Citrus Sinensis ID: 011249

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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
Protein Sequence
MTSKYLVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWISS
Secondary Structure (PSIPRED)
ccccHHHHHcccHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccccHHHHHHHHccccccccEEcHHHHHHHHHccccHHHHHHHHHHHHHccccccccHHHHHHHHHccccHHHHHHHHHHHHHccHHHHHHHHHHcccccHHHHHHHHHHHHHcccHHHHHHHHHccccccHHHHHHHHHHHHccccHHHHHHHHccccccccEEHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccHHHHHHHHHHHHHHcccccccHHHHHHHHHHccccHHHHHHHHccccccccccHHHHHHHHHccccHHHHHHHHHHHHHcccccccHHHHHHHHHcccccHHHHHHHHHHHcHHHcccccccccHHHHHHHHcccccHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHccccHHHHHHHHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHcHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccHHHHHHHHHHccccccEEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHccHHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccEEEEc
Coil and Loop (DISEMBL)
mtskylvprsktfNQLKQVHSYLLKTltkphdqyHYYAQFLIRLLqlpgdnlsYARQVFdqipkcktQFLWTSLIRNHVLHAHFRQSILLYAKMHRLgvltsgftFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKvfdeisepdasCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVdegccdrtnYVSNALIHMHSKCGYLDLAWREFsriknkdviSYSSMITAFADHGKSQEALDMFLKMRnegiepnqvTFIGVLTAcshgglvedgckQFELMTRvfgikpltEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLelgpektgnSALLANIYASMGKWKDSEIVKMMISEtekkkspgcswiss
Flexible Loop (DISEMBL)
mtskylvprsktfnqLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMIsetekkkspgcswiss
Low Complexity Region (SEG)
MTSKYLVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWISS
Disordered region (IsUnstruct)
***********TFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIV********************
Disordered Region (DISOPRED)
MTSKYLVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWISS
Disordered Region (DISEMBL)
MTSKYLVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISE**************
Disordered Region (DISPRO)
MTSKYLVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWISS
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTSKYLVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWISS
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	490	2.2.26 [Sep-21-2011]
Q9FFG8	657	Pentatricopeptide repeat-	yes	no	0.940	0.701	0.374	2e-87
Q9SY02	781	Pentatricopeptide repeat-	no	no	0.883	0.554	0.338	3e-81
Q9FIF7	544	Putative pentatricopeptid	no	no	0.934	0.841	0.356	4e-78
Q9LXF2	548	Pentatricopeptide repeat-	no	no	0.889	0.795	0.357	5e-77
Q9LTV8	694	Pentatricopeptide repeat-	no	no	0.948	0.670	0.315	2e-76
Q56XI1	705	Pentatricopeptide repeat-	no	no	0.881	0.612	0.322	5e-76
Q9FHR3	550	Putative pentatricopeptid	no	no	0.871	0.776	0.330	2e-75
Q9LS72	600	Pentatricopeptide repeat-	no	no	0.969	0.791	0.296	2e-75
O23337	722	Pentatricopeptide repeat-	no	no	0.965	0.655	0.296	5e-75
O82380	738	Pentatricopeptide repeat-	no	no	0.869	0.577	0.361	6e-75

>sp|Q9FFG8|PP417_ARATH Pentatricopeptide repeat-containing protein At5g44230 OS=Arabidopsis thaliana GN=PCMP-H17 PE=2 SV=1

 Score =  323 bits (829), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 181/483 (37%), Positives = 270/483 (55%), Gaps = 22/483 (4%)

Query: 12  TFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQ---LPGDNLSYARQVFDQIPKCKTQ 68
             NQ+KQ+H ++L+   K  DQ  Y    LIR L    +P D   YAR+V + + + +  
Sbjct: 61  NLNQIKQIHGHVLR---KGLDQSCYILTKLIRTLTKLGVPMD--PYARRVIEPV-QFRNP 114

Query: 69  FLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYT 128
           FLWT++IR + +   F ++I +Y  M +  +    FTFS++L AC  +  L         
Sbjct: 115 FLWTAVIRGYAIEGKFDEAIAMYGCMRKEEITPVSFTFSALLKACGTMKDL--------- 165

Query: 129 KIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAG 188
            +G    AQ  F       V   + M+  Y  C ++  A++ +D M E++ ++W  +IA 
Sbjct: 166 NLGRQFHAQT-FRLRGFCFVYVGNTMIDMYVKCESIDCARKVFDEMPERDVISWTELIAA 224

Query: 189 YGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAM 248
           Y + G +  A ++F+ +   D   W AM   + QN   + A+E +  M +  +R  EV +
Sbjct: 225 YARVGNMECAAELFESLPTKDMVAWTAMVTGFAQNAKPQEALEYFDRMEKSGIRADEVTV 284

Query: 249 VGAISACTQLGDVEMAAILAKHVDEGCCDRTNYV--SNALIHMHSKCGYLDLAWREFSRI 306
            G ISAC QLG  + A    +   +     +++V   +ALI M+SKCG ++ A   F  +
Sbjct: 285 AGYISACAQLGASKYADRAVQIAQKSGYSPSDHVVIGSALIDMYSKCGNVEEAVNVFMSM 344

Query: 307 KNKDVISYSSMITAFADHGKSQEALDMFLKMRNEG-IEPNQVTFIGVLTACSHGGLVEDG 365
            NK+V +YSSMI   A HG++QEAL +F  M  +  I+PN VTF+G L ACSH GLV+ G
Sbjct: 345 NNKNVFTYSSMILGLATHGRAQEALHLFHYMVTQTEIKPNTVTFVGALMACSHSGLVDQG 404

Query: 366 CKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACK 425
            + F+ M + FG++P  +H TCMVDLLGR+G+L++A  LI         G WGALLGAC+
Sbjct: 405 RQVFDSMYQTFGVQPTRDHYTCMVDLLGRTGRLQEALELIKTMSVEPHGGVWGALLGACR 464

Query: 426 VHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGC 485
           +H N E+ EIAA HL EL P+  GN  LL+N+YAS G W     V+ +I E   KK+P  
Sbjct: 465 IHNNPEIAEIAAEHLFELEPDIIGNYILLSNVYASAGDWGGVLRVRKLIKEKGLKKTPAV 524

Query: 486 SWI 488
           SW+
Sbjct: 525 SWV 527

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SY02|PP301_ARATH Pentatricopeptide repeat-containing protein At4g02750 OS=Arabidopsis thaliana GN=PCMP-H24 PE=3 SV=1

 Score =  302 bits (774), Expect = 3e-81,   Method: Compositional matrix adjust.
 Identities = 162/478 (33%), Positives = 264/478 (55%), Gaps = 45/478 (9%)

Query: 55  ARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGV-----LTSGF----- 104
           AR VFD++P+ K    W +L+  +V ++   ++ +L+       +     L  GF     
Sbjct: 176 ARSVFDRMPE-KNDVSWNALLSAYVQNSKMEEACMLFKSRENWALVSWNCLLGGFVKKKK 234

Query: 105 -----------------TFSSVLNACARVPSLLEA-----------------VICGYTKI 130
                            ++++++   A+   + EA                 ++ GY + 
Sbjct: 235 IVEARQFFDSMNVRDVVSWNTIITGYAQSGKIDEARQLFDESPVQDVFTWTAMVSGYIQN 294

Query: 131 GLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYG 190
            ++++A+ LFD M ERN +SW+AM+AGY     M+ AKE +D M  +N  TW  MI GY 
Sbjct: 295 RMVEEARELFDKMPERNEVSWNAMLAGYVQGERMEMAKELFDVMPCRNVSTWNTMITGYA 354

Query: 191 KCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVG 250
           +CG++ EAK +FD++ + D   WAAM   Y Q+G++  A+ ++  M +E  R++  +   
Sbjct: 355 QCGKISEAKNLFDKMPKRDPVSWAAMIAGYSQSGHSFEALRLFVQMEREGGRLNRSSFSS 414

Query: 251 AISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKD 310
           A+S C  +  +E+   L   + +G  +   +V NAL+ M+ KCG ++ A   F  +  KD
Sbjct: 415 ALSTCADVVALELGKQLHGRLVKGGYETGCFVGNALLLMYCKCGSIEEANDLFKEMAGKD 474

Query: 311 VISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFE 370
           ++S+++MI  ++ HG  + AL  F  M+ EG++P+  T + VL+ACSH GLV+ G + F 
Sbjct: 475 IVSWNTMIAGYSRHGFGEVALRFFESMKREGLKPDDATMVAVLSACSHTGLVDKGRQYFY 534

Query: 371 LMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNA 430
            MT+ +G+ P ++H  CMVDLLGR+G LE AH+L+ +     DA  WG LLGA +VH N 
Sbjct: 535 TMTQDYGVMPNSQHYACMVDLLGRAGLLEDAHNLMKNMPFEPDAAIWGTLLGASRVHGNT 594

Query: 431 ELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI 488
           EL E AA  +  + PE +G   LL+N+YAS G+W D   +++ + +   KK PG SWI
Sbjct: 595 ELAETAADKIFAMEPENSGMYVLLSNLYASSGRWGDVGKLRVRMRDKGVKKVPGYSWI 652

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FIF7|PP435_ARATH Putative pentatricopeptide repeat-containing protein At5g59200, chloroplastic OS=Arabidopsis thaliana GN=PCMP-E41 PE=3 SV=1

 Score =  292 bits (748), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 171/479 (35%), Positives = 263/479 (54%), Gaps = 21/479 (4%)

Query: 11  KTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFL 70
           K    +  +H+ +++T    HDQ  +    LIR+     D++ YA  VF  +      +L
Sbjct: 40  KNIAHVPSIHAKIIRTF---HDQDAFVVFELIRVCSTL-DSVDYAYDVFSYVSNPNV-YL 94

Query: 71  WTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNAC-ARVPSLLEAVICGYTK 129
           +T++I   V        + LY +M    VL   +  +SVL AC  +V   + A +    K
Sbjct: 95  YTAMIDGFVSSGRSADGVSLYHRMIHNSVLPDNYVITSVLKACDLKVCREIHAQVL---K 151

Query: 130 IGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGY 189
           +G            + R+V     M+  Y   G +  AK+ +D M +++ V    MI  Y
Sbjct: 152 LGFG----------SSRSV--GLKMMEIYGKSGELVNAKKMFDEMPDRDHVAATVMINCY 199

Query: 190 GKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMV 249
            +CG ++EA ++F ++   D  CW AM    V+N     A+E+++ M+ ENV  +E   V
Sbjct: 200 SECGFIKEALELFQDVKIKDTVCWTAMIDGLVRNKEMNKALELFREMQMENVSANEFTAV 259

Query: 250 GAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK 309
             +SAC+ LG +E+   +   V+    + +N+V NALI+M+S+CG ++ A R F  +++K
Sbjct: 260 CVLSACSDLGALELGRWVHSFVENQRMELSNFVGNALINMYSRCGDINEARRVFRVMRDK 319

Query: 310 DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQF 369
           DVISY++MI+  A HG S EA++ F  M N G  PNQVT + +L ACSHGGL++ G + F
Sbjct: 320 DVISYNTMISGLAMHGASVEAINEFRDMVNRGFRPNQVTLVALLNACSHGGLLDIGLEVF 379

Query: 370 ELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVN 429
             M RVF ++P  EH  C+VDLLGR G+LE+A+  I +     D    G LL ACK+H N
Sbjct: 380 NSMKRVFNVEPQIEHYGCIVDLLGRVGRLEEAYRFIENIPIEPDHIMLGTLLSACKIHGN 439

Query: 430 AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI 488
            ELGE  A+ L E     +G   LL+N+YAS GKWK+S  ++  + ++  +K PGCS I
Sbjct: 440 MELGEKIAKRLFESENPDSGTYVLLSNLYASSGKWKESTEIRESMRDSGIEKEPGCSTI 498

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LXF2|PP385_ARATH Pentatricopeptide repeat-containing protein At5g15300 OS=Arabidopsis thaliana GN=PCMP-E40 PE=2 SV=2

 Score =  288 bits (738), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 170/475 (35%), Positives = 259/475 (54%), Gaps = 39/475 (8%)

Query: 45  LQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFR-----QSILLYAKMHRLGV 99
           L +PG  L YA ++FD+IPK          I NHVL    +     +++ LY +M + GV
Sbjct: 56  LSVPG-ALKYAHKLFDEIPKPDVS------ICNHVLRGSAQSMKPEKTVSLYTEMEKRGV 108

Query: 100 LTSGFTFSSVLNACARVP---------------------SLLEAVICGYTKIGLMDDAQR 138
               +TF+ VL AC+++                       +  A+I  +   G +  A  
Sbjct: 109 SPDRYTFTFVLKACSKLEWRSNGFAFHGKVVRHGFVLNEYVKNALILFHANCGDLGIASE 168

Query: 139 LFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREA 198
           LFD  A+ + ++WS+M +GYA  G +  A   +D M  K+ V W  MI G  KC E+  A
Sbjct: 169 LFDDSAKAHKVAWSSMTSGYAKRGKIDEAMRLFDEMPYKDQVAWNVMITGCLKCKEMDSA 228

Query: 199 KKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQL 258
           +++FD  +E D   W AM   YV  GY K A+ ++K MR        V ++  +SAC  L
Sbjct: 229 RELFDRFTEKDVVTWNAMISGYVNCGYPKEALGIFKEMRDAGEHPDVVTILSLLSACAVL 288

Query: 259 GDVEMAAILAKHVDE-GCCDRTNYVS----NALIHMHSKCGYLDLAWREFSRIKNKDVIS 313
           GD+E    L  ++ E      + YV     NALI M++KCG +D A   F  +K++D+ +
Sbjct: 289 GDLETGKRLHIYILETASVSSSIYVGTPIWNALIDMYAKCGSIDRAIEVFRGVKDRDLST 348

Query: 314 YSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMT 373
           ++++I   A H  ++ +++MF +M+   + PN+VTFIGV+ ACSH G V++G K F LM 
Sbjct: 349 WNTLIVGLALH-HAEGSIEMFEEMQRLKVWPNEVTFIGVILACSHSGRVDEGRKYFSLMR 407

Query: 374 RVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELG 433
            ++ I+P  +H  CMVD+LGR+GQLE+A   +   K   +A  W  LLGACK++ N ELG
Sbjct: 408 DMYNIEPNIKHYGCMVDMLGRAGQLEEAFMFVESMKIEPNAIVWRTLLGACKIYGNVELG 467

Query: 434 EIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI 488
           + A   LL +  +++G+  LL+NIYAS G+W   + V+ M  +T  KK  G S I
Sbjct: 468 KYANEKLLSMRKDESGDYVLLSNIYASTGQWDGVQKVRKMFDDTRVKKPTGVSLI 522

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LTV8|PP224_ARATH Pentatricopeptide repeat-containing protein At3g12770 OS=Arabidopsis thaliana GN=PCMP-H43 PE=2 SV=1

 Score =  286 bits (732), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 170/539 (31%), Positives = 276/539 (51%), Gaps = 74/539 (13%)

Query: 15  QLKQVHSYLLKTLTKPHDQYHYYAQFLI-RLLQLPGD--NLSYARQVFDQIPKCKTQFLW 71
           QLKQ+H+ LL    +       ++ FLI +L+       ++++ARQVFD +P+ +  F W
Sbjct: 36  QLKQIHARLLVLGLQ-------FSGFLITKLIHASSSFGDITFARQVFDDLPRPQI-FPW 87

Query: 72  TSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLL----------- 120
            ++IR +  + HF+ ++L+Y+ M    V    FTF  +L AC+ +  L            
Sbjct: 88  NAIIRGYSRNNHFQDALLMYSNMQLARVSPDSFTFPHLLKACSGLSHLQMGRFVHAQVFR 147

Query: 121 ----------EAVICGYTKIGLMDDAQRLFD--SMAERNVISWSAMVAGYANCGNMKAAK 168
                       +I  Y K   +  A+ +F+   + ER ++SW+A+V+ YA  G    A 
Sbjct: 148 LGFDADVFVQNGLIALYAKCRRLGSARTVFEGLPLPERTIVSWTAIVSAYAQNGEPMEAL 207

Query: 169 EFYDRMTEKN-SVTWVAMIA--------------------------------------GY 189
           E + +M + +    WVA+++                                       Y
Sbjct: 208 EIFSQMRKMDVKPDWVALVSVLNAFTCLQDLKQGRSIHASVVKMGLEIEPDLLISLNTMY 267

Query: 190 GKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMV 249
            KCG+V  AK +FD++  P+   W AM   Y +NGYA+ AI+M+  M  ++VR   +++ 
Sbjct: 268 AKCGQVATAKILFDKMKSPNLILWNAMISGYAKNGYAREAIDMFHEMINKDVRPDTISIT 327

Query: 250 GAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK 309
            AISAC Q+G +E A  + ++V         ++S+ALI M +KCG ++ A   F R  ++
Sbjct: 328 SAISACAQVGSLEQARSMYEYVGRSDYRDDVFISSALIDMFAKCGSVEGARLVFDRTLDR 387

Query: 310 DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQF 369
           DV+ +S+MI  +  HG+++EA+ ++  M   G+ PN VTF+G+L AC+H G+V +G   F
Sbjct: 388 DVVVWSAMIVGYGLHGRAREAISLYRAMERGGVHPNDVTFLGLLMACNHSGMVREGWWFF 447

Query: 370 ELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVN 429
             M     I P  +H  C++DLLGR+G L++A+ +I           WGALL ACK H +
Sbjct: 448 NRMAD-HKINPQQQHYACVIDLLGRAGHLDQAYEVIKCMPVQPGVTVWGALLSACKKHRH 506

Query: 430 AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI 488
            ELGE AA+ L  + P  TG+   L+N+YA+   W     V++ + E    K  GCSW+
Sbjct: 507 VELGEYAAQQLFSIDPSNTGHYVQLSNLYAAARLWDRVAEVRVRMKEKGLNKDVGCSWV 565

Arabidopsis thaliana (taxid: 3702)

>sp|Q56XI1|PPR25_ARATH Pentatricopeptide repeat-containing protein At1g09410 OS=Arabidopsis thaliana GN=PCMP-H18 PE=2 SV=2

 Score =  285 bits (730), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 154/478 (32%), Positives = 261/478 (54%), Gaps = 46/478 (9%)

Query: 55  ARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLG-----VLTSGFTFSSV 109
           AR+VFD +P+ +    WT+L++ +V +     +  L+ KM         V+  GF     
Sbjct: 98  ARKVFDLMPE-RNVVSWTALVKGYVHNGKVDVAESLFWKMPEKNKVSWTVMLIGFLQDGR 156

Query: 110 LNACARVPSLLE--------AVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANC 161
           ++   ++  ++         ++I G  K G +D+A+ +FD M+ER+VI+W+ MV GY   
Sbjct: 157 IDDACKLYEMIPDKDNIARTSMIHGLCKEGRVDEAREIFDEMSERSVITWTTMVTGYGQN 216

Query: 162 GNMKAAKEFYDRMTEKNSVTWV-------------------------------AMIAGYG 190
             +  A++ +D M EK  V+W                                AMI+G G
Sbjct: 217 NRVDDARKIFDVMPEKTEVSWTSMLMGYVQNGRIEDAEELFEVMPVKPVIACNAMISGLG 276

Query: 191 KCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVG 250
           + GE+ +A++VFD + E + + W  +   + +NG+   A++++ +M+++ VR +   ++ 
Sbjct: 277 QKGEIAKARRVFDSMKERNDASWQTVIKIHERNGFELEALDLFILMQKQGVRPTFPTLIS 336

Query: 251 AISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKD 310
            +S C  L  +     +   +     D   YV++ L+ M+ KCG L  +   F R  +KD
Sbjct: 337 ILSVCASLASLHHGKQVHAQLVRCQFDVDVYVASVLMTMYIKCGELVKSKLIFDRFPSKD 396

Query: 311 VISYSSMITAFADHGKSQEALDMFLKMRNEG-IEPNQVTFIGVLTACSHGGLVEDGCKQF 369
           +I ++S+I+ +A HG  +EAL +F +M   G  +PN+VTF+  L+ACS+ G+VE+G K +
Sbjct: 397 IIMWNSIISGYASHGLGEEALKVFCEMPLSGSTKPNEVTFVATLSACSYAGMVEEGLKIY 456

Query: 370 ELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVN 429
           E M  VFG+KP+T H  CMVD+LGR+G+  +A  +I       DA  WG+LLGAC+ H  
Sbjct: 457 ESMESVFGVKPITAHYACMVDMLGRAGRFNEAMEMIDSMTVEPDAAVWGSLLGACRTHSQ 516

Query: 430 AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSW 487
            ++ E  A+ L+E+ PE +G   LL+N+YAS G+W D   ++ ++     +KSPGCSW
Sbjct: 517 LDVAEFCAKKLIEIEPENSGTYILLSNMYASQGRWADVAELRKLMKTRLVRKSPGCSW 574

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FHR3|PP403_ARATH Putative pentatricopeptide repeat-containing protein At5g37570 OS=Arabidopsis thaliana GN=PCMP-E37 PE=3 SV=1

 Score =  283 bits (724), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 162/490 (33%), Positives = 259/490 (52%), Gaps = 63/490 (12%)

Query: 58  VFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSG-FTFSSVLNACA-- 114
           VF+++P   T +LW  LI+ +     F +++ +  +M R G+     +TF  V+  C+  
Sbjct: 65  VFERVPSPGT-YLWNHLIKGYSNKFLFFETVSILMRMMRTGLARPDEYTFPLVMKVCSNN 123

Query: 115 ---RVPSLLE-----------------------------------------------AVI 124
              RV S +                                                A++
Sbjct: 124 GQVRVGSSVHGLVLRIGFDKDVVVGTSFVDFYGKCKDLFSARKVFGEMPERNAVSWTALV 183

Query: 125 CGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVA 184
             Y K G +++A+ +FD M ERN+ SW+A+V G    G++  AK+ +D M +++ +++ +
Sbjct: 184 VAYVKSGELEEAKSMFDLMPERNLGSWNALVDGLVKSGDLVNAKKLFDEMPKRDIISYTS 243

Query: 185 MIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRIS 244
           MI GY K G++  A+ +F+E    D   W+A+ + Y QNG    A +++  M  +NV+  
Sbjct: 244 MIDGYAKGGDMVSARDLFEEARGVDVRAWSALILGYAQNGQPNEAFKVFSEMCAKNVKPD 303

