)
T 4fhn_B          888 I-AEKYHHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLST  966 (1139)
T ss_dssp             H-HHTTTSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHH
T ss_pred             c-cccccccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCC
Confidence            1 110000010 1457777777778888888887777666542212 22  2368889999999999999998887664 


Q ss_pred             CCCCHHHHHHHHHHHHhcCCHH------------HHHHHHHHchhcc-CCCCcccHHHHHHHHHHhcCChHHHHHH-HHH
Q 044988          407 MKPNDAVLGSLLLGCRIHNNAE------------LASQVAQKLVAEI-DPEQAAGYLALVANVYAAAKRWQDVAAV-RQK  472 (538)
Q Consensus       407 ~~p~~~~~~~l~~~~~~~~~~~------------~A~~~~~~~~~~~-~p~~~~~~~~~l~~~~~~~g~~~~A~~~-~~~  472 (538)
                      ..--...+..|+...+..|..+            +..+++..--... .+.+...|...|-.-+...|++..|..+ |+.
T Consensus       967 ~~~r~~cLr~LV~~lce~~~~~~L~~lpf~gl~~~Vd~IL~~kAr~~~~~~~~p~Yy~iLYs~ri~r~dyR~AA~vmYe~ 1046 (1139)
T 4fhn_B          967 TPLKKSCLLDFVNQLTKQGKINQLLNYSMPTLRQDVDNLLERKAFQMINVESQPCWYNILFSWRYKHQNYRDAAAIIYEK 1046 (1139)
T ss_dssp             SSSCHHHHHHHHHHHHHHCCHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCChhhhhCCCCccHHHHHHHHHHHHHHhCCccccCCCHHHHhHhhhhccCChHHHHHHHHHH
Confidence            1122456677777666666543            3334433221111 2222212443666666777777766654 454


Q ss_pred             HH
Q 044988          473 MI  474 (538)
Q Consensus       473 m~  474 (538)
                      ..
T Consensus      1047 ~~ 1048 (1139)
T 4fhn_B         1047 LS 1048 (1139)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3ltm_A Alpha-REP4; protein engineering, heat-like repeat, protein binding; HET: 1PE 12P; 2.15A {Synthetic}

Probab=87.46  E-value=11  Score=31.16  Aligned_cols=91  Identities=7%  Similarity=0.031  Sum_probs=38.4

Q ss_pred             CchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHH
Q 044988          151 SNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQ  230 (538)
Q Consensus       151 ~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~  230 (538)
                      ++..+-...+.+..+.|+   .+....+.+.+..++...-...+.++.+.|..+....+...+..++..+-...+.++.+
T Consensus        93 ~~~~vr~~a~~aL~~~~~---~~~~~~L~~~l~d~~~~vr~~a~~aL~~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~  169 (211)
T 3ltm_A           93 EDGWVRQSAAVALGQIGD---ERAVEPLIKALKDEDWFVRIAAAFALGEIGDERAVEPLIKALKDEDGWVRQSAADALGE  169 (211)
T ss_dssp             SSHHHHHHHHHHHHHHCC---GGGHHHHHHHTTCSSHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCc---HHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            333444444444444444   32222333333334444444444444444444333333333444554444444555555


Q ss_pred             cCCHHHHHHHHHHHH
Q 044988          231 NGKSRQALSLFNEMR  245 (538)
Q Consensus       231 ~~~~~~a~~~~~~m~  245 (538)
                      .+. .++...+..+.
T Consensus       170 ~~~-~~~~~~L~~~l  183 (211)
T 3ltm_A          170 IGG-ERVRAAMEKLA  183 (211)
T ss_dssp             HCS-HHHHHHHHHHH
T ss_pred             hCc-hhHHHHHHHHH
Confidence            544 33444444443

>1v54_E Cytochrome C oxidase polypeptide VA; oxidoreductase; HET: FME TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus} SCOP: a.118.11.1 PDB: 1oco_E* 1occ_E* 1ocz_E* 1ocr_E* 1v55_E* 2dyr_E* 2dys_E* 2eij_E* 2eik_E* 2eil_E* 2eim_E* 2ein_E* 2occ_E* 2ybb_P* 2zxw_E* 3abk_E* 3abl_E* 3abm_E* 3ag1_E* 3ag2_E* ...

Probab=86.92  E-value=3.1  Score=29.59  Aligned_cols=62  Identities=11%  Similarity=0.079  Sum_probs=45.4

Q ss_pred             CchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHH
Q 044988           98 TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLM  160 (538)
Q Consensus        98 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  160 (538)
                      +.-+..+-++.+....+.|++....+.+++|.+.+++..|.++++-++..- .+...+|..++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~l   86 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI   86 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHH
Confidence            344566677777777888999999999999999999999999888887653 33344555443

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=85.25  E-value=28  Score=36.41  Aligned_cols=26  Identities=8%  Similarity=0.045  Sum_probs=19.2

Q ss_pred             cHHHHHHHHhccCChHHHHHHHHHHH
Q 044988           19 TTRQIFSLLQIRNTTKTLFQIHSQII   44 (538)
Q Consensus        19 ~~~~ll~~~~~~~~~~~a~~~~~~~~   44 (538)
                      -|..+++...+.++.+.+.++|..+.
T Consensus       232 dy~~a~~~ai~LnD~~li~~if~~l~  257 (963)
T 4ady_A          232 DYLTLNKVVVNLNDAGLALQLFKKLK  257 (963)
T ss_dssp             CHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45667777777778888888888765

>3ltj_A Alpharep-4; protein engineering, heat-like repeat, protein binding; 1.80A {Synthetic}

Probab=85.25  E-value=14  Score=30.21  Aligned_cols=90  Identities=7%  Similarity=0.031  Sum_probs=36.1

Q ss_pred             chhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHc
Q 044988          152 NVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQN  231 (538)
Q Consensus       152 ~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~  231 (538)
                      +..+-...+.++.+.++   .+....+...+..++...-...+.++.+.++.+....+...+..++..+-...+.++.+.
T Consensus        89 ~~~vr~~a~~aL~~~~~---~~~~~~L~~~l~d~~~~vr~~a~~aL~~~~~~~~~~~L~~~l~d~~~~vr~~A~~aL~~~  165 (201)
T 3ltj_A           89 DGWVRQSAAVALGQIGD---ERAVEPLIKALKDEDWFVRIAAAFALGEIGDERAVEPLIKALKDEDGWVRQSAADALGEI  165 (201)
T ss_dssp             SHHHHHHHHHHHHHHCC---GGGHHHHHHHTTCSSHHHHHHHHHHHHHHTCGGGHHHHHHHTTCSSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCc---HHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            33344444444444444   322222233333334333344444444444433333333333344444444444444444


Q ss_pred             CCHHHHHHHHHHHH
Q 044988          232 GKSRQALSLFNEMR  245 (538)
Q Consensus       232 ~~~~~a~~~~~~m~  245 (538)
                      |. .++...+..+.
T Consensus       166 ~~-~~~~~~L~~~l  178 (201)
T 3ltj_A          166 GG-ERVRAAMEKLA  178 (201)
T ss_dssp             CS-HHHHHHHHHHH
T ss_pred             Cc-hhHHHHHHHHH
Confidence            44 23333333333

>3ltm_A Alpha-REP4; protein engineering, heat-like repeat, protein binding; HET: 1PE 12P; 2.15A {Synthetic}

Probab=85.13  E-value=15  Score=30.37  Aligned_cols=143  Identities=9%  Similarity=0.002  Sum_probs=91.6

Q ss_pred             CCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHH
Q 044988           49 SQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVC  128 (538)
Q Consensus        49 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~  128 (538)
                      .++..+-...+..+.+.|..+....+.+.+..++...-...+.++.+.++.+ +...+..+..   .++...-...+.++
T Consensus        30 ~~~~~vR~~A~~~L~~~~~~~~~~~L~~~l~~~~~~vr~~a~~aL~~~~~~~-~~~~L~~~l~---~~~~~vr~~a~~aL  105 (211)
T 3ltm_A           30 DDSYYVRRAAAYALGKIGDERAVEPLIKALKDEDAWVRRAAADALGQIGDER-AVEPLIKALK---DEDGWVRQSAAVAL  105 (211)
T ss_dssp             CSSHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSCHHHHHHHHHHHHHHCCGG-GHHHHHHHTT---CSSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhCCccHHHHHHHHHcCCCHHHHHHHHHHHHhhCCHH-HHHHHHHHHc---CCCHHHHHHHHHHH
Confidence            3566666667777777777555555556666677766666677777777644 4444444443   46777777777888


Q ss_pred             HccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCC
Q 044988          129 ARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGD  202 (538)
Q Consensus       129 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~  202 (538)
                      .+.++.+.. ..+..+.+   .++..+-...+.++.+.|+   .+....+..-+..++...-...+.++.+.+.
T Consensus       106 ~~~~~~~~~-~~L~~~l~---d~~~~vr~~a~~aL~~~~~---~~~~~~L~~~l~d~~~~vr~~a~~aL~~~~~  172 (211)
T 3ltm_A          106 GQIGDERAV-EPLIKALK---DEDWFVRIAAAFALGEIGD---ERAVEPLIKALKDEDGWVRQSAADALGEIGG  172 (211)
T ss_dssp             HHHCCGGGH-HHHHHHTT---CSSHHHHHHHHHHHHHHCC---GGGHHHHHHHTTCSSHHHHHHHHHHHHHHCS
T ss_pred             HHhCcHHHH-HHHHHHHh---CCCHHHHHHHHHHHHHcCC---HHHHHHHHHHHcCCCHHHHHHHHHHHHHhCc
Confidence            888775443 33333432   5677777888888888887   5544445555555666666666777777665

>3ltj_A Alpharep-4; protein engineering, heat-like repeat, protein binding; 1.80A {Synthetic}

Probab=84.98  E-value=15  Score=30.13  Aligned_cols=144  Identities=10%  Similarity=0.007  Sum_probs=84.3

Q ss_pred             CChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHH
Q 044988           50 QKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCA  129 (538)
Q Consensus        50 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~  129 (538)
                      ++..+-...+..+...+..+....+.+.+..++...-...+.++.+.++.+. ...+..+..   .++...-...+.++.
T Consensus        26 ~~~~vr~~A~~~L~~~~~~~~~~~L~~~l~~~~~~vr~~a~~~L~~~~~~~~-~~~L~~~l~---d~~~~vr~~a~~aL~  101 (201)
T 3ltj_A           26 DSYYVRRAAAYALGKIGDERAVEPLIKALKDEDAWVRRAAADALGQIGDERA-VEPLIKALK---DEDGWVRQSAAVALG  101 (201)
T ss_dssp             SCHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHHHHHCCGGG-HHHHHHHTT---CSSHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhcCChhHHHHHHHHHcCCCHHHHHHHHHHHHhhCCHHH-HHHHHHHHc---CCCHHHHHHHHHHHH
Confidence            4555555555555555554444445555555666555556666666665543 344444443   466667777777777


Q ss_pred             ccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHH
Q 044988          130 RCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDID  204 (538)
Q Consensus       130 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~  204 (538)
                      ..++.+....+ ..+..   .++..+-...+.+..+.++   .+....+...+..++...-...+.++.+.|..+
T Consensus       102 ~~~~~~~~~~L-~~~l~---d~~~~vr~~a~~aL~~~~~---~~~~~~L~~~l~d~~~~vr~~A~~aL~~~~~~~  169 (201)
T 3ltj_A          102 QIGDERAVEPL-IKALK---DEDWFVRIAAAFALGEIGD---ERAVEPLIKALKDEDGWVRQSAADALGEIGGER  169 (201)
T ss_dssp             HHCCGGGHHHH-HHHTT---CSSHHHHHHHHHHHHHHTC---GGGHHHHHHHTTCSSHHHHHHHHHHHHHHCSHH
T ss_pred             HhCcHHHHHHH-HHHHc---CCCHHHHHHHHHHHHHhCC---HHHHHHHHHHHcCCCHHHHHHHHHHHHHhCchh
Confidence            77765433333 33332   4677777777888888887   544444445555566666666677777766543

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=84.46  E-value=8.9  Score=30.33  Aligned_cols=115  Identities=7%  Similarity=0.022  Sum_probs=65.3

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHccCC-----CCCh-------HHHHHHHHHHHHcCCHHHHHHHHHHHHHC-CCCC-CHH
Q 044988          189 SWNSLLKGYVKRGDIDGAWKIFDEMP-----HRNV-------VSWTTMISGCAQNGKSRQALSLFNEMRRA-RVGL-DQV  254 (538)
Q Consensus       189 ~~~~li~~~~~~g~~~~A~~~~~~m~-----~~~~-------~~~~~li~~~~~~~~~~~a~~~~~~m~~~-g~~p-~~~  254 (538)
                      .+-.-++.+...|.++.|+-+.+.+.     .+++       .++..+..++...|++..|...|++..+. ..-+ +..
T Consensus        22 ~l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~s  101 (167)
T 3ffl_A           22 NVIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTSK  101 (167)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC-----
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            44455677777888888877766643     1332       24556667778888888888888876542 1111 111


Q ss_pred             HHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          255 ALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       255 ~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      +...+-   .......          ..    ..+.+..+---+..+|.+.|++++|+.+++.++.
T Consensus       102 ~~~~~~---~~ss~p~----------s~----~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~  150 (167)
T 3ffl_A          102 VRPSTG---NSASTPQ----------SQ----CLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPS  150 (167)
T ss_dssp             --------------------------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCG
T ss_pred             cccccc---ccCCCcc----------cc----cccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCc
Confidence            111110   0000000          00    1233444445688999999999999999999865

>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A {Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3 b.26.1.2 PDB: 2fez_A*

Probab=84.14  E-value=3  Score=38.94  Aligned_cols=68  Identities=9%  Similarity=-0.003  Sum_probs=52.8

Q ss_pred             HHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHH-----hCCCCchhHH
Q 044988           88 QMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLA-----SGYCSNVFIR  156 (538)
Q Consensus        88 ~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~~~  156 (538)
                      .++..+...|++++++..+..+.... +.+...|..+|.++.+.|+..+|.+.|+...+     .|+.|...+-
T Consensus       176 ~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~  248 (388)
T 2ff4_A          176 AKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  248 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            34556677889999998888887653 45777899999999999999999998887754     4888876543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=83.40  E-value=4.7  Score=41.08  Aligned_cols=122  Identities=16%  Similarity=0.027  Sum_probs=77.0

Q ss_pred             HHHHHHhcCC-HHHHHHHHccCCC--CChHHH--HHHHHHHHHcC-CHHHHHHHHHHHHHC------CCCC-CHH-----
Q 044988          193 LLKGYVKRGD-IDGAWKIFDEMPH--RNVVSW--TTMISGCAQNG-KSRQALSLFNEMRRA------RVGL-DQV-----  254 (538)
Q Consensus       193 li~~~~~~g~-~~~A~~~~~~m~~--~~~~~~--~~li~~~~~~~-~~~~a~~~~~~m~~~------g~~p-~~~-----  254 (538)
                      ++..+...|+ .+.|.++|+++.+  |...++  ..++..+.+.+ +--+|.+++.+..+.      ...+ +..     
T Consensus       254 Ll~~~~~t~~~~~~a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~~~~~  333 (754)
T 4gns_B          254 LKSFIAITPSLVDFTIDYLKGLTKKDPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADSARLM  333 (754)
T ss_dssp             HHHHHHTCGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHHHH
T ss_pred             HHHHHcccccHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccccccc
Confidence            4444444555 5778888888764  333322  22233222222 223455555554321      1222 111     


Q ss_pred             -----HHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcC
Q 044988          255 -----ALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQ  319 (538)
Q Consensus       255 -----~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  319 (538)
                           ....-..-|.+.|+++.|..+-+.....     .|..-.+|..|..+|...|+++.|.-.++.++
T Consensus       334 ~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~~-----aPseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          334 NCMSDLLNIQTNFLLNRGDYELALGVSNTSTEL-----ALDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             CcchHHHHHHHHHHhccCcHHHHHHHHHHHHhc-----CchhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence                 1111123356789999999999999987     89999999999999999999999999999886

>2y69_E Cytochrome C oxidase subunit 5A; electron transport, complex IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV DMU; 1.95A {Bos taurus}

Probab=82.70  E-value=11  Score=28.39  Aligned_cols=62  Identities=16%  Similarity=0.143  Sum_probs=48.8

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHH
Q 044988          233 KSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALI  299 (538)
Q Consensus       233 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~  299 (538)
                      |.-+..+-++.+....+.|+.......+++|-+.+++..|.++++-++..     ..+...+|..++
T Consensus        68 D~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K-----~~~~~~iY~y~l  129 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK-----AGPHKEIYPYVI  129 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----TTTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHh-----cCCchhhHHHHH
Confidence            45567777777878889999999999999999999999999999998887     222344555554

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	538
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.9
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.88
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.56
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.45
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.11
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.0
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.92
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.89
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.88
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.85
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.84
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.84
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.83
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.75
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.68
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.55
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.49
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.48
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.45
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.38
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.37
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.35
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.33
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.24
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.19
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.14
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.11
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.09
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.06
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.98
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.97
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.95
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.94
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.93
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.88
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.83
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.79
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.78
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.76
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.67
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.66
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.58
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	97.47
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.46
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	97.32
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.29
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.22
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.16
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.01
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.93
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.87
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	96.68
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	96.67
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.64
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	96.33
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	96.09
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	94.22
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	93.47
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	92.82
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	91.99
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	88.08
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	87.41
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	86.95
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	86.38

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=2.5e-20  Score=176.83  Aligned_cols=368  Identities=14%  Similarity=0.087  Sum_probs=242.4

Q ss_pred             HHHHccCChhHHHHHHhcCC--CC-CcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHH
Q 044988           60 AFYVTSGYLINAHKVFEKTE--NP-STAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFRE  136 (538)
Q Consensus        60 ~~~~~~g~~~~a~~~~~~~~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~  136 (538)
                      ..+.+.|++++|++.|+++.  .| +...+..+...+.+.|++++|+..|++..+.. +-+..+|..+...+.+.|++++
T Consensus         7 ~~~~~~G~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~   85 (388)
T d1w3ba_           7 HREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQE   85 (388)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhccccc
Confidence            33444555555555555443  12 33445555555555555555555555555432 1233455555555555566666


Q ss_pred             HHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcC---CCCCchhHHHHHHHHHhcCCHHHHHHHHccC
Q 044988          137 GEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDM---PARSVVSWNSLLKGYVKRGDIDGAWKIFDEM  213 (538)
Q Consensus       137 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~---~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  213 (538)
                      |...+....+.. +.+..............+.   ...+.......   ..................+....+...+...
T Consensus        86 A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (388)
T d1w3ba_          86 AIEHYRHALRLK-PDFIDGYINLAAALVAAGD---MEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKA  161 (388)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSC---SSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             cccccccccccc-ccccccccccccccccccc---ccccccccccccccccccccccccccccccccchhhhhHHHHHHh
Confidence            655555555543 2222333333333333333   22222222111   1123333444444555556666666655554


Q ss_pred             C--CC-ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCc
Q 044988          214 P--HR-NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPV  290 (538)
Q Consensus       214 ~--~~-~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~  290 (538)
                      .  .| +...+..+...+...|++++|...+++..+.. +-+...+..+...+...|++++|...+......     .+.
T Consensus       162 ~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-----~~~  235 (388)
T d1w3ba_         162 IETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYLRALSL-----SPN  235 (388)
T ss_dssp             HHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH-----CTT
T ss_pred             hccCcchhHHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHHHhHHH-----hhh
Confidence            3  23 45567778888888899999999998887742 224567788888888999999999999888886     556


Q ss_pred             chhHHHHHHHHHHhCCCHHHHHHHHHhcCC--C-CcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHH
Q 044988          291 LVSLNNALIHMYASCGEIEEAYGVFRKMQR--R-NTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFE  367 (538)
Q Consensus       291 ~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--~-~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~  367 (538)
                      ....+..+...+.+.|++++|...|++..+  | +..+|..+...+...|                    ++++|.+.++
T Consensus       236 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~--------------------~~~~A~~~~~  295 (388)
T d1w3ba_         236 HAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKG--------------------SVAEAEDCYN  295 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHS--------------------CHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC--------------------CHHHHHHHHH
Confidence            666777888999999999999999987654  2 3445555555555554                    7777778888


Q ss_pred             HhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC
Q 044988          368 CMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ  445 (538)
Q Consensus       368 ~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~  445 (538)
                      .....  .+.+...+..+...+...|++++|++.|++.. ..|+ ..++..+...+...|++++|...|+++ .++.|++
T Consensus       296 ~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~a-l~l~P~~  372 (388)
T d1w3ba_         296 TALRL--CPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEA-IRISPTF  372 (388)
T ss_dssp             HHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHH-HTTCTTC
T ss_pred             hhhcc--CCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCCCC
Confidence            77765  24467888899999999999999999998863 4565 677888899999999999999999999 9999999


Q ss_pred             cccHHHHHHHHHHhcCC
Q 044988          446 AAGYLALVANVYAAAKR  462 (538)
Q Consensus       446 ~~~~~~~l~~~~~~~g~  462 (538)
                      +.++. .|+.+|.+.|+
T Consensus       373 ~~a~~-~lg~~~~~~~D  388 (388)
T d1w3ba_         373 ADAYS-NMGNTLKEMQD  388 (388)
T ss_dssp             HHHHH-HHHHHHHHTCC
T ss_pred             HHHHH-HHHHHHHHcCC
Confidence            98888 99999988875

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: O-GlcNAc transferase p110 subunit, OGT
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.88  E-value=9.5e-20  Score=172.80  Aligned_cols=351  Identities=15%  Similarity=0.108  Sum_probs=278.0

Q ss_pred             HHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCC
Q 044988           89 MIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGG  168 (538)
Q Consensus        89 li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  168 (538)
                      +...+.+.|++++|++.|+++.+.. +-+...+..+...+.+.|++++|...+++.++.. +.+..++..+..+|.+.|+
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~   82 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQ   82 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhcc
Confidence            3456778899999999999998753 2356688888999999999999999999999875 5567889999999999999


Q ss_pred             CCChhHHHHHhhcCCCC---CchhHHHHHHHHHhcCCHHHHHHHHccCC---CCChHHHHHHHHHHHHcCCHHHHHHHHH
Q 044988          169 ECGVGCARLLFDDMPAR---SVVSWNSLLKGYVKRGDIDGAWKIFDEMP---HRNVVSWTTMISGCAQNGKSRQALSLFN  242 (538)
Q Consensus       169 ~~~~~~a~~~~~~~~~~---~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~  242 (538)
                         +++|...+....+.   +...+..........+....+........   .................+....+...+.
T Consensus        83 ---~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  159 (388)
T d1w3ba_          83 ---LQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYL  159 (388)
T ss_dssp             ---HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHH
T ss_pred             ---ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhhHHHHH
Confidence               99999998887642   33344444444444455444444443322   2444555666667777888888888888


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC--
Q 044988          243 EMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR--  320 (538)
Q Consensus       243 ~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~--  320 (538)
                      ...... +-+...+..+...+...|+++.|...+....+.     .|.+...+..+...+...|++++|...+++...  
T Consensus       160 ~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~-----~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  233 (388)
T d1w3ba_         160 KAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTL-----DPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS  233 (388)
T ss_dssp             HHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC
T ss_pred             HhhccC-cchhHHHHhhcccccccCcHHHHHHHHHHHHHh-----CcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh
Confidence            877642 334667777888888999999999999998887     677788888999999999999999999987654  


Q ss_pred             -CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHH
Q 044988          321 -RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEA  398 (538)
Q Consensus       321 -~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A  398 (538)
                       .+...+..+...+.+.                    |++++|...|++..+.   .| +..++..+...+...|++++|
T Consensus       234 ~~~~~~~~~l~~~~~~~--------------------~~~~~A~~~~~~al~~---~p~~~~~~~~l~~~~~~~~~~~~A  290 (388)
T d1w3ba_         234 PNHAVVHGNLACVYYEQ--------------------GLIDLAIDTYRRAIEL---QPHFPDAYCNLANALKEKGSVAEA  290 (388)
T ss_dssp             TTCHHHHHHHHHHHHHT--------------------TCHHHHHHHHHHHHHT---CSSCHHHHHHHHHHHHHHSCHHHH
T ss_pred             hhHHHHHHHHHHHHHHC--------------------CCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHH
Confidence             3334444444444444                    5778888888888764   45 477899999999999999999


Q ss_pred             HHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          399 FSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       399 ~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .+.++...  .+.+...+..+...+...|++++|+..++++ .+..|+++.++. .++.+|.+.|++++|++.|++..+
T Consensus       291 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a-l~~~p~~~~~~~-~la~~~~~~g~~~~A~~~~~~al~  367 (388)
T d1w3ba_         291 EDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKA-LEVFPEFAAAHS-NLASVLQQQGKLQEALMHYKEAIR  367 (388)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHH-TTSCTTCHHHHH-HHHHHHHTTTCCHHHHHHHHHHHT
T ss_pred             HHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99998874  4566788889999999999999999999999 999999999888 999999999999999999999886

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.5e-13  Score=126.27  Aligned_cols=239  Identities=14%  Similarity=0.009  Sum_probs=174.2

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHH
Q 044988          223 TMISGCAQNGKSRQALSLFNEMRRARVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHM  301 (538)
Q Consensus       223 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  301 (538)
                      .....+.+.|++++|+..|+++.+.  .| +..++..+..++...|+++.|...+..+.+.     .|.+...+..+...
T Consensus        24 ~~g~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~-----~p~~~~~~~~la~~   96 (323)
T d1fcha_          24 EEGLRRLQEGDLPNAVLLFEAAVQQ--DPKHMEAWQYLGTTQAENEQELLAISALRRCLEL-----KPDNQTALMALAVS   96 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhcc-----cccccccccccccc
Confidence            3455677788888888888888774  34 4667777778888888888888888888876     56677777788888


Q ss_pred             HHhCCCHHHHHHHHHhcCC--CCcc-hHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCcc
Q 044988          302 YASCGEIEEAYGVFRKMQR--RNTV-SWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPR  378 (538)
Q Consensus       302 ~~~~g~~~~a~~~~~~m~~--~~~~-~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~  378 (538)
                      |...|++++|.+.+++...  |+.. .+........ ...    .......+..+...+...+|...|.+..+...-.++
T Consensus        97 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~----~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~  171 (323)
T d1fcha_          97 FTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAG-GAG----LGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSID  171 (323)
T ss_dssp             HHHTTCHHHHHHHHHHHHHTSTTTGGGCC--------------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCC
T ss_pred             ccccccccccccchhhHHHhccchHHHHHhhhhhhh-hcc----cccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccc
Confidence            8888888888888877653  2111 0000000000 000    000111112222334677788888887765333345


Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ..++..+...+...|++++|+..+++.. ..| +...|..+...+...|++++|.+.++++ .+..|+++.++. .++.+
T Consensus       172 ~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a-l~~~p~~~~a~~-~lg~~  249 (323)
T d1fcha_         172 PDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRA-LELQPGYIRSRY-NLGIS  249 (323)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHH
T ss_pred             cccchhhHHHHHHHHHHhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHH-HHHhhccHHHHH-HHHHH
Confidence            7788899999999999999999999863 334 4788889999999999999999999999 899999999888 99999


Q ss_pred             HHhcCChHHHHHHHHHHHh
Q 044988          457 YAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       457 ~~~~g~~~~A~~~~~~m~~  475 (538)
                      |.+.|++++|++.|++..+
T Consensus       250 ~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         250 CINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             HHHHTCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH
Confidence            9999999999999999876

>d1fcha_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=1.9e-12  Score=118.57  Aligned_cols=234  Identities=12%  Similarity=-0.003  Sum_probs=139.1

Q ss_pred             HHHHccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHH
Q 044988           60 AFYVTSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFRE  136 (538)
Q Consensus        60 ~~~~~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~  136 (538)
                      ..+.+.|++++|+..|++..   +.+..+|..+..++...|++++|+..|++..+.. +-+...|..+...+...|++++
T Consensus        27 ~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~  105 (323)
T d1fcha_          27 LRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQRQ  105 (323)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-cccccccccccccccccccccc
Confidence            33445555555555555543   1233445555555555555555555555555421 1123344555555555555555


Q ss_pred             HHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCC--
Q 044988          137 GEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMP--  214 (538)
Q Consensus       137 a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~--  214 (538)
                      |.+.++......  |+..............                  .+.......+..+...+.+.+|...|.+..  
T Consensus       106 A~~~~~~~~~~~--~~~~~~~~~~~~~~~~------------------~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~  165 (323)
T d1fcha_         106 ACEILRDWLRYT--PAYAHLVTPAEEGAGG------------------AGLGPSKRILGSLLSDSLFLEVKELFLAAVRL  165 (323)
T ss_dssp             HHHHHHHHHHTS--TTTGGGCC---------------------------------CTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccchhhHHHhc--cchHHHHHhhhhhhhh------------------cccccchhhHHHHHHhhHHHHHHHHHHHHHHH
Confidence            555555554432  1111000000000000                  000011111223344455667777766543  


Q ss_pred             ---CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcc
Q 044988          215 ---HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVL  291 (538)
Q Consensus       215 ---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~  291 (538)
                         ..+...+..+...+...|++++|+..|++..... +-+...+..+...+...|++++|...++.+.+.     .|.+
T Consensus       166 ~p~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~-----~p~~  239 (323)
T d1fcha_         166 DPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVAAYRRALEL-----QPGY  239 (323)
T ss_dssp             STTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTC
T ss_pred             hhcccccccchhhHHHHHHHHHHhhhhcccccccccc-cccccchhhhhhcccccccchhHHHHHHHHHHH-----hhcc
Confidence               1345678888888899999999999999987743 224677888888899999999999999998887     6777


Q ss_pred             hhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          292 VSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       292 ~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      ..++..+..+|.+.|++++|...|++..+
T Consensus       240 ~~a~~~lg~~~~~~g~~~~A~~~~~~al~  268 (323)
T d1fcha_         240 IRSRYNLGISCINLGAHREAVEHFLEALN  268 (323)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            78888899999999999999999987654

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.11  E-value=5.6e-08  Score=89.21  Aligned_cols=207  Identities=12%  Similarity=0.006  Sum_probs=104.0

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHH----CCCCC--C-HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcch
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRR----ARVGL--D-QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLV  292 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~----~g~~p--~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  292 (538)
                      ++..+...+...|++..+...+.....    .+..+  . ...+..+...+...|+++.+...+..........+.....
T Consensus        93 ~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~  172 (366)
T d1hz4a_          93 SLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQL  172 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHH
Confidence            445556667777888888877776643    11111  1 1233344455566677777776666666553322233333


Q ss_pred             hHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          293 SLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       293 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                      ..+..+...+...++...+...+.+..                                            .++....  
T Consensus       173 ~~~~~~~~~~~~~~~~~~a~~~~~~a~--------------------------------------------~~~~~~~--  206 (366)
T d1hz4a_         173 QCLAMLIQCSLARGDLDNARSQLNRLE--------------------------------------------NLLGNGK--  206 (366)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHH--------------------------------------------HHHTTSC--
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHH--------------------------------------------HHHHHhc--
Confidence            333444445555555555554443321                                            1111000  


Q ss_pred             cCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CC-----CCHHHHHHHHHHHHhcCCHHHHHHHHHHch-----hc
Q 044988          373 WGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MK-----PNDAVLGSLLLGCRIHNNAELASQVAQKLV-----AE  440 (538)
Q Consensus       373 ~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~-----p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~-----~~  440 (538)
                       ...+ ....+..+...+...|++++|...++... ..     .....+..+..++...|++++|...++++.     .+
T Consensus       207 -~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~  285 (366)
T d1hz4a_         207 -YHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLR  285 (366)
T ss_dssp             -CCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             -ccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcc
Confidence             0011 12234444555555666666666665542 11     112334445555666666666666666553     13


Q ss_pred             cCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          441 IDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       441 ~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      ..|.....+. .++.+|.+.|++++|.+.+++..
T Consensus       286 ~~~~~~~~~~-~la~~~~~~g~~~~A~~~l~~Al  318 (366)
T d1hz4a_         286 LMSDLNRNLL-LLNQLYWQAGRKSDAQRVLLDAL  318 (366)
T ss_dssp             CHHHHHHHHH-HHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             cChHHHHHHH-HHHHHHHHCCCHHHHHHHHHHHH
Confidence            3344444445 56666666666666666666554

>d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Transcription factor MalT domain III
domain: Transcription factor MalT domain III
species: Escherichia coli [TaxId: 562]

Probab=99.00  E-value=9.8e-08  Score=87.51  Aligned_cols=270  Identities=10%  Similarity=-0.033  Sum_probs=149.5

Q ss_pred             HHHHHhccCChHHHHHHHHHHHHhCCCCC----hhHHHHHHHHHHccCChhHHHHHHhcCCC-----CC----cchHHHH
Q 044988           23 IFSLLQIRNTTKTLFQIHSQIIINGFSQK----NYILAKLLAFYVTSGYLINAHKVFEKTEN-----PS----TAIWNQM   89 (538)
Q Consensus        23 ll~~~~~~~~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-----~~----~~~~~~l   89 (538)
                      ....+...|+++.|...++..++.....+    ..++..+..+|...|++++|+..|++..+     ++    ...+..+
T Consensus        18 rA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   97 (366)
T d1hz4a_          18 RAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQ   97 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHH
Confidence            34556677888888888888776542222    23556666777788888888888876542     11    1234555


Q ss_pred             HHHHhcCCCchHHHHHHHHhHh----CCCCCCc---chHHHHHHHHHccCCcHHHHHHHHHHHHhCCC----CchhHHhH
Q 044988           90 IRGHARSETPEKSVYLYKQMID----KETEPDE---YTYSFLLSVCARCGLFREGEQVHGRVLASGYC----SNVFIRTN  158 (538)
Q Consensus        90 i~~~~~~~~~~~a~~~~~~m~~----~~~~p~~---~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~----~~~~~~~~  158 (538)
                      ...+...|++..+...+.....    .+.....   ..+..+...+...|+++.+...+.........    .....+..
T Consensus        98 ~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  177 (366)
T d1hz4a_          98 SEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAM  177 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHH
Confidence            6667777888888777776543    1111111   23444556677778888888777777664321    11233444