Query: 245 EVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTN-----YVSNALIHMHSKCGYLDLA 299
           E  MVG +SAC+Q+G  E    L + VD     R N     YV  ALI M++KCG++D A
Sbjct: 304 EFIMVGLMSACSQMGCFE----LCEKVDSYLHQRMNKFSSHYVVPALIDMNAKCGHMDRA 359

Query: 300 WREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHG 359
            + F  +  +D++SY SM+   A HG   EA+ +F KM +EGI P++V F  +L  C   
Sbjct: 360 AKLFEEMPQRDLVSYCSMMEGMAIHGCGSEAIRLFEKMVDEGIVPDEVAFTVILKVCGQS 419

Query: 360 GLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGA 419
            LVE+G + FELM + + I    +H +C+V+LL R+G+L++A+ LI        A  WG+
Sbjct: 420 RLVEEGLRYFELMRKKYSILASPDHYSCIVNLLSRTGKLKEAYELIKSMPFEAHASAWGS 479

Query: 420 LLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK 479
           LLG C +H N E+ E+ ARHL EL P+  G+  LL+NIYA++ +W D   ++  ++E   
Sbjct: 480 LLGGCSLHGNTEIAEVVARHLFELEPQSAGSYVLLSNIYAALDRWTDVAHLRDKMNENGI 539

Query: 480 KKSPGCSWIS 489
            K  G SWIS
Sbjct: 540 TKICGRSWIS 549

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LS72|PP261_ARATH Pentatricopeptide repeat-containing protein At3g29230 OS=Arabidopsis thaliana GN=PCMP-E27 PE=2 SV=1

 Score =  283 bits (724), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 159/536 (29%), Positives = 273/536 (50%), Gaps = 61/536 (11%)

Query: 7   VPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCK 66
           +P+    NQ+KQ+H+ +++     H+  H   + +  L      NL  A +VF+Q+ +  
Sbjct: 26  LPKCANLNQVKQLHAQIIRR--NLHEDLHIAPKLISALSLCRQTNL--AVRVFNQVQEPN 81

Query: 67  TQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACA------------ 114
              L  SLIR H  ++   Q+  ++++M R G+    FT+  +L AC+            
Sbjct: 82  VH-LCNSLIRAHAQNSQPYQAFFVFSEMQRFGLFADNFTYPFLLKACSGQSWLPVVKMMH 140

Query: 115 ------------RVPSLL------------------------------EAVICGYTKIGL 132
                        VP+ L                               +++ G  K G 
Sbjct: 141 NHIEKLGLSSDIYVPNALIDCYSRCGGLGVRDAMKLFEKMSERDTVSWNSMLGGLVKAGE 200

Query: 133 MDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKC 192
           + DA+RLFD M +R++ISW+ M+ GYA C  M  A E +++M E+N+V+W  M+ GY K 
Sbjct: 201 LRDARRLFDEMPQRDLISWNTMLDGYARCREMSKAFELFEKMPERNTVSWSTMVMGYSKA 260

Query: 193 GEVREAKKVFDEISEP--DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVG 250
           G++  A+ +FD++  P  +   W  +   Y + G  K A  +   M    ++    A++ 
Sbjct: 261 GDMEMARVMFDKMPLPAKNVVTWTIIIAGYAEKGLLKEADRLVDQMVASGLKFDAAAVIS 320

Query: 251 AISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKD 310
            ++ACT+ G + +   +   +         YV NAL+ M++KCG L  A+  F+ I  KD
Sbjct: 321 ILAACTESGLLSLGMRIHSILKRSNLGSNAYVLNALLDMYAKCGNLKKAFDVFNDIPKKD 380

Query: 311 VISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFE 370
           ++S+++M+     HG  +EA+++F +MR EGI P++VTFI VL +C+H GL+++G   F 
Sbjct: 381 LVSWNTMLHGLGVHGHGKEAIELFSRMRREGIRPDKVTFIAVLCSCNHAGLIDEGIDYFY 440

Query: 371 LMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNA 430
            M +V+ + P  EH  C+VDLLGR G+L++A  ++       +   WGALLGAC++H   
Sbjct: 441 SMEKVYDLVPQVEHYGCLVDLLGRVGRLKEAIKVVQTMPMEPNVVIWGALLGACRMHNEV 500

Query: 431 ELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCS 486
           ++ +    +L++L P   GN +LL+NIYA+   W+    ++  +     +K  G S
Sbjct: 501 DIAKEVLDNLVKLDPCDPGNYSLLSNIYAAAEDWEGVADIRSKMKSMGVEKPSGAS 556

Arabidopsis thaliana (taxid: 3702)

>sp|O23337|PP311_ARATH Pentatricopeptide repeat-containing protein At4g14820 OS=Arabidopsis thaliana GN=PCMP-H3 PE=2 SV=1

 Score =  282 bits (721), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 169/570 (29%), Positives = 272/570 (47%), Gaps = 97/570 (17%)

Query: 11  KTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLS-YARQVFDQIPKCKTQF 69
           K+ N +KQ+H+++L+T+       H    FL  L          YA  VF  IP      
Sbjct: 23  KSLNHIKQLHAHILRTVIN-----HKLNSFLFNLSVSSSSINLSYALNVFSSIPSPPESI 77

Query: 70  LWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLE-------- 121
           ++   +R+    +  R +IL Y ++  +G     F+F  +L A ++V +L E        
Sbjct: 78  VFNPFLRDLSRSSEPRATILFYQRIRHVGGRLDQFSFLPILKAVSKVSALFEGMELHGVA 137

Query: 122 ---AVICG-----------------------------------------YTKIGLMDDAQ 137
              A +C                                          Y + GL+D+A 
Sbjct: 138 FKIATLCDPFVETGFMDMYASCGRINYARNVFDEMSHRDVVTWNTMIERYCRFGLVDEAF 197

Query: 138 RLFDSMAERNVIS---------------------------------------WSAMVAGY 158
           +LF+ M + NV+                                         +A+V  Y
Sbjct: 198 KLFEEMKDSNVMPDEMILCNIVSACGRTGNMRYNRAIYEFLIENDVRMDTHLLTALVTMY 257

Query: 159 ANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTV 218
           A  G M  A+EF+ +M+ +N     AM++GY KCG + +A+ +FD+  + D  CW  M  
Sbjct: 258 AGAGCMDMAREFFRKMSVRNLFVSTAMVSGYSKCGRLDDAQVIFDQTEKKDLVCWTTMIS 317

Query: 219 CYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDR 278
            YV++ Y + A+ +++ M    ++   V+M   ISAC  LG ++ A  +   +     + 
Sbjct: 318 AYVESDYPQEALRVFEEMCCSGIKPDVVSMFSVISACANLGILDKAKWVHSCIHVNGLES 377

Query: 279 TNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMR 338
              ++NALI+M++KCG LD     F ++  ++V+S+SSMI A + HG++ +AL +F +M+
Sbjct: 378 ELSINNALINMYAKCGGLDATRDVFEKMPRRNVVSWSSMINALSMHGEASDALSLFARMK 437

Query: 339 NEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQL 398
            E +EPN+VTF+GVL  CSH GLVE+G K F  MT  + I P  EH  CMVDL GR+  L
Sbjct: 438 QENVEPNEVTFVGVLYGCSHSGLVEEGKKIFASMTDEYNITPKLEHYGCMVDLFGRANLL 497

Query: 399 EKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY 458
            +A  +I       +   WG+L+ AC++H   ELG+ AA+ +LEL P+  G   L++NIY
Sbjct: 498 REALEVIESMPVASNVVIWGSLMSACRIHGELELGKFAAKRILELEPDHDGALVLMSNIY 557

Query: 459 ASMGKWKDSEIVKMMISETEKKKSPGCSWI 488
           A   +W+D   ++ ++ E    K  G S I
Sbjct: 558 AREQRWEDVRNIRRVMEEKNVFKEKGLSRI 587

Arabidopsis thaliana (taxid: 3702)

>sp|O82380|PP175_ARATH Pentatricopeptide repeat-containing protein At2g29760, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H33 PE=2 SV=1

 Score =  281 bits (720), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 159/440 (36%), Positives = 242/440 (55%), Gaps = 14/440 (3%)

Query: 51  NLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVL 110
           +L  A +VF  I K K    W S+I   V      +++ L+ KM    V  S  T   VL
Sbjct: 181 DLDSACKVFTTI-KEKDVVSWNSMINGFVQKGSPDKALELFKKMESEDVKASHVTMVGVL 239

Query: 111 NACARVPSL-LEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKE 169
           +ACA++ +L     +C Y +           ++    N+   +AM+  Y  CG+++ AK 
Sbjct: 240 SACAKIRNLEFGRQVCSYIE-----------ENRVNVNLTLANAMLDMYTKCGSIEDAKR 288

Query: 170 FYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYA-KA 228
            +D M EK++VTW  M+ GY    +   A++V + + + D   W A+   Y QNG   +A
Sbjct: 289 LFDAMEEKDNVTWTTMLDGYAISEDYEAAREVLNSMPQKDIVAWNALISAYEQNGKPNEA 348

Query: 229 AIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIH 288
            I  +++  Q+N++++++ +V  +SAC Q+G +E+   +  ++ +       +V++ALIH
Sbjct: 349 LIVFHELQLQKNMKLNQITLVSTLSACAQVGALELGRWIHSYIKKHGIRMNFHVTSALIH 408

Query: 289 MHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVT 348
           M+SKCG L+ +   F+ ++ +DV  +S+MI   A HG   EA+DMF KM+   ++PN VT
Sbjct: 409 MYSKCGDLEKSREVFNSVEKRDVFVWSAMIGGLAMHGCGNEAVDMFYKMQEANVKPNGVT 468

Query: 349 FIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDY 408
           F  V  ACSH GLV++    F  M   +GI P  +H  C+VD+LGRSG LEKA   I   
Sbjct: 469 FTNVFCACSHTGLVDEAESLFHQMESNYGIVPEEKHYACIVDVLGRSGYLEKAVKFIEAM 528

Query: 409 KDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSE 468
                   WGALLGACK+H N  L E+A   LLEL P   G   LL+NIYA +GKW++  
Sbjct: 529 PIPPSTSVWGALLGACKIHANLNLAEMACTRLLELEPRNDGAHVLLSNIYAKLGKWENVS 588

Query: 469 IVKMMISETEKKKSPGCSWI 488
            ++  +  T  KK PGCS I
Sbjct: 589 ELRKHMRVTGLKKEPGCSSI 608

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	490
356498888	552	PREDICTED: putative pentatricopeptide re	0.975	0.865	0.522	1e-156
357480561	598	Pentatricopeptide repeat-containing prot	0.971	0.795	0.513	1e-154
357445603	558	Pentatricopeptide repeat-containing prot	0.979	0.860	0.504	1e-152
449446907	456	PREDICTED: putative pentatricopeptide re	0.814	0.875	0.537	1e-136
449516776	427	PREDICTED: putative pentatricopeptide re	0.755	0.866	0.502	1e-121
225440783	561	PREDICTED: putative pentatricopeptide re	0.963	0.841	0.364	7e-93
147799847	546	hypothetical protein VITISV_017037 [Viti	0.975	0.875	0.362	6e-90
225431281	647	PREDICTED: pentatricopeptide repeat-cont	0.940	0.712	0.374	1e-89
356510957	617	PREDICTED: pentatricopeptide repeat-cont	0.961	0.763	0.375	8e-89
449525261	650	PREDICTED: pentatricopeptide repeat-cont	0.944	0.712	0.382	1e-88

>gi|356498888|ref|XP_003518279.1| PREDICTED: putative pentatricopeptide repeat-containing protein At5g37570-like [Glycine max]

 Score =  557 bits (1436), Expect = e-156,   Method: Compositional matrix adjust.
 Identities = 280/536 (52%), Positives = 360/536 (67%), Gaps = 58/536 (10%)

Query: 6   LVPRSKTFNQLKQVHSYLLKTL-TKPHDQYHYY-AQFLIRLLQLPGD--NLSYARQVFDQ 61
           L+  +KT + LKQ H+  LK L  +P   YHY+  + L ++L+  G+  NL YA Q+FD 
Sbjct: 10  LLNAAKTIDHLKQTHALFLKLLRQQPPHHYHYFMGRLLHQVLRCTGEKTNLCYAHQLFDT 69

Query: 62  IPKCKTQFLWTSLIRNHVLH-AHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLL 120
           +P C + FLWTSLIR  + H AH    I  Y++MH+ GVL SGFTFSS+L+AC RVP+L 
Sbjct: 70  MPNCPSSFLWTSLIRALLSHQAHLHHCISTYSRMHQNGVLPSGFTFSSILSACGRVPALF 129

Query: 121 E----------------------------------------------------AVICGYT 128
           E                                                    A++CGY 
Sbjct: 130 EGKQVHARVMQSGFHGNKIVQTALLDMYAKSGCISDARAVFDGMDDRDVVAWTAMVCGYA 189

Query: 129 KIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAG 188
           K+G+M DAQ LFD M ERN  +W+AMVAGYANC +MK AK+ YD M +KN VTWVAMIAG
Sbjct: 190 KVGMMVDAQWLFDKMGERNSFTWTAMVAGYANCEDMKTAKKLYDVMNDKNEVTWVAMIAG 249

Query: 189 YGKCGEVREAKKVFDEISEPD-ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVA 247
           YGK G VREA++VFD I  P  AS  AAM  CY Q+GYAK AI+MY+ MR+  ++I+EVA
Sbjct: 250 YGKLGNVREARRVFDGIPVPQGASACAAMLACYAQHGYAKEAIDMYEKMREAKIKITEVA 309

Query: 248 MVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIK 307
           MVGAISAC QL D+ M+  L  H++EGCCDRT+ VS ALIHMHSKCG ++LA  EF+ ++
Sbjct: 310 MVGAISACAQLRDIRMSNTLTGHLEEGCCDRTHIVSTALIHMHSKCGNINLALSEFTTMR 369

Query: 308 NKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCK 367
            +DV +YS+MI AFA+HGKSQ+A+D+FLKM+ EG++PNQVTFIGVL AC   G +E+GC+
Sbjct: 370 YRDVYTYSAMIAAFAEHGKSQDAIDLFLKMQKEGLKPNQVTFIGVLNACGSSGYIEEGCR 429

Query: 368 QFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVH 427
            F++MT VFGI+PL EH TC+VDLLG++GQLE+A+ LI       DA TWG+LL  C+++
Sbjct: 430 FFQIMTGVFGIEPLPEHYTCIVDLLGKAGQLERAYDLIKQNASSADATTWGSLLATCRLY 489

Query: 428 VNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSP 483
            N ELGEIAARHL E+ PE +GN  LLAN YAS  KW+ ++ VK +ISE   KK P
Sbjct: 490 GNVELGEIAARHLFEIDPEDSGNYVLLANTYASKDKWEHAQEVKKLISEKGMKKKP 545

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357480561|ref|XP_003610566.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|355511621|gb|AES92763.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  550 bits (1418), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 276/537 (51%), Positives = 359/537 (66%), Gaps = 61/537 (11%)

Query: 10  SKTFNQLKQVHSYLLKTLTK--PHDQYHYYAQFLIRLLQLPGD--NLSYARQVFDQIPKC 65
           +K  + LKQ+H+  LK L +  PH   H++ + L R+L    +  NL YA ++FD +P C
Sbjct: 20  AKNISHLKQIHALFLKHLPQNAPH---HFFDRLLFRVLHFSAEKSNLYYAHKLFDTMPNC 76

Query: 66  KTQFLWTSLIRNHVLH-AHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLE--- 121
              F+WTSLIR  + H  HFR  I  +A MH+ G+L SGFTFSSVLNAC RVP++ E   
Sbjct: 77  SNCFIWTSLIRAFLSHHTHFRHCISTFAIMHQKGILPSGFTFSSVLNACGRVPAVFEGKQ 136

Query: 122 -------------------------------------------------AVICGYTKIGL 132
                                                            A+ICGY K G 
Sbjct: 137 VHARLVQSGFLGNKIVQTALLDMYAKCGYVCDARDVFDGMVDRDVVAWTAMICGYAKAGR 196

Query: 133 MDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKC 192
           M DA+ LFD+M ERN  +W+ MVAGYAN G+MKAA E YD M  K  VTWVAMIAGYGK 
Sbjct: 197 MVDARLLFDNMGERNSFTWTTMVAGYANYGDMKAAMELYDVMNGKEEVTWVAMIAGYGKL 256

Query: 193 GEVREAKKVFDEISEP-DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGA 251
           G V EA+++FDEI  P + S  AA+  CY QNG+A+ AIEMY+ MR+  +++++VAMVGA
Sbjct: 257 GNVSEARRIFDEIPVPLNPSTCAALLACYAQNGHAREAIEMYEKMRRAKIKVTDVAMVGA 316

Query: 252 ISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDV 311
           ISAC QL D+ M+ +L   ++EG C++T+ VSNALIHM SKCG +DLAWREF+ ++N+D+
Sbjct: 317 ISACAQLRDIRMSNLLTYDIEEGFCEKTHIVSNALIHMQSKCGNIDLAWREFNIMRNRDL 376

Query: 312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFEL 371
            +YS+MI AFA+HGKSQ+A+D+FLKM+ EG+ PNQVTF+GVL ACS  GL+E+GC+ F++
Sbjct: 377 YTYSAMIAAFAEHGKSQDAIDLFLKMQQEGLTPNQVTFVGVLNACSTSGLIEEGCRFFQI 436

Query: 372 MTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAE 431
           MT V+GI+PL EH TCMVDLLGR+GQLEKA+SLI +     DA TWG+LL AC+V+ N E
Sbjct: 437 MTGVYGIEPLPEHYTCMVDLLGRAGQLEKAYSLIKENSTSADATTWGSLLAACRVYGNVE 496

Query: 432 LGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI 488
           LGEIAARHL E+ P  +GN  LLAN YAS  KW+ +E VK ++S+   KK  G SWI
Sbjct: 497 LGEIAARHLFEIDPTDSGNYVLLANTYASNDKWERAEEVKKLMSKKGMKKPSGYSWI 553

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357445603|ref|XP_003593079.1| Pentatricopeptide repeat-containing protein [Medicago truncatula] gi|124360447|gb|ABN08457.1| Tetratricopeptide-like helical [Medicago truncatula] gi|355482127|gb|AES63330.1| Pentatricopeptide repeat-containing protein [Medicago truncatula]

 Score =  543 bits (1400), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 273/541 (50%), Positives = 361/541 (66%), Gaps = 61/541 (11%)

Query: 6   LVPRSKTFNQLKQVHSYLLKTLTK--PHDQYHYYAQFLIRLLQLPGD--NLSYARQVFDQ 61
            +  +K  + LKQ+H+  LK L +  PH   H++ + L R+L    +  NL YA ++FD 
Sbjct: 16  FLNNAKNISHLKQIHALFLKHLPQNAPH---HFFNRLLFRVLHFSAEKSNLYYAHKLFDT 72

Query: 62  IPKCKTQFLWTSLIRNHVLH-AHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLL 120
           +P C   F+WTSLIR  + H  HF   I  +A+MH+ G+L SGFTFS VLNAC RVP+  
Sbjct: 73  MPNCSNCFIWTSLIRAFLSHHTHFCHCISTFARMHQKGILPSGFTFSLVLNACGRVPAGF 132

Query: 121 E----------------------------------------------------AVICGYT 128
           E                                                    A+ICGY 
Sbjct: 133 EGKQVHARLVQSGFLGNKIVQTALLDMYAKCGHVCDARDVFDGIVDRDVVAWTAMICGYA 192

Query: 129 KIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAG 188
           K G M DA+ LFD+M ERN  +W+ MVAGYAN G+MKAA E YD M  K+ VTWVAMIAG
Sbjct: 193 KAGRMVDARFLFDNMGERNSFTWTTMVAGYANYGDMKAAMELYDVMNGKDEVTWVAMIAG 252

Query: 189 YGKCGEVREAKKVFDEISEP-DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVA 247
           YGK G V EA+++FDEI+ P + S  AA+  CY QNG+A+ AIEMY+ MR+  +++++VA
Sbjct: 253 YGKLGNVSEARRIFDEITVPWNPSTCAALLACYAQNGHAREAIEMYEKMRRAKIKVTDVA 312

Query: 248 MVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIK 307
           MVGAISAC QL D+ M+  L  +++EG C++T+ VSNALIHM SKCG +DLAWREF+ ++
Sbjct: 313 MVGAISACAQLRDIRMSNSLTYNIEEGFCEKTHIVSNALIHMQSKCGNIDLAWREFNIMR 372

Query: 308 NKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCK 367
           N+D+ +YS+MI AFA+HGKSQ+A+D+FLKM+ EG++PNQVTF+GVL ACS  GL+E+GC+
Sbjct: 373 NRDLYTYSAMIAAFAEHGKSQDAIDLFLKMQQEGLKPNQVTFVGVLNACSTSGLIEEGCR 432

Query: 368 QFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVH 427
            F++MT ++GI+PL EH TCMVDLLGR+GQLEKA+SLI +     DA TWG+LL AC+V+
Sbjct: 433 FFQIMTEMYGIEPLPEHYTCMVDLLGRAGQLEKAYSLIKENSTSADATTWGSLLAACRVY 492

Query: 428 VNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSW 487
            N ELGEIAARHL E+ P  +GN  LLAN YAS  KW+ +E VK ++S+   KK  G SW
Sbjct: 493 GNVELGEIAARHLFEIDPTDSGNYVLLANTYASNDKWECAEEVKKLMSKKGMKKPSGYSW 552

Query: 488 I 488
           I
Sbjct: 553 I 553

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446907|ref|XP_004141212.1| PREDICTED: putative pentatricopeptide repeat-containing protein At5g37570-like [Cucumis sativus]

 Score =  491 bits (1265), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 243/452 (53%), Positives = 314/452 (69%), Gaps = 53/452 (11%)

Query: 90  LYAKMHRLGVLTSGFTFSSVLNACARVP-------------------------SLLE--- 121
           LYA+M + G+L S FTFSSVL+A AR+P                         SL++   
Sbjct: 3   LYARMQKAGILESEFTFSSVLSASARMPALYLGRQVHARVIQLGFLSNKIVLTSLMDMYA 62

Query: 122 ------------------------AVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAG 157
                                   ++I GY+K+G+MDDAQ LFD M +RN  SW+ MVAG
Sbjct: 63  KCGFILDAESLFFAIDDKDIVAWTSMIRGYSKLGMMDDAQDLFDKMGQRNSFSWTTMVAG 122