Q ss_pred             HHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCC---ChHHHHHHHHHHHHcCCHH
Q 044988          159 LMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR---NVVSWTTMISGCAQNGKSR  235 (538)
Q Consensus       159 l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~---~~~~~~~li~~~~~~~~~~  235 (538)
                      ....+...++   ...+...+.                        .+..++......   ....+......+...|+++
T Consensus       178 ~~~~~~~~~~---~~~a~~~~~------------------------~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  230 (366)
T d1hz4a_         178 LIQCSLARGD---LDNARSQLN------------------------RLENLLGNGKYHSDWISNANKVRVIYWQMTGDKA  230 (366)
T ss_dssp             HHHHHHHHTC---HHHHHHHHH------------------------HHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHhhhh---HHHHHHHHH------------------------HHHHHHHHhcccCchHHHHHHHHHHHHHhcccHH
Confidence            4445555555   544444332                        222222222221   1123444445555666666


Q ss_pred             HHHHHHHHHHHCCCC---CCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccC-CCCCcchhHHHHHHHHHHhCCCHHHH
Q 044988          236 QALSLFNEMRRARVG---LDQVALVAALSACAEIGDLKLGKWIHSYVEENFSV-GREPVLVSLNNALIHMYASCGEIEEA  311 (538)
Q Consensus       236 ~a~~~~~~m~~~g~~---p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~g~~~~a  311 (538)
                      +|...++........   .....+..+...+...|+++.|...++.+...... +..+.....+..+...|.+.|++++|
T Consensus       231 ~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  310 (366)
T d1hz4a_         231 AAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDA  310 (366)
T ss_dssp             HHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHH
Confidence            666666655432211   11233444555566666666666666655433211 12233445566677777777777777


Q ss_pred             HHHHHhcC
Q 044988          312 YGVFRKMQ  319 (538)
Q Consensus       312 ~~~~~~m~  319 (538)
                      .+.+++..
T Consensus       311 ~~~l~~Al  318 (366)
T d1hz4a_         311 QRVLLDAL  318 (366)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77776643

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.92  E-value=3.3e-08  Score=88.98  Aligned_cols=210  Identities=7%  Similarity=0.030  Sum_probs=147.2

Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHccCCC--C-ChHHHHHHHHHHHHcC-CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 044988          189 SWNSLLKGYVKRGDIDGAWKIFDEMPH--R-NVVSWTTMISGCAQNG-KSRQALSLFNEMRRARVGLDQVALVAALSACA  264 (538)
Q Consensus       189 ~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~~~~~~~li~~~~~~~-~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~  264 (538)
                      .|+.+...+.+.+.+++|+.++++..+  | +...|+....++...| ++++|+..++...+.. +-+..+|..+...+.
T Consensus        45 a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~~~~  123 (315)
T d2h6fa1          45 VYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVLVE  123 (315)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCchHHHHHHHHHHHHHCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhHHHH
Confidence            455566667777788888888888663  4 4456777777777765 4888888888887742 234677777777888


Q ss_pred             ccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccH
Q 044988          265 EIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQE  341 (538)
Q Consensus       265 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~  341 (538)
                      +.|++++|...+..+.+.     .|.+..+|..+...+...|++++|.+.++++.+   .+...|+.+...+.+.+....
T Consensus       124 ~l~~~~eAl~~~~kal~~-----dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~~p~n~~a~~~r~~~l~~~~~~~~  198 (315)
T d2h6fa1         124 WLRDPSQELEFIADILNQ-----DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKEDVRNNSVWNQRYFVISNTTGYND  198 (315)
T ss_dssp             HHTCCTTHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCSCS
T ss_pred             hhccHHHHHHHHhhhhhh-----hhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHHCCccHHHHHHHHHHHHHccccch
Confidence            888888888888888887     778888888888888888888888888888775   355667776666666665443


Q ss_pred             HHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC----CCCCHHHHHH
Q 044988          342 ALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP----MKPNDAVLGS  416 (538)
Q Consensus       342 a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~p~~~~~~~  416 (538)
                      +              +.+++|...+....+.   .| +...|+.+...+...| .+++.+.++...    ...+...+..
T Consensus       199 ~--------------~~~~~ai~~~~~al~~---~P~~~~~~~~l~~ll~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~  260 (315)
T d2h6fa1         199 R--------------AVLEREVQYTLEMIKL---VPHNESAWNYLKGILQDRG-LSKYPNLLNQLLDLQPSHSSPYLIAF  260 (315)
T ss_dssp             H--------------HHHHHHHHHHHHHHHH---STTCHHHHHHHHHHHTTTC-GGGCHHHHHHHHHHTTTCCCHHHHHH
T ss_pred             h--------------hhhHHhHHHHHHHHHh---CCCchHHHHHHHHHHHhcC-hHHHHHHHHHHHHhCCCcCCHHHHHH
Confidence            3              3577888888887765   45 5777777766655443 455555554432    2234555666


Q ss_pred             HHHHHH
Q 044988          417 LLLGCR  422 (538)
Q Consensus       417 l~~~~~  422 (538)
                      ++..+.
T Consensus       261 l~~~y~  266 (315)
T d2h6fa1         261 LVDIYE  266 (315)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            666553

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=3.8e-08  Score=88.56  Aligned_cols=224  Identities=10%  Similarity=0.109  Sum_probs=154.7

Q ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccC-ChHHHHHHHHHHHHhccCCCCCcchhHHH
Q 044988          219 VSWTTMISGCAQNGKSRQALSLFNEMRRARVGLD-QVALVAALSACAEIG-DLKLGKWIHSYVEENFSVGREPVLVSLNN  296 (538)
Q Consensus       219 ~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~-~~~~~~li~~~~~~~-~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  296 (538)
                      ..|+.+...+.+.+.+++|+.+++++.+  +.|+ ...|.....++...| ++++|...++.+.+.     .|.+..+|.
T Consensus        44 ~a~~~~~~~~~~~e~~~~Al~~~~~ai~--lnP~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~-----~p~~~~a~~  116 (315)
T d2h6fa1          44 DVYDYFRAVLQRDERSERAFKLTRDAIE--LNAANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEE-----QPKNYQVWH  116 (315)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH-----CTTCHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHH--HCCCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHH-----HHhhhhHHH
Confidence            3677777788888999999999999988  4565 445666666666665 588999999988887     788888888


Q ss_pred             HHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc
Q 044988          297 ALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       297 ~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  373 (538)
                      .+...+.+.|++++|...++++.+   .+...|..+...+...|                    ++++|.+.++.+.+. 
T Consensus       117 ~~~~~~~~l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~~~~--------------------~~~~Al~~~~~al~~-  175 (315)
T d2h6fa1         117 HRRVLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFK--------------------LWDNELQYVDQLLKE-  175 (315)
T ss_dssp             HHHHHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHT--------------------CCTTHHHHHHHHHHH-
T ss_pred             HHhHHHHhhccHHHHHHHHhhhhhhhhcchHHHHHHHHHHHHHH--------------------hhHHHHHHHHHHHHH-
Confidence            888889999999999999888775   35566666666666666                    555667888888865 


Q ss_pred             CCCc-cHHHHHHHHHHhhhcCC------hHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCC
Q 044988          374 GIKP-RIEHYGCMVDLFSRAGL------MDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPE  444 (538)
Q Consensus       374 ~~~p-~~~~~~~l~~~~~~~g~------~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~  444 (538)
                        .| +...|+.+..++.+.+.      +++|++.+.... ..| +...|+.+...+.. ...+++.+.++.. .++.|+
T Consensus       176 --~p~n~~a~~~r~~~l~~~~~~~~~~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~~-~~~~~~~~~~~~~-~~l~~~  251 (315)
T d2h6fa1         176 --DVRNNSVWNQRYFVISNTTGYNDRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQD-RGLSKYPNLLNQL-LDLQPS  251 (315)
T ss_dssp             --CTTCHHHHHHHHHHHHHTTCSCSHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTT-TCGGGCHHHHHHH-HHHTTT
T ss_pred             --CCccHHHHHHHHHHHHHccccchhhhhHHhHHHHHHHHHhCCCchHHHHHHHHHHHh-cChHHHHHHHHHH-HHhCCC
Confidence              45 56677777666665554      567777776652 344 46666666555443 4457777888877 666666


Q ss_pred             CcccHH-HHHHHHHHhc--CChHHHHHHHHHHH
Q 044988          445 QAAGYL-ALVANVYAAA--KRWQDVAAVRQKMI  474 (538)
Q Consensus       445 ~~~~~~-~~l~~~~~~~--g~~~~A~~~~~~m~  474 (538)
                      ....+. ..++.+|...  +..+.+...+++..
T Consensus       252 ~~~~~~~~~l~~~y~~~~~~~~~~~~~~~~ka~  284 (315)
T d2h6fa1         252 HSSPYLIAFLVDIYEDMLENQCDNKEDILNKAL  284 (315)
T ss_dssp             CCCHHHHHHHHHHHHHHHHTTCSSHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            544332 1445555432  44555555555544

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.88  E-value=1.1e-07  Score=85.51  Aligned_cols=192  Identities=10%  Similarity=-0.000  Sum_probs=133.7

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHH
Q 044988          233 KSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAY  312 (538)
Q Consensus       233 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  312 (538)
                      ..++|..+|++..+...+.+...+...+....+.|+++.|..+++.+.+.    .......+|..++..+.+.|+.+.|+
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~----~~~~~~~~w~~~~~~~~~~~~~~~ar  154 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI----EDIDPTLVYIQYMKFARRAEGIKSGR  154 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTS----SSSCTHHHHHHHHHHHHHHHCHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHH----hcCChHHHHHHHHHHHHHcCChHHHH
Confidence            45778888888876544455666677777777888888888888888775    23333446778888888888888888


Q ss_pred             HHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhc
Q 044988          313 GVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRA  392 (538)
Q Consensus       313 ~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  392 (538)
                      ++|+++.+..+.++...+...                ..-+...|+.+.|..+|+.+.+.+  +.+...|...++.+.+.
T Consensus       155 ~i~~~al~~~~~~~~~~~~~a----------------~~e~~~~~~~~~a~~i~e~~l~~~--p~~~~~w~~y~~~~~~~  216 (308)
T d2onda1         155 MIFKKAREDARTRHHVYVTAA----------------LMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYIDYLSHL  216 (308)
T ss_dssp             HHHHHHHTSTTCCTHHHHHHH----------------HHHHHTSCCHHHHHHHHHHHHHHH--TTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhCCCcHHHHHHHH----------------HHHHHhccCHHHHHHHHHHHHHhh--hhhHHHHHHHHHHHHHc
Confidence            888887653322222211100                001122357788888888888762  33467888888888889


Q ss_pred             CChHHHHHHHHhCC----CCCC--HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          393 GLMDEAFSLVQNMP----MKPN--DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       393 g~~~~A~~~~~~~~----~~p~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      |+.+.|..+|++..    ..|+  ...|...+..-...|+.+.+..+++++ .+..|....
T Consensus       217 g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~-~~~~~~~~~  276 (308)
T d2onda1         217 NEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRR-FTAFREEYE  276 (308)
T ss_dssp             CCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHH-HHHTTTTTS
T ss_pred             CChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHHCccccc
Confidence            99999999988752    2232  457888888878889999999988888 777776654

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.85  E-value=3.4e-07  Score=82.04  Aligned_cols=160  Identities=9%  Similarity=0.022  Sum_probs=102.7

Q ss_pred             hhHHHHHHHHHhcCCHHHHHHHHccCCC--C-C-hHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH-H
Q 044988          188 VSWNSLLKGYVKRGDIDGAWKIFDEMPH--R-N-VVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALS-A  262 (538)
Q Consensus       188 ~~~~~li~~~~~~g~~~~A~~~~~~m~~--~-~-~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~-~  262 (538)
                      ..|...+....+.|+++.|..+|+++..  | + ...|...+..+.+.|+.+.|.++|+++.+.+... ...|..... -
T Consensus       100 ~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~~~-~~~~~~~a~~e  178 (308)
T d2onda1         100 LLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTR-HHVYVTAALME  178 (308)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCC-THHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCc-HHHHHHHHHHH
Confidence            3445555555556666666666665432  2 2 3367777888888888888888888887654332 233333222 2


Q ss_pred             HHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCC---C----cchHHHHHHHHHh
Q 044988          263 CAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRR---N----TVSWTSMITGFAK  335 (538)
Q Consensus       263 ~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~---~----~~~~~~li~~~~~  335 (538)
                      +...|+.+.|..+|+.+.+.     .|.+...|...++.+.+.|+++.|+.+|++..+.   +    ...|...+.--..
T Consensus       179 ~~~~~~~~~a~~i~e~~l~~-----~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~  253 (308)
T d2onda1         179 YYCSKDKSVAFKIFELGLKK-----YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESN  253 (308)
T ss_dssp             HHTSCCHHHHHHHHHHHHHH-----HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHHHh-----hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHH
Confidence            34457888888888888886     6777888888888888889999999988886431   1    1234444443333


Q ss_pred             cCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc
Q 044988          336 QGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       336 ~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  373 (538)
                      .                    |+.+.+..+++++.+.+
T Consensus       254 ~--------------------G~~~~~~~~~~r~~~~~  271 (308)
T d2onda1         254 I--------------------GDLASILKVEKRRFTAF  271 (308)
T ss_dssp             H--------------------SCHHHHHHHHHHHHHHT
T ss_pred             c--------------------CCHHHHHHHHHHHHHHC
Confidence            4                    46666667777666553

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.84  E-value=1.5e-08  Score=88.79  Aligned_cols=94  Identities=10%  Similarity=-0.157  Sum_probs=67.4

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHH
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRARVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNAL  298 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l  298 (538)
                      +|..+...|.+.|++++|+..|++..+.  .| +..+|..+..++.+.|++++|...|+.+.+.     .|.+..++..+
T Consensus        39 ~~~~~G~~y~~~g~~~~A~~~~~~al~l--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~-----~p~~~~a~~~l  111 (259)
T d1xnfa_          39 LLYERGVLYDSLGLRALARNDFSQALAI--RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL-----DPTYNYAHLNR  111 (259)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCTHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHhhcc--CCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHH-----HhhhhhhHHHH
Confidence            5666677777777788887777777763  33 4566777777777777777777777777776     55566666677


Q ss_pred             HHHHHhCCCHHHHHHHHHhcCC
Q 044988          299 IHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       299 ~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      ..+|...|++++|...|++..+
T Consensus       112 g~~~~~~g~~~~A~~~~~~al~  133 (259)
T d1xnfa_         112 GIALYYGGRDKLAQDDLLAFYQ  133 (259)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHh
Confidence            7777777777777777776654

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.84  E-value=3.9e-08  Score=85.98  Aligned_cols=120  Identities=13%  Similarity=-0.131  Sum_probs=87.6

Q ss_pred             chhHHHHHHHHHhcCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 044988          187 VVSWNSLLKGYVKRGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSAC  263 (538)
Q Consensus       187 ~~~~~~li~~~~~~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~  263 (538)
                      ..+|..+...|.+.|++++|+..|++..+   .++.+|+.+..+|.+.|++++|+..|+++.+... -+..++..+..++
T Consensus        37 a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~  115 (259)
T d1xnfa_          37 AQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDP-TYNYAHLNRGIAL  115 (259)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHHh-hhhhhHHHHHHHH
Confidence            35677778888999999999999988653   4567888899999999999999999999887431 2355677788888


Q ss_pred             HccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHH
Q 044988          264 AEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAY  312 (538)
Q Consensus       264 ~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  312 (538)
                      ...|+++.|...++...+.     .|.+......+...+.+.+..+.+.
T Consensus       116 ~~~g~~~~A~~~~~~al~~-----~p~~~~~~~~~~~~~~~~~~~~~~~  159 (259)
T d1xnfa_         116 YYGGRDKLAQDDLLAFYQD-----DPNDPFRSLWLYLAEQKLDEKQAKE  159 (259)
T ss_dssp             HHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHCHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHhh-----ccccHHHHHHHHHHHHHhhhHHHHH
Confidence            8899999999999988887     4544444333444444444433333

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.83  E-value=3.1e-08  Score=90.31  Aligned_cols=247  Identities=9%  Similarity=-0.040  Sum_probs=168.6

Q ss_pred             CHHHHHHHHccCC--CCChH-HHHHHHHH----------HHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC-
Q 044988          202 DIDGAWKIFDEMP--HRNVV-SWTTMISG----------CAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIG-  267 (538)
Q Consensus       202 ~~~~A~~~~~~m~--~~~~~-~~~~li~~----------~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~-  267 (538)
                      ..++|++++++..  .|+.. .|+..-..          +...|++++|+.+++...+.. +-+...+..+..++...+ 
T Consensus        44 ~~~~al~~~~~~l~~~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~~~~~~~~~~~~~~  122 (334)
T d1dcea1          44 LDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPE  122 (334)
T ss_dssp             CSHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSS
T ss_pred             ccHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHHHHHhhHHHHHhcc
Confidence            3467777777654  34433 34332222          233455788888888887642 224555555655555544 


Q ss_pred             -ChHHHHHHHHHHHHhccCCCCCcchhHHH-HHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHH
Q 044988          268 -DLKLGKWIHSYVEENFSVGREPVLVSLNN-ALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEA  342 (538)
Q Consensus       268 -~~~~a~~~~~~~~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a  342 (538)
                       +++.+...+..+.+.     .|.+...+. .....+...|..+.|...++++.+   .+..+|+.+...+.+.|++++|
T Consensus       123 ~~~~~a~~~~~~al~~-----~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~p~~~~a~~~l~~~~~~~~~~~~A  197 (334)
T d1dcea1         123 PNWARELELCARFLEA-----DERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDS  197 (334)
T ss_dssp             CCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCS
T ss_pred             ccHHHHHHHHHHHHhh-----CchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCHHHH
Confidence             578888888888887     555555543 445677778999999999998886   3566788888889999988887