Query: 158 YANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMT 217
           YAN GNMKAAK+ YD M EKN V+ +AMIAGYG+CG+V EA+++F EI  PD+SC AAM 
Sbjct: 123 YANWGNMKAAKQLYDAMPEKNPVSQLAMIAGYGRCGDVAEAERIFGEILVPDSSCCAAMV 182

Query: 218 VCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCD 277
            CY QNGY K AIEMYK M+++N+  +EVA+VGA+SAC QLGDVEMA+ L   VDEGCCD
Sbjct: 183 ACYSQNGYGKEAIEMYKQMKEKNLGTNEVALVGALSACVQLGDVEMASKLIDQVDEGCCD 242

Query: 278 RTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKM 337
           RT +VSNALIH HSK G ++ A  EF+R+K++DV++YS++I A ADHGK++EALD+F KM
Sbjct: 243 RTLFVSNALIHKHSKFGNIERAQEEFNRMKDRDVVTYSTLIIALADHGKAKEALDLFSKM 302

Query: 338 RNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ 397
             EGI+PNQ+ FIGVL AC+H GL+E GCK FELM + FGI+P   H  CMVDLLGR+G+
Sbjct: 303 EEEGIKPNQICFIGVLNACAHAGLIEQGCKYFELMRKGFGIEPQKGHYACMVDLLGRAGE 362

Query: 398 LEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANI 457
           +E A+++I   ++  DA TWG+LLGACK+H N E+GEIAA+HL E+ PE TGN  LLAN 
Sbjct: 363 VEMAYNVIKGAREI-DAKTWGSLLGACKIHGNLEVGEIAAKHLFEMEPENTGNYVLLANT 421

Query: 458 YASMGKWKDSEIVKMMISETEKKKSPGCSWIS 489
           YA M +W ++E V+ ++ E   KK PG SW+S
Sbjct: 422 YAQMKEWNEAEKVRNVMVERGIKKFPGYSWVS 453

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449516776|ref|XP_004165422.1| PREDICTED: putative pentatricopeptide repeat-containing protein At5g37570-like [Cucumis sativus]

 Score =  440 bits (1131), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 227/452 (50%), Positives = 293/452 (64%), Gaps = 82/452 (18%)

Query: 90  LYAKMHRLGVLTSGFTFSSVLNACARVP-------------------------SLLE--- 121
           LYA+M + G+L S FTFSSVL+A AR+P                         SL++   
Sbjct: 3   LYARMQKAGILESEFTFSSVLSASARMPALYLGRQVHARVIQLGFLSNKIVLTSLMDMYA 62

Query: 122 ------------------------AVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAG 157
                                   ++I GY+K+G+MDDAQ LFD M +RN  SW+ MVAG
Sbjct: 63  KCGFILDAESLFFAIDDKDIVAWTSMIRGYSKLGMMDDAQDLFDKMGQRNSFSWTTMVAG 122

Query: 158 YANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMT 217
           YAN GNMKAAK+ YD M EKN V+ +AMIAGYG+CG+V EA+++F EI  PD+SC AAM 
Sbjct: 123 YANWGNMKAAKQLYDAMPEKNPVSQLAMIAGYGRCGDVAEAERIFGEILVPDSSCCAAM- 181

Query: 218 VCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCD 277
                                       VA+VGA+SAC QLGDVEMA+ L   VDEGCCD
Sbjct: 182 ----------------------------VALVGALSACVQLGDVEMASKLIDQVDEGCCD 213

Query: 278 RTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKM 337
           RT +VSNALIH HSK G ++ A  EF+R+K++DV++YS++I A ADHGK++EALD+F KM
Sbjct: 214 RTLFVSNALIHKHSKFGNIERAQEEFNRMKDRDVVTYSTLIIALADHGKAKEALDLFSKM 273

Query: 338 RNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ 397
             EGI+PNQ+ FIGVL AC+H GL+E GCK FELM + FGI+P   H  CMVDLLGR+G+
Sbjct: 274 EEEGIKPNQICFIGVLNACAHAGLIEQGCKYFELMRKGFGIEPQKGHYACMVDLLGRAGE 333

Query: 398 LEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANI 457
           +E A+++I   ++  DA TWG+LLGACK+H N E+GEIAA+HL E+ PE TGN  LLAN 
Sbjct: 334 VEMAYNVIKGAREI-DAKTWGSLLGACKIHGNLEVGEIAAKHLFEMEPENTGNYVLLANT 392

Query: 458 YASMGKWKDSEIVKMMISETEKKKSPGCSWIS 489
           YA M +W ++E V+ ++ E   KK PG SW+S
Sbjct: 393 YAQMKEWNEAEKVRNVMVERGIKKFPGYSWVS 424

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225440783|ref|XP_002275884.1| PREDICTED: putative pentatricopeptide repeat-containing protein At5g37570 [Vitis vinifera]

 Score =  347 bits (891), Expect = 7e-93,   Method: Compositional matrix adjust.
 Identities = 193/530 (36%), Positives = 294/530 (55%), Gaps = 58/530 (10%)

Query: 12  TFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLW 71
           T + L+QVH+ +++     H  +   +QFL     L   N SY   VF+ +    T  LW
Sbjct: 37  TTSTLEQVHARIIRK--GLHQDHFIISQFLTLCNSL--SNFSYTTSVFNGVSSPST-VLW 91

Query: 72  TSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLE-------AVI 124
            + I+ +  +     ++ L+ +M R   +   FT+ S++ AC++V  + E       AV 
Sbjct: 92  NTYIKGYSENYSVSLTVSLFIRMKRSDAVPDKFTYPSLIKACSKVCGVKEGVAFHGSAVR 151

Query: 125 CG--------------YTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEF 170
           CG              Y K G +  A+++FD M ERNV+SW+AM+AGYA+  ++  A++ 
Sbjct: 152 CGVGGDVFVMTSLIDLYGKCGEILCARKVFDEMGERNVVSWTAMIAGYASFSDLVEARKL 211

Query: 171 YDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEIS------------------------ 206
           +D M EKN+V+W A+I+GY KCG++R A+K+FDE+                         
Sbjct: 212 FDEMPEKNAVSWNAIISGYVKCGDLRSARKMFDEMPHRNVVSFTTMIDGYAKSGDMASAR 271

Query: 207 -------EPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLG 259
                  E D   W+A+   YVQNG    A++++  M   NV+  E  MV  +SAC+Q+G
Sbjct: 272 FVFEEAPERDVVAWSALISGYVQNGQPNEAVKIFLEMCSRNVKPDEFIMVSLMSACSQMG 331

Query: 260 DVEMAAILAKHVDEGCCD-RTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMI 318
            +E+A  +  +V +   D    +V  ALI M++KCG +D A + F  +  +D+ISY SM+
Sbjct: 332 SLELAKWVDDYVRKSSIDVHRAHVIAALIDMNAKCGSMDRATKLFEEMPKRDLISYCSMM 391

Query: 319 TAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGI 378
              + HG   +A+ +F +M NEG+ P+ V F  +LTACS  GLV++GC  FE M   + I
Sbjct: 392 QGLSIHGCGPQAVSLFSRMLNEGLTPDDVAFTVILTACSRAGLVDEGCYYFESMKTDYSI 451

Query: 379 KPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAAR 438
            P  +H  CMVDLLGR+G+L++A+ L+        AG WGALLGACK+H + ELGE+ A 
Sbjct: 452 VPSPDHYACMVDLLGRAGRLKEAYELLKSMPVEPHAGAWGALLGACKLHCDIELGEVVAD 511

Query: 439 HLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI 488
            L EL P+  GN  LL+NIYA+  +W D  +++  + E   +K PGCSWI
Sbjct: 512 QLFELEPQNAGNYVLLSNIYAAAEQWLDVSLLRNKMRERGIRKIPGCSWI 561

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147799847|emb|CAN66059.1| hypothetical protein VITISV_017037 [Vitis vinifera]

 Score =  337 bits (865), Expect = 6e-90,   Method: Compositional matrix adjust.
 Identities = 189/521 (36%), Positives = 294/521 (56%), Gaps = 43/521 (8%)

Query: 6   LVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKC 65
           L+    T + L+QVH+ +++     H  +   +QFL     L   N SY   VF+ +   
Sbjct: 31  LLKACTTTSTLEQVHARIIRK--GLHQDHFLISQFLTLCNSL--SNFSYTTSVFNGVSSP 86

Query: 66  KTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLE---- 121
            T  LW + I+ +  +     ++ L+ +M R   +   FT+ S++ AC++V  + E    
Sbjct: 87  ST-VLWNTYIKGYSENYSVSLTVSLFIRMKRSDAVPDKFTYPSLIKACSKVCGVKEGVAF 145

Query: 122 ---AVICG--------------YTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNM 164
              AV CG              Y K G +  A+++FD M ERNV+SW+AM+AGYA+  ++
Sbjct: 146 HGSAVRCGVGGDVFVMTSLIDLYGKCGEILCARKVFDEMGERNVVSWTAMIAGYASFSDL 205

Query: 165 KAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNG 224
             A++ +D M EKN+V+W A+I+GY KCG++R A+K+FDE+   +   +  M   Y ++G
Sbjct: 206 VEARKLFDEMPEKNAVSWNAIISGYVKCGDLRSARKMFDEMPHRNVVSFTTMIDGYAKSG 265

Query: 225 ---YAKAAIE-------------MYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILA 268
               A+   E             +++V  + NV+  E  MV  +SAC+Q+G +E+A  + 
Sbjct: 266 DMASARFVFEEAPERDVVAWSALIFRVCAEWNVKPDEFIMVSLMSACSQMGSLELAKWVD 325

Query: 269 KHVDEGCCD-RTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKS 327
            +V +   D    +V  ALI M++KCG +D A + F  +  +D+ISY SM+   + HG  
Sbjct: 326 DYVRKSSIDVHRAHVIAALIDMNAKCGSMDRATKLFEEMPKRDLISYCSMMQGLSIHGCG 385

Query: 328 QEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTC 387
            +A+ +F +M NEG+ P+ V F  +LTACS  GLV++GC  FE M   + I P  +H  C
Sbjct: 386 PQAVSLFSRMLNEGLTPDDVAFTVILTACSRAGLVDEGCYYFESMKTDYSIVPSPDHYAC 445

Query: 388 MVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK 447
           MVDLLGR+G+L++A+ L+        AG WGALLGACK+H + ELGE+ A  L EL P+ 
Sbjct: 446 MVDLLGRAGRLKEAYELLKSMPVEPHAGAWGALLGACKLHCDIELGEVVADQLFELEPQN 505

Query: 448 TGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI 488
            GN  LL+NIYA+  +W D  +++  + E   +K PGCSWI
Sbjct: 506 AGNYVLLSNIYAAAEQWLDVSLLRNKMRERGIRKIPGCSWI 546

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225431281|ref|XP_002268784.1| PREDICTED: pentatricopeptide repeat-containing protein At5g44230-like [Vitis vinifera]

 Score =  337 bits (863), Expect = 1e-89,   Method: Compositional matrix adjust.
 Identities = 180/481 (37%), Positives = 274/481 (56%), Gaps = 20/481 (4%)

Query: 13  FNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLL---QLPGDNLSYARQVFDQIPKCKTQF 69
            NQ+KQVH+++ +   K  +Q  +    L+R L    +P D   Y R VF Q+ +    F
Sbjct: 52  INQVKQVHAHIFR---KGLEQCCFVLAKLLRTLTKLDVPMD--PYPRLVFQQV-EYPNPF 105

Query: 70  LWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTK 129
           LWT+LIR + L   F +S+LLY  M R G+    FTF+++L AC+    +          
Sbjct: 106 LWTALIRGYALQGPFMESVLLYNSMRRQGIGPVSFTFTALLKACSAALDV---------N 156

Query: 130 IGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGY 189
           +G     Q +       ++   + ++  Y  CG +      +D M +++ ++W ++I  Y
Sbjct: 157 LGRQVHTQTILIGGFGSDLYVGNTLIDMYVKCGCLGCGHRVFDEMLDRDVISWTSLIVAY 216

Query: 190 GKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMV 249
            K G +  A ++FD +   D   W AM   Y QN   + A+E+++ M+   V+  EV +V
Sbjct: 217 AKVGNMEAASELFDGLPMKDMVAWTAMVTGYAQNARPREALEVFERMQAAGVKTDEVTLV 276

Query: 250 GAISACTQLGDVEMAAILAKHVDEGCCDRTN--YVSNALIHMHSKCGYLDLAWREFSRIK 307
           G ISAC QLG  + A  +    ++     T+   V +ALI M++KCG ++ A++ F R++
Sbjct: 277 GVISACAQLGAAKYANWVRDVAEQSGFGPTSNVVVGSALIDMYAKCGSVEDAYKVFERME 336

Query: 308 NKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCK 367
            ++V SYSSMI  FA HG +  A+++F +M    I+PN+VTFIGVLTACSH G+VE G +
Sbjct: 337 ERNVYSYSSMIVGFAMHGLAGAAMELFDEMLKTEIKPNRVTFIGVLTACSHAGMVEQGQQ 396

Query: 368 QFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVH 427
            F +M    G+ P  +H  CMVDLLGR+G+LE+A +L+         G WGALLGAC++H
Sbjct: 397 LFAMMEECHGVAPSEDHYACMVDLLGRAGRLEEALNLVKMMPMNPHGGVWGALLGACRIH 456

Query: 428 VNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSW 487
            N ++ +IAA HL EL P   GN  LL+NIYAS G+W D   V+ ++     KK+PGCSW
Sbjct: 457 GNPDMAQIAASHLFELEPNGIGNYILLSNIYASAGRWDDVSKVRKLMRAKGLKKNPGCSW 516

Query: 488 I 488
           +
Sbjct: 517 V 517

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356510957|ref|XP_003524199.1| PREDICTED: pentatricopeptide repeat-containing protein At5g44230-like [Glycine max]

 Score =  333 bits (855), Expect = 8e-89,   Method: Compositional matrix adjust.
 Identities = 184/490 (37%), Positives = 273/490 (55%), Gaps = 19/490 (3%)

Query: 6   LVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQ-LPGDNL-SYARQVFDQIP 63
           ++ R  + NQ K+VH+   +   K   Q  Y    L+RL+  LP   L SY R +F Q+ 
Sbjct: 14  ILERCSSLNQAKEVHA---QIYIKNLQQSSYVLTKLLRLVTALPHVPLHSYPRLLFSQL- 69

Query: 64  KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAV 123
                F WT+LIR + L     Q++  Y+ M +  V    FTFS++ +ACA V       
Sbjct: 70  HTPNPFAWTALIRAYALRGPLSQALSFYSSMRKRRVSPISFTFSALFSACAAVR------ 123

Query: 124 ICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWV 183
              ++ +G    AQ L       ++   +A++  Y  CG+++ A+  +D M E++ ++W 
Sbjct: 124 ---HSALGAQLHAQTLLLGGFSSDLYVNNAVIDMYVKCGSLRCARMVFDEMPERDVISWT 180

Query: 184 AMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRI 243
            +I  Y + G++R A+ +FD +   D   W AM   Y QN     A+E+++ +R E V I
Sbjct: 181 GLIVAYTRIGDMRAARDLFDGLPVKDMVTWTAMVTGYAQNAMPMDALEVFRRLRDEGVEI 240

Query: 244 SEVAMVGAISACTQLGDVEMAAIL---AKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAW 300
            EV +VG ISAC QLG  + A  +   A+    G  D    V +ALI M+SKCG ++ A+
Sbjct: 241 DEVTLVGVISACAQLGASKYANWIRDIAESSGFGVGDNV-LVGSALIDMYSKCGNVEEAY 299

Query: 301 REFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGG 360
             F  ++ ++V SYSSMI  FA HG+++ A+ +F  M   G++PN VTF+GVLTACSH G
Sbjct: 300 DVFKGMRERNVFSYSSMIVGFAIHGRARAAIKLFYDMLETGVKPNHVTFVGVLTACSHAG 359

Query: 361 LVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGAL 420
           LV+ G + F  M + +G+ P  E   CM DLL R+G LEKA  L+       D   WGAL
Sbjct: 360 LVDQGQQLFASMEKCYGVAPTAELYACMTDLLSRAGYLEKALQLVETMPMESDGAVWGAL 419

Query: 421 LGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK 480
           LGA  VH N ++ EIA++ L EL P+  GN  LL+N YAS G+W D   V+ ++ E   K
Sbjct: 420 LGASHVHGNPDVAEIASKRLFELEPDNIGNYLLLSNTYASAGRWDDVSKVRKLLREKNLK 479

Query: 481 KSPGCSWISS 490
           K+PG SW+ +
Sbjct: 480 KNPGWSWVEA 489

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449525261|ref|XP_004169636.1| PREDICTED: pentatricopeptide repeat-containing protein At5g44230-like [Cucumis sativus]

 Score =  333 bits (855), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 183/479 (38%), Positives = 269/479 (56%), Gaps = 16/479 (3%)

Query: 13  FNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLL-QLPGDNLSYARQVFDQIPKCKTQFLW 71
           F+Q+KQVH+++++       Q  Y    LIR+L ++     SY   VF Q+      FLW
Sbjct: 55  FSQIKQVHAHIIRNGLS---QCSYVLTKLIRMLTKVDVPMGSYPLLVFGQV-NYPNPFLW 110

Query: 72  TSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIG 131
           T++IR + L     +S   Y +M R GV    FTFS++  AC    ++          +G
Sbjct: 111 TAMIRGYALQGLLSESTNFYTRMRRDGVGPVSFTFSALFKACGAALNM---------DLG 161

Query: 132 LMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGK 191
               AQ +       ++   ++M+  Y  CG +  A++ +D M+E++ V+W  +I  Y K
Sbjct: 162 KQVHAQTILIGGFASDLYVGNSMIDLYVKCGFLGCARKVFDEMSERDVVSWTELIVAYAK 221

Query: 192 CGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGA 251
            G++  A  +FD++   D   W AM   Y QNG  K A+E ++ M+   +   EV + G 
Sbjct: 222 YGDMESASGLFDDLPSKDMVAWTAMVTGYAQNGRPKEALEYFQKMQDVGMETDEVTLAGV 281

Query: 252 ISACTQLGDVEMAAILAKHVDE-GCCDRTNYV-SNALIHMHSKCGYLDLAWREFSRIKNK 309
           ISAC QLG V+ A  +    +  G     N V  +ALI M+SKCG  D A++ F  +K +
Sbjct: 282 ISACAQLGAVKHANWIRDIAERSGFGPSGNVVVGSALIDMYSKCGSPDEAYKVFEVMKER 341

Query: 310 DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQF 369
           +V SYSSMI  +A HG++  AL +F  M    I PN+VTFIG+L+ACSH GLVE G + F
Sbjct: 342 NVFSYSSMILGYAMHGRAHSALQLFHDMLKTEIRPNKVTFIGILSACSHAGLVEQGRQLF 401

Query: 370 ELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVN 429
             M + FG+ P  +H  CMVDLLGR+G LE+A  L+       + G WGALLGAC++H N
Sbjct: 402 AKMEKFFGVAPSPDHYACMVDLLGRAGCLEEALDLVKTMPMEPNGGVWGALLGACRIHGN 461

Query: 430 AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI 488
            ++ +IAA  L +L P   GN  LL+NIYAS G+W++   ++ +I E   KK+PGCSW 
Sbjct: 462 PDIAQIAANELFKLEPNGIGNYILLSNIYASAGRWEEVSKLRKVIREKGFKKNPGCSWF 520

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	490
TAIR|locus:2167593	657	AT5G44230 [Arabidopsis thalian	0.940	0.701	0.375	4.1e-81
TAIR|locus:2140235	781	AT4G02750 [Arabidopsis thalian	0.748	0.469	0.397	1.5e-74
TAIR|locus:2060640	738	OTP81 "ORGANELLE TRANSCRIPT PR	0.895	0.594	0.368	1.8e-71
TAIR|locus:2151694	550	AT5G37570 "AT5G37570" [Arabido	0.751	0.669	0.373	8.9e-70
TAIR|locus:2027554	704	AT1G56690 [Arabidopsis thalian	0.746	0.519	0.379	2.4e-69
TAIR|locus:2012295	705	AT1G09410 [Arabidopsis thalian	0.742	0.516	0.367	2.4e-69
TAIR|locus:2154855	620	AT5G66520 "AT5G66520" [Arabido	0.938	0.741	0.345	5.6e-68
TAIR|locus:2006927	538	AT1G33350 [Arabidopsis thalian	0.957	0.871	0.323	1.2e-67
TAIR|locus:2154389	646	LPA66 "LOW PSII ACCUMULATION 6	0.946	0.718	0.339	1.9e-67
TAIR|locus:2130354	722	AT4G14820 "AT4G14820" [Arabido	0.867	0.588	0.328	2.4e-67

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

 Score = 814 (291.6 bits), Expect = 4.1e-81, P = 4.1e-81
 Identities = 180/479 (37%), Positives = 269/479 (56%)

Query:    14 NQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLS-YARQVFDQIPKCKTQFLWT 72
             NQ+KQ+H ++L+   K  DQ  Y    LIR L   G  +  YAR+V + + + +  FLWT
Sbjct:    63 NQIKQIHGHVLR---KGLDQSCYILTKLIRTLTKLGVPMDPYARRVIEPV-QFRNPFLWT 118

Query:    73 SLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGL 132
             ++IR + +   F ++I +Y  M +  +    FTFS++L AC  +  L          +G 
Sbjct:   119 AVIRGYAIEGKFDEAIAMYGCMRKEEITPVSFTFSALLKACGTMKDL---------NLGR 169

Query:   133 MDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKC 192
                AQ  F       V   + M+  Y  C ++  A++ +D M E++ ++W  +IA Y + 
Sbjct:   170 QFHAQT-FRLRGFCFVYVGNTMIDMYVKCESIDCARKVFDEMPERDVISWTELIAAYARV 228

Query:   193 GEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAI 252
             G +  A ++F+ +   D   W AM   + QN   + A+E +  M +  +R  EV + G I
Sbjct:   229 GNMECAAELFESLPTKDMVAWTAMVTGFAQNAKPQEALEYFDRMEKSGIRADEVTVAGYI 288

Query:   253 SACTQLGDVEMAAILAKHVDEGCCDRTNYV--SNALIHMHSKCGYLDLAWREFSRIKNKD 310
             SAC QLG  + A    +   +     +++V   +ALI M+SKCG ++ A   F  + NK+
Sbjct:   289 SACAQLGASKYADRAVQIAQKSGYSPSDHVVIGSALIDMYSKCGNVEEAVNVFMSMNNKN 348

Query:   311 VISYSSMITAFADHGKSQEALDMFLKMRNEG-IEPNQVTFIGVLTACSHGGLVEDGCKQF 369
             V +YSSMI   A HG++QEAL +F  M  +  I+PN VTF+G L ACSH GLV+ G + F
Sbjct:   349 VFTYSSMILGLATHGRAQEALHLFHYMVTQTEIKPNTVTFVGALMACSHSGLVDQGRQVF 408

Query:   370 ELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVN 429
             + M + FG++P  +H TCMVDLLGR+G+L++A  LI         G WGALLGAC++H N
Sbjct:   409 DSMYQTFGVQPTRDHYTCMVDLLGRTGRLQEALELIKTMSVEPHGGVWGALLGACRIHNN 468

Query:   430 AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI 488
              E+ EIAA HL EL P+  GN  LL+N+YAS G W     V+ +I E   KK+P  SW+
Sbjct:   469 PEIAEIAAEHLFELEPDIIGNYILLSNVYASAGDWGGVLRVRKLIKEKGLKKTPAVSWV 527

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2140235 AT4G02750 [Arabidopsis thaliana (taxid:3702)]

 Score = 752 (269.8 bits), Expect = 1.5e-74, P = 1.5e-74
 Identities = 146/367 (39%), Positives = 227/367 (61%)

Query:   122 AVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVT 181
             A++ GY +  ++++A+ LFD M ERN +SW+AM+AGY     M+ AKE +D M  +N  T
Sbjct:   286 AMVSGYIQNRMVEEARELFDKMPERNEVSWNAMLAGYVQGERMEMAKELFDVMPCRNVST 345

Query:   182 WVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENV 241
             W  MI GY +CG++ EAK +FD++ + D   WAAM   Y Q+G++  A+ ++  M +E  
Sbjct:   346 WNTMITGYAQCGKISEAKNLFDKMPKRDPVSWAAMIAGYSQSGHSFEALRLFVQMEREGG 405

Query:   242 RISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWR 301
             R++  +   A+S C  +  +E+   L   + +G  +   +V NAL+ M+ KCG ++ A  
Sbjct:   406 RLNRSSFSSALSTCADVVALELGKQLHGRLVKGGYETGCFVGNALLLMYCKCGSIEEAND 465

Query:   302 EFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGL 361
              F  +  KD++S+++MI  ++ HG  + AL  F  M+ EG++P+  T + VL+ACSH GL
Sbjct:   466 LFKEMAGKDIVSWNTMIAGYSRHGFGEVALRFFESMKREGLKPDDATMVAVLSACSHTGL 525

Query:   362 VEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALL 421
             V+ G + F  MT+ +G+ P ++H  CMVDLLGR+G LE AH+L+ +     DA  WG LL
Sbjct:   526 VDKGRQYFYTMTQDYGVMPNSQHYACMVDLLGRAGLLEDAHNLMKNMPFEPDAAIWGTLL 585

Query:   422 GACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKK 481
             GA +VH N EL E AA  +  + PE +G   LL+N+YAS G+W D   +++ + +   KK
Sbjct:   586 GASRVHGNTELAETAADKIFAMEPENSGMYVLLSNLYASSGRWGDVGKLRVRMRDKGVKK 645

Query:   482 SPGCSWI 488
              PG SWI
Sbjct:   646 VPGYSWI 652

GO:0005739 "mitochondrion" evidence=ISM

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

 Score = 723 (259.6 bits), Expect = 1.8e-71, P = 1.8e-71
 Identities = 168/456 (36%), Positives = 249/456 (54%)

Query:    36 YYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMH 95
             + A  LI      GD L  A +VF  I K K    W S+I   V      +++ L+ KM 
Sbjct:   167 FVANSLIHCYFSCGD-LDSACKVFTTI-KEKDVVSWNSMINGFVQKGSPDKALELFKKME 224

Query:    96 RLGVLTSGFTFSSVLNACARVPSL-LEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAM 154
                V  S  T   VL+ACA++ +L     +C Y +           ++    N+   +AM
Sbjct:   225 SEDVKASHVTMVGVLSACAKIRNLEFGRQVCSYIE-----------ENRVNVNLTLANAM 273

Query:   155 VAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWA 214
             +  Y  CG+++ AK  +D M EK++VTW  M+ GY    +   A++V + + + D   W 
Sbjct:   274 LDMYTKCGSIEDAKRLFDAMEEKDNVTWTTMLDGYAISEDYEAAREVLNSMPQKDIVAWN 333

Query:   215 AMTVCYVQNGYA-KAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDE 273
             A+   Y QNG   +A I  +++  Q+N++++++ +V  +SAC Q+G +E+   +  ++ +
Sbjct:   334 ALISAYEQNGKPNEALIVFHELQLQKNMKLNQITLVSTLSACAQVGALELGRWIHSYIKK 393

Query:   274 GCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDM 333
                    +V++ALIHM+SKCG L+ +   F+ ++ +DV  +S+MI   A HG   EA+DM
Sbjct:   394 HGIRMNFHVTSALIHMYSKCGDLEKSREVFNSVEKRDVFVWSAMIGGLAMHGCGNEAVDM 453

Query:   334 FLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLG 393
             F KM+   ++PN VTF  V  ACSH GLV++    F  M   +GI P  +H  C+VD+LG
Sbjct:   454 FYKMQEANVKPNGVTFTNVFCACSHTGLVDEAESLFHQMESNYGIVPEEKHYACIVDVLG 513

Query:   394 RSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSAL 453
             RSG LEKA   I           WGALLGACK+H N  L E+A   LLEL P   G   L
Sbjct:   514 RSGYLEKAVKFIEAMPIPPSTSVWGALLGACKIHANLNLAEMACTRLLELEPRNDGAHVL 573

Query:   454 LANIYASMGKWKD-SEIVKMMISETEKKKSPGCSWI 488
             L+NIYA +GKW++ SE+ K M   T  KK PGCS I
Sbjct:   574 LSNIYAKLGKWENVSELRKHM-RVTGLKKEPGCSSI 608

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0031425 "chloroplast RNA processing" evidence=IMP

TAIR|locus:2151694 AT5G37570 "AT5G37570" [Arabidopsis thaliana (taxid:3702)]

 Score = 707 (253.9 bits), Expect = 8.9e-70, P = 8.9e-70
 Identities = 138/369 (37%), Positives = 225/369 (60%)

Query:   122 AVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVT 181
             A++  Y K G +++A+ +FD M ERN+ SW+A+V G    G++  AK+ +D M +++ ++
Sbjct:   181 ALVVAYVKSGELEEAKSMFDLMPERNLGSWNALVDGLVKSGDLVNAKKLFDEMPKRDIIS 240

Query:   182 WVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENV 241
             + +MI GY K G++  A+ +F+E    D   W+A+ + Y QNG    A +++  M  +NV
Sbjct:   241 YTSMIDGYAKGGDMVSARDLFEEARGVDVRAWSALILGYAQNGQPNEAFKVFSEMCAKNV 300

Query:   242 RISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCD-RTNYVSNALIHMHSKCGYLDLAW 300
             +  E  MVG +SAC+Q+G  E+   +  ++ +      ++YV  ALI M++KCG++D A 
Sbjct:   301 KPDEFIMVGLMSACSQMGCFELCEKVDSYLHQRMNKFSSHYVVPALIDMNAKCGHMDRAA 360

Query:   301 REFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGG 360
             + F  +  +D++SY SM+   A HG   EA+ +F KM +EGI P++V F  +L  C    
Sbjct:   361 KLFEEMPQRDLVSYCSMMEGMAIHGCGSEAIRLFEKMVDEGIVPDEVAFTVILKVCGQSR 420

Query:   361 LVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGAL 420
             LVE+G + FELM + + I    +H +C+V+LL R+G+L++A+ LI        A  WG+L
Sbjct:   421 LVEEGLRYFELMRKKYSILASPDHYSCIVNLLSRTGKLKEAYELIKSMPFEAHASAWGSL 480

Query:   421 LGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK 480
             LG C +H N E+ E+ ARHL EL P+  G+  LL+NIYA++ +W D   ++  ++E    
Sbjct:   481 LGGCSLHGNTEIAEVVARHLFELEPQSAGSYVLLSNIYAALDRWTDVAHLRDKMNENGIT 540

Query:   481 KSPGCSWIS 489
             K  G SWIS
Sbjct:   541 KICGRSWIS 549

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2027554 AT1G56690 [Arabidopsis thaliana (taxid:3702)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 139/366 (37%), Positives = 218/366 (59%)

Query:   123 VICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTW 182
             +I GY +   +D A++LF+ M E+  +SW++M+ GY   G ++ A+EF++ M  K  +  
Sbjct:   209 MITGYRQNNRVDVARKLFEVMPEKTEVSWTSMLLGYTLSGRIEDAEEFFEVMPMKPVIAC 268

Query:   183 VAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVR 242
              AMI G+G+ GE+ +A++VFD + + D + W  M   Y + G+   A++++  M+++ VR
Sbjct:   269 NAMIVGFGEVGEISKARRVFDLMEDRDNATWRGMIKAYERKGFELEALDLFAQMQKQGVR 328

Query:   243 ISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWRE 302
              S  +++  +S C  L  ++    +  H+     D   YV++ L+ M+ KCG L  A   
Sbjct:   329 PSFPSLISILSVCATLASLQYGRQVHAHLVRCQFDDDVYVASVLMTMYVKCGELVKAKLV 388

Query:   303 FSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLV 362
             F R  +KD+I ++S+I+ +A HG  +EAL +F +M + G  PN+VT I +LTACS+ G +
Sbjct:   389 FDRFSSKDIIMWNSIISGYASHGLGEEALKIFHEMPSSGTMPNKVTLIAILTACSYAGKL 448

Query:   363 EDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLG 422
             E+G + FE M   F + P  EH +C VD+LGR+GQ++KA  LI       DA  WGALLG
Sbjct:   449 EEGLEIFESMESKFCVTPTVEHYSCTVDMLGRAGQVDKAMELIESMTIKPDATVWGALLG 508

Query:   423 ACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKS 482
             ACK H   +L E+AA+ L E  P+  G   LL++I AS  KW D  +V+  +      K 
Sbjct:   509 ACKTHSRLDLAEVAAKKLFENEPDNAGTYVLLSSINASRSKWGDVAVVRKNMRTNNVSKF 568

Query:   483 PGCSWI 488
             PGCSWI
Sbjct:   569 PGCSWI 574

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2012295 AT1G09410 [Arabidopsis thaliana (taxid:3702)]

 Score = 703 (252.5 bits), Expect = 2.4e-69, P = 2.4e-69
 Identities = 135/367 (36%), Positives = 227/367 (61%)

Query:   123 VICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTW 182
             ++ GY +   +DDA+++FD M E+  +SW++M+ GY   G ++ A+E ++ M  K  +  
Sbjct:   209 MVTGYGQNNRVDDARKIFDVMPEKTEVSWTSMLMGYVQNGRIEDAEELFEVMPVKPVIAC 268

Query:   183 VAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVR 242
              AMI+G G+ GE+ +A++VFD + E + + W  +   + +NG+   A++++ +M+++ VR
Sbjct:   269 NAMISGLGQKGEIAKARRVFDSMKERNDASWQTVIKIHERNGFELEALDLFILMQKQGVR 328

Query:   243 ISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWRE 302
              +   ++  +S C  L  +     +   +     D   YV++ L+ M+ KCG L  +   
Sbjct:   329 PTFPTLISILSVCASLASLHHGKQVHAQLVRCQFDVDVYVASVLMTMYIKCGELVKSKLI 388

Query:   303 FSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEG-IEPNQVTFIGVLTACSHGGL 361
             F R  +KD+I ++S+I+ +A HG  +EAL +F +M   G  +PN+VTF+  L+ACS+ G+
Sbjct:   389 FDRFPSKDIIMWNSIISGYASHGLGEEALKVFCEMPLSGSTKPNEVTFVATLSACSYAGM 448

Query:   362 VEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALL 421
             VE+G K +E M  VFG+KP+T H  CMVD+LGR+G+  +A  +I       DA  WG+LL
Sbjct:   449 VEEGLKIYESMESVFGVKPITAHYACMVDMLGRAGRFNEAMEMIDSMTVEPDAAVWGSLL 508

Query:   422 GACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKD-SEIVKMMISETEKK 480
             GAC+ H   ++ E  A+ L+E+ PE +G   LL+N+YAS G+W D +E+ K+M +   +K
Sbjct:   509 GACRTHSQLDVAEFCAKKLIEIEPENSGTYILLSNMYASQGRWADVAELRKLMKTRLVRK 568

Query:   481 KSPGCSW 487
              SPGCSW
Sbjct:   569 -SPGCSW 574

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 690 (248.0 bits), Expect = 5.6e-68, P = 5.6e-68
 Identities = 165/478 (34%), Positives = 258/478 (53%)

Query:    15 QLKQVHSYLLKTLTKPHDQYHYYAQFL-IRLLQLPGDNLSYARQVFDQIPKCKTQFLWTS 73
             +LKQ+H+ +LKT     D Y    +FL   +     D L YA+ VFD   +  T FLW  
Sbjct:    29 ELKQIHARMLKTGLM-QDSYAI-TKFLSFCISSTSSDFLPYAQIVFDGFDRPDT-FLWNL 85

Query:    74 LIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEA--VICGYTKIG 131
             +IR         +S+LLY +M       + +TF S+L AC+ + +  E   +    TK+G
Sbjct:    86 MIRGFSCSDEPERSLLLYQRMLCSSAPHNAYTFPSLLKACSNLSAFEETTQIHAQITKLG 145

Query:   132 LMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGK 191
                          E +V + ++++  YA  GN K A   +DR+ E + V+W ++I GY K
Sbjct:   146 Y------------ENDVYAVNSLINSYAVTGNFKLAHLLFDRIPEPDDVSWNSVIKGYVK 193

Query:   192 CGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGA 251
              G++  A  +F +++E +A  W  M   YVQ    K A++++  M+  +V    V++  A
Sbjct:   194 AGKMDIALTLFRKMAEKNAISWTTMISGYVQADMNKEALQLFHEMQNSDVEPDNVSLANA 253

Query:   252 ISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDV 311
             +SAC QLG +E    +  ++++      + +   LI M++KCG ++ A   F  IK K V
Sbjct:   254 LSACAQLGALEQGKWIHSYLNKTRIRMDSVLGCVLIDMYAKCGEMEEALEVFKNIKKKSV 313

Query:   312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFEL 371
              +++++I+ +A HG  +EA+  F++M+  GI+PN +TF  VLTACS+ GLVE+G   F  
Sbjct:   314 QAWTALISGYAYHGHGREAISKFMEMQKMGIKPNVITFTAVLTACSYTGLVEEGKLIFYS 373

Query:   372 MTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAE 431
             M R + +KP  EH  C+VDLLGR+G L++A   I +     +A  WGALL AC++H N E
Sbjct:   374 MERDYNLKPTIEHYGCIVDLLGRAGLLDEAKRFIQEMPLKPNAVIWGALLKACRIHKNIE 433

Query:   432 LGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWIS 489
             LGE     L+ + P   G     ANI+A   KW  +   + ++ E    K PGCS IS
Sbjct:   434 LGEEIGEILIAIDPYHGGRYVHKANIHAMDKKWDKAAETRRLMKEQGVAKVPGCSTIS 491

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0016556 "mRNA modification" evidence=RCA

TAIR|locus:2006927 AT1G33350 [Arabidopsis thaliana (taxid:3702)]

 Score = 687 (246.9 bits), Expect = 1.2e-67, P = 1.2e-67
 Identities = 159/491 (32%), Positives = 266/491 (54%)

Query:     6 LVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKC 65
             ++ +S+  N LKQV S+++ +    H   H+    L+R   L   NLSYAR +FD+    
Sbjct:    30 VISKSRHLNHLKQVQSFMIVSGLS-HS--HFLCFKLLRFCTLRLCNLSYARFIFDRFSFP 86

Query:    66 KTQFLWTSLIRNHV--LHAHFRQSILLYAKMHRLGV-LTSGFTFSSVLNACARVPSLLEA 122
              T  L+ +++  +   L  H   +   +  M    V   + F +  VL +   + S    
Sbjct:    87 NTH-LYAAVLTAYSSSLPLHASSAFSFFRLMVNRSVPRPNHFIYPLVLKSTPYLSSAFST 145

Query:   123 VICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANC-GNMKAAKEFYDRMTEKNSVT 181
              +  +T          LF S     V+  +A++  YA+   ++  A++ +D M+E+N V+
Sbjct:   146 PLV-HT---------HLFKSGFHLYVVVQTALLHSYASSVSHITLARQLFDEMSERNVVS 195

Query:   182 WVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQE-N 240
             W AM++GY + G++  A  +F+++ E D   W A+     QNG    A+ +++ M  E +
Sbjct:   196 WTAMLSGYARSGDISNAVALFEDMPERDVPSWNAILAACTQNGLFLEAVSLFRRMINEPS 255

Query:   241 VRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAW 300
             +R +EV +V  +SAC Q G +++A  +             +VSN+L+ ++ KCG L+ A 
Sbjct:   256 IRPNEVTVVCVLSACAQTGTLQLAKGIHAFAYRRDLSSDVFVSNSLVDLYGKCGNLEEAS 315

Query:   301 REFSRIKNKDVISYSSMITAFADHGKSQEALDMF---LKMRNEGIEPNQVTFIGVLTACS 357
               F     K + +++SMI  FA HG+S+EA+ +F   +K+    I+P+ +TFIG+L AC+
Sbjct:   316 SVFKMASKKSLTAWNSMINCFALHGRSEEAIAVFEEMMKLNINDIKPDHITFIGLLNACT 375

Query:   358 HGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTW 417
             HGGLV  G   F+LMT  FGI+P  EH  C++DLLGR+G+ ++A  ++   K   D   W
Sbjct:   376 HGGLVSKGRGYFDLMTNRFGIEPRIEHYGCLIDLLGRAGRFDEALEVMSTMKMKADEAIW 435

Query:   418 GALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET 477
             G+LL ACK+H + +L E+A ++L+ L P   G  A++AN+Y  MG W+++   + MI   
Sbjct:   436 GSLLNACKIHGHLDLAEVAVKNLVALNPNNGGYVAMMANLYGEMGNWEEARRARKMIKHQ 495

Query:   478 EKKKSPGCSWI 488
                K PG S I
Sbjct:   496 NAYKPPGWSRI 506

GO:0005739 "mitochondrion" evidence=ISM

TAIR|locus:2154389 LPA66 "LOW PSII ACCUMULATION 66" [Arabidopsis thaliana (taxid:3702)]

 Score = 685 (246.2 bits), Expect = 1.9e-67, P = 1.9e-67
 Identities = 169/498 (33%), Positives = 270/498 (54%)

Query:    11 KTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLL---QLPGDNLSYARQVFDQIPKCKT 67
             +T   L Q+H+  +K+  +  D     A  ++R      L   +L YA ++F+Q+P+ + 
Sbjct:    34 RTIRDLSQIHAVFIKS-GQMRDTLA--AAEILRFCATSDLHHRDLDYAHKIFNQMPQ-RN 89

Query:    68 QFLWTSLIRNHVLHAHFRQSI---LLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVI 124
              F W ++IR        +  I   L Y  M    V  + FTF SVL ACA+   + E   
Sbjct:    90 CFSWNTIIRGFSESDEDKALIAITLFYEMMSDEFVEPNRFTFPSVLKACAKTGKIQE--- 146

Query:   125 CGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKE-FYDRMTEKNSVT-- 181
              G    GL   A + +    +  V+S   +V  Y  CG MK A+  FY  + EK+ V   
Sbjct:   147 -GKQIHGL---ALK-YGFGGDEFVMS--NLVRMYVMCGFMKDARVLFYKNIIEKDMVVMT 199

Query:   182 -----------WVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAI 230
                        W  MI GY + G+ + A+ +FD++ +     W  M   Y  NG+ K A+
Sbjct:   200 DRRKRDGEIVLWNVMIDGYMRLGDCKAARMLFDKMRQRSVVSWNTMISGYSLNGFFKDAV 259

Query:   231 EMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMH 290
             E+++ M++ ++R + V +V  + A ++LG +E+   L  + ++      + + +ALI M+
Sbjct:   260 EVFREMKKGDIRPNYVTLVSVLPAISRLGSLELGEWLHLYAEDSGIRIDDVLGSALIDMY 319

Query:   291 SKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFI 350
             SKCG ++ A   F R+  ++VI++S+MI  FA HG++ +A+D F KMR  G+ P+ V +I
Sbjct:   320 SKCGIIEKAIHVFERLPRENVITWSAMINGFAIHGQAGDAIDCFCKMRQAGVRPSDVAYI 379

Query:   351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKD 410
              +LTACSHGGLVE+G + F  M  V G++P  EH  CMVDLLGRSG L++A   I++   
Sbjct:   380 NLLTACSHGGLVEEGRRYFSQMVSVDGLEPRIEHYGCMVDLLGRSGLLDEAEEFILNMPI 439

Query:   411 FCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIV 470
               D   W ALLGAC++  N E+G+  A  L+++ P  +G    L+N+YAS G W +   +
Sbjct:   440 KPDDVIWKALLGACRMQGNVEMGKRVANILMDMVPHDSGAYVALSNMYASQGNWSEVSEM 499

Query:   471 KMMISETEKKKSPGCSWI 488
             ++ + E + +K PGCS I
Sbjct:   500 RLRMKEKDIRKDPGCSLI 517

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0007020 "microtubule nucleation" evidence=RCA

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

 Score = 684 (245.8 bits), Expect = 2.4e-67, P = 2.4e-67
 Identities = 144/438 (32%), Positives = 245/438 (55%)

Query:    52 LSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLN 111
             ++YAR VFD++   +    W ++I  +       ++  L+ +M    V+       ++++
Sbjct:   162 INYARNVFDEMSH-RDVVTWNTMIERYCRFGLVDEAFKLFEEMKDSNVMPDEMILCNIVS 220

Query:   112 ACARVPSL-LEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEF 170
             AC R  ++     I  +    L+++  R+     + ++++  A+V  YA  G M  A+EF
Sbjct:   221 ACGRTGNMRYNRAIYEF----LIENDVRM-----DTHLLT--ALVTMYAGAGCMDMAREF 269