Q ss_pred             H----------HHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-
Q 044988          343 L----------LTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-  410 (538)
Q Consensus       343 ~----------~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-  410 (538)
                      .          .........+...+..+.+...+......  -+++...+..+...+...|+.++|...+.+.. ..|+ 
T Consensus       198 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~a~~~~~~~l~~--~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~p~~  275 (334)
T d1dcea1         198 GPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLG--RAEPLFRCELSVEKSTVLQSELESCKELQELEPENKWC  275 (334)
T ss_dssp             SSCCSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHS--CCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHHHHhHHhHHHHHHHHHHHHHhcchhHHHHHHHHHHHh--CcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhCchH
Confidence            6          22222333444456666777777776654  13345566677778888899999999888764 3343 


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHH
Q 044988          411 DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYA  458 (538)
Q Consensus       411 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~  458 (538)
                      ..+|..+...+...|++++|.+.++++ .++.|++...|. .|...+.
T Consensus       276 ~~~~~~l~~~~~~~~~~~eA~~~~~~a-i~ldP~~~~y~~-~L~~~~~  321 (334)
T d1dcea1         276 LLTIILLMRALDPLLYEKETLQYFSTL-KAVDPMRAAYLD-DLRSKFL  321 (334)
T ss_dssp             HHHHHHHHHHHCTGGGHHHHHHHHHHH-HHHCGGGHHHHH-HHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHH-HHHCcccHHHHH-HHHHHHh
Confidence            467777888899999999999999999 999998887455 5655544

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.75  E-value=1.1e-08  Score=93.30  Aligned_cols=259  Identities=8%  Similarity=-0.026  Sum_probs=133.4

Q ss_pred             CChHHHHHHHHHHHHhCCCCChhHHHHHHHH---HH-------ccCChhHHHHHHhcCC---CCCcchHHHHHHHHhcCC
Q 044988           31 NTTKTLFQIHSQIIINGFSQKNYILAKLLAF---YV-------TSGYLINAHKVFEKTE---NPSTAIWNQMIRGHARSE   97 (538)
Q Consensus        31 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~---~~-------~~g~~~~a~~~~~~~~---~~~~~~~~~li~~~~~~~   97 (538)
                      +..++|..+++..++..+. +...|+..-..   +.       ..|.+++|+.+++...   +.+...|..+..++...+
T Consensus        43 ~~~~~al~~~~~~l~~~P~-~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~pk~~~~~~~~~~~~~~~~  121 (334)
T d1dcea1          43 ELDESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLLSRLP  121 (334)
T ss_dssp             CCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTCS
T ss_pred             cccHHHHHHHHHHHHHCCC-cHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhCCCcHHHHHHhhHHHHHhc
Confidence            3446777777777765422 23334332222   11       2233566666666554   234445555555554443


Q ss_pred             --CchHHHHHHHHhHhCCCCCCcchHH-HHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhH
Q 044988           98 --TPEKSVYLYKQMIDKETEPDEYTYS-FLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGC  174 (538)
Q Consensus        98 --~~~~a~~~~~~m~~~~~~p~~~~~~-~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~  174 (538)
                        ++++|+..++.+.+.. +++...+. .....+...+..+.|...++.+++.. +.+...|+.+..++.+.|+   .++
T Consensus       122 ~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~-p~~~~a~~~l~~~~~~~~~---~~~  196 (334)
T d1dcea1         122 EPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCLLPQLHP---QPD  196 (334)
T ss_dssp             SCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHHHHHHSC---CCC
T ss_pred             cccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcC---HHH
Confidence              3567777777766542 22333433 33345555666777777776666654 4455666666777777776   555


Q ss_pred             HHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCC---CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC
Q 044988          175 ARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMP---HRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGL  251 (538)
Q Consensus       175 a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p  251 (538)
                      |...+....+..... ......+...+..+++...+....   .++...+..+...+...++.++|...+.+..+.  .|
T Consensus       197 A~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~p  273 (334)
T d1dcea1         197 SGPQGRLPENVLLKE-LELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELSVEKSTVLQSELESCKELQELEPE--NK  273 (334)
T ss_dssp             SSSCCSSCHHHHHHH-HHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTT--CH
T ss_pred             HHHHHHHhHHhHHHH-HHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhh--Cc
Confidence            544444333211111 112222334444444544444321   123334444555555566666666666655442  22


Q ss_pred             -CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHH
Q 044988          252 -DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYA  303 (538)
Q Consensus       252 -~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  303 (538)
                       +..++..+..++.+.|+.++|...++.+.+.     .|.....|..|...+.
T Consensus       274 ~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l-----dP~~~~y~~~L~~~~~  321 (334)
T d1dcea1         274 WCLLTIILLMRALDPLLYEKETLQYFSTLKAV-----DPMRAAYLDDLRSKFL  321 (334)
T ss_dssp             HHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH-----CGGGHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-----CcccHHHHHHHHHHHh
Confidence             3344555555666666666666666666665     4555555555544443

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.68  E-value=6.9e-07  Score=79.18  Aligned_cols=202  Identities=11%  Similarity=-0.017  Sum_probs=132.6

Q ss_pred             HHHHccCChHHHHHHHHHHHHhccCCC-CCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCc
Q 044988          261 SACAEIGDLKLGKWIHSYVEENFSVGR-EPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYA  339 (538)
Q Consensus       261 ~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~  339 (538)
                      ..|...+++++|...|..+.+.....+ .+....+|..+..+|.+.|++++|.+.+++.           +..+...|..
T Consensus        45 ~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a-----------~~~~~~~~~~  113 (290)
T d1qqea_          45 TIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENA-----------IQIFTHRGQF  113 (290)
T ss_dssp             HHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-----------HHHHHHTTCH
T ss_pred             HHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHh-----------hHHhhhcccc
Confidence            345566677777777666655422112 2233456778889999999999998877664           4455666777


Q ss_pred             cHHHHHHHHHHHHhc-ccCcHHHHHHHHHHhhhhc---CCCcc-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CC-----
Q 044988          340 QEALLTFLGVLSACS-HGGFVDEGRQFFECMNQNW---GIKPR-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MK-----  408 (538)
Q Consensus       340 ~~a~~~~~~ll~~~~-~~~~~~~a~~~~~~~~~~~---~~~p~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~-----  408 (538)
                      ..+...+..+...|. ..|++++|.+.+++..+..   +..+. ..++..+...|...|++++|.+.|+++. ..     
T Consensus       114 ~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~  193 (290)
T d1qqea_         114 RRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRL  193 (290)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTT
T ss_pred             hhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchh
Confidence            777777777777774 4688999998888765431   22222 4568889999999999999999998863 11     


Q ss_pred             --CCH-HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCccc--H--HHHHHHHHHh--cCChHHHHHHHHHHH
Q 044988          409 --PND-AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAG--Y--LALVANVYAA--AKRWQDVAAVRQKMI  474 (538)
Q Consensus       409 --p~~-~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~--~--~~~l~~~~~~--~g~~~~A~~~~~~m~  474 (538)
                        ... ..+...+..+...|+++.|.+.+++. .+..|.....  +  ...++.++..  .+++++|+..|+++.
T Consensus       194 ~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~-~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~  267 (290)
T d1qqea_         194 SQWSLKDYFLKKGLCQLAATDAVAAARTLQEG-QSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFM  267 (290)
T ss_dssp             TGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGG-GCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             hhhhHHHHHHHHHHHHHHhccHHHHHHHHHHH-HHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence              111 23344555677899999999999999 8877764432  1  1144555544  346888888876544

>d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Vesicular transport protein sec17
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.55  E-value=4.3e-06  Score=73.90  Aligned_cols=211  Identities=10%  Similarity=-0.065  Sum_probs=138.6

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCC-CCcchhH
Q 044988          221 WTTMISGCAQNGKSRQALSLFNEMRRA----RVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGR-EPVLVSL  294 (538)
Q Consensus       221 ~~~li~~~~~~~~~~~a~~~~~~m~~~----g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~-~~~~~~~  294 (538)
                      |......|...|++++|...|.+..+.    +-++ -..+|..+..+|.+.|++++|...++...+.....+ ......+
T Consensus        40 y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~  119 (290)
T d1qqea_          40 CVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANF  119 (290)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHH
Confidence            344566777788888888888877652    2222 235677778888888888888888887766532212 2222444


Q ss_pred             HHHHHHHHHh-CCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhc
Q 044988          295 NNALIHMYAS-CGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNW  373 (538)
Q Consensus       295 ~~~l~~~~~~-~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~  373 (538)
                      +..+...|.. .|++++|.+.+++..           ..+...+....+..++..+...+...|++++|...|+++....
T Consensus       120 ~~~l~~~~~~~~~~~~~A~~~~~~A~-----------~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~  188 (290)
T d1qqea_         120 KFELGEILENDLHDYAKAIDCYELAG-----------EWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSS  188 (290)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHH-----------HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHhHhhHHHHHHHHHHHHHHHH-----------HHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhC
Confidence            5566666744 699999999988753           3334444444455667777888888889999999999877652


Q ss_pred             CCCc----c-HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC------HHHHHHHHHHHHh--cCCHHHHHHHHHHchh
Q 044988          374 GIKP----R-IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN------DAVLGSLLLGCRI--HNNAELASQVAQKLVA  439 (538)
Q Consensus       374 ~~~p----~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~------~~~~~~l~~~~~~--~~~~~~A~~~~~~~~~  439 (538)
                      ...+    . ...+...+..+...|+++.|...+++.. ..|+      ......++.++..  .+.+++|+..|+++ .
T Consensus       189 ~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~-~  267 (290)
T d1qqea_         189 MGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNF-M  267 (290)
T ss_dssp             SSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTS-S
T ss_pred             ccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH-h
Confidence            1111    1 1234455667778999999999999884 3332      2345566666654  34588898888887 6


Q ss_pred             ccCC
Q 044988          440 EIDP  443 (538)
Q Consensus       440 ~~~p  443 (538)
                      .+.|
T Consensus       268 ~lD~  271 (290)
T d1qqea_         268 RLDK  271 (290)
T ss_dssp             CCCH
T ss_pred             hcCH
Confidence            5544

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.49  E-value=9.9e-07  Score=65.83  Aligned_cols=102  Identities=11%  Similarity=0.001  Sum_probs=74.0

Q ss_pred             HHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCC
Q 044988          350 LSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNN  426 (538)
Q Consensus       350 l~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~  426 (538)
                      ...+...|++++|..+|.+..+.   .| +...|..+..+|...|++++|+..++...  .+.+...|..+..++...|+
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~---~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~   86 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKL---DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNR   86 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhc---CCcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccC
Confidence            34556667777888888887765   45 46678888888888888888888887763  33456777777778888888


Q ss_pred             HHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          427 AELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       427 ~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      +++|+..+++. ....|+++..+. .+.++
T Consensus        87 ~~~A~~~~~~a-~~~~p~~~~~~~-~l~~l  114 (117)
T d1elwa_          87 FEEAKRTYEEG-LKHEANNPQLKE-GLQNM  114 (117)
T ss_dssp             HHHHHHHHHHH-HTTCTTCHHHHH-HHHHH
T ss_pred             HHHHHHHHHHH-HHhCCCCHHHHH-HHHHH
Confidence            88888888888 778888877444 55443

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.48  E-value=5.3e-07  Score=75.05  Aligned_cols=96  Identities=10%  Similarity=-0.084  Sum_probs=55.3

Q ss_pred             HHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhc
Q 044988          348 GVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIH  424 (538)
Q Consensus       348 ~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~  424 (538)
                      .....+...|++++|...|.+..+.   .| +...|..+..+|.+.|++++|+..|++.. ..|+ ..+|..+..++...
T Consensus         9 ~~Gn~~~~~g~~~~Ai~~~~kal~~---~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~~~~~l   85 (201)
T d2c2la1           9 EQGNRLFVGRKYPEAAACYGRAITR---NPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQLEM   85 (201)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH---CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHHHHHHHC
Confidence            3445555666666666666665544   33 35556666666666666666666665553 3343 45555666666666


Q ss_pred             CCHHHHHHHHHHchhccCCCCcc
Q 044988          425 NNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       425 ~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      |++++|+..|+++ ..+.|+...
T Consensus        86 ~~~~~A~~~~~~a-l~l~p~~~~  107 (201)
T d2c2la1          86 ESYDEAIANLQRA-YSLAKEQRL  107 (201)
T ss_dssp             TCHHHHHHHHHHH-HHHHHHTTC
T ss_pred             CCHHHHHHHHHHH-HHhCcccHH
Confidence            6666666666666 555554443

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.45  E-value=3.1e-06  Score=69.43  Aligned_cols=121  Identities=10%  Similarity=-0.045  Sum_probs=97.9

Q ss_pred             HHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCH
Q 044988          350 LSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNA  427 (538)
Q Consensus       350 l~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~  427 (538)
                      ...+...|+++.|.+.|.++.     +|+..+|..+..+|...|++++|++.|++.. ..| +...|..+..++.+.|++
T Consensus        12 g~~~~~~~d~~~Al~~~~~i~-----~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~~g~~   86 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAVQ-----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKY   86 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSS-----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHCCCHHHHHHHHHhcC-----CCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHhhccH
Confidence            445567789999999998653     5678889999999999999999999999874 334 478899999999999999


Q ss_pred             HHHHHHHHHchhccCCCCc----------------ccHHHHHHHHHHhcCChHHHHHHHHHHHhCC
Q 044988          428 ELASQVAQKLVAEIDPEQA----------------AGYLALVANVYAAAKRWQDVAAVRQKMIKMG  477 (538)
Q Consensus       428 ~~A~~~~~~~~~~~~p~~~----------------~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~  477 (538)
                      ++|+..|++. ....|.+.                ..+. .++.++.+.|++++|.+.++...+..
T Consensus        87 ~~A~~~~~kA-l~~~~~n~~~~~~~~~~~~~~~~~e~~~-n~a~~~~~~~~~~~A~~~l~~A~~~~  150 (192)
T d1hh8a_          87 DLAIKDLKEA-LIQLRGNQLIDYKILGLQFKLFACEVLY-NIAFMYAKKEEWKKAEEQLALATSMK  150 (192)
T ss_dssp             HHHHHHHHHH-HHTTTTCSEEECGGGTBCCEEEHHHHHH-HHHHHHHHTTCHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHH-HHhCccCchHHHHHhhhhcccchHHHHH-HHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            9999999998 54433322                1234 67888999999999999999887643

>d1elwa_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.38  E-value=1.5e-06  Score=64.78  Aligned_cols=91  Identities=13%  Similarity=0.117  Sum_probs=82.1

Q ss_pred             HHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcC
Q 044988          384 CMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAK  461 (538)
Q Consensus       384 ~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g  461 (538)
                      .-...+.+.|++++|+..|++..  .+.+...|..+..++...|++++|+..++++ ..+.|+++..|. .++.++...|
T Consensus         8 ~~g~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~a-l~~~p~~~~~~~-~~g~~~~~~~   85 (117)
T d1elwa_           8 EKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKT-VDLKPDWGKGYS-RKAAALEFLN   85 (117)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhH-HHhccchhhHHH-HHHHHHHHcc
Confidence            34667888999999999999874  3445788999999999999999999999999 999999999999 9999999999


Q ss_pred             ChHHHHHHHHHHHhC
Q 044988          462 RWQDVAAVRQKMIKM  476 (538)
Q Consensus       462 ~~~~A~~~~~~m~~~  476 (538)
                      ++++|+..+++..+.
T Consensus        86 ~~~~A~~~~~~a~~~  100 (117)
T d1elwa_          86 RFEEAKRTYEEGLKH  100 (117)
T ss_dssp             CHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999999874

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.37  E-value=2.6e-06  Score=67.56  Aligned_cols=118  Identities=8%  Similarity=-0.008  Sum_probs=95.5

Q ss_pred             HHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHh
Q 044988          347 LGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRI  423 (538)
Q Consensus       347 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~  423 (538)
                      ......|.+.|++++|...|++..+.   .| +...|..+..+|...|++++|+..|+++. ..| +...|..+..++..
T Consensus        14 ~~~gn~~~~~~~y~~A~~~~~~al~~---~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~   90 (159)
T d1a17a_          14 KTQANDYFKAKDYENAIKFYSQAIEL---NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMA   90 (159)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH---STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHhhhcccc---chhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHH
Confidence            34455667788999999999999876   56 58899999999999999999999999874 344 46899999999999


Q ss_pred             cCCHHHHHHHHHHchhccCCCCcccHHHHHHHHH--HhcCChHHHHHH
Q 044988          424 HNNAELASQVAQKLVAEIDPEQAAGYLALVANVY--AAAKRWQDVAAV  469 (538)
Q Consensus       424 ~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~--~~~g~~~~A~~~  469 (538)
                      .|++++|...++++ ..+.|+++..+. .+..+.  .+.+.+++|...
T Consensus        91 ~g~~~eA~~~~~~a-~~~~p~~~~~~~-~l~~~~~~~~~~~~~~a~~~  136 (159)
T d1a17a_          91 LGKFRAALRDYETV-VKVKPHDKDAKM-KYQECNKIVKQKAFERAIAG  136 (159)
T ss_dssp             TTCHHHHHHHHHHH-HHHSTTCHHHHH-HHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH-HHcCCCCHHHHH-HHHHHHHHHHHHHHHHHHhC
Confidence            99999999999999 999999988665 555443  344556666654

>d1hh8a_ a.118.8.1 (A:) Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Neutrophil cytosolic factor 2 (NCF-2, p67-phox)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.35  E-value=1.3e-05  Score=65.55  Aligned_cols=126  Identities=11%  Similarity=-0.065  Sum_probs=92.1

Q ss_pred             HHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHH
Q 044988          194 LKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGK  273 (538)
Q Consensus       194 i~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~  273 (538)
                      ...+...|+++.|++.|+++..++..+|..+...|...|++++|++.|++..+.. +-+...|..+..++.+.|++++|.
T Consensus        12 g~~~~~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~   90 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAI   90 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHH
Confidence            4456778888888888888877888888888888888888888888888888743 234667777888888888888888


Q ss_pred             HHHHHHHHhccCCC--------C---CcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          274 WIHSYVEENFSVGR--------E---PVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       274 ~~~~~~~~~~~~~~--------~---~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      ..|+..........        .   .....++..+..++.+.|++++|.+.|....+
T Consensus        91 ~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~  148 (192)
T d1hh8a_          91 KDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATS  148 (192)
T ss_dssp             HHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            88887766421100        0   01123445677888888999999888887654

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=98.33  E-value=1e-06  Score=65.18  Aligned_cols=90  Identities=14%  Similarity=0.006  Sum_probs=80.2

Q ss_pred             HHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhc
Q 044988          383 GCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAA  460 (538)
Q Consensus       383 ~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~  460 (538)
                      ..+...+.+.|++++|...|++.. ..| +...|..+..++.+.|++++|+..++++ ..+.|++..++. .++.+|...
T Consensus        20 ~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~a-l~~~p~~~~a~~-~la~~y~~~   97 (112)
T d1hxia_          20 MEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHA-RMLDPKDIAVHA-ALAVSHTNE   97 (112)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhcccccc-cccccccccchH-HHHHHHHHC
Confidence            345677889999999999999874 445 4788999999999999999999999999 999999999888 999999999


Q ss_pred             CChHHHHHHHHHHH
Q 044988          461 KRWQDVAAVRQKMI  474 (538)
Q Consensus       461 g~~~~A~~~~~~m~  474 (538)
                      |++++|.+.+++..
T Consensus        98 g~~~~A~~~l~~~l  111 (112)
T d1hxia_          98 HNANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHh
Confidence            99999999998853

>d1a17a_ a.118.8.1 (A:) Protein phosphatase 5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Protein phosphatase 5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=3.9e-06  Score=66.51  Aligned_cols=93  Identities=15%  Similarity=0.113  Sum_probs=82.7

Q ss_pred             HHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHh
Q 044988          382 YGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAA  459 (538)
Q Consensus       382 ~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~  459 (538)
                      +......|.+.|++++|+..|++..  .+.+...|..+..++...|++++|...|+++ .++.|++..+|. .++.+|..
T Consensus        13 l~~~gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~ka-l~~~p~~~~a~~-~~g~~~~~   90 (159)
T d1a17a_          13 LKTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRA-IELDKKYIKGYY-RRAASNMA   90 (159)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHH-HHHcccchHHHH-HHHHHHHH
Confidence            3445667889999999999999874  3345788999999999999999999999999 999999998898 99999999


Q ss_pred             cCChHHHHHHHHHHHhC
Q 044988          460 AKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       460 ~g~~~~A~~~~~~m~~~  476 (538)
                      .|++++|...+++....
T Consensus        91 ~g~~~eA~~~~~~a~~~  107 (159)
T d1a17a_          91 LGKFRAALRDYETVVKV  107 (159)
T ss_dssp             TTCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHc
Confidence            99999999999999874

>d2c2la1 a.118.8.1 (A:24-224) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.19  E-value=3.6e-06  Score=69.79  Aligned_cols=97  Identities=10%  Similarity=0.011  Sum_probs=87.1

Q ss_pred             ccHHHHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHH
Q 044988          377 PRIEHYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVA  454 (538)
Q Consensus       377 p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~  454 (538)
                      |+...+......|.+.|++++|+..|++.. . +.+...|..+..+|.+.|++++|+..|+++ ..+.|++..+|. .++
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~a-l~l~p~~~~a~~-~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRA-LELDGQSVKAHF-FLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHH-TTSCTTCHHHHH-HHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHhhhhhhhhhhHHHHHH-HHhCCCcHHHHH-HHH
Confidence            677777888999999999999999998863 3 345788999999999999999999999999 999999999899 999


Q ss_pred             HHHHhcCChHHHHHHHHHHHh
Q 044988          455 NVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       455 ~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .+|.+.|++++|+..|++..+
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~  100 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYS  100 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHH
Confidence            999999999999999998764

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.14  E-value=5.9e-06  Score=61.66  Aligned_cols=103  Identities=12%  Similarity=0.022  Sum_probs=82.0

Q ss_pred             HHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCC---hHHHHHHHHhCC-CCCCH---HHHHHHH
Q 044988          347 LGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGL---MDEAFSLVQNMP-MKPND---AVLGSLL  418 (538)
Q Consensus       347 ~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~-~~p~~---~~~~~l~  418 (538)
                      ..+++.+...+++++|++.|++....   .| +..++..+..++.+.++   +++|+.+|+++. ..|+.   .+|..+.
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~---~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg   79 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAA---GSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLA   79 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHH---SCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhh---CCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHH
Confidence            34566777778999999999999876   45 57888999999987655   456999999874 34443   3677888


Q ss_pred             HHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHH
Q 044988          419 LGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVA  454 (538)
Q Consensus       419 ~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~  454 (538)
                      .+|.+.|++++|++.|+++ ..+.|++..+.. ++.
T Consensus        80 ~~y~~~g~~~~A~~~~~~a-L~~~P~~~~A~~-l~~  113 (122)
T d1nzna_          80 VGNYRLKEYEKALKYVRGL-LQTEPQNNQAKE-LER  113 (122)
T ss_dssp             HHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHH
T ss_pred             HHHHHHhhhHHHHHHHHHH-HHhCcCCHHHHH-HHH
Confidence            8999999999999999999 999999987444 443

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=98.11  E-value=0.0003  Score=62.07  Aligned_cols=268  Identities=12%  Similarity=0.006  Sum_probs=148.9

Q ss_pred             ccccHHHHHHHHhccCChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCCCCCcchHHHHHHHHhc
Q 044988           16 KALTTRQIFSLLQIRNTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTENPSTAIWNQMIRGHAR   95 (538)
Q Consensus        16 ~~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~li~~~~~   95 (538)
                      +..-...+...|-..|.++.|..++..         ..-|..++..+.+.++++.|.+.+.+.  .+..+|..+...+.+
T Consensus        13 n~~d~~~i~~~c~~~~lye~A~~lY~~---------~~d~~rl~~~~v~l~~~~~avd~~~k~--~~~~~~k~~~~~l~~   81 (336)
T d1b89a_          13 NNAHIQQVGDRCYDEKMYDAAKLLYNN---------VSNFGRLASTLVHLGEYQAAVDGARKA--NSTRTWKEVCFACVD   81 (336)
T ss_dssp             ----------------CTTTHHHHHHH---------TTCHHHHHHHHHTTTCHHHHHHHHHHH--TCHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHCCCHHHHHHHHHh---------CCCHHHHHHHHHhhccHHHHHHHHHHc--CCHHHHHHHHHHHHh
Confidence            344556777888899999999999873         445788889999999999999888765  356688888888887


Q ss_pred             CCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHHHHHHhcCCCCChhHH
Q 044988           96 SETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLMNLYLMSGGECGVGCA  175 (538)
Q Consensus        96 ~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~a  175 (538)
                      .....-+     .+.......++.....++..|-..|.++....+++...... ..+...++.++.+|++.+.    ++.
T Consensus        82 ~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~-~~~~~~~~~L~~lyak~~~----~kl  151 (336)
T d1b89a_          82 GKEFRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKP----QKM  151 (336)
T ss_dssp             TTCHHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCH----HHH
T ss_pred             CcHHHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCC-ccchHHHHHHHHHHHHhCh----HHH
Confidence            7655443     22223334566677788999999999999999998876432 5667788899999998764    444


Q ss_pred             HHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCC------------ChHHHHHHHHHHHHcCCHHHHHHHHHH
Q 044988          176 RLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHR------------NVVSWTTMISGCAQNGKSRQALSLFNE  243 (538)
Q Consensus       176 ~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~------------~~~~~~~li~~~~~~~~~~~a~~~~~~  243 (538)
                      .+.+.....  ......++..|.+.+.++++.-++.++...            +......++..+.+..+.+...++...
T Consensus       152 ~e~l~~~s~--~y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~~~~~~~~~f~e~~~k~~N~e~~~~~i~~  229 (336)
T d1b89a_         152 REHLELFWS--RVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQF  229 (336)
T ss_dssp             HHHHHHHST--TSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHH
T ss_pred             HHHHHhccc--cCCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcchhhhhHHHHHHHHHccCChHHHHHHHHH
Confidence            444443221  122233344444444444444444444321            222233445555566655555444444


Q ss_pred             HHHCCCCCCHHHHHH-------------HHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHH
Q 044988          244 MRRARVGLDQVALVA-------------ALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEE  310 (538)
Q Consensus       244 m~~~g~~p~~~~~~~-------------li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  310 (538)
                      ..+.  .|+  ..+.             ++..+.+.+++......+..+.+.    +   +..+.+++.+.|...++++.
T Consensus       230 yL~~--~p~--~i~~lL~~v~~~~d~~r~V~~~~k~~~l~li~p~Le~v~~~----n---~~~vn~al~~lyie~~d~~~  298 (336)
T d1b89a_         230 YLEF--KPL--LLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNH----N---NKSVNESLNNLFITEEDYQA  298 (336)
T ss_dssp             HHHH--CGG--GHHHHHHHHGGGCCHHHHHHHHHHTTCTTTTHHHHHHHHTT----C---CHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHc--CHH--HHHHHHHHhccCCCHHHHHHHHHhcCCcHHHHHHHHHHHHc----C---hHHHHHHHHHHHhCcchhHH
Confidence            4331  232  1222             233333444444444444443322    1   23456667777777776655


Q ss_pred             HHHHHHh
Q 044988          311 AYGVFRK  317 (538)
Q Consensus       311 a~~~~~~  317 (538)
                      -++..+.
T Consensus       299 l~~~i~~  305 (336)
T d1b89a_         299 LRTSIDA  305 (336)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5444433

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.09  E-value=2.8e-05  Score=62.09  Aligned_cols=84  Identities=15%  Similarity=0.038  Sum_probs=70.1

Q ss_pred             HHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHH
Q 044988          380 EHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVY  457 (538)
Q Consensus       380 ~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~  457 (538)
                      .+|+.+..+|.+.|++++|+..++... ..| +...|..+..++...|++++|+..|+++ ..+.|+++.+.. .+..+.
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~a-l~l~P~n~~~~~-~l~~~~  140 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKV-LQLYPNNKAAKT-QLAVCQ  140 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCSSCHHHHH-HHHHHH
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHH
Confidence            467778889999999999999998874 445 6888999999999999999999999999 999999998666 777776


Q ss_pred             HhcCChHH
Q 044988          458 AAAKRWQD  465 (538)
Q Consensus       458 ~~~g~~~~  465 (538)
                      .+.+...+
T Consensus       141 ~~~~~~~~  148 (170)
T d1p5qa1         141 QRIRRQLA  148 (170)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            65555443

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=98.06  E-value=0.0015  Score=56.06  Aligned_cols=228  Identities=10%  Similarity=-0.012  Sum_probs=140.1

Q ss_pred             ChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----cCChHHHHHHHHHHHHhccCCCCCcch
Q 044988          217 NVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAE----IGDLKLGKWIHSYVEENFSVGREPVLV  292 (538)
Q Consensus       217 ~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~~~~~~~~~~  292 (538)
                      |+..+..|...+.+.+++++|+++|++..+.|   +...+..|-..|..    ..+...+...+....+.    +.+   
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~----~~~---   70 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDL----NYS---   70 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT----TCH---
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccc----ccc---
Confidence            34556667777777888888888888887765   44445555555554    45677777777776665    322   


Q ss_pred             hHHHHHHHHHHh----CCCHHHHHHHHHhcCCCC-cchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHH
Q 044988          293 SLNNALIHMYAS----CGEIEEAYGVFRKMQRRN-TVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFE  367 (538)
Q Consensus       293 ~~~~~l~~~~~~----~g~~~~a~~~~~~m~~~~-~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~  367 (538)
                      .....+...+..    ..+.+.|...++...+.+ ......+...+...                .........+...+.
T Consensus        71 ~a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~l~~~~~~~----------------~~~~~~~~~a~~~~~  134 (265)
T d1ouva_          71 NGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDG----------------KVVTRDFKKAVEYFT  134 (265)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHC----------------SSSCCCHHHHHHHHH
T ss_pred             chhhccccccccccccchhhHHHHHHHhhhhhhhhhhHHHhhcccccCC----------------CcccchhHHHHHHhh
Confidence            222334443332    356677777776654332 22222222222211                112335566666666


Q ss_pred             HhhhhcCCCccHHHHHHHHHHhhh----cCChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHHHHHchh
Q 044988          368 CMNQNWGIKPRIEHYGCMVDLFSR----AGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRI----HNNAELASQVAQKLVA  439 (538)
Q Consensus       368 ~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~  439 (538)
                      ....    ..+...+..|...|..    ..+...+...++......+......+...+..    ..++++|+..|++. .
T Consensus       135 ~~~~----~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~a-a  209 (265)
T d1ouva_         135 KACD----LNDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKA-C  209 (265)
T ss_dssp             HHHH----TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHH-H
T ss_pred             hhhc----ccccchhhhhhhhhccCCCcccccccchhhhhccccccccccccchhhhcccCcccccchhhhhhhHhhh-h
Confidence            6543    2345566667666664    45666777777766444567766667666655    56899999999998 5


Q ss_pred             ccCCCCcccHHHHHHHHHHh----cCChHHHHHHHHHHHhCCC
Q 044988          440 EIDPEQAAGYLALVANVYAA----AKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       440 ~~~p~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~~~  478 (538)
                      +..  ++..+. .|+.+|.+    .++.++|.++|++..+.|.
T Consensus       210 ~~g--~~~a~~-~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g~  249 (265)
T d1ouva_         210 ELE--NGGGCF-NLGAMQYNGEGVTRNEKQAIENFKKGCKLGA  249 (265)
T ss_dssp             HTT--CHHHHH-HHHHHHHTTSSSSCCSTTHHHHHHHHHHHTC
T ss_pred             ccc--CHHHHH-HHHHHHHcCCCCccCHHHHHHHHHHHHHCcC
Confidence            543  444566 78888876    4478999999999887765

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.98  E-value=3.7e-05  Score=57.94  Aligned_cols=94  Identities=13%  Similarity=0.123  Sum_probs=73.7

Q ss_pred             HHHHHHHHhhhcCChHHHHHHHHhCC-C-CCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH------HH
Q 044988          381 HYGCMVDLFSRAGLMDEAFSLVQNMP-M-KPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL------AL  452 (538)
Q Consensus       381 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~------~~  452 (538)
                      .+..+...|.+.|++++|++.|++.. . +.+...+..+..++.+.|++++|++.++++ .++.|++...+.      ..
T Consensus         6 ~~k~~G~~~~~~~~y~~Ai~~y~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~a-l~l~~~~~~~~~~~a~~~~~   84 (128)
T d1elra_           6 KEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKA-IEVGRENREDYRQIAKAYAR   84 (128)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHHHHHSTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHhHHHHHHHcCchHHHHHHHHHH-HHhCcccHHHHHHHHHHHHH
Confidence            34567778888999999999998763 3 345778888888999999999999999999 777887765444      04


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHh
Q 044988          453 VANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       453 l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ++.++...+++++|++.+++...
T Consensus        85 lg~~~~~~~~~~~A~~~~~kal~  107 (128)
T d1elra_          85 IGNSYFKEEKYKDAIHFYNKSLA  107 (128)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHh
Confidence            56677788899999999987664

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.97  E-value=6.6e-05  Score=59.81  Aligned_cols=63  Identities=17%  Similarity=0.099  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          412 AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       412 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      .+|+.+..+|.+.|++++|+..++++ ..+.|+++.++. .++.+|...|++++|+..|++..+.
T Consensus        63 ~~~~nla~~y~k~~~~~~A~~~~~~a-l~~~p~~~~a~~-~~g~~~~~~g~~~~A~~~~~~al~l  125 (170)
T d1p5qa1          63 ASHLNLAMCHLKLQAFSAAIESCNKA-LELDSNNEKGLS-RRGEAHLAVNDFELARADFQKVLQL  125 (170)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcccccchhhhh-hhccccchhhhH-HHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            35666778899999999999999999 999999999898 9999999999999999999999874

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.95  E-value=2.7e-05  Score=57.98  Aligned_cols=91  Identities=4%  Similarity=-0.076  Sum_probs=74.0

Q ss_pred             HHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcC---CHHHHHHHHHHchhccCCCC--cccHHHHHHH
Q 044988          383 GCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHN---NAELASQVAQKLVAEIDPEQ--AAGYLALVAN  455 (538)
Q Consensus       383 ~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~---~~~~A~~~~~~~~~~~~p~~--~~~~~~~l~~  455 (538)
                      ..++..+...+++++|.+.|++..  .+.+..++..+..++.+.+   ++++|+.+++++ ....|..  ..++. .|+.
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~-l~~~~~~~~~~~~~-~Lg~   80 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEEL-LPKGSKEEQRDYVF-YLAV   80 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHH-TTTSCHHHHHHHHH-HHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-HhccCCchHHHHHH-HHHH
Confidence            457778888999999999999874  3456788888888887655   456799999999 7666654  33567 8999