Query:   171 YDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAI 230
             + +M+ +N     AM++GY KCG + +A+ +FD+  + D  CW  M   YV++ Y + A+
Sbjct:   270 FRKMSVRNLFVSTAMVSGYSKCGRLDDAQVIFDQTEKKDLVCWTTMISAYVESDYPQEAL 329

Query:   231 EMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMH 290
              +++ M    ++   V+M   ISAC  LG ++ A  +   +     +    ++NALI+M+
Sbjct:   330 RVFEEMCCSGIKPDVVSMFSVISACANLGILDKAKWVHSCIHVNGLESELSINNALINMY 389

Query:   291 SKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFI 350
             +KCG LD     F ++  ++V+S+SSMI A + HG++ +AL +F +M+ E +EPN+VTF+
Sbjct:   390 AKCGGLDATRDVFEKMPRRNVVSWSSMINALSMHGEASDALSLFARMKQENVEPNEVTFV 449

Query:   351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKD 410
             GVL  CSH GLVE+G K F  MT  + I P  EH  CMVDL GR+  L +A  +I     
Sbjct:   450 GVLYGCSHSGLVEEGKKIFASMTDEYNITPKLEHYGCMVDLFGRANLLREALEVIESMPV 509

Query:   411 FCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIV 470
               +   WG+L+ AC++H   ELG+ AA+ +LEL P+  G   L++NIYA   +W+D   +
Sbjct:   510 ASNVVIWGSLMSACRIHGELELGKFAAKRILELEPDHDGALVLMSNIYAREQRWEDVRNI 569

Query:   471 KMMISETEKKKSPGCSWI 488
             + ++ E    K  G S I
Sbjct:   570 RRVMEEKNVFKEKGLSRI 587

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00021552001 SubName- Full=Chromosome chr8 scaffold_23, whole genome shotgun sequence; (561 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

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	490
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-79
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-75
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-34
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-25
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	2e-19
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-13
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	3e-10
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-09
pfam13041	50	pfam13041, PPR_2, PPR repeat family	3e-06
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-05
pfam01535	31	pfam01535, PPR, PPR repeat	8e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	2e-04
pfam01535	31	pfam01535, PPR, PPR repeat	3e-04
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.001
pfam13041	50	pfam13041, PPR_2, PPR repeat family	0.001
pfam01535	31	pfam01535, PPR, PPR repeat	0.004

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

 Score =  260 bits (666), Expect = 3e-79
 Identities = 149/502 (29%), Positives = 236/502 (47%), Gaps = 77/502 (15%)

Query: 57  QVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGF-TFSSVLNACAR 115
              D     K+     S I   V     R+++ L+  +      T    T+ +++ AC  
Sbjct: 76  ARLDDTQIRKSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIA 135

Query: 116 VPS---------------------LLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAM 154
           + S                     ++  V+  + K G++ DA+RLFD M ERN+ SW  +
Sbjct: 136 LKSIRCVKAVYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTI 195

Query: 155 VAGYANCGNMKAAKEFYDRMTEKNSV----TWVAMI----------AG------------ 188
           + G  + GN + A   +  M E  S     T+V M+          AG            
Sbjct: 196 IGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGV 255

Query: 189 -------------YGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKV 235
                        Y KCG++ +A+ VFD + E     W +M   Y  +GY++ A+ +Y  
Sbjct: 256 VGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYE 315

Query: 236 MRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDR---TNYVSN-ALIHMHS 291
           MR   V I +      I   ++L  +E     AK    G        + V+N AL+ ++S
Sbjct: 316 MRDSGVSIDQFTFSIMIRIFSRLALLE----HAKQAHAGLIRTGFPLDIVANTALVDLYS 371

Query: 292 KCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIG 351
           K G ++ A   F R+  K++IS++++I  + +HG+  +A++MF +M  EG+ PN VTF+ 
Sbjct: 372 KWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLA 431

Query: 352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDF 411
           VL+AC + GL E G + F+ M+    IKP   H  CM++LLGR G L++A+++I      
Sbjct: 432 VLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFK 491

Query: 412 CDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVK 471
                W ALL AC++H N ELG +AA  L  +GPEK  N  +L N+Y S G+  ++  V 
Sbjct: 492 PTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKV- 550

Query: 472 MMISETEKKKS----PGCSWIS 489
               ET K+K     P C+WI 
Sbjct: 551 ---VETLKRKGLSMHPACTWIE 569

Length = 697

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

 Score =  253 bits (647), Expect = 2e-75
 Identities = 146/501 (29%), Positives = 246/501 (49%), Gaps = 66/501 (13%)

Query: 49  GDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSS 108
           GD +S AR VFD++P+ +    W ++I  +  +    + + L+  M  L V     T +S
Sbjct: 236 GDVVS-ARLVFDRMPR-RDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITS 293

Query: 109 VLNACARVP---------------------SLLEAVICGYTKIGLMDDAQRLFDSMAERN 147
           V++AC  +                      S+  ++I  Y  +G   +A+++F  M  ++
Sbjct: 294 VISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKD 353

Query: 148 VISWSAMVAGYANCGNMKAAKEFYDRMTEKNSV--------------------------- 180
            +SW+AM++GY   G    A E Y  + E+++V                           
Sbjct: 354 AVSWTAMISGYEKNGLPDKALETY-ALMEQDNVSPDEITIASVLSACACLGDLDVGVKLH 412

Query: 181 ---------TWV----AMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAK 227
                    ++V    A+I  Y KC  + +A +VF  I E D   W ++      N    
Sbjct: 413 ELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCF 472

Query: 228 AAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALI 287
            A+  ++ M    ++ + V ++ A+SAC ++G +     +  HV         ++ NAL+
Sbjct: 473 EALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALL 531

Query: 288 HMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV 347
            ++ +CG ++ AW +F+    KDV+S++ ++T +  HGK   A+++F +M   G+ P++V
Sbjct: 532 DLYVRCGRMNYAWNQFN-SHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEV 590

Query: 348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMD 407
           TFI +L ACS  G+V  G + F  M   + I P  +H  C+VDLLGR+G+L +A++ I  
Sbjct: 591 TFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINK 650

Query: 408 YKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDS 467
                D   WGALL AC++H + ELGE+AA+H+ EL P   G   LL N+YA  GKW + 
Sbjct: 651 MPITPDPAVWGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEV 710

Query: 468 EIVKMMISETEKKKSPGCSWI 488
             V+  + E      PGCSW+
Sbjct: 711 ARVRKTMRENGLTVDPGCSWV 731

Length = 857

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

 Score =  137 bits (346), Expect = 2e-34
 Identities = 80/292 (27%), Positives = 130/292 (44%), Gaps = 39/292 (13%)

Query: 122 AVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRM------- 174
           A++  + + G +  A  +F  M ER++ SW+ +V GYA  G    A   Y RM       
Sbjct: 126 AMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRP 185

Query: 175 ----------TEKNSVTWV----------------------AMIAGYGKCGEVREAKKVF 202
                     T                              A+I  Y KCG+V  A+ VF
Sbjct: 186 DVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVF 245

Query: 203 DEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVE 262
           D +   D   W AM   Y +NG     +E++  MR+ +V    + +   ISAC  LGD  
Sbjct: 246 DRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDER 305

Query: 263 MAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFA 322
           +   +  +V +        V N+LI M+   G    A + FSR++ KD +S+++MI+ + 
Sbjct: 306 LGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYE 365

Query: 323 DHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTR 374
            +G   +AL+ +  M  + + P+++T   VL+AC+  G ++ G K  EL  R
Sbjct: 366 KNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAER 417

Length = 857

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

 Score =  109 bits (273), Expect = 3e-25
 Identities = 80/284 (28%), Positives = 131/284 (46%), Gaps = 40/284 (14%)

Query: 17  KQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIR 76
           +Q+H  +LKT     D +   A  LI +    GD +  AR VFD +P+ KT   W S++ 
Sbjct: 244 QQLHCCVLKT-GVVGDTFVSCA--LIDMYSKCGD-IEDARCVFDGMPE-KTTVAWNSMLA 298

Query: 77  NHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSL--------------LEA 122
            + LH +  +++ LY +M   GV    FTFS ++   +R+  L                 
Sbjct: 299 GYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPL 358

Query: 123 VICG-------YTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMT 175
            I         Y+K G M+DA+ +FD M  +N+ISW+A++AGY N G    A E ++RM 
Sbjct: 359 DIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMI 418

Query: 176 EK----NSVTWVAMIAGYGKCGEVREAKKVFDEISE-----PDASCWAAMTVCYVQNGYA 226
            +    N VT++A+++     G   +  ++F  +SE     P A  +A M     + G  
Sbjct: 419 AEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLL 478

Query: 227 KAAIEMYKVMRQENVRISEVAMVGA-ISACTQLGDVEMAAILAK 269
             A  M +           V M  A ++AC    ++E+  + A+
Sbjct: 479 DEAYAMIR----RAPFKPTVNMWAALLTACRIHKNLELGRLAAE 518

Length = 697

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

 Score = 91.1 bits (226), Expect = 2e-19
 Identities = 90/356 (25%), Positives = 153/356 (42%), Gaps = 36/356 (10%)

Query: 82  AHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFD 141
            H R+      +   L V  S  + +   N+  R        +C +   G ++ A +L +
Sbjct: 32  FHGRK------RSRGLSVAASSSSSTHDSNSQLRA-------LCSH---GQLEQALKLLE 75

Query: 142 SMAERNV-ISWSAMVAGYANCGNMKAAKE-FYDRMTEKNSVTWV------AMIAGYGKCG 193
           SM E  V +   A VA +  C   +A +E         +S   +      AM++ + + G
Sbjct: 76  SMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALSSHPSLGVRLGNAMLSMFVRFG 135

Query: 194 EVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAIS 253
           E+  A  VF ++ E D   W  +   Y + GY   A+ +Y  M    VR         + 
Sbjct: 136 ELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLR 195

Query: 254 ACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVIS 313
            C  + D+     +  HV     +    V NALI M+ KCG +  A   F R+  +D IS
Sbjct: 196 TCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCIS 255

Query: 314 YSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFEL-- 371
           +++MI+ + ++G+  E L++F  MR   ++P+ +T   V++AC    L+ D     E+  
Sbjct: 256 WNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISAC---ELLGDERLGREMHG 312

Query: 372 --MTRVFGIK-PLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGAC 424
             +   F +   +   L  M   LG  G+ EK  S  M+ K   DA +W A++   
Sbjct: 313 YVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSR-METK---DAVSWTAMISGY 364

Length = 857

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

 Score = 73.4 bits (180), Expect = 1e-13
 Identities = 83/364 (22%), Positives = 153/364 (42%), Gaps = 75/364 (20%)

Query: 65  CKTQ------FLWTSLIRNHVLHAHFRQSILLYAKMHR------LGVL----TSGFT--- 105
           CK Q      F +  LIRN  L + F  ++L+            L VL     +G     
Sbjct: 416 CKKQRAVKEAFRFAKLIRNPTL-STF--NMLMSVCASSQDIDGALRVLRLVQEAGLKADC 472

Query: 106 --FSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMA----ERNVISWSAMVAGYA 159
             ++++++ CA              K G +D    +F  M     E NV ++ A++ G A
Sbjct: 473 KLYTTLISTCA--------------KSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCA 518

Query: 160 NCGNMKAAKEFYDRMTEKN----SVTWVAMIAGYGKCGEVREAKKVFDEISE-------- 207
             G +  A   Y  M  KN     V + A+I+  G+ G V  A   FD ++E        
Sbjct: 519 RAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRA---FDVLAEMKAETHPI 575

Query: 208 -PD-ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAA 265
            PD  +  A M  C    G    A E+Y+++ + N++ +      A+++C+Q GD + A 
Sbjct: 576 DPDHITVGALMKAC-ANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFAL 634

Query: 266 ILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKD-------VISYSSMI 318
            +   + +          +AL+ +    G LD A   F  +++          +SYSS++
Sbjct: 635 SIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKA---FEILQDARKQGIKLGTVSYSSLM 691

Query: 319 TAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRV--F 376
            A ++    ++AL+++  +++  + P   T   ++TA   G  +    K  E+++ +   
Sbjct: 692 GACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLP---KALEVLSEMKRL 748

Query: 377 GIKP 380
           G+ P
Sbjct: 749 GLCP 752

Length = 1060

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

 Score = 62.6 bits (152), Expect = 3e-10
 Identities = 59/252 (23%), Positives = 105/252 (41%), Gaps = 47/252 (18%)

Query: 185 MIAGYGKCGEVREAKKVFDEIS----EPDASCWAAMTVCYVQNGYAKA-----AIEMYKV 235
           +I+   K G+V    +VF E+     E +   + A+      +G A+A     A   Y +
Sbjct: 478 LISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALI-----DGCARAGQVAKAFGAYGI 532

Query: 236 MRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGY 295
           MR +NV+   V     ISAC Q G V+ A                   + L  M +    
Sbjct: 533 MRSKNVKPDRVVFNALISACGQSGAVDRAF------------------DVLAEMKA---- 570

Query: 296 LDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTA 355
                 E   I   D I+  +++ A A+ G+   A +++  +    I+     +   + +
Sbjct: 571 ------ETHPID-PDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNS 623

Query: 356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDA 414
           CS  G  +     ++ M +  G+KP     + +VD+ G +G L+KA  ++ D +      
Sbjct: 624 CSQKGDWDFALSIYDDMKKK-GVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKL 682

Query: 415 GT--WGALLGAC 424
           GT  + +L+GAC
Sbjct: 683 GTVSYSSLMGAC 694

Length = 1060

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

 Score = 53.6 bits (130), Expect = 1e-09
 Identities = 16/50 (32%), Positives = 30/50 (60%)

Query: 309 KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSH 358
            DV++Y+++I  +   GK +EAL +F +M+  GI+PN  T+  ++     
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 = 43.9 bits (105), Expect = 3e-06
 Identities = 11/49 (22%), Positives = 27/49 (55%), Gaps = 4/49 (8%)

Query: 147 NVISWSAMVAGYANCGNMKAAKEFYDRMTEK----NSVTWVAMIAGYGK 191
           +V++++ ++ GY   G ++ A + ++ M ++    N  T+  +I G  K
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|213555 TIGR00756, PPR, pentatricopeptide repeat domain (PPR motif)

 Score = 41.3 bits (98), Expect = 2e-05
 Identities = 12/34 (35%), Positives = 24/34 (70%)

Query: 312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN 345
           ++Y+++I      G+ +EAL++F +M+  GIEP+
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|144943 pfam01535, PPR, PPR repeat

 Score = 39.4 bits (93), Expect = 8e-05
 Identities = 11/31 (35%), Positives = 24/31 (77%)

Query: 312 ISYSSMITAFADHGKSQEALDMFLKMRNEGI 342
           ++Y+S+I+ +   GK +EAL++F +M+ +G+
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|205222 pfam13041, PPR_2, PPR repeat family

 Score = 38.5 bits (91), Expect = 2e-04
 Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 4/44 (9%)

Query: 284 NALIHMHSKCGYLDLAWREFSRIKNK----DVISYSSMITAFAD 323
           N LI  + K G ++ A + F+ +K +    +V +YS +I     
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 = 37.4 bits (88), Expect = 3e-04
 Identities = 12/28 (42%), Positives = 21/28 (75%)

Query: 180 VTWVAMIAGYGKCGEVREAKKVFDEISE 207
           VT+ ++I+GY K G++ EA ++F E+ E
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKE 28

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|205222 pfam13041, PPR_2, PPR repeat family

 Score = 37.0 bits (87), Expect = 0.001
 Identities = 13/28 (46%), Positives = 19/28 (67%)

Query: 177 KNSVTWVAMIAGYGKCGEVREAKKVFDE 204
            + VT+  +I GY K G+V EA K+F+E
Sbjct: 1   PDVVTYNTLIDGYCKKGKVEEALKLFNE 28

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 = 36.6 bits (86), Expect = 0.001
 Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 4/43 (9%)

Query: 122 AVICGYTKIGLMDDAQRLFDSMAER----NVISWSAMVAGYAN 160
            +I GY K G +++A +LF+ M +R    NV ++S ++ G   
Sbjct: 8   TLIDGYCKKGKVEEALKLFNEMKKRGIKPNVYTYSILIDGLCK 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 = 34.4 bits (80), Expect = 0.004
 Identities = 8/30 (26%), Positives = 19/30 (63%)