Q ss_pred             HHHhcCChHHHHHHHHHHHh
Q 044988          456 VYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       456 ~~~~~g~~~~A~~~~~~m~~  475 (538)
                      +|.+.|++++|++.|++..+
T Consensus        81 ~y~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          81 GNYRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHhhhHHHHHHHHHHHH
Confidence            99999999999999999987

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.94  E-value=5.5e-05  Score=55.39  Aligned_cols=89  Identities=12%  Similarity=-0.038  Sum_probs=74.5

Q ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHH
Q 044988          223 TMISGCAQNGKSRQALSLFNEMRRARVGL-DQVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHM  301 (538)
Q Consensus       223 ~li~~~~~~~~~~~a~~~~~~m~~~g~~p-~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~  301 (538)
                      .....+.+.|++++|+..|++..+.  .| +...|..+..++.+.|++++|...++.+.+.     .|.+..++..+...
T Consensus        21 ~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~-----~p~~~~a~~~la~~   93 (112)
T d1hxia_          21 EEGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNHARML-----DPKDIAVHAALAVS   93 (112)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhccc--ccccchhhhhhhhhhhhhhhHHHhhccccccccc-----ccccccchHHHHHH
Confidence            4566778889999999999988874  34 5777888888888999999999999998887     77888888899999


Q ss_pred             HHhCCCHHHHHHHHHhc
Q 044988          302 YASCGEIEEAYGVFRKM  318 (538)
Q Consensus       302 ~~~~g~~~~a~~~~~~m  318 (538)
                      |...|++++|.+.|++.
T Consensus        94 y~~~g~~~~A~~~l~~~  110 (112)
T d1hxia_          94 HTNEHNANAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHH
Confidence            99999999999988763

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.93  E-value=3.1e-05  Score=60.53  Aligned_cols=62  Identities=11%  Similarity=-0.027  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          412 AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       412 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .+|..+..++.+.|++++|++.++++ .++.|++..+|. .++.+|...|++++|+..|++..+
T Consensus        68 ~~~~Nla~~~~~l~~~~~Al~~~~~a-l~~~p~~~ka~~-~~g~~~~~lg~~~~A~~~~~~al~  129 (153)
T d2fbna1          68 SCNLNLATCYNKNKDYPKAIDHASKV-LKIDKNNVKALY-KLGVANMYFGFLEEAKENLYKAAS  129 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHH-HHHSTTCHHHHH-HHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHhcccchhhhhhhcc-ccccchhhhhhH-HhHHHHHHcCCHHHHHHHHHHHHH
Confidence            35666777888899999999999998 888999988888 899999999999999999988876

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.88  E-value=9.3e-05  Score=58.80  Aligned_cols=93  Identities=15%  Similarity=0.058  Sum_probs=73.6

Q ss_pred             HHHHHHHHHhhhcCChHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHH
Q 044988          380 EHYGCMVDLFSRAGLMDEAFSLVQNMP--MKPNDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVY  457 (538)
Q Consensus       380 ~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~p~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~  457 (538)
                      .+|+.+..+|.+.|++++|+..++...  .+.+...|..+..++...|++++|...|+++ ..+.|++..... .+..+.
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~a-l~l~P~n~~~~~-~l~~~~  142 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKV-LEVNPQNKAARL-QIFMCQ  142 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHSCTTCHHHHH-HHHHHH
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHH
Confidence            456678888999999999999998874  3455788999999999999999999999999 999999998666 776666


Q ss_pred             HhcCChH-HHHHHHHHHH
Q 044988          458 AAAKRWQ-DVAAVRQKMI  474 (538)
Q Consensus       458 ~~~g~~~-~A~~~~~~m~  474 (538)
                      .+.+... ...+++.+|.
T Consensus       143 ~~~~~~~e~~kk~~~~~f  160 (168)
T d1kt1a1         143 KKAKEHNERDRRTYANMF  160 (168)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHH
Confidence            6555443 3445555554

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.83  E-value=0.00013  Score=56.76  Aligned_cols=76  Identities=13%  Similarity=0.008  Sum_probs=64.0

Q ss_pred             HHHHHHHHHHhhhcCChHHHHHHHHhCC-CCC-CHHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          379 IEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKP-NDAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       379 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      ..+|..+..+|.+.|++++|++.++... ..| +..+|..+..++...|++++|+..|+++ ..+.|++..+.. .+..+
T Consensus        67 ~~~~~Nla~~~~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~a-l~l~P~n~~~~~-~l~~~  144 (153)
T d2fbna1          67 ISCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKA-ASLNPNNLDIRN-SYELC  144 (153)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHHSTTCHHHHH-HHHHH
T ss_pred             HHHHhhHHHHHHHhcccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHH
Confidence            4577788999999999999999998863 344 5789999999999999999999999999 999999988555 55443

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.79  E-value=8.6e-05  Score=59.10  Aligned_cols=63  Identities=14%  Similarity=0.041  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          411 DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       411 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      ...|..+..++.+.|++++|+..++++ .++.|+++.+|. .++.+|.+.|++++|++.|++..+
T Consensus        77 ~~~~~nla~~~~~~~~~~~Ai~~~~~a-l~~~p~~~~a~~-~~g~~~~~l~~~~~A~~~~~~al~  139 (169)
T d1ihga1          77 LSCVLNIGACKLKMSDWQGAVDSCLEA-LEIDPSNTKALY-RRAQGWQGLKEYDQALADLKKAQE  139 (169)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHH-HTTCTTCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcccchhhhhhhhh-hhhhhhhhhHHH-hHHHHHHHccCHHHHHHHHHHHHH
Confidence            345666677788888888888888888 888888888788 888888888888888888888876

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.78  E-value=0.00016  Score=54.32  Aligned_cols=98  Identities=9%  Similarity=0.093  Sum_probs=65.5

Q ss_pred             HHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHH
Q 044988          257 VAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGF  333 (538)
Q Consensus       257 ~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~  333 (538)
                      ..+...+...|++++|...|....+.     .|.+..++..+..+|.+.|++++|...++++.+   .+...|..+..+|
T Consensus         8 k~~G~~~~~~~~y~~Ai~~y~~al~~-----~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~   82 (128)
T d1elra_           8 KELGNDAYKKKDFDTALKHYDKAKEL-----DPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAY   82 (128)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHh-----CcccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            34455667777777777777777776     566777777888888888888888888887654   2333444444333


Q ss_pred             HhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhh
Q 044988          334 AKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQN  372 (538)
Q Consensus       334 ~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~  372 (538)
                      .+             +...+...+++++|...|......
T Consensus        83 ~~-------------lg~~~~~~~~~~~A~~~~~kal~~  108 (128)
T d1elra_          83 AR-------------IGNSYFKEEKYKDAIHFYNKSLAE  108 (128)
T ss_dssp             HH-------------HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HH-------------HHHHHHHhCCHHHHHHHHHHHHhc
Confidence            33             334445556778888888776654

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.76  E-value=0.0001  Score=58.60  Aligned_cols=125  Identities=14%  Similarity=0.017  Sum_probs=85.3

Q ss_pred             HHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhC
Q 044988          327 TSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNM  405 (538)
Q Consensus       327 ~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~  405 (538)
                      ......+...|++.+|+..|...+..+...    .+........   .+.| +...|..+..+|.+.|++++|+..++++
T Consensus        31 ~~~~~~~~~~~~y~~Ai~~y~~al~~~~~~----~~~~~~~~~~---~~~~~~~~~~~nla~~~~~~~~~~~Ai~~~~~a  103 (169)
T d1ihga1          31 KNIGNTFFKSQNWEMAIKKYTKVLRYVEGS----RAAAEDADGA---KLQPVALSCVLNIGACKLKMSDWQGAVDSCLEA  103 (169)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHH----HHHSCHHHHG---GGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhhhhh----hhhhhhHHHH---HhChhhHHHHHHHHHHHHhhcccchhhhhhhhh
Confidence            344555667777777765555444321100    0000000000   1234 4667888899999999999999999887


Q ss_pred             C-CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhc
Q 044988          406 P-MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAA  460 (538)
Q Consensus       406 ~-~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~  460 (538)
                      . ..|+ ...|..+..++...|++++|++.|+++ .++.|++..+.. .+..+..+.
T Consensus       104 l~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~a-l~l~p~n~~~~~-~l~~~~~~l  158 (169)
T d1ihga1         104 LEIDPSNTKALYRRAQGWQGLKEYDQALADLKKA-QEIAPEDKAIQA-ELLKVKQKI  158 (169)
T ss_dssp             HTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHH
T ss_pred             hhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHH-HHhCCCCHHHHH-HHHHHHHHH
Confidence            3 4444 788999999999999999999999999 999999988666 666554443

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.67  E-value=0.00015  Score=57.98  Aligned_cols=123  Identities=8%  Similarity=0.034  Sum_probs=83.6

Q ss_pred             HHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 044988          346 FLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRIHN  425 (538)
Q Consensus       346 ~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~~~  425 (538)
                      ...........|+++.|.+.|......+.-.+-.        .+....-......-++.    -....+..+...+...|
T Consensus        14 ~~~~g~~~~~~g~~e~A~~~~~~AL~l~rG~~l~--------~~~~~~w~~~~r~~l~~----~~~~a~~~la~~~~~~g   81 (179)
T d2ff4a2          14 EKTAGVHAAAAGRFEQASRHLSAALREWRGPVLD--------DLRDFQFVEPFATALVE----DKVLAHTAKAEAEIACG   81 (179)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHTTCCSSTTG--------GGTTSTTHHHHHHHHHH----HHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhhCcccccc--------cCcchHHHHHHHHHHHH----HHHHHHHHHHHHHHHCC
Confidence            3344456677788888888888777543111100        00000001111111111    12356677888899999


Q ss_pred             CHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH-----hCCCCCCC
Q 044988          426 NAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI-----KMGVRKPP  482 (538)
Q Consensus       426 ~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~-----~~~~~~~~  482 (538)
                      ++++|+..++++ ....|.+...|. .++.+|.+.|++.+|++.|++..     +.|+.|.+
T Consensus        82 ~~~~Al~~~~~a-l~~~P~~e~~~~-~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~  141 (179)
T d2ff4a2          82 RASAVIAELEAL-TFEHPYREPLWT-QLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGP  141 (179)
T ss_dssp             CHHHHHHHHHHH-HHHSTTCHHHHH-HHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCH
T ss_pred             CchHHHHHHHHH-HHhCCccHHHHH-HHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCH
Confidence            999999999999 999999999899 99999999999999999999985     35776654

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.66  E-value=0.0002  Score=56.80  Aligned_cols=62  Identities=10%  Similarity=0.095  Sum_probs=56.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          413 VLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       413 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      .|..+..++.+.|++++|+..++++ ..+.|++..+|. .++.+|...|++++|...|++..+.
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~a-l~l~p~~~~a~~-~~~~~~~~l~~~~~A~~~~~~al~l  127 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKA-LGLDSANEKGLY-RRGEAQLLMNEFESAKGDFEKVLEV  127 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHS
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhh-hhcccchHHHHH-HHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4556777889999999999999999 999999999999 9999999999999999999999874

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.58  E-value=0.02  Score=50.04  Aligned_cols=132  Identities=11%  Similarity=0.089  Sum_probs=57.5

Q ss_pred             CCcchHHHHHHHHhcCCCchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHHH
Q 044988           81 PSTAIWNQMIRGHARSETPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNLM  160 (538)
Q Consensus        81 ~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~  160 (538)
                      ||..--..+..-|.+.|.++.|..+|..+..         |..++..+.+.++++.|.++..+.      .+..+|..+.
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~d---------~~rl~~~~v~l~~~~~avd~~~k~------~~~~~~k~~~   76 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVSN---------FGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVC   76 (336)
T ss_dssp             C----------------CTTTHHHHHHHTTC---------HHHHHHHHHTTTCHHHHHHHHHHH------TCHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCCC---------HHHHHHHHHhhccHHHHHHHHHHc------CCHHHHHHHH
Confidence            4444444556666677777777777765542         566666667777777666655432      2344555555


Q ss_pred             HHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCC---CCChHHHHHHHHHHHHc
Q 044988          161 NLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMP---HRNVVSWTTMISGCAQN  231 (538)
Q Consensus       161 ~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~~~~~~~~li~~~~~~  231 (538)
                      ..+.....   ...|.- .......+......++..|-..|.++....+++...   ..+...++.++..|++.
T Consensus        77 ~~l~~~~e---~~la~i-~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~~~~~~~~~~L~~lyak~  146 (336)
T d1b89a_          77 FACVDGKE---FRLAQM-CGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKF  146 (336)
T ss_dssp             HHHHHTTC---HHHHHH-TTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTT
T ss_pred             HHHHhCcH---HHHHHH-HHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCCccchHHHHHHHHHHHHh
Confidence            55555554   333211 111111222333344555555555555555555321   23333445555555443

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=97.47  E-value=0.0078  Score=51.22  Aligned_cols=78  Identities=8%  Similarity=-0.060  Sum_probs=41.8

Q ss_pred             CHHHHHHHHccCCC-CChHHHHHHHHHHHH----cCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----cCChHHH
Q 044988          202 DIDGAWKIFDEMPH-RNVVSWTTMISGCAQ----NGKSRQALSLFNEMRRARVGLDQVALVAALSACAE----IGDLKLG  272 (538)
Q Consensus       202 ~~~~A~~~~~~m~~-~~~~~~~~li~~~~~----~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~----~~~~~~a  272 (538)
                      +...+...++...+ .+..+...+...|..    ..++++|+.+|+...+.|   +...+..|...|.+    ..+.+.|
T Consensus       161 ~~~~~~~~~~~a~~~g~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g---~~~a~~~LG~~y~~G~g~~~n~~~A  237 (265)
T d1ouva_         161 DLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE---NGGGCFNLGAMQYNGEGVTRNEKQA  237 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHTTSSSSCCSTTH
T ss_pred             ccccchhhhhccccccccccccchhhhcccCcccccchhhhhhhHhhhhccc---CHHHHHHHHHHHHcCCCCccCHHHH
Confidence            34444444444322 344455555545544    456777777777777665   23444444444443    2356666


Q ss_pred             HHHHHHHHHh
Q 044988          273 KWIHSYVEEN  282 (538)
Q Consensus       273 ~~~~~~~~~~  282 (538)
                      ...|+...+.
T Consensus       238 ~~~~~kAa~~  247 (265)
T d1ouva_         238 IENFKKGCKL  247 (265)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHC
Confidence            6666666555

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.46  E-value=0.00013  Score=69.38  Aligned_cols=130  Identities=9%  Similarity=-0.096  Sum_probs=62.3

Q ss_pred             cCCHHHHHHHHccCCC---CChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHH
Q 044988          200 RGDIDGAWKIFDEMPH---RNVVSWTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIH  276 (538)
Q Consensus       200 ~g~~~~A~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~  276 (538)
                      .+.++.|+..+....+   ++...+..+...+.+.|+.+.|...+.......  | ..++..+...+...|+++.|...|
T Consensus        99 ~~~Y~~ai~~l~~~~~l~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~--~-~~~~~~LG~l~~~~~~~~~A~~~y  175 (497)
T d1ya0a1          99 SGFYTQLLQELCTVFNVDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYI--C-QHCLVHLGDIARYRNQTSQAESYY  175 (497)
T ss_dssp             HHHHHHHHHHHTC-------------------------------CCHHHHHH--H-HHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCC--H-HHHHHHHHHHHHHcccHHHHHHHH
Confidence            3445555555554332   233455556666666666666666665544311  1 234555666666677777777777


Q ss_pred             HHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcC
Q 044988          277 SYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQG  337 (538)
Q Consensus       277 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~  337 (538)
                      ..+.+.     .|.+...|+.|...+...|+..+|...|.+...   |...++..|...+.+..
T Consensus       176 ~~A~~l-----~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~~~~  234 (497)
T d1ya0a1         176 RHAAQL-----VPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKAL  234 (497)
T ss_dssp             HHHHHH-----CTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHH-----CCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhh
Confidence            777766     666666777777777777777777777765543   45556666666665544

>d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: SMG-7
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.32  E-value=1.2e-05  Score=76.91  Aligned_cols=99  Identities=10%  Similarity=-0.047  Sum_probs=51.5

Q ss_pred             CCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHH
Q 044988          374 GIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLA  451 (538)
Q Consensus       374 ~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~  451 (538)
                      ++.| +...+..+...+.+.|+.++|...++... .++ ...+..+...+...|++++|...|+++ ..+.|++...|. 
T Consensus       114 ~l~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al-~~~~~~~~~~LG~l~~~~~~~~~A~~~y~~A-~~l~P~~~~~~~-  190 (497)
T d1ya0a1         114 NVDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSC-SYICQHCLVHLGDIARYRNQTSQAESYYRHA-AQLVPSNGQPYN-  190 (497)
T ss_dssp             -----------------------------CCHHH-HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTBSHHHH-
T ss_pred             CCChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHh-CCCHHHHHHHHHHHHHHcccHHHHHHHHHHH-HHHCCCchHHHH-
Confidence            3344 35566677777777777777776554432 122 345666777778888888888888888 888888887777 


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHh
Q 044988          452 LVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       452 ~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                      .|+.++...|+..+|+..|.+...
T Consensus       191 ~Lg~~~~~~~~~~~A~~~y~ral~  214 (497)
T d1ya0a1         191 QLAILASSKGDHLTTIFYYCRSIA  214 (497)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHS
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHh
Confidence            888888888888888887777665