Query: 149 ISWSAMVAGYANCGNMKAAKEFYDRMTEKN 178
           ++++++++GY   G ++ A E +  M EK 
Sbjct: 1   VTYNSLISGYCKAGKLEEALELFKEMKEKG 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	490
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	100.0
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	100.0
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.96
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.95
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.95
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.94
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.93
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.92
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.91
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.91
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.91
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.9
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.9
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.89
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.89
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.89
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.88
PRK14574	822	hmsH outer membrane protein; Provisional	99.86
PRK14574	822	hmsH outer membrane protein; Provisional	99.86
KOG2003	840	consensus TPR repeat-containing protein [General f	99.85
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	99.82
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.79
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.78
KOG2076	895	consensus RNA polymerase III transcription factor	99.77
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.75
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.74
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.74
KOG2003	840	consensus TPR repeat-containing protein [General f	99.74
KOG0495	913	consensus HAT repeat protein [RNA processing and m	99.72
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.71
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.7
KOG2076	895	consensus RNA polymerase III transcription factor	99.7
KOG1126	638	consensus DNA-binding cell division cycle control	99.69
KOG1915	677	consensus Cell cycle control protein (crooked neck	99.68
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.68
KOG1126	638	consensus DNA-binding cell division cycle control	99.68
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.67
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.66
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.65
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.65
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.62
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.61
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.59
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.56
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.55
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.55
KOG0547	606	consensus Translocase of outer mitochondrial membr	99.54
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.54
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.52
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.49
KOG1129	478	consensus TPR repeat-containing protein [General f	99.47
PRK12370	553	invasion protein regulator; Provisional	99.45
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.45
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.44
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	99.44
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.44
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.44
KOG2047	835	consensus mRNA splicing factor [RNA processing and	99.43
KOG1129	478	consensus TPR repeat-containing protein [General f	99.43
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	99.43
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.39
PRK12370	553	invasion protein regulator; Provisional	99.39
PRK11189	296	lipoprotein NlpI; Provisional	99.37
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	99.37
PRK11189	296	lipoprotein NlpI; Provisional	99.36
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.34
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.32
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.3
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.3
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	99.29
PF13041	50	PPR_2: PPR repeat family	99.27
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.27
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.27
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	99.26
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.26
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.25
KOG3785	557	consensus Uncharacterized conserved protein [Funct	99.25
PF13041	50	PPR_2: PPR repeat family	99.25
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	99.24
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	99.24
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	99.24
KOG4340	459	consensus Uncharacterized conserved protein [Funct	99.23
KOG2376	652	consensus Signal recognition particle, subunit Srp	99.19
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	99.16
KOG3616	1636	consensus Selective LIM binding factor [Transcript	99.16
PRK04841	903	transcriptional regulator MalT; Provisional	99.12
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.11
KOG1125	579	consensus TPR repeat-containing protein [General f	99.1
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	99.08
PRK10370	198	formate-dependent nitrite reductase complex subuni	99.04
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	99.03
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	99.03
KOG3616	1636	consensus Selective LIM binding factor [Transcript	99.01
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.99
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.99
PRK04841	903	transcriptional regulator MalT; Provisional	98.97
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	98.97
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.96
PRK15359	144	type III secretion system chaperone protein SscB;	98.95
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	98.95
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.91
PRK15359	144	type III secretion system chaperone protein SscB;	98.89
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.89
KOG1125	579	consensus TPR repeat-containing protein [General f	98.89
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.88
PLN02789	320	farnesyltranstransferase	98.86
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.83
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	98.81
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.79
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.79
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.77
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.75
PLN02789	320	farnesyltranstransferase	98.72
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.72
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.72
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.7
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.7
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.7
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.69
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.69
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.69
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	98.69
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.68
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.63
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.62
PRK14720	906	transcript cleavage factor/unknown domain fusion p	98.55
KOG3060	289	consensus Uncharacterized conserved protein [Funct	98.52
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.51
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.5
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	98.49
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.48
PF12854	34	PPR_1: PPR repeat	98.46
PF12854	34	PPR_1: PPR repeat	98.41
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	98.37
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	98.34
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	98.34
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	98.33
COG3898	531	Uncharacterized membrane-bound protein [Function u	98.32
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.31
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	98.31
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	98.3
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.28
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.28
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	98.26
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.25
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	98.25
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	98.24
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	98.23
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	98.22
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	98.19
KOG0553	304	consensus TPR repeat-containing protein [General f	98.18
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.16
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	98.16
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	98.08
KOG0553	304	consensus TPR repeat-containing protein [General f	98.08
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.06
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	98.05
KOG2041	1189	consensus WD40 repeat protein [General function pr	98.04
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.04
PRK15331	165	chaperone protein SicA; Provisional	98.03
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	98.01
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	98.01
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	98.01
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	98.0
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.99
PF13371	73	TPR_9: Tetratricopeptide repeat	97.96
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.94
COG4700	251	Uncharacterized protein conserved in bacteria cont	97.92
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	97.92
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.91
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.9
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.89
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.89
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	97.88
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.85
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.83
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	97.82
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.79
PF12688	120	TPR_5: Tetratrico peptide repeat	97.74
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.73
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.72
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.72
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	97.7
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.69
PRK10803	263	tol-pal system protein YbgF; Provisional	97.68
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.68
PF12688	120	TPR_5: Tetratrico peptide repeat	97.67
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.66
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	97.65
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	97.65
KOG2796	366	consensus Uncharacterized conserved protein [Funct	97.64
PF13431	34	TPR_17: Tetratricopeptide repeat	97.63
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.58
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.58
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.56
PF13428	44	TPR_14: Tetratricopeptide repeat	97.55
KOG1258	577	consensus mRNA processing protein [RNA processing	97.54
PF13371	73	TPR_9: Tetratricopeptide repeat	97.54
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	97.52
COG3898	531	Uncharacterized membrane-bound protein [Function u	97.5
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	97.45
PRK10803	263	tol-pal system protein YbgF; Provisional	97.43
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.42
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.41
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.41
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.41
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.23
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	97.18
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.16
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.16
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.12
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	97.1
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	97.05
PF13512	142	TPR_18: Tetratricopeptide repeat	97.03
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	97.01
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.0
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	97.0
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	96.93
PRK15331	165	chaperone protein SicA; Provisional	96.92
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.9
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	96.89
KOG1585	308	consensus Protein required for fusion of vesicles	96.88
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.82
PRK11906	458	transcriptional regulator; Provisional	96.72
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.69
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.62
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.54
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.53
KOG4555	175	consensus TPR repeat-containing protein [Function	96.51
COG0457	291	NrfG FOG: TPR repeat [General function prediction	96.5
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	96.48
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.47
KOG1258	577	consensus mRNA processing protein [RNA processing	96.44
KOG2610	491	consensus Uncharacterized conserved protein [Funct	96.4
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.38
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	96.38
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	96.38
COG0457	291	NrfG FOG: TPR repeat [General function prediction	96.37
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	96.35
KOG1941	518	consensus Acetylcholine receptor-associated protei	96.29
KOG2610	491	consensus Uncharacterized conserved protein [Funct	96.17
PRK11906	458	transcriptional regulator; Provisional	96.15
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	96.15
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	96.15
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	96.14
COG4105	254	ComL DNA uptake lipoprotein [General function pred	96.08
COG3118	304	Thioredoxin domain-containing protein [Posttransla	96.07
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	96.04
KOG4234	271	consensus TPR repeat-containing protein [General f	96.03
PRK11619	644	lytic murein transglycosylase; Provisional	96.01
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	95.98
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	95.94
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	95.82
PF13512	142	TPR_18: Tetratricopeptide repeat	95.81
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	95.79
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.64
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.64
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	95.61
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	95.42
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	95.3
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	95.28
KOG1585	308	consensus Protein required for fusion of vesicles	95.14
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	95.11
PRK09687	280	putative lyase; Provisional	95.05
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	95.04
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	95.04
KOG4555	175	consensus TPR repeat-containing protein [Function	95.04
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	94.99
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	94.82
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	94.74
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	94.69
KOG3941	406	consensus Intermediate in Toll signal transduction	94.58
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	94.51
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	94.41
KOG3941	406	consensus Intermediate in Toll signal transduction	94.38
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	94.31
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	94.31
KOG4234	271	consensus TPR repeat-containing protein [General f	94.27
COG2976	207	Uncharacterized protein conserved in bacteria [Fun	94.2
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	94.15
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	94.14
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	94.11
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	94.08
KOG4648	536	consensus Uncharacterized conserved protein, conta	93.96
PF13428	44	TPR_14: Tetratricopeptide repeat	93.9
KOG1586	288	consensus Protein required for fusion of vesicles	93.89
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	93.87
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	93.75
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	93.75
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	93.72
COG3629	280	DnrI DNA-binding transcriptional activator of the	93.68
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	93.51
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	93.44
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	93.31
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	93.23
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	93.16
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	93.08
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	93.06
COG4105	254	ComL DNA uptake lipoprotein [General function pred	92.98
COG1747	711	Uncharacterized N-terminal domain of the transcrip	92.92
KOG1550	552	consensus Extracellular protein SEL-1 and related	92.75
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	92.58
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	92.57
PRK09687	280	putative lyase; Provisional	92.49
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	92.46
KOG4648	536	consensus Uncharacterized conserved protein, conta	92.38
smart00299	140	CLH Clathrin heavy chain repeat homology.	92.3
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	92.27
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	92.21
COG3629	280	DnrI DNA-binding transcriptional activator of the	92.16
COG3947	361	Response regulator containing CheY-like receiver a	92.15
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	92.14
PF10345	608	Cohesin_load: Cohesin loading factor; InterPro: IP	92.08
PF06552	186	TOM20_plant: Plant specific mitochondrial import r	92.05
KOG0890	2382	consensus Protein kinase of the PI-3 kinase family	91.52
KOG0545	329	consensus Aryl-hydrocarbon receptor-interacting pr	91.44
KOG1586	288	consensus Protein required for fusion of vesicles	91.37
COG1747	711	Uncharacterized N-terminal domain of the transcrip	91.35
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	91.34
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	91.27
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	91.25
PF14853	53	Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repe	91.08
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	91.06
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	90.95
PF13174	33	TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_	90.92
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	90.72
PF13431	34	TPR_17: Tetratricopeptide repeat	90.7
PRK10941	269	hypothetical protein; Provisional	90.4
smart00028	34	TPR Tetratricopeptide repeats. Repeats present in	90.3
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	90.21
KOG1308	377	consensus Hsp70-interacting protein Hip/Transient	89.84
KOG0276	794	consensus Vesicle coat complex COPI, beta' subunit	89.63
KOG4279	1226	consensus Serine/threonine protein kinase [Signal	89.18
PF13181	34	TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_	88.97
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	88.87
COG4455	273	ImpE Protein of avirulence locus involved in tempe	88.54
PRK15180	831	Vi polysaccharide biosynthesis protein TviD; Provi	87.99
KOG2396	568	consensus HAT (Half-A-TPR) repeat-containing prote	87.72
COG5159	421	RPN6 26S proteasome regulatory complex component [	87.63
PRK12798	421	chemotaxis protein; Reviewed	87.59
KOG4570	418	consensus Uncharacterized conserved protein [Funct	87.59
PF14561	90	TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S	87.54
PF04910	360	Tcf25: Transcriptional repressor TCF25; InterPro:	87.32
KOG2063	877	consensus Vacuolar assembly/sorting proteins VPS39	87.31
PF09986	214	DUF2225: Uncharacterized protein conserved in bact	87.28
KOG4642	284	consensus Chaperone-dependent E3 ubiquitin protein	87.19
KOG2066	846	consensus Vacuolar assembly/sorting protein VPS41	87.03
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	86.78
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	86.7
KOG4507	886	consensus Uncharacterized conserved protein, conta	86.56
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	86.47
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	86.08
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	85.9
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	85.89
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	85.81
KOG2471	696	consensus TPR repeat-containing protein [General f	85.69
KOG2063	877	consensus Vacuolar assembly/sorting proteins VPS39	85.42
PF07721	26	TPR_4: Tetratricopeptide repeat; InterPro: IPR0117	85.07
smart00386	33	HAT HAT (Half-A-TPR) repeats. Present in several R	84.88
TIGR03504	44	FimV_Cterm FimV C-terminal domain. This protein is	83.68
smart00028	34	TPR Tetratricopeptide repeats. Repeats present in	82.97
PRK11619	644	lytic murein transglycosylase; Provisional	82.72
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	82.59
PRK13800	897	putative oxidoreductase/HEAT repeat-containing pro	82.2
PF13929	292	mRNA_stabil: mRNA stabilisation	82.08
PF04097	613	Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic9	81.11
KOG2300	629	consensus Uncharacterized conserved protein [Funct	80.93
KOG1498	439	consensus 26S proteasome regulatory complex, subun	80.25

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=1.4e-72  Score=577.61  Aligned_cols=480  Identities=31%  Similarity=0.585  Sum_probs=459.6

Q ss_pred             cccchhhhhh---chhhHHHHHHHHhhhcCCC--CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCCCCCceehHHHHH
Q 011249            2 TSKYLVPRSK---TFNQLKQVHSYLLKTLTKP--HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIR   76 (490)
Q Consensus         2 ~~~~l~~~~~---~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~l~~   76 (490)
                      ||..++++|+   ++..+.++|..+.+   .|  +++.  +++.|+.+|++.|+ +++|.++|++|+.||. .+||++|.
T Consensus       189 t~~~ll~~~~~~~~~~~~~~~~~~~~~---~g~~~~~~--~~n~Li~~y~k~g~-~~~A~~lf~~m~~~d~-~s~n~li~  261 (857)
T PLN03077        189 TFPCVLRTCGGIPDLARGREVHAHVVR---FGFELDVD--VVNALITMYVKCGD-VVSARLVFDRMPRRDC-ISWNAMIS  261 (857)
T ss_pred             HHHHHHHHhCCccchhhHHHHHHHHHH---cCCCcccc--hHhHHHHHHhcCCC-HHHHHHHHhcCCCCCc-chhHHHHH
Confidence            5677888876   45678899999999   77  8899  99999999999999 9999999999999999 99999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChH---------------------HHHHHHHHhcCCHHH
Q 011249           77 NHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLL---------------------EAVICGYTKIGLMDD  135 (490)
Q Consensus        77 ~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~---------------------~~l~~~~~~~g~~~~  135 (490)
                      +|++.|++++|+++|++|.+.|+.||..||+.++.+|++.++..                     ++++.+|++.|++++
T Consensus       262 ~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~  341 (857)
T PLN03077        262 GYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGE  341 (857)
T ss_pred             HHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHHHHHHHHHhcCCHHH
Confidence            99999999999999999999999999999999999999988765                     789999999999999


Q ss_pred             HHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhcc----CC---------------------------------
Q 011249          136 AQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTE----KN---------------------------------  178 (490)
Q Consensus       136 A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~---------------------------------  178 (490)
                      |.++|++|.+||..+||.++.+|++.|++++|+++|++|.+    ||                                 
T Consensus       342 A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~a~~l~~~~~~~g~~  421 (857)
T PLN03077        342 AEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKLHELAERKGLI  421 (857)
T ss_pred             HHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHHHHHHHHHHHHhCCC
Confidence            99999999999999999999999999999999999999953    33                                 


Q ss_pred             --chhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHh
Q 011249          179 --SVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACT  256 (490)
Q Consensus       179 --~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~  256 (490)
                        ..+|+.|+.+|++.|++++|.++|++|.++|..+|+.++.+|.+.|+.++|+++|++|.. ++.||..||..++.+|+
T Consensus       422 ~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~  500 (857)
T PLN03077        422 SYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACA  500 (857)
T ss_pred             cchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHh
Confidence              445678888899999999999999999999999999999999999999999999999986 58999999999999999


Q ss_pred             ccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHH
Q 011249          257 QLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLK  336 (490)
Q Consensus       257 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  336 (490)
                      +.|+++.+.+++..+.+.|+.++..++++|+.+|+++|++++|.++|+.+ .+|..+|+++|.+|++.|+.++|+++|++
T Consensus       501 ~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~-~~d~~s~n~lI~~~~~~G~~~~A~~lf~~  579 (857)
T PLN03077        501 RIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGSMAVELFNR  579 (857)
T ss_pred             hhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhc-CCChhhHHHHHHHHHHcCCHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999 89999999999999999999999999999


Q ss_pred             HHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhh
Q 011249          337 MRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGT  416 (490)
Q Consensus       337 ~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~  416 (490)
                      |.+.|+.||..||+.++.+|.+.|++++|.++|+.|.+.+|+.|+..+|+.++++|.+.|++++|.+++++|+.+|+..+
T Consensus       580 M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~~~pd~~~  659 (857)
T PLN03077        580 MVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAV  659 (857)
T ss_pred             HHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHCCCCCCHHH
Confidence            99999999999999999999999999999999999996679999999999999999999999999999999998999999


Q ss_pred             HHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccccCCCccccCC
Q 011249          417 WGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWISS  490 (490)
Q Consensus       417 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~  490 (490)
                      |++|+.+|..+|+.+.++...+++.+++|+++..|..|+++|...|+|++|.++.+.|++.|++++||+|||++
T Consensus       660 ~~aLl~ac~~~~~~e~~e~~a~~l~~l~p~~~~~y~ll~n~ya~~g~~~~a~~vr~~M~~~g~~k~~g~s~ie~  733 (857)
T PLN03077        660 WGALLNACRIHRHVELGELAAQHIFELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEV  733 (857)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHhhCCCCcchHHHHHHHHHHCCChHHHHHHHHHHHHcCCCCCCCccEEEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999985

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

Probab=100.00  E-value=9.2e-69  Score=536.95  Aligned_cols=442  Identities=31%  Similarity=0.525  Sum_probs=415.1

Q ss_pred             CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC-----CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhh
Q 011249           31 HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP-----KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFT  105 (490)
Q Consensus        31 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~  105 (490)
                      .+..  .|+.++..|.+.|+ +++|.++|+.|.     .|+. .+|+.++.+|.+.++++.+.+++..|.+.|+.||..+
T Consensus        85 ~~~~--~~~~~i~~l~~~g~-~~~Al~~f~~m~~~~~~~~~~-~t~~~ll~a~~~~~~~~~a~~l~~~m~~~g~~~~~~~  160 (697)
T PLN03081         85 KSGV--SLCSQIEKLVACGR-HREALELFEILEAGCPFTLPA-STYDALVEACIALKSIRCVKAVYWHVESSGFEPDQYM  160 (697)
T ss_pred             CCce--eHHHHHHHHHcCCC-HHHHHHHHHHHHhcCCCCCCH-HHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCcchHH
Confidence            4556  78999999999999 999999999885     3455 8999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhcc---------
Q 011249          106 FSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTE---------  176 (490)
Q Consensus       106 ~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---------  176 (490)
                      |+.++..              |++.|++++|.++|++|.+||..+||.++.+|++.|++++|+++|++|.+         
T Consensus       161 ~n~Li~~--------------y~k~g~~~~A~~lf~~m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t  226 (697)
T PLN03081        161 MNRVLLM--------------HVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRT  226 (697)
T ss_pred             HHHHHHH--------------HhcCCCHHHHHHHHhcCCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhh
Confidence            9998886              66777777777777777777777777777777777777777777777742         


Q ss_pred             ------------------------------CCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCCh
Q 011249          177 ------------------------------KNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYA  226 (490)
Q Consensus       177 ------------------------------~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~  226 (490)
                                                    +|..+|+.++.+|++.|++++|.++|++|.++|..+||.++.+|++.|++
T Consensus       227 ~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~  306 (697)
T PLN03081        227 FVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYS  306 (697)
T ss_pred             HHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHHHHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCH
Confidence                                          35667789999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcc
Q 011249          227 KAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRI  306 (490)
Q Consensus       227 ~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~  306 (490)
                      ++|+++|++|.+.|+.||..||+.++.+|++.|++++|.+++..+.+.|++|+..++++|+.+|++.|++++|.++|++|
T Consensus       307 ~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m  386 (697)
T PLN03081        307 EEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRM  386 (697)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHH
Q 011249          307 KNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLT  386 (490)
Q Consensus       307 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  386 (490)
                      .++|..+||+||.+|++.|+.++|.++|++|.+.|+.||..||+.++.+|.+.|.+++|.++|+.|.+.+|+.|+..+|+
T Consensus       387 ~~~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        387 PRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYA  466 (697)
T ss_pred             CCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchH
Confidence            99999999999999999999999999999999999999999999999999999999999999999998779999999999


Q ss_pred             HHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcch
Q 011249          387 CMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKD  466 (490)
Q Consensus       387 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  466 (490)
                      .++++|++.|++++|.++++++...|+..+|++++.+|...|+++.|..+++++.+.+|+++..|..|+++|.+.|+|++
T Consensus       467 ~li~~l~r~G~~~eA~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L~~~y~~~G~~~~  546 (697)
T PLN03081        467 CMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAE  546 (697)
T ss_pred             hHHHHHHhcCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCcchHHHHHHHHhCCCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhcccccCCCccccCC
Q 011249          467 SEIVKMMISETEKKKSPGCSWISS  490 (490)
Q Consensus       467 A~~~~~~~~~~~~~~~~~~~~~~~  490 (490)
                      |.++++.|.+.|+++.||+|||++
T Consensus       547 A~~v~~~m~~~g~~k~~g~s~i~~  570 (697)
T PLN03081        547 AAKVVETLKRKGLSMHPACTWIEV  570 (697)
T ss_pred             HHHHHHHHHHcCCccCCCeeEEEE
Confidence            999999999999999999999974

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=5.6e-65  Score=521.63  Aligned_cols=468  Identities=28%  Similarity=0.398  Sum_probs=425.7

Q ss_pred             ccchhhhhh---chhhHHHHHHHHhhhcCCC--CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCCCCCceehHHHHHH
Q 011249            3 SKYLVPRSK---TFNQLKQVHSYLLKTLTKP--HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRN   77 (490)
Q Consensus         3 ~~~l~~~~~---~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~l~~~   77 (490)
                      +..+++.|.   .++.+.++|.++.+   .+  ++..  +++.|+.+|++.|+ ++.|+++|++|+.|+. .+||++|.+
T Consensus        89 ~~~ll~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~--~~n~li~~~~~~g~-~~~A~~~f~~m~~~d~-~~~n~li~~  161 (857)
T PLN03077         89 YVALFRLCEWKRAVEEGSRVCSRALS---SHPSLGVR--LGNAMLSMFVRFGE-LVHAWYVFGKMPERDL-FSWNVLVGG  161 (857)
T ss_pred             HHHHHHHHhhCCCHHHHHHHHHHHHH---cCCCCCch--HHHHHHHHHHhCCC-hHHHHHHHhcCCCCCe-eEHHHHHHH
Confidence            445566653   56778999999998   66  7778  99999999999999 9999999999999999 999999999


Q ss_pred             HHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChH---------------------HHHHHHHHhcCCHHHH
Q 011249           78 HVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLL---------------------EAVICGYTKIGLMDDA  136 (490)
Q Consensus        78 ~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~---------------------~~l~~~~~~~g~~~~A  136 (490)
                      |++.|++++|+++|++|...|+.||..||+.++.+|+..+++.                     ++++.+|++.|++++|
T Consensus       162 ~~~~g~~~~A~~~f~~M~~~g~~Pd~~t~~~ll~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A  241 (857)
T PLN03077        162 YAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVKCGDVVSA  241 (857)
T ss_pred             HHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHhCCccchhhHHHHHHHHHHcCCCcccchHhHHHHHHhcCCCHHHH
Confidence            9999999999999999999999999999999999998876653                     7899999999999999


Q ss_pred             HHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhcc---------------------------------------C
Q 011249          137 QRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTE---------------------------------------K  177 (490)
Q Consensus       137 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---------------------------------------~  177 (490)
                      .++|++|.+||..+||.++.+|++.|++++|+++|++|.+                                       |
T Consensus       242 ~~lf~~m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~  321 (857)
T PLN03077        242 RLVFDRMPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAV  321 (857)
T ss_pred             HHHHhcCCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCcc
Confidence            9999999999999999999999999999999999999963                                       3


Q ss_pred             CchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhc
Q 011249          178 NSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQ  257 (490)
Q Consensus       178 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~  257 (490)
                      |..+|+.++.+|++.|++++|.++|++|.+||..+|+.++.+|.+.|++++|+++|++|.+.|+.||..||..++.+|++
T Consensus       322 d~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~  401 (857)
T PLN03077        322 DVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACAC  401 (857)
T ss_pred             chHHHHHHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhc
Confidence            56677888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHH
Q 011249          258 LGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKM  337 (490)
Q Consensus       258 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  337 (490)
                      .|+++.|.++++.+.+.|+.++..++++|+.+|++.|++++|.++|++|.++|..+|+.++.+|++.|+.++|+.+|++|
T Consensus       402 ~g~~~~a~~l~~~~~~~g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m  481 (857)
T PLN03077        402 LGDLDVGVKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLNNRCFEALIFFRQM  481 (857)
T ss_pred             cchHHHHHHHHHHHHHhCCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhH
Q 011249          338 RNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTW  417 (490)
Q Consensus       338 ~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  417 (490)
                      .. ++.||..||..++.+|++.|.++.+.+++..+.+. |+.++..+++.|+++|.++|++++|.++|+.+  .+|..+|
T Consensus       482 ~~-~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~-g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~--~~d~~s~  557 (857)
T PLN03077        482 LL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRT-GIGFDGFLPNALLDLYVRCGRMNYAWNQFNSH--EKDVVSW  557 (857)
T ss_pred             Hh-CCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHh-CCCccceechHHHHHHHHcCCHHHHHHHHHhc--CCChhhH
Confidence            86 59999999999999999999999999999999985 99888888888888888888888888888877  6788888


Q ss_pred             HHHHHHHhhhCChHHHHHHHHHHHhcC--CCCCchHHHHHHHHHhcCCcchHHHHHHHhh-hcccccC
Q 011249          418 GALLGACKVHVNAELGEIAARHLLELG--PEKTGNSALLANIYASMGKWKDSEIVKMMIS-ETEKKKS  482 (490)
Q Consensus       418 ~~l~~~~~~~g~~~~a~~~~~~~~~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~~  482 (490)
                      ++++.+|.+.|+.++|.++|++|.+.+  |+ ..+|..++.+|.+.|++++|.++|+.|. +.|+.|+
T Consensus       558 n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd-~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~  624 (857)
T PLN03077        558 NILLTGYVAHGKGSMAVELFNRMVESGVNPD-EVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPN  624 (857)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHcCCCCC-cccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCc
Confidence            888888888888888888888887754  44 5567777778888888888888888887 4566554

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=1.1e-60  Score=481.19  Aligned_cols=466  Identities=16%  Similarity=0.206  Sum_probs=419.5

Q ss_pred             hhhchhhHHHHHHHHhhhcCCC---CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCCCCCceehHHHHHHHHhcCChh
Q 011249            9 RSKTFNQLKQVHSYLLKTLTKP---HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFR   85 (490)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~   85 (490)
                      .+|+++.+..+++.+.+   .+   ++..  .++.++..|.+.|. +++|..+|+.|+.|+. .+|+.++.+|++.|+++
T Consensus       382 r~G~l~eAl~Lfd~M~~---~gvv~~~~v--~~~~li~~~~~~g~-~~eAl~lf~~M~~pd~-~Tyn~LL~a~~k~g~~e  454 (1060)
T PLN03218        382 RDGRIKDCIDLLEDMEK---RGLLDMDKI--YHAKFFKACKKQRA-VKEAFRFAKLIRNPTL-STFNMLMSVCASSQDID  454 (1060)
T ss_pred             HCcCHHHHHHHHHHHHh---CCCCCchHH--HHHHHHHHHHHCCC-HHHHHHHHHHcCCCCH-HHHHHHHHHHHhCcCHH
Confidence            34888999999999998   66   5666  88889999999999 9999999999999888 99999999999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChH---------------------HHHHHHHHhcCCHHHHHHHHhhcC
Q 011249           86 QSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLL---------------------EAVICGYTKIGLMDDAQRLFDSMA  144 (490)
Q Consensus        86 ~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~---------------------~~l~~~~~~~g~~~~A~~~~~~~~  144 (490)
                      .|.++|+.|.+.|+.||..+|+.+|.+|++.|+..                     +.++.+|++.|++++|.++|+.|.
T Consensus       455 ~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~  534 (1060)
T PLN03218        455 GALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAYGIMR  534 (1060)
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            99999999999999999999999999999998876                     678999999999999999999996