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.29  E-value=0.00033  Score=53.80  Aligned_cols=112  Identities=14%  Similarity=0.155  Sum_probs=82.6

Q ss_pred             ccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhc----------CChHHHHHHHHhCC-CCCC-HHHHHHHHHHH
Q 044988          355 HGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRA----------GLMDEAFSLVQNMP-MKPN-DAVLGSLLLGC  421 (538)
Q Consensus       355 ~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~----------g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~  421 (538)
                      +.+.+++|...|+...+.   .| +..++..+..+|...          +.+++|++.|++.. ..|+ ..+|..+..++
T Consensus         9 r~~~fe~A~~~~e~al~~---~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y   85 (145)
T d1zu2a1           9 RILLFEQIRQDAENTYKS---NPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAY   85 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHccHHHHHHHHHHHHhh---CCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHHH
Confidence            345789999999999876   56 577888888887643          45678888888774 4454 77888888887


Q ss_pred             HhcC-----------CHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCC
Q 044988          422 RIHN-----------NAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       422 ~~~~-----------~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~  478 (538)
                      ...|           ++++|.+.|+++ .++.|++...+. .|...       .+|.+++.+..+.|+
T Consensus        86 ~~~g~~~~~~~~~~~~~~~A~~~~~ka-l~l~P~~~~~~~-~L~~~-------~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1          86 TSFAFLTPDETEAKHNFDLATQFFQQA-VDEQPDNTHYLK-SLEMT-------AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             HHHHHHCCCHHHHHHHHHHHHHHHHHH-HHHCTTCHHHHH-HHHHH-------HTHHHHHHHHHHSSS
T ss_pred             HHcccchhhHHHHHHhHHHhhhhhhcc-cccCCCHHHHHH-HHHHH-------HHHHHHHHHHHHHhc
Confidence            6654           368899999999 999999988344 55433       456777777766654

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=97.22  E-value=0.00065  Score=52.92  Aligned_cols=94  Identities=15%  Similarity=0.025  Sum_probs=66.4

Q ss_pred             HHHHHH--HHHhhhcCChHHHHHHHHhCC----CCCC----------HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCC
Q 044988          380 EHYGCM--VDLFSRAGLMDEAFSLVQNMP----MKPN----------DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDP  443 (538)
Q Consensus       380 ~~~~~l--~~~~~~~g~~~~A~~~~~~~~----~~p~----------~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p  443 (538)
                      .+|..+  ...+.+.|++++|++.|++..    ..|+          ...|+.+..++...|++++|...+++. ..+.|
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~a-l~~~~   86 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKA-LHYFN   86 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhh-hhccc
Confidence            345545  445556788888877777652    1121          356778888899999999999888888 43322


Q ss_pred             -------CCc----ccHHHHHHHHHHhcCChHHHHHHHHHHHh
Q 044988          444 -------EQA----AGYLALVANVYAAAKRWQDVAAVRQKMIK  475 (538)
Q Consensus       444 -------~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~  475 (538)
                             +..    .++. .++.+|.+.|++++|++.|++..+
T Consensus        87 ~~~~~~~~~~~~~~~a~~-~~g~~~~~lg~~eeA~~~~~~Al~  128 (156)
T d2hr2a1          87 RRGELNQDEGKLWISAVY-SRALALDGLGRGAEAMPEFKKVVE  128 (156)
T ss_dssp             HHCCTTSTHHHHHHHHHH-HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ccccccccccchhHHHHh-hhHHHHHHHHHHHHHHHHHHHHHH
Confidence                   211    2355 788999999999999999999875

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=97.16  E-value=0.00024  Score=60.71  Aligned_cols=119  Identities=11%  Similarity=0.083  Sum_probs=83.5

Q ss_pred             cccCcHHHHHHHHHHhhhhcCCCc-cHHHHHHHHHHhhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHhcCCHHHH
Q 044988          354 SHGGFVDEGRQFFECMNQNWGIKP-RIEHYGCMVDLFSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRIHNNAELA  430 (538)
Q Consensus       354 ~~~~~~~~a~~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~~~~~~~A  430 (538)
                      .+.|++++|...+++..+.   .| |...+..+...|+..|++++|.+.|+... ..|+ ...+..+...+...+..+++
T Consensus         7 L~~G~l~eAl~~l~~al~~---~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l~P~~~~~~~~l~~ll~a~~~~~~a   83 (264)
T d1zbpa1           7 LSEGQLQQALELLIEAIKA---SPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAAQARKDF   83 (264)
T ss_dssp             TTTTCHHHHHHHHHHHHHT---CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhccccHHH
Confidence            4568999999999999876   56 68899999999999999999999999874 4565 44444444444444444443


Q ss_pred             HHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          431 SQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       431 ~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      ............|+....+. ..+..+...|+.++|.+.++++.+.
T Consensus        84 ~~~~~~~~~~~~p~~~~~~l-~~a~~~~~~gd~~~A~~~~~~a~e~  128 (264)
T d1zbpa1          84 AQGAATAKVLGENEELTKSL-VSFNLSMVSQDYEQVSELALQIEEL  128 (264)
T ss_dssp             TTSCCCEECCCSCHHHHHHH-HHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHhhhhhcccCchHHHHHH-HHHHHHHhCCCHHHHHHHHHHHHhc
Confidence            33222220222343333344 5677788999999999999998764

>d2ff4a2 a.118.8.3 (A:105-283) Probable regulatory protein EmbR, middle domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: BTAD-like
domain: Probable regulatory protein EmbR, middle domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.01  E-value=0.005  Score=48.75  Aligned_cols=56  Identities=18%  Similarity=0.269  Sum_probs=27.1

Q ss_pred             HHHHHHHHHhCCCHHHHHHHHHhcCC---CCcchHHHHHHHHHhcCCccHHHHHHHHHH
Q 044988          295 NNALIHMYASCGEIEEAYGVFRKMQR---RNTVSWTSMITGFAKQGYAQEALLTFLGVL  350 (538)
Q Consensus       295 ~~~l~~~~~~~g~~~~a~~~~~~m~~---~~~~~~~~li~~~~~~~~~~~a~~~~~~ll  350 (538)
                      +..+...+.+.|++++|...++++.+   -+...|..++.+|.+.|+..+|+..|..+.
T Consensus        70 ~~~la~~~~~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~  128 (179)
T d2ff4a2          70 HTAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVK  128 (179)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence            33444555555555555555554443   233445555555555555555554444443

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.93  E-value=0.0015  Score=45.55  Aligned_cols=70  Identities=16%  Similarity=0.050  Sum_probs=55.6

Q ss_pred             HHHHHHHHHhhhcCChHHHHHHHHhCC--------CCCC-HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHH
Q 044988          380 EHYGCMVDLFSRAGLMDEAFSLVQNMP--------MKPN-DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYL  450 (538)
Q Consensus       380 ~~~~~l~~~~~~~g~~~~A~~~~~~~~--------~~p~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~  450 (538)
                      ..+-.+...+.+.|++++|...|++..        ..++ ..+++.+..++.+.|++++|+..++++ .++.|+++.++.
T Consensus         6 ddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~a-L~l~P~~~~a~~   84 (95)
T d1tjca_           6 EDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKL-LELDPEHQRANG   84 (95)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHCTTCHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHH-HHhCcCCHHHHH
Confidence            344567778888888888888887652        1223 567888999999999999999999999 999999988666

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=96.87  E-value=0.0027  Score=49.15  Aligned_cols=91  Identities=14%  Similarity=0.019  Sum_probs=64.2

Q ss_pred             cccCcHHHHHHHHHHhhhhcCCCc----------cHHHHHHHHHHhhhcCChHHHHHHHHhCC--------CCCC-----
Q 044988          354 SHGGFVDEGRQFFECMNQNWGIKP----------RIEHYGCMVDLFSRAGLMDEAFSLVQNMP--------MKPN-----  410 (538)
Q Consensus       354 ~~~~~~~~a~~~~~~~~~~~~~~p----------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--------~~p~-----  410 (538)
                      ...|++++|++.|++..+...-.|          ...+|+.+..+|...|++++|.+.+++..        ..++     
T Consensus        20 ~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~~   99 (156)
T d2hr2a1          20 LVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLW   99 (156)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccchh
Confidence            344566666666666654322122          14678899999999999999998887752        2232     


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCC
Q 044988          411 DAVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQ  445 (538)
Q Consensus       411 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~  445 (538)
                      ...+..+..++...|++++|+..|+++ .++.|..
T Consensus       100 ~~a~~~~g~~~~~lg~~eeA~~~~~~A-l~l~~~~  133 (156)
T d2hr2a1         100 ISAVYSRALALDGLGRGAEAMPEFKKV-VEMIEER  133 (156)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHH-HHHHHHC
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHHHH-HHhhHHh
Confidence            235677788899999999999999999 5555443

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=96.68  E-value=0.00064  Score=52.09  Aligned_cols=85  Identities=15%  Similarity=0.078  Sum_probs=67.4

Q ss_pred             hhhcCChHHHHHHHHhCC-CCCC-HHHHHHHHHHHHh----------cCCHHHHHHHHHHchhccCCCCcccHHHHHHHH
Q 044988          389 FSRAGLMDEAFSLVQNMP-MKPN-DAVLGSLLLGCRI----------HNNAELASQVAQKLVAEIDPEQAAGYLALVANV  456 (538)
Q Consensus       389 ~~~~g~~~~A~~~~~~~~-~~p~-~~~~~~l~~~~~~----------~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~  456 (538)
                      |-+.+.+++|++.|+... ..|+ ...+..+..++..          .+.+++|+..|+++ .++.|++..+|. .++.+
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kA-l~l~P~~~~a~~-~lG~~   84 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEA-LLIDPKKDEAVW-CIGNA   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHH-HHHCTTCHHHHH-HHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHH-HHhcchhhHHHh-hHHHH
Confidence            456677999999999873 3444 6677777777653          34568899999999 999999999899 89999


Q ss_pred             HHhcCC-----------hHHHHHHHHHHHh
Q 044988          457 YAAAKR-----------WQDVAAVRQKMIK  475 (538)
Q Consensus       457 ~~~~g~-----------~~~A~~~~~~m~~  475 (538)
                      |...|+           +++|.+.|++..+
T Consensus        85 y~~~g~~~~~~~~~~~~~~~A~~~~~kal~  114 (145)
T d1zu2a1          85 YTSFAFLTPDETEAKHNFDLATQFFQQAVD  114 (145)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcccchhhHHHHHHhHHHhhhhhhcccc
Confidence            987654           6888888888876

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=96.67  E-value=0.23  Score=45.48  Aligned_cols=256  Identities=9%  Similarity=0.000  Sum_probs=137.6

Q ss_pred             HHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHccCChHH
Q 044988          193 LLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQNGKSRQALSLFNEMRRAR-VGLDQVALVAALSACAEIGDLKL  271 (538)
Q Consensus       193 li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~m~~~g-~~p~~~~~~~li~~~~~~~~~~~  271 (538)
                      .+..+.+.+++......+...+ .+...-.....+....|+..+|...+..+-..| ..|+                  .
T Consensus        78 ~l~~L~~~~~w~~~~~~~~~~p-~~~~~~c~~~~A~~~~g~~~~a~~~~~~lW~~~~~~p~------------------~  138 (450)
T d1qsaa1          78 FVNELARREDWRGLLAFSPEKP-GTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTGKSQPN------------------A  138 (450)
T ss_dssp             HHHHHHHTTCHHHHHHHCCSCC-SSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCSSCCCT------------------H
T ss_pred             HHHHHHhccCHHHHHHhccCCC-CCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCCCch------------------H
Confidence            3455666777776666554322 234444456677777888888887777665543 2222                  2


Q ss_pred             HHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCCCCcchHHHHHHHHHhcCCccHHH-------H
Q 044988          272 GKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQRRNTVSWTSMITGFAKQGYAQEAL-------L  344 (538)
Q Consensus       272 a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~-------~  344 (538)
                      ...++..+.+.    +.......+ .-+......|+...|..+...+...........+.....-.......       .
T Consensus       139 c~~l~~~~~~~----~~lt~~~~~-~R~~~~l~~~~~~~a~~l~~~l~~~~~~~~~a~~~l~~~p~~~~~~~~~~~~~~~  213 (450)
T d1qsaa1         139 CDKLFSVWRAS----GKQDPLAYL-ERIRLAMKAGNTGLVTVLAGQMPADYQTIASAIISLANNPNTVLTFARTTGATDF  213 (450)
T ss_dssp             HHHHHHHHHHT----TCSCHHHHH-HHHHHHHHTTCHHHHHHHHHTCCGGGHHHHHHHHHHHHCGGGHHHHHHHSCCCHH
T ss_pred             HHHHHHHHHhc----CCCCHHHHH-HHHHHHHHcCChhhHHHHHhhCChhHHHHHHHHHHHHhChHhHHHHHhcCCCChh
Confidence            22233333332    222222222 34444555566777777666655433222333332222111111111       0


Q ss_pred             HHHHHHHHhcc--cCcHHHHHHHHHHhhhhcCCCccHH--HHHHHHHHhhhcCChHHHHHHHHhCC-CCCCHHHHHHHHH
Q 044988          345 TFLGVLSACSH--GGFVDEGRQFFECMNQNWGIKPRIE--HYGCMVDLFSRAGLMDEAFSLVQNMP-MKPNDAVLGSLLL  419 (538)
Q Consensus       345 ~~~~ll~~~~~--~~~~~~a~~~~~~~~~~~~~~p~~~--~~~~l~~~~~~~g~~~~A~~~~~~~~-~~p~~~~~~~l~~  419 (538)
                      ....+..++.+  ..+.+.+...+..........++..  ....+...+...+..+.+...+.... ...+.....-.+.
T Consensus       214 ~~~~~~~~l~rla~~d~~~a~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~w~~~  293 (450)
T d1qsaa1         214 TRQMAAVAFASVARQDAENARLMIPSLAQAQQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQSTSLIERRVR  293 (450)
T ss_dssp             HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTCCCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHhccChhHHHHHHHhhhhcccccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcccccchHHHHHHHH
Confidence            01111111111  2367778888887776544443321  22233344455667777777776553 2344444445555


Q ss_pred             HHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHH
Q 044988          420 GCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMI  474 (538)
Q Consensus       420 ~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~  474 (538)
                      .....+++..+...++.+ ............ -++.++...|+.++|...|....
T Consensus       294 ~al~~~~~~~~~~~~~~l-~~~~~~~~r~~Y-W~gRa~~~~G~~~~A~~~~~~~a  346 (450)
T d1qsaa1         294 MALGTGDRRGLNTWLARL-PMEAKEKDEWRY-WQADLLLERGREAEAKEILHQLM  346 (450)
T ss_dssp             HHHHHTCHHHHHHHHHHS-CTTGGGSHHHHH-HHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCChHHHHHHHHhc-CcccccHHHHHH-HHHHHHHHcCChhhHHHHHHHHh
Confidence            667778889888888888 433333344345 78888889999999998888865

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=96.64  E-value=0.0025  Score=54.19  Aligned_cols=51  Identities=18%  Similarity=0.171  Sum_probs=30.7

Q ss_pred             ccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHHHHHHHhcCC
Q 044988          265 EIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEAYGVFRKMQR  320 (538)
Q Consensus       265 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  320 (538)
                      +.|++++|...++..++.     .|.+...+..+...|+..|++++|...|+...+
T Consensus         8 ~~G~l~eAl~~l~~al~~-----~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~   58 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKA-----SPKDASLRSSFIELLCIDGDFERADEQLMQSIK   58 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHT-----CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHH-----CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            445566666666655554     556666666666666666666666666665543

>d1tjca_ a.118.8.1 (A:) Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Prolyl 4-hydroxylase alpha-1 subunit, P4HA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.33  E-value=0.032  Score=38.39  Aligned_cols=74  Identities=15%  Similarity=0.029  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHC-----CCCCC-HHHHHHHHHHHHccCChHHHHHHHHHHHHhccCCCCCcchh
Q 044988          220 SWTTMISGCAQNGKSRQALSLFNEMRRA-----RVGLD-QVALVAALSACAEIGDLKLGKWIHSYVEENFSVGREPVLVS  293 (538)
Q Consensus       220 ~~~~li~~~~~~~~~~~a~~~~~~m~~~-----g~~p~-~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  293 (538)
                      .+-.+...+.+.|++++|...|++..+.     ...++ ..++..+..++.+.|++++|...++.+.+.     .|.+..
T Consensus         7 dc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l-----~P~~~~   81 (95)
T d1tjca_           7 DSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLEL-----DPEHQR   81 (95)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-----CTTCHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHh-----CcCCHH
Confidence            3445667777888888888888877642     11222 456677777777888888888888877776     566665


Q ss_pred             HHHHH
Q 044988          294 LNNAL  298 (538)
Q Consensus       294 ~~~~l  298 (538)
                      +++.+
T Consensus        82 a~~Nl   86 (95)
T d1tjca_          82 ANGNL   86 (95)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55544

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=96.09  E-value=0.12  Score=36.53  Aligned_cols=119  Identities=12%  Similarity=0.149  Sum_probs=80.9