Q ss_pred             C----CCHhHHHHHHHHHHhCCChHHHHHHHHHhc------cCCchhHHHHHHHHHhcCChhHHHHHHhhcCC----CCH
Q 011249          145 E----RNVISWSAMVAGYANCGNMKAAKEFYDRMT------EKNSVTWVAMIAGYGKCGEVREAKKVFDEISE----PDA  210 (490)
Q Consensus       145 ~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~  210 (490)
                      +    ||..+|+.++.+|++.|++++|.++|++|.      .||..+|+.++.+|++.|++++|.++|+.|.+    |+.
T Consensus       535 ~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k~G~ldeA~elf~~M~e~gi~p~~  614 (1060)
T PLN03218        535 SKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRAKEVYQMIHEYNIKGTP  614 (1060)
T ss_pred             HcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCh
Confidence            4    899999999999999999999999999995      36889999999999999999999999999975    788


Q ss_pred             HhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 011249          211 SCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMH  290 (490)
Q Consensus       211 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  290 (490)
                      .+|+.+|.+|++.|++++|.++|++|.+.|+.||..+|+.++.+|++.|++++|.++++.|.+.|++|+..+|+.++.+|
T Consensus       615 ~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~l~~eM~k~G~~pd~~tynsLI~ay  694 (1060)
T PLN03218        615 EVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGAC  694 (1060)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhcCChHHHHHHHhccc----CCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHH
Q 011249          291 SKCGYLDLAWREFSRIK----NKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGC  366 (490)
Q Consensus       291 ~~~~~~~~A~~~~~~~~----~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~  366 (490)
                      ++.|++++|.++|++|.    .||..+|+.||.+|++.|++++|.++|++|.+.|+.||..||+.++.+|++.|++++|.
T Consensus       695 ~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~  774 (1060)
T PLN03218        695 SNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLSEMKRLGLCPNTITYSILLVASERKDDADVGL  774 (1060)
T ss_pred             HhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHH
Confidence            99999999999999985    48999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHcCCCCCchHHHHHHHHHhh----c-------------------CChHHHHHHHHhcc---CCCChhhHHHH
Q 011249          367 KQFELMTRVFGIKPLTEHLTCMVDLLGR----S-------------------GQLEKAHSLIMDYK---DFCDAGTWGAL  420 (490)
Q Consensus       367 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~-------------------g~~~~A~~~~~~~~---~~~~~~~~~~l  420 (490)
                      ++++.|.+. |+.|+..+|+.++..|.+    +                   +..++|..+|++|.   ..|+..+|+.+
T Consensus       775 ~l~~~M~k~-Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n~w~~~Al~lf~eM~~~Gi~Pd~~T~~~v  853 (1060)
T PLN03218        775 DLLSQAKED-GIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIENKWTSWALMVYRETISAGTLPTMEVLSQV  853 (1060)
T ss_pred             HHHHHHHHc-CCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccccccchHHHHHHHHHHHHHCCCCCCHHHHHHH
Confidence            999999985 999999999998876432    1                   12367889999888   67999999999


Q ss_pred             HHHHhhhCChHHHHHHHHHHHhc-CCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccccCCC
Q 011249          421 LGACKVHVNAELGEIAARHLLEL-GPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPG  484 (490)
Q Consensus       421 ~~~~~~~g~~~~a~~~~~~~~~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~  484 (490)
                      +.++...+..+.+..+++.+... .+.+...|..|+..+.+.  .++|..+++.|...|+.|+-.
T Consensus       854 L~cl~~~~~~~~~~~m~~~m~~~~~~~~~~~y~~Li~g~~~~--~~~A~~l~~em~~~Gi~p~~~  916 (1060)
T PLN03218        854 LGCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGFGEY--DPRAFSLLEEAASLGVVPSVS  916 (1060)
T ss_pred             HHHhcccccHHHHHHHHHHhccCCCCcchhhhHHHHHhhccC--hHHHHHHHHHHHHcCCCCCcc
Confidence            97777888888888888876643 356678899999887322  358999999999999987754

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=2.7e-57  Score=456.72  Aligned_cols=431  Identities=16%  Similarity=0.229  Sum_probs=397.7

Q ss_pred             CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCCCCC----ceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhH
Q 011249           31 HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKT----QFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTF  106 (490)
Q Consensus        31 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~  106 (490)
                      ++..  .+..++..+++.|+ +++|+++|++|+.++.    ...++.++..|.+.|..++|..+|+.|..    ||..+|
T Consensus       368 ~~~~--~~~~~y~~l~r~G~-l~eAl~Lfd~M~~~gvv~~~~v~~~~li~~~~~~g~~~eAl~lf~~M~~----pd~~Ty  440 (1060)
T PLN03218        368 RKSP--EYIDAYNRLLRDGR-IKDCIDLLEDMEKRGLLDMDKIYHAKFFKACKKQRAVKEAFRFAKLIRN----PTLSTF  440 (1060)
T ss_pred             CCch--HHHHHHHHHHHCcC-HHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHCCCHHHHHHHHHHcCC----CCHHHH
Confidence            6677  88999999999999 9999999999986544    13566778889999999999999999975    999999


Q ss_pred             HHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC----CCHhHHHHHHHHHHhCCChHHHHHHHHHhc----cCC
Q 011249          107 SSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE----RNVISWSAMVAGYANCGNMKAAKEFYDRMT----EKN  178 (490)
Q Consensus       107 ~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~----~~~  178 (490)
                      +.+|.+              |++.|+++.|.++|+.|.+    ||..+|+.++.+|++.|++++|.++|++|.    .||
T Consensus       441 n~LL~a--------------~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~Pd  506 (1060)
T PLN03218        441 NMLMSV--------------CASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEAN  506 (1060)
T ss_pred             HHHHHH--------------HHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCC
Confidence            999987              6788999999999999975    899999999999999999999999999998    479


Q ss_pred             chhHHHHHHHHHhcCChhHHHHHHhhcCC----CCHHhHHHHHHHHHhcCChHHHHHHHHHHHH--cCcccChhhHHHHH
Q 011249          179 SVTWVAMIAGYGKCGEVREAKKVFDEISE----PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQ--ENVRISEVAMVGAI  252 (490)
Q Consensus       179 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~p~~~~~~~l~  252 (490)
                      ..+|+.+|.+|++.|++++|.++|++|.+    ||..+|+.++.+|++.|++++|.++|++|..  .|+.||..+|+.++
T Consensus       507 vvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI  586 (1060)
T PLN03218        507 VHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALM  586 (1060)
T ss_pred             HHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHH
Confidence            99999999999999999999999999964    9999999999999999999999999999986  67899999999999


Q ss_pred             HHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC----CChhHHHHHHHHHHhcCChH
Q 011249          253 SACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN----KDVISYSSMITAFADHGKSQ  328 (490)
Q Consensus       253 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~  328 (490)
                      .+|++.|++++|.++|+.|.+.+++|+..+|+.++.+|++.|++++|.++|++|.+    ||..+|+.++.+|++.|+++
T Consensus       587 ~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~e  666 (1060)
T PLN03218        587 KACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLD  666 (1060)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHH
Confidence            99999999999999999999999999999999999999999999999999999985    79999999999999999999


Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhc
Q 011249          329 EALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDY  408 (490)
Q Consensus       329 ~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  408 (490)
                      +|.+++++|.+.|+.||..+|+.++.+|++.|++++|.++|++|.+. ++.|+..+|+.|+.+|++.|++++|.++|++|
T Consensus       667 eA~~l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~-g~~PdvvtyN~LI~gy~k~G~~eeAlelf~eM  745 (1060)
T PLN03218        667 KAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSI-KLRPTVSTMNALITALCEGNQLPKALEVLSEM  745 (1060)
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999985 99999999999999999999999999999998


Q ss_pred             c---CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC-CCCCchHHHHHHHHH----hcC------------------
Q 011249          409 K---DFCDAGTWGALLGACKVHVNAELGEIAARHLLELG-PEKTGNSALLANIYA----SMG------------------  462 (490)
Q Consensus       409 ~---~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-p~~~~~~~~l~~~~~----~~g------------------  462 (490)
                      .   ..||..+|+.++.+|.+.|++++|.++++++.+.+ ..+..+|..++.++.    +++                  
T Consensus       746 ~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~~~n  825 (1060)
T PLN03218        746 KRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQIEN  825 (1060)
T ss_pred             HHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccccccc
Confidence            7   67999999999999999999999999999999876 334677888776543    221                  


Q ss_pred             -CcchHHHHHHHhhhcccccCC
Q 011249          463 -KWKDSEIVKMMISETEKKKSP  483 (490)
Q Consensus       463 -~~~~A~~~~~~~~~~~~~~~~  483 (490)
                       ..++|..+|++|.+.|+.|+.
T Consensus       826 ~w~~~Al~lf~eM~~~Gi~Pd~  847 (1060)
T PLN03218        826 KWTSWALMVYRETISAGTLPTM  847 (1060)
T ss_pred             chHHHHHHHHHHHHHCCCCCCH
Confidence             236799999999999998774

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

Probab=100.00  E-value=2.2e-56  Score=447.71  Aligned_cols=454  Identities=19%  Similarity=0.235  Sum_probs=404.6

Q ss_pred             cccchhhhhh---chhhHHHHHHHHhhhcCCC--CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCCCCCceehHHHHH
Q 011249            2 TSKYLVPRSK---TFNQLKQVHSYLLKTLTKP--HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIR   76 (490)
Q Consensus         2 ~~~~l~~~~~---~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~l~~   76 (490)
                      ||..++++|.   +.+.+.++|..+.+   .|  |++.  +++.|+++|++.|+ +++|.++|++|+.|+. .+||+++.
T Consensus       125 t~~~ll~a~~~~~~~~~a~~l~~~m~~---~g~~~~~~--~~n~Li~~y~k~g~-~~~A~~lf~~m~~~~~-~t~n~li~  197 (697)
T PLN03081        125 TYDALVEACIALKSIRCVKAVYWHVES---SGFEPDQY--MMNRVLLMHVKCGM-LIDARRLFDEMPERNL-ASWGTIIG  197 (697)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHHH---hCCCcchH--HHHHHHHHHhcCCC-HHHHHHHHhcCCCCCe-eeHHHHHH
Confidence            4556666664   56678999999999   77  8899  99999999999999 9999999999999999 99999999


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC----CCHhHHH
Q 011249           77 NHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE----RNVISWS  152 (490)
Q Consensus        77 ~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~~~~~~  152 (490)
                      +|++.|++++|+++|++|.+.|+.|+..+|+.++.+              +++.|..+.+.+++..+.+    +|..+|+
T Consensus       198 ~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a--------------~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n  263 (697)
T PLN03081        198 GLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRA--------------SAGLGSARAGQQLHCCVLKTGVVGDTFVSC  263 (697)
T ss_pred             HHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHH--------------HhcCCcHHHHHHHHHHHHHhCCCccceeHH
Confidence            999999999999999999999999999999999987              4667888889988877754    7999999


Q ss_pred             HHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCC----CCHHhHHHHHHHHHhcCChHH
Q 011249          153 AMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISE----PDASCWAAMTVCYVQNGYAKA  228 (490)
Q Consensus       153 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~~~~~~l~~~~~~~g~~~~  228 (490)
                      .|+.+|++.|++++|.++|++|.++|..+|+.++.+|++.|++++|.++|++|.+    ||..+|+.++.+|++.|++++
T Consensus       264 ~Li~~y~k~g~~~~A~~vf~~m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~  343 (697)
T PLN03081        264 ALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEH  343 (697)
T ss_pred             HHHHHHHHCCCHHHHHHHHHhCCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHH
Confidence            9999999999999999999999999999999999999999999999999999953    999999999999999999999


Q ss_pred             HHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC
Q 011249          229 AIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN  308 (490)
Q Consensus       229 A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  308 (490)
                      |.+++..|.+.|+.||..+++.++..|++.|++++|.++|+.|.    .+|..+||+++.+|++.|+.++|.++|++|.+
T Consensus       344 a~~i~~~m~~~g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~----~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~  419 (697)
T PLN03081        344 AKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMP----RKNLISWNALIAGYGNHGRGTKAVEMFERMIA  419 (697)
T ss_pred             HHHHHHHHHHhCCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC----CCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999985    47889999999999999999999999999975


Q ss_pred             ----CChhHHHHHHHHHHhcCChHHHHHHHHHHHH-cCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCch
Q 011249          309 ----KDVISYSSMITAFADHGKSQEALDMFLKMRN-EGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTE  383 (490)
Q Consensus       309 ----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  383 (490)
                          ||..||+.++.+|.+.|..++|.++|+.|.+ .|+.|+..+|+.++.+|.+.|++++|.++++++    +..|+..
T Consensus       420 ~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~----~~~p~~~  495 (697)
T PLN03081        420 EGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRA----PFKPTVN  495 (697)
T ss_pred             hCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHC----CCCCCHH
Confidence                8999999999999999999999999999986 699999999999999999999999999998876    7889999


Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCC--CCCchHHHH-----
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGP--EKTGNSALL-----  454 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p--~~~~~~~~l-----  454 (490)
                      +|+.++.+|...|+++.|..+++++. ..| +..+|..+++.|.+.|++++|.+++++|.+.+-  .....|..+     
T Consensus       496 ~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g~~k~~g~s~i~~~~~~~  575 (697)
T PLN03081        496 MWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDH  575 (697)
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHcCCccCCCeeEEEECCeEE
Confidence            99999999999999999999998876 334 567999999999999999999999999998651  111111000     


Q ss_pred             ---HH--HH-HhcCCcchHHHHHHHhhhcccccCCC
Q 011249          455 ---AN--IY-ASMGKWKDSEIVKMMISETEKKKSPG  484 (490)
Q Consensus       455 ---~~--~~-~~~g~~~~A~~~~~~~~~~~~~~~~~  484 (490)
                         +.  .+ ....-++...++..+|.+.|..+++.
T Consensus       576 ~f~~~d~~h~~~~~i~~~l~~l~~~~~~~gy~~~~~  611 (697)
T PLN03081        576 SFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEEN  611 (697)
T ss_pred             EEccCCCCCccHHHHHHHHHHHHHHHHHcCCCCCcc
Confidence               00  00 00112445667788888888877654

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

Probab=100.00  E-value=4.8e-31  Score=277.01  Aligned_cols=459  Identities=13%  Similarity=0.054  Sum_probs=256.9

Q ss_pred             hhhhhchhhHHHHHHHHhhhcCCC-CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCC
Q 011249            7 VPRSKTFNQLKQVHSYLLKTLTKP-HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAH   83 (490)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~   83 (490)
                      +...|+++.+...++...+   .. .++.  .+..+...+...|+ +++|.+.|+++.  .|+.......++..+.+.|+
T Consensus       373 ~~~~g~~~~A~~~~~~~~~---~~~~~~~--~~~~l~~~~~~~~~-~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~  446 (899)
T TIGR02917       373 YLALGDFEKAAEYLAKATE---LDPENAA--ARTQLGISKLSQGD-PSEAIADLETAAQLDPELGRADLLLILSYLRSGQ  446 (899)
T ss_pred             HHHCCCHHHHHHHHHHHHh---cCCCCHH--HHHHHHHHHHhCCC-hHHHHHHHHHHHhhCCcchhhHHHHHHHHHhcCC
Confidence            3344555555555555544   33 3444  45555555555555 555555555443  12221333334444444444


Q ss_pred             hhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChH--------------------HHHHHHHHhcCCHHHHHHHHhhc
Q 011249           84 FRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLL--------------------EAVICGYTKIGLMDDAQRLFDSM  143 (490)
Q Consensus        84 ~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~--------------------~~l~~~~~~~g~~~~A~~~~~~~  143 (490)
                      +++|..+++.+... .+++..++..+...+...++..                    ..+...+...|++++|...|+++
T Consensus       447 ~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~  525 (899)
T TIGR02917       447 FDKALAAAKKLEKK-QPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIEPDFFPAAANLARIDIQEGNPDDAIQRFEKV  525 (899)
T ss_pred             HHHHHHHHHHHHHh-CCCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            44444444444432 1222333333333333333332                    22344556667777777777666


Q ss_pred             CC---CCHhHHHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHH
Q 011249          144 AE---RNVISWSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWA  214 (490)
Q Consensus       144 ~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~  214 (490)
                      .+   .+..++..+...+.+.|++++|...++++.+.   +...+..++..+...|++++|..+++.+.+   .+...|.
T Consensus       526 ~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~  605 (899)
T TIGR02917       526 LTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPDSPEAWL  605 (899)
T ss_pred             HHhCcCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHH
Confidence            54   24556666666666667777777766666532   444555666666666666666666666543   3455666


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcC
Q 011249          215 AMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCG  294 (490)
Q Consensus       215 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  294 (490)
                      .++.++...|++++|+..|+++.+.. +.+...+..+..++...|++++|..+++.+.+.. +.+...+..++..+...|
T Consensus       606 ~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~  683 (899)
T TIGR02917       606 MLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLAQLLLAAK  683 (899)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcC
Confidence            66666666666666666666666543 2244555666666666666666666666666554 444555666666666666


Q ss_pred             ChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHH
Q 011249          295 YLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFEL  371 (490)
Q Consensus       295 ~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~  371 (490)
                      ++++|.++++.+.+   .+...+..+...+...|++++|...|+++...  .|+..++..++.++...|++++|.+.+++
T Consensus       684 ~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  761 (899)
T TIGR02917       684 RTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKR--APSSQNAIKLHRALLASGNTAEAVKTLEA  761 (899)
T ss_pred             CHHHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            66666666666554   24445555666666666666666666666653  34445555555566666666666666666


Q ss_pred             HHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          372 MTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       372 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                      +.+  ..+.+...+..++..|...|++++|.+.|+++.  .++++.++..++..+...|+ .+|+..++++.+..|+++.
T Consensus       762 ~l~--~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~~~~~~  838 (899)
T TIGR02917       762 WLK--THPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPDNAVVLNNLAWLYLELKD-PRALEYAEKALKLAPNIPA  838 (899)
T ss_pred             HHH--hCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhCCCCcH
Confidence            655  334445555566666666666666666665554  33344555555555555555 5566666666665566555


Q ss_pred             hHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          450 NSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       450 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .+..++.++...|++++|.++++++.+.++
T Consensus       839 ~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~  868 (899)
T TIGR02917       839 ILDTLGWLLVEKGEADRALPLLRKAVNIAP  868 (899)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            555566666666666666666665555443

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=100.00  E-value=6e-31  Score=276.25  Aligned_cols=431  Identities=12%  Similarity=0.030  Sum_probs=207.3

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhc
Q 011249           37 YAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACA  114 (490)
Q Consensus        37 ~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~  114 (490)
                      ....++..+.+.|+ +++|.++++++.  .|+....|+.+...+...|++++|.+.|+++.+.. +.+...+..+...+.
T Consensus       433 ~~~~l~~~~~~~~~-~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~  510 (899)
T TIGR02917       433 ADLLLILSYLRSGQ-FDKALAAAKKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSIE-PDFFPAAANLARIDI  510 (899)
T ss_pred             hHHHHHHHHHhcCC-HHHHHHHHHHHHHhCCCCcHHHHHHHHHHHhCCCHHHHHHHHHHHHhhC-CCcHHHHHHHHHHHH
Confidence            33444455555555 555555555443  22222445555555555555555555555554431 111222222333333


Q ss_pred             CCCChH--------------------HHHHHHHHhcCCHHHHHHHHhhcCC---CCHhHHHHHHHHHHhCCChHHHHHHH
Q 011249          115 RVPSLL--------------------EAVICGYTKIGLMDDAQRLFDSMAE---RNVISWSAMVAGYANCGNMKAAKEFY  171 (490)
Q Consensus       115 ~~~~~~--------------------~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~  171 (490)
                      ..|+..                    ..+...+.+.|+.++|..+++++.+   .+...+..++..+...|++++|..++
T Consensus       511 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~  590 (899)
T TIGR02917       511 QEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAIL  590 (899)
T ss_pred             HCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchhHHHHHHHHHHHCCCHHHHHHHH
Confidence            333322                    2234444455555555555555432   13334444555555555555555555


Q ss_pred             HHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccCh
Q 011249          172 DRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISE  245 (490)
Q Consensus       172 ~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~  245 (490)
                      +++.+.   +...|..++.++...|++++|...|+++.+   .+...+..++.++...|++++|...|+++.+.. +.+.
T Consensus       591 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~  669 (899)
T TIGR02917       591 NEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNT  669 (899)
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCH
Confidence            555421   344455555555555555555555554432   233444555555555555555555555554432 1234


Q ss_pred             hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--CChhHHHHHHHHHHh
Q 011249          246 VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KDVISYSSMITAFAD  323 (490)
Q Consensus       246 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~  323 (490)
                      .++..++..+...|++++|..+++.+.+.. +.+...+..+...+...|++++|.+.|+.+..  |+..++..++.++.+
T Consensus       670 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~  748 (899)
T TIGR02917       670 EAQIGLAQLLLAAKRTESAKKIAKSLQKQH-PKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLA  748 (899)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHH
Confidence            444555555555555555555555554443 33444444455555555555555555555433  333444445555555


Q ss_pred             cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHH
Q 011249          324 HGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHS  403 (490)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  403 (490)
                      .|++++|...++++.+.. +.+...+..+...|...|++++|..+|+++.+  ..++++..+..++..+...|+ .+|+.
T Consensus       749 ~g~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~--~~p~~~~~~~~l~~~~~~~~~-~~A~~  824 (899)
T TIGR02917       749 SGNTAEAVKTLEAWLKTH-PNDAVLRTALAELYLAQKDYDKAIKHYRTVVK--KAPDNAVVLNNLAWLYLELKD-PRALE  824 (899)
T ss_pred             CCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHhcCc-HHHHH
Confidence            555555555555555431 22334444455555555555555555555554  223344445555555555555 44555


Q ss_pred             HHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          404 LIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       404 ~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      +++++.  .+.++..+..+...+...|++++|.+.++++++.+|.++.++..++.++.+.|++++|.+++++|+
T Consensus       825 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  898 (899)
T TIGR02917       825 YAEKALKLAPNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPEAAAIRYHLALALLATGRKAEARKELDKLL  898 (899)
T ss_pred             HHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence            554443  222333444445555555555555555555555555555555555555555555555555555543

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.