Q ss_pred             ccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCC--------------------CCCCHHHH
Q 044988          355 HGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMP--------------------MKPNDAVL  414 (538)
Q Consensus       355 ~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--------------------~~p~~~~~  414 (538)
                      -.|.++++.++..+....    .+..-||-+|--....-+-+...+.++.+.                    ...+...+
T Consensus        14 ldG~ve~Gveii~k~~~s----s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~Nlk~vv~C~~~~n~~se~v   89 (161)
T d1wy6a1          14 LDGYIDEGVKIVLEITKS----STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQNLKSVVECGVINNTLNEHV   89 (161)
T ss_dssp             HTTCHHHHHHHHHHHHHH----SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCSCTHHHHHHHHHTTCCCHHH
T ss_pred             HhhhHHhHHHHHHHHccc----CCccccceeeeecccccchHHHHHHHHHHhhhcCchhhhcHHHHHHHHHHhcchHHHH
Confidence            346788888888887754    233334444433333334444444444332                    12345566


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHHHHHHHHHhCCCC
Q 044988          415 GSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVAAVRQKMIKMGVR  479 (538)
Q Consensus       415 ~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~~~~  479 (538)
                      +..++....+|+-++-.++++.+ .+.....+.... -++.+|.+-|...++-+++.+..++|++
T Consensus        90 dlALd~lv~~~kkd~Ld~i~~~l-~kn~~i~~~~ll-kia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          90 NKALDILVIQGKRDKLEEIGREI-LKNNEVSASILV-AIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHH-C--CCSCHHHHH-HHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHhccHHHHHHHHHHH-HhcCCCCHHHHH-HHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            77788899999999999999996 444444555456 8999999999999999999999999873

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=94.22  E-value=0.3  Score=35.68  Aligned_cols=111  Identities=12%  Similarity=0.006  Sum_probs=79.4

Q ss_pred             cHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhhcCChHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCCHHHHHHH
Q 044988          358 FVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSRAGLMDEAFSLVQNMPMKPNDAVLGSLLLGCRI----HNNAELASQV  433 (538)
Q Consensus       358 ~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~p~~~~~~~l~~~~~~----~~~~~~A~~~  433 (538)
                      ++++|...|++..+. |.   ...+..|.  .....+.++|.+++++....-+......|...|..    ..+.++|.++
T Consensus         8 d~~~A~~~~~kaa~~-g~---~~a~~~l~--~~~~~~~~~a~~~~~~aa~~g~~~a~~~Lg~~y~~g~~~~~d~~~A~~~   81 (133)
T d1klxa_           8 DLKKAIQYYVKACEL-NE---MFGCLSLV--SNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQY   81 (133)
T ss_dssp             HHHHHHHHHHHHHHT-TC---TTHHHHHH--TCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHH
T ss_pred             CHHHHHHHHHHHHHC-CC---hhhhhhhc--cccccCHHHHHHHHhhhhcccchhhhhhHHHhhhhccccchhhHHHHHH
Confidence            788999999998765 42   22233333  34557889999999887544566666666666654    4578999999


Q ss_pred             HHHchhccCCCCcccHHHHHHHHHHh----cCChHHHHHHHHHHHhCCC
Q 044988          434 AQKLVAEIDPEQAAGYLALVANVYAA----AKRWQDVAAVRQKMIKMGV  478 (538)
Q Consensus       434 ~~~~~~~~~p~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~~~  478 (538)
                      |++. .+.  .++.... .|+.+|..    ..+.++|.+++++..+.|.
T Consensus        82 ~~~a-a~~--g~~~a~~-~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_          82 YSKA-CGL--NDQDGCL-ILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  126 (133)
T ss_dssp             HHHH-HHT--TCHHHHH-HHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             Hhhh-hcc--CcchHHH-HHHHHHHcCCccCCCHHHHHHHHHHHHHCCC
Confidence            9998 543  3344455 77778776    4589999999999888775

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.47  E-value=0.28  Score=35.02  Aligned_cols=69  Identities=12%  Similarity=0.063  Sum_probs=33.1

Q ss_pred             cHHHHHHHHHHhhhcC---ChHHHHHHHHhCC-CCC-CH-HHHHHHHHHHHhcCCHHHHHHHHHHchhccCCCCcc
Q 044988          378 RIEHYGCMVDLFSRAG---LMDEAFSLVQNMP-MKP-ND-AVLGSLLLGCRIHNNAELASQVAQKLVAEIDPEQAA  447 (538)
Q Consensus       378 ~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~-~~p-~~-~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~  447 (538)
                      ...+--....++.+..   +.++++.+|+++. ..| +. ..+-.|.-+|.+.|++++|.+.++++ .++.|++..
T Consensus        34 s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~-L~ieP~n~q  108 (124)
T d2pqrb1          34 TIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTL-FEHERNNKQ  108 (124)
T ss_dssp             CHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHH-HHHCTTCHH
T ss_pred             CcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHH-HccCCCcHH
Confidence            3344444444444433   2345555555442 122 21 23344444555556666666666655 555555544

>d1wy6a1 a.118.20.1 (A:7-167) Hypothetical protein ST1625 {Archaeon Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Hypothetical protein ST1625
family: Hypothetical protein ST1625
domain: Hypothetical protein ST1625
species: Archaeon Sulfolobus tokodaii [TaxId: 111955]

Probab=92.82  E-value=1.1  Score=31.73  Aligned_cols=61  Identities=15%  Similarity=0.080  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          221 WTTMISGCAQNGKSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       221 ~~~li~~~~~~~~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      .+..+....++|+-+.-.+++..+.+. -+|++.....+..+|.+.|...++..++..+.+.
T Consensus        89 vdlALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~ACe~  149 (161)
T d1wy6a1          89 VNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKK  149 (161)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHH
Confidence            334444445555555555555554432 2444444555555555555555555555555444

>d1qsaa1 a.118.5.1 (A:1-450) 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Bacterial muramidases
family: Bacterial muramidases
domain: 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain
species: Escherichia coli [TaxId: 562]

Probab=91.99  E-value=4.1  Score=36.64  Aligned_cols=272  Identities=10%  Similarity=0.010  Sum_probs=138.5

Q ss_pred             HHHHHHHhcCCCCChhHHHHHhhcCCCCCchhHHHHHHHHHhcCCHHHHHHHHccCCCCChHHHHHHHHHHHH--cCCHH
Q 044988          158 NLMNLYLMSGGECGVGCARLLFDDMPARSVVSWNSLLKGYVKRGDIDGAWKIFDEMPHRNVVSWTTMISGCAQ--NGKSR  235 (538)
Q Consensus       158 ~l~~~~~~~g~~~~~~~a~~~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~~~~~~~~li~~~~~--~~~~~  235 (538)
                      .-+......|+   ...|..+...+...........+.....   ...+........ .+......+..++.+  ..+.+
T Consensus       159 ~R~~~~l~~~~---~~~a~~l~~~l~~~~~~~~~a~~~l~~~---p~~~~~~~~~~~-~~~~~~~~~~~~l~rla~~d~~  231 (450)
T d1qsaa1         159 ERIRLAMKAGN---TGLVTVLAGQMPADYQTIASAIISLANN---PNTVLTFARTTG-ATDFTRQMAAVAFASVARQDAE  231 (450)
T ss_dssp             HHHHHHHHTTC---HHHHHHHHHTCCGGGHHHHHHHHHHHHC---GGGHHHHHHHSC-CCHHHHHHHHHHHHHHHHHCHH
T ss_pred             HHHHHHHHcCC---hhhHHHHHhhCChhHHHHHHHHHHHHhC---hHhHHHHHhcCC-CChhhhHHHHHHHHHHhccChh
Confidence            34444455566   6777777666654444444444444433   222233222222 222222233333332  25677


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHH----HHccCChHHHHHHHHHHHHhccCCCCCcchhHHHHHHHHHHhCCCHHHH
Q 044988          236 QALSLFNEMRRARVGLDQVALVAALSA----CAEIGDLKLGKWIHSYVEENFSVGREPVLVSLNNALIHMYASCGEIEEA  311 (538)
Q Consensus       236 ~a~~~~~~m~~~g~~p~~~~~~~li~~----~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a  311 (538)
                      .+..++........ .+......+-..    ....+..+.+..........    ...  .....-.+......+++..+
T Consensus       232 ~a~~~l~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~----~~~--~~~~~w~~~~al~~~~~~~~  304 (450)
T d1qsaa1         232 NARLMIPSLAQAQQ-LNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMR----SQS--TSLIERRVRMALGTGDRRGL  304 (450)
T ss_dssp             HHHHHHHHHHHHTT-CCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHT----CCC--HHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHhhhhccc-ccHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhccc----ccc--hHHHHHHHHHHHHcCChHHH
Confidence            78888777665321 222222222222    23445667776666665544    222  22223345555667888888


Q ss_pred             HHHHHhcCCCCcchHHHHHHHHHhcCCccHHHHHHHHHHHHhcccCcHHHHHHHHHHhhhhcCCCccHHHHHHHHHHhhh
Q 044988          312 YGVFRKMQRRNTVSWTSMITGFAKQGYAQEALLTFLGVLSACSHGGFVDEGRQFFECMNQNWGIKPRIEHYGCMVDLFSR  391 (538)
Q Consensus       312 ~~~~~~m~~~~~~~~~~li~~~~~~~~~~~a~~~~~~ll~~~~~~~~~~~a~~~~~~~~~~~~~~p~~~~~~~l~~~~~~  391 (538)
                      ...++.|....... .                .-.--+..++...|+.+.|...|..+..    .++  -|..|...-  
T Consensus       305 ~~~~~~l~~~~~~~-~----------------r~~YW~gRa~~~~G~~~~A~~~~~~~a~----~~~--fYG~LAa~~--  359 (450)
T d1qsaa1         305 NTWLARLPMEAKEK-D----------------EWRYWQADLLLERGREAEAKEILHQLMQ----QRG--FYPMVAAQR--  359 (450)
T ss_dssp             HHHHHHSCTTGGGS-H----------------HHHHHHHHHHHHTTCHHHHHHHHHHHHT----SCS--HHHHHHHHH--
T ss_pred             HHHHHhcCcccccH-H----------------HHHHHHHHHHHHcCChhhHHHHHHHHhc----CCC--hHHHHHHHH--
Confidence            88888876421110 0                0111223445556688888899888763    233  344443221  


Q ss_pred             cCChHHHHHHHHhCCCCCC-HHHH---HHHHHHHHhcCCHHHHHHHHHHchhccCCCCcccHHHHHHHHHHhcCChHHHH
Q 044988          392 AGLMDEAFSLVQNMPMKPN-DAVL---GSLLLGCRIHNNAELASQVAQKLVAEIDPEQAAGYLALVANVYAAAKRWQDVA  467 (538)
Q Consensus       392 ~g~~~~A~~~~~~~~~~p~-~~~~---~~l~~~~~~~~~~~~A~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~  467 (538)
                      .|..-.. . .......+. ...-   ..-+..+...|....|...+..+ ....+  +.... .++....+.|.++.|+
T Consensus       360 Lg~~~~~-~-~~~~~~~~~~~~~~~~~~~ra~~L~~~g~~~~A~~e~~~l-~~~~~--~~~~~-~la~lA~~~g~~~~aI  433 (450)
T d1qsaa1         360 IGEEYEL-K-IDKAPQNVDSALTQGPEMARVRELMYWNLDNTARSEWANL-VKSKS--KTEQA-QLARYAFNNQWWDLSV  433 (450)
T ss_dssp             TTCCCCC-C-CCCCCSCCCCHHHHSHHHHHHHHHHHTTCHHHHHHHHHHH-HTTCC--HHHHH-HHHHHHHHTTCHHHHH
T ss_pred             cCCCCCC-C-cCCCCccHHHhhhcChHHHHHHHHHHcCCchHHHHHHHHH-HhCCC--HHHHH-HHHHHHHHCCChhHHH
Confidence            2211000 0 000111111 1111   12244577889999999999888 43322  22255 7788889999999999


Q ss_pred             HHHHHHH
Q 044988          468 AVRQKMI  474 (538)
Q Consensus       468 ~~~~~m~  474 (538)
                      ....+..
T Consensus       434 ~a~~~~~  440 (450)
T d1qsaa1         434 QATIAGK  440 (450)
T ss_dssp             HHHHHTT
T ss_pred             HHHHHHH
Confidence            8877654

>d2pqrb1 a.118.8.1 (B:5-128) Mitochondria fission protein Fis1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=88.08  E-value=1.5  Score=31.03  Aligned_cols=66  Identities=3%  Similarity=-0.053  Sum_probs=47.6

Q ss_pred             CCHHHHHHHHHHHHhcC---CHHHHHHHHHHchhccCCCCc-ccHHHHHHHHHHhcCChHHHHHHHHHHHhC
Q 044988          409 PNDAVLGSLLLGCRIHN---NAELASQVAQKLVAEIDPEQA-AGYLALVANVYAAAKRWQDVAAVRQKMIKM  476 (538)
Q Consensus       409 p~~~~~~~l~~~~~~~~---~~~~A~~~~~~~~~~~~p~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~  476 (538)
                      |...|--....++.+..   +.++|+.+++.+ ....|.+. ..+. .|+-+|.+.|++++|.+.++.+.+.
T Consensus        33 ~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~-~~~~p~~~rd~lY-~Lav~yyklgdy~~A~~~~~~~L~i  102 (124)
T d2pqrb1          33 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDI-YKEAESRRRECLY-YLTIGCYKLGEYSMAKRYVDTLFEH  102 (124)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHH-HHHCGGGHHHHHH-HHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             CCcchHHHHHHHHHcCCcHHHHHHHHHHHHHH-HhcCchhHHHHHH-HHHHHHHHHhhHHHHHHHHHHHHcc
Confidence            44555555556666554   456888888888 66677654 4456 7888899999999999999988863

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=87.41  E-value=2.5  Score=28.14  Aligned_cols=50  Identities=18%  Similarity=0.195  Sum_probs=43.7

Q ss_pred             CHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCChHHHHHHHHHHHHh
Q 044988          233 KSRQALSLFNEMRRARVGLDQVALVAALSACAEIGDLKLGKWIHSYVEEN  282 (538)
Q Consensus       233 ~~~~a~~~~~~m~~~g~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~  282 (538)
                      +.-++.+-++.+....+.|++....+.+++|-+.+++..|.++++.++..
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K   70 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK   70 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            55677777888888889999999999999999999999999999988876

>d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein B (HcpB)
species: Helicobacter pylori [TaxId: 210]

Probab=86.95  E-value=2.8  Score=30.10  Aligned_cols=110  Identities=9%  Similarity=-0.091  Sum_probs=62.9

Q ss_pred             CChHHHHHHHHHHHHhCCCCChhHHHHHHHHHHccCChhHHHHHHhcCC-CCCcchHHHHHHHHhc----CCCchHHHHH
Q 044988           31 NTTKTLFQIHSQIIINGFSQKNYILAKLLAFYVTSGYLINAHKVFEKTE-NPSTAIWNQMIRGHAR----SETPEKSVYL  105 (538)
Q Consensus        31 ~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-~~~~~~~~~li~~~~~----~~~~~~a~~~  105 (538)
                      .|+++|...|....+.|..   .....|..  ....+.++|...+++.- .-++..+..|...|..    ..+.++|+++
T Consensus         7 kd~~~A~~~~~kaa~~g~~---~a~~~l~~--~~~~~~~~a~~~~~~aa~~g~~~a~~~Lg~~y~~g~~~~~d~~~A~~~   81 (133)
T d1klxa_           7 KDLKKAIQYYVKACELNEM---FGCLSLVS--NSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQY   81 (133)
T ss_dssp             HHHHHHHHHHHHHHHTTCT---THHHHHHT--CTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHCCCh---hhhhhhcc--ccccCHHHHHHHHhhhhcccchhhhhhHHHhhhhccccchhhHHHHHH
Confidence            3667788888887777632   22333322  23456677777776544 2344455555555443    3456777777


Q ss_pred             HHHhHhCCCCCCcchHHHHHHHHHc----cCCcHHHHHHHHHHHHhC
Q 044988          106 YKQMIDKETEPDEYTYSFLLSVCAR----CGLFREGEQVHGRVLASG  148 (538)
Q Consensus       106 ~~~m~~~~~~p~~~~~~~li~~~~~----~~~~~~a~~~~~~~~~~~  148 (538)
                      |++..+.|   ++.....|...|..    ..+.+.|..+|++..+.|
T Consensus        82 ~~~aa~~g---~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          82 YSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HhhhhccC---cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            77777654   23334444444433    346667777777776665

>d1v54e_ a.118.11.1 (E:) Cytochrome c oxidase subunit E {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Cytochrome c oxidase subunit E
family: Cytochrome c oxidase subunit E
domain: Cytochrome c oxidase subunit E
species: Cow (Bos taurus) [TaxId: 9913]

Probab=86.38  E-value=1.7  Score=29.01  Aligned_cols=61  Identities=11%  Similarity=0.067  Sum_probs=45.6

Q ss_pred             CchHHHHHHHHhHhCCCCCCcchHHHHHHHHHccCCcHHHHHHHHHHHHhCCCCchhHHhHH
Q 044988           98 TPEKSVYLYKQMIDKETEPDEYTYSFLLSVCARCGLFREGEQVHGRVLASGYCSNVFIRTNL  159 (538)
Q Consensus        98 ~~~~a~~~~~~m~~~~~~p~~~~~~~li~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~l  159 (538)
                      +.-++.+-++.+....+.|++....+.+++|.+.+|+..|.++++-.+... .++...|.-+
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~-~~~k~~y~yi   81 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYV   81 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCcHHHHHHH
Confidence            344566677777777888999999999999999999999999998887653 3344455444