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.96  E-value=1.3e-24  Score=229.18  Aligned_cols=460  Identities=11%  Similarity=0.057  Sum_probs=282.0

Q ss_pred             chhhhhhchhhHHHHHHHHhhhcCCC-CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhc
Q 011249            5 YLVPRSKTFNQLKQVHSYLLKTLTKP-HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLH   81 (490)
Q Consensus         5 ~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~   81 (490)
                      .++...|+++.|...++.+.+   .. ++.. .....+.......++ .++|++.++++.  .|+....+..+...+...
T Consensus       120 ~ll~~~g~~~eA~~~~~~~l~---~~p~~~~-la~~y~~~~~~~~g~-~~~A~~~L~~ll~~~P~~~~~~~~LA~ll~~~  194 (1157)
T PRK11447        120 RLLATTGRTEEALASYDKLFN---GAPPELD-LAVEYWRLVAKLPAQ-RPEAINQLQRLNADYPGNTGLRNTLALLLFSS  194 (1157)
T ss_pred             HHHHhCCCHHHHHHHHHHHcc---CCCCChH-HHHHHHHHHhhCCcc-HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHcc
Confidence            356677899999999999887   54 3332 122222223334588 999999999986  466556788899999999


Q ss_pred             CChhHHHHHHHHHHhcCCC----------------CCH---hhHHHHHHHhcCCCChH--------------------HH
Q 011249           82 AHFRQSILLYAKMHRLGVL----------------TSG---FTFSSVLNACARVPSLL--------------------EA  122 (490)
Q Consensus        82 g~~~~A~~~~~~m~~~g~~----------------p~~---~~~~~ll~~~~~~~~~~--------------------~~  122 (490)
                      |++++|++.++++.+....                ++.   ..+...+..+.......                    ..
T Consensus       195 g~~~eAl~~l~~~~~~~~~~~~aa~~~~~~l~~~~~~~~~~~~l~~~l~~~p~~~~~~~A~~~L~~~~~~~~dp~~~~~~  274 (1157)
T PRK11447        195 GRRDEGFAVLEQMAKSPAGRDAAAQLWYGQIKDMPVSDASVAALQKYLQVFSDGDSVAAARSQLAEQQKQLADPAFRARA  274 (1157)
T ss_pred             CCHHHHHHHHHHHhhCCCchHHHHHHHHHHHhccCCChhhHHHHHHHHHHCCCchHHHHHHHHHHHHHHhccCcchHHHH
Confidence            9999999999998654210                000   01111122221111111                    12


Q ss_pred             HHHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCCChHHHHHHHHHhccCCc-----hhH------------
Q 011249          123 VICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCGNMKAAKEFYDRMTEKNS-----VTW------------  182 (490)
Q Consensus       123 l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----~~~------------  182 (490)
                      ....+...|++++|+..|++..+  | +...+..+..++.+.|++++|+..|++..+.++     ..+            
T Consensus       275 ~G~~~~~~g~~~~A~~~l~~aL~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~  354 (1157)
T PRK11447        275 QGLAAVDSGQGGKAIPELQQAVRANPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLL  354 (1157)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHH
Confidence            24567788999999999998876  4 678899999999999999999999999886321     111            


Q ss_pred             HHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHH-----
Q 011249          183 VAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISA-----  254 (490)
Q Consensus       183 ~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~-----  254 (490)
                      ......+.+.|++++|+..|+++.+   .+...+..+..++...|++++|++.|++..+.... +...+..+...     
T Consensus       355 ~~~g~~~~~~g~~~eA~~~~~~Al~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~p~-~~~a~~~L~~l~~~~~  433 (1157)
T PRK11447        355 IQQGDAALKANNLAQAERLYQQARQVDNTDSYAVLGLGDVAMARKDYAAAERYYQQALRMDPG-NTNAVRGLANLYRQQS  433 (1157)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHhcC
Confidence            2234567789999999999998875   45667888899999999999999999999875322 23333333333     


Q ss_pred             -------------------------------------HhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChH
Q 011249          255 -------------------------------------CTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLD  297 (490)
Q Consensus       255 -------------------------------------~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  297 (490)
                                                           +...|++++|...++++.+.. |.++..+..+...|.+.|+++
T Consensus       434 ~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~~-P~~~~~~~~LA~~~~~~G~~~  512 (1157)
T PRK11447        434 PEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLALD-PGSVWLTYRLAQDLRQAGQRS  512 (1157)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHH
Confidence                                                 334566666666666665554 334555555666666666666


Q ss_pred             HHHHHHhcccC--C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHH---------HHHHHHHHhcCCCChHHH
Q 011249          298 LAWREFSRIKN--K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV---------TFIGVLTACSHGGLVEDG  365 (490)
Q Consensus       298 ~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~---------~~~~l~~~~~~~g~~~~a  365 (490)
                      +|...++++.+  | ++..+..+...+...+++++|...++.+......++..         .+......+...|+.++|
T Consensus       513 ~A~~~l~~al~~~P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA  592 (1157)
T PRK11447        513 QADALMRRLAQQKPNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEA  592 (1157)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHH
Confidence            66666665543  2 33333333333444455555555444432211111100         011122333444444444


Q ss_pred             HHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhc
Q 011249          366 CKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLEL  443 (490)
Q Consensus       366 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  443 (490)
                      ..+++      ..++++..+..+...+.+.|++++|++.|+++.  .+.+...+..++..+...|++++|++.++++.+.
T Consensus       593 ~~~l~------~~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~  666 (1157)
T PRK11447        593 EALLR------QQPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPAT  666 (1157)
T ss_pred             HHHHH------hCCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcc
Confidence            44443      123344445556666666666666666665554  2334556666666666666666666666666666


Q ss_pred             CCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          444 GPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       444 ~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      .|+++..+..++.++...|++++|.++++++...
T Consensus       667 ~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~  700 (1157)
T PRK11447        667 ANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQ  700 (1157)
T ss_pred             CCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            6666666666666666666666666666666554

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.95  E-value=4.8e-23  Score=217.36  Aligned_cols=454  Identities=12%  Similarity=0.061  Sum_probs=272.3

Q ss_pred             hhhchhhHHHHHHHHhhhcCCC-CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceeh--------------
Q 011249            9 RSKTFNQLKQVHSYLLKTLTKP-HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLW--------------   71 (490)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~--------------   71 (490)
                      +.++.+.+.+..+++..   .. .++.  ++..++..+.+.|+ .++|.+.++++.  .|+....+              
T Consensus        40 ~~~~~d~a~~~l~kl~~---~~p~~p~--~~~~~~~~~l~~g~-~~~A~~~l~~l~~~~P~~~~~~~~~~~~~~~~~~~~  113 (1157)
T PRK11447         40 ATHREDLVRQSLYRLEL---IDPNNPD--VIAARFRLLLRQGD-SDGAQKLLDRLSQLAPDSNAYRSSRTTMLLSTPEGR  113 (1157)
T ss_pred             hhCChHHHHHHHHHHHc---cCCCCHH--HHHHHHHHHHhCCC-HHHHHHHHHHHHhhCCCChHHHHHHHHHHhcCCchh
Confidence            44567777777777766   55 7888  99999999999999 999999999886  34431221              


Q ss_pred             --HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHh-cCCCChH--------------------HHHHHHHH
Q 011249           72 --TSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNAC-ARVPSLL--------------------EAVICGYT  128 (490)
Q Consensus        72 --~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~-~~~~~~~--------------------~~l~~~~~  128 (490)
                        ..+...+...|++++|++.|+.+.+.+ +|+...-....... ...+...                    ..+...+.
T Consensus       114 ~~l~~A~ll~~~g~~~eA~~~~~~~l~~~-p~~~~la~~y~~~~~~~~g~~~~A~~~L~~ll~~~P~~~~~~~~LA~ll~  192 (1157)
T PRK11447        114 QALQQARLLATTGRTEEALASYDKLFNGA-PPELDLAVEYWRLVAKLPAQRPEAINQLQRLNADYPGNTGLRNTLALLLF  192 (1157)
T ss_pred             hHHHHHHHHHhCCCHHHHHHHHHHHccCC-CCChHHHHHHHHHHhhCCccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence              233446788999999999999988753 23321111111111 1111111                    34555566


Q ss_pred             hcCCHHHHHHHHhhcCCC-C-----Hh-----------------HHH---------------------------------
Q 011249          129 KIGLMDDAQRLFDSMAER-N-----VI-----------------SWS---------------------------------  152 (490)
Q Consensus       129 ~~g~~~~A~~~~~~~~~~-~-----~~-----------------~~~---------------------------------  152 (490)
                      ..|+.++|+..++++.+. .     ..                 .+.                                 
T Consensus       193 ~~g~~~eAl~~l~~~~~~~~~~~~aa~~~~~~l~~~~~~~~~~~~l~~~l~~~p~~~~~~~A~~~L~~~~~~~~dp~~~~  272 (1157)
T PRK11447        193 SSGRRDEGFAVLEQMAKSPAGRDAAAQLWYGQIKDMPVSDASVAALQKYLQVFSDGDSVAAARSQLAEQQKQLADPAFRA  272 (1157)
T ss_pred             ccCCHHHHHHHHHHHhhCCCchHHHHHHHHHHHhccCCChhhHHHHHHHHHHCCCchHHHHHHHHHHHHHHhccCcchHH
Confidence            666666666666654320 0     00                 000                                 


Q ss_pred             -HHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhHHHHHHhhcCC--CCH---HhHH---------
Q 011249          153 -AMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVREAKKVFDEISE--PDA---SCWA---------  214 (490)
Q Consensus       153 -~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~---~~~~---------  214 (490)
                       .....+...|++++|+..|++..+  | +...+..+..++.+.|++++|+..|++..+  |+.   ..|.         
T Consensus       273 ~~~G~~~~~~g~~~~A~~~l~~aL~~~P~~~~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~  352 (1157)
T PRK11447        273 RAQGLAAVDSGQGGKAIPELQQAVRANPKDSEALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYW  352 (1157)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHH
Confidence             012234445556666666655553  2 444555555666666666666666655443  211   1111         


Q ss_pred             ---HHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHH
Q 011249          215 ---AMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHS  291 (490)
Q Consensus       215 ---~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  291 (490)
                         .....+.+.|++++|+..|+++.+... .+...+..+..++...|++++|.+.|+++.+.. +.+...+..+...|.
T Consensus       353 ~~~~~g~~~~~~g~~~eA~~~~~~Al~~~P-~~~~a~~~Lg~~~~~~g~~~eA~~~y~~aL~~~-p~~~~a~~~L~~l~~  430 (1157)
T PRK11447        353 LLIQQGDAALKANNLAQAERLYQQARQVDN-TDSYAVLGLGDVAMARKDYAAAERYYQQALRMD-PGNTNAVRGLANLYR  430 (1157)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence               112344555666666666666555421 233444455555566666666666666655543 333334444444432


Q ss_pred             hcCChHHHHHHHhcccCCC------------hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc-HHHHHHHHHHhcC
Q 011249          292 KCGYLDLAWREFSRIKNKD------------VISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN-QVTFIGVLTACSH  358 (490)
Q Consensus       292 ~~~~~~~A~~~~~~~~~~~------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~  358 (490)
                       .++.++|..+++.+....            ...+..+...+...|++++|+..|++.++.  .|+ ...+..+...|..
T Consensus       431 -~~~~~~A~~~l~~l~~~~~~~~~~~~~~l~~~~~~~~a~~~~~~g~~~eA~~~~~~Al~~--~P~~~~~~~~LA~~~~~  507 (1157)
T PRK11447        431 -QQSPEKALAFIASLSASQRRSIDDIERSLQNDRLAQQAEALENQGKWAQAAELQRQRLAL--DPGSVWLTYRLAQDLRQ  507 (1157)
T ss_pred             -hcCHHHHHHHHHhCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHH
Confidence             233444444444332210            112233445566678888888888887773  453 4466667777888


Q ss_pred             CCChHHHHHHHHHHHHHcCCCCCchHHHHH--------------------------------------------HHHHhh
Q 011249          359 GGLVEDGCKQFELMTRVFGIKPLTEHLTCM--------------------------------------------VDLLGR  394 (490)
Q Consensus       359 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l--------------------------------------------~~~~~~  394 (490)
                      .|++++|...++++.+.  .+.++..+..+                                            +..+..
T Consensus       508 ~G~~~~A~~~l~~al~~--~P~~~~~~~a~al~l~~~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~  585 (1157)
T PRK11447        508 AGQRSQADALMRRLAQQ--KPNDPEQVYAYGLYLSGSDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRD  585 (1157)
T ss_pred             cCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHhCCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHH
Confidence            88888888888887652  22233333222                                            334445


Q ss_pred             cCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          395 SGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       395 ~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      .|+.++|.++++.  .++++..+..+...+...|++++|+..|+++++..|+++.++..++.+|...|++++|++.++++
T Consensus       586 ~G~~~eA~~~l~~--~p~~~~~~~~La~~~~~~g~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~l  663 (1157)
T PRK11447        586 SGKEAEAEALLRQ--QPPSTRIDLTLADWAQQRGDYAAARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKL  663 (1157)
T ss_pred             CCCHHHHHHHHHh--CCCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            5566666665552  23455667778888999999999999999999999999999999999999999999999999988


Q ss_pred             hhcc
Q 011249          475 SETE  478 (490)
Q Consensus       475 ~~~~  478 (490)
                      .+..
T Consensus       664 l~~~  667 (1157)
T PRK11447        664 PATA  667 (1157)
T ss_pred             hccC
Confidence            7643

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

Probab=99.95  E-value=6.6e-25  Score=197.83  Aligned_cols=387  Identities=16%  Similarity=0.144  Sum_probs=322.3

Q ss_pred             CCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcC
Q 011249           65 CKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMA  144 (490)
Q Consensus        65 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  144 (490)
                      |....+|..+...+-.+|++.+|+.+|+.+.+.  .|+...-.+-+.+             ++...|+.+.|.+.|....
T Consensus       113 ~q~ae~ysn~aN~~kerg~~~~al~~y~~aiel--~p~fida~inla~-------------al~~~~~~~~a~~~~~~al  177 (966)
T KOG4626|consen  113 PQGAEAYSNLANILKERGQLQDALALYRAAIEL--KPKFIDAYINLAA-------------ALVTQGDLELAVQCFFEAL  177 (966)
T ss_pred             chHHHHHHHHHHHHHHhchHHHHHHHHHHHHhc--CchhhHHHhhHHH-------------HHHhcCCCcccHHHHHHHH
Confidence            333367888999999999999999999999986  5654433322222             4788899999999999888


Q ss_pred             C--CCHh-HHHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCCCC---HHhHHH
Q 011249          145 E--RNVI-SWSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISEPD---ASCWAA  215 (490)
Q Consensus       145 ~--~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~---~~~~~~  215 (490)
                      +  |+.. ....+...+-..|+.++|...|.+..+.   -...|..|.-.+-..|+...|+..|++..+.|   ...|-.
T Consensus       178 qlnP~l~ca~s~lgnLlka~Grl~ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkldP~f~dAYiN  257 (966)
T KOG4626|consen  178 QLNPDLYCARSDLGNLLKAEGRLEEAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKLDPNFLDAYIN  257 (966)
T ss_pred             hcCcchhhhhcchhHHHHhhcccchhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcCCCcchHHHhh
Confidence            7  4433 3344566677789999999999988864   45688999999999999999999999988733   467889


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCccc-ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcC
Q 011249          216 MTVCYVQNGYAKAAIEMYKVMRQENVRI-SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCG  294 (490)
Q Consensus       216 l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  294 (490)
                      |...|-..+.+++|+..|.+....  .| ....+..+...|...|.++.|+..|++..+.. |.-+..|+.|..++-..|
T Consensus       258 LGnV~ke~~~~d~Avs~Y~rAl~l--rpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~-P~F~~Ay~NlanALkd~G  334 (966)
T KOG4626|consen  258 LGNVYKEARIFDRAVSCYLRALNL--RPNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQ-PNFPDAYNNLANALKDKG  334 (966)
T ss_pred             HHHHHHHHhcchHHHHHHHHHHhc--CCcchhhccceEEEEeccccHHHHHHHHHHHHhcC-CCchHHHhHHHHHHHhcc
Confidence            999999999999999999988765  34 45678888888999999999999999998876 556788999999999999


Q ss_pred             ChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcH-HHHHHHHHHhcCCCChHHHHHHHH
Q 011249          295 YLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQ-VTFIGVLTACSHGGLVEDGCKQFE  370 (490)
Q Consensus       295 ~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~  370 (490)
                      ++.+|.+.|.+...   ....+.+.|...|...|.+++|..+|....+  +.|.- ..++.|...|-++|++++|+..++
T Consensus       335 ~V~ea~~cYnkaL~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~--v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Yk  412 (966)
T KOG4626|consen  335 SVTEAVDCYNKALRLCPNHADAMNNLGNIYREQGKIEEATRLYLKALE--VFPEFAAAHNNLASIYKQQGNLDDAIMCYK  412 (966)
T ss_pred             chHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHh--hChhhhhhhhhHHHHHHhcccHHHHHHHHH
Confidence            99999999998876   3567889999999999999999999999988  56765 478889999999999999999999


Q ss_pred             HHHHHcCCCCC-chHHHHHHHHHhhcCChHHHHHHHHhcc-CCCC-hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC
Q 011249          371 LMTRVFGIKPL-TEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD-AGTWGALLGACKVHVNAELGEIAARHLLELGPEK  447 (490)
Q Consensus       371 ~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~  447 (490)
                      +..+   +.|+ ...|+.+...|...|+.+.|.+.+.+.. ..|. ...++.|...+...|+..+|++.|+.++++.|+.
T Consensus       413 ealr---I~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLklkPDf  489 (966)
T KOG4626|consen  413 EALR---IKPTFADALSNMGNTYKEMGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAIQSYRTALKLKPDF  489 (966)
T ss_pred             HHHh---cCchHHHHHHhcchHHHHhhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHccCCCC
Confidence            9975   5666 7788999999999999999999998776 4443 5688999999999999999999999999999999


Q ss_pred             CchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          448 TGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       448 ~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      |.+|..++-++.--.+|.+-.+.++++
T Consensus       490 pdA~cNllh~lq~vcdw~D~d~~~~kl  516 (966)
T KOG4626|consen  490 PDAYCNLLHCLQIVCDWTDYDKRMKKL  516 (966)
T ss_pred             chhhhHHHHHHHHHhcccchHHHHHHH
Confidence            999999998888777887755555444

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

Probab=99.94  E-value=1.1e-23  Score=190.09  Aligned_cols=351  Identities=15%  Similarity=0.147  Sum_probs=305.3

Q ss_pred             HHHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhH---HHHHHHHHhcCChh
Q 011249          123 VICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTW---VAMIAGYGKCGEVR  196 (490)
Q Consensus       123 l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~---~~l~~~~~~~~~~~  196 (490)
                      +...+-..|++++|+.+++.+.+  | .+..|..+..++...|+.+.|.+.|.+.++-|+..|   ..+...+-..|+++
T Consensus       122 ~aN~~kerg~~~~al~~y~~aiel~p~fida~inla~al~~~~~~~~a~~~~~~alqlnP~l~ca~s~lgnLlka~Grl~  201 (966)
T KOG4626|consen  122 LANILKERGQLQDALALYRAAIELKPKFIDAYINLAAALVTQGDLELAVQCFFEALQLNPDLYCARSDLGNLLKAEGRLE  201 (966)
T ss_pred             HHHHHHHhchHHHHHHHHHHHHhcCchhhHHHhhHHHHHHhcCCCcccHHHHHHHHhcCcchhhhhcchhHHHHhhcccc
Confidence            44567889999999999999986  3 567899999999999999999999999997655433   45666677789999


Q ss_pred             HHHHHHhhcCC--C-CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccC-hhhHHHHHHHHhccCChHHHHHHHHHHH
Q 011249          197 EAKKVFDEISE--P-DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRIS-EVAMVGAISACTQLGDVEMAAILAKHVD  272 (490)
Q Consensus       197 ~A~~~~~~~~~--~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~  272 (490)
                      +|...+.+..+  | -...|..|...+-.+|+...|+..|++..+.  .|+ ...|..|...|...+.++.|...|.+..
T Consensus       202 ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvkl--dP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl  279 (966)
T KOG4626|consen  202 EAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVKL--DPNFLDAYINLGNVYKEARIFDRAVSCYLRAL  279 (966)
T ss_pred             hhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhcC--CCcchHHHhhHHHHHHHHhcchHHHHHHHHHH
Confidence            99999988765  3 3457999999999999999999999999875  444 4689999999999999999999999988


Q ss_pred             hcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--CC-hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcH-HH
Q 011249          273 EGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KD-VISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQ-VT  348 (490)
Q Consensus       273 ~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~  348 (490)
                      ... +....++..+...|-.+|.++-|+..|++..+  |+ +..|+.|..++...|+..+|...|.+...  +.|+. ..
T Consensus       280 ~lr-pn~A~a~gNla~iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~--l~p~hada  356 (966)
T KOG4626|consen  280 NLR-PNHAVAHGNLACIYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALR--LCPNHADA  356 (966)
T ss_pred             hcC-CcchhhccceEEEEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHH--hCCccHHH
Confidence            765 55677778888899999999999999999887  43 56899999999999999999999999998  46654 58


Q ss_pred             HHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCC-hhhHHHHHHHHhh
Q 011249          349 FIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD-AGTWGALLGACKV  426 (490)
Q Consensus       349 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~-~~~~~~l~~~~~~  426 (490)
                      .+.|...+...|.+++|..+|....+  -.+.-...++.|...|..+|++++|+..|++.. +.|+ ...++.+...|..
T Consensus       357 m~NLgni~~E~~~~e~A~~ly~~al~--v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke  434 (966)
T KOG4626|consen  357 MNNLGNIYREQGKIEEATRLYLKALE--VFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKE  434 (966)
T ss_pred             HHHHHHHHHHhccchHHHHHHHHHHh--hChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHH
Confidence            89999999999999999999999986  334446778999999999999999999998776 6665 4699999999999


Q ss_pred             hCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          427 HVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       427 ~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      .|+.+.|++.+.+++..+|.-.++++.|+.+|...|+..+|+.-++...+..+.
T Consensus       435 ~g~v~~A~q~y~rAI~~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLklkPD  488 (966)
T KOG4626|consen  435 MGDVSAAIQCYTRAIQINPTFAEAHSNLASIYKDSGNIPEAIQSYRTALKLKPD  488 (966)
T ss_pred             hhhHHHHHHHHHHHHhcCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHccCCC
Confidence            999999999999999999999999999999999999999999999998876553

>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=99.93  E-value=2.8e-21  Score=191.73  Aligned_cols=386  Identities=12%  Similarity=0.019  Sum_probs=281.3

Q ss_pred             hHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--C-C
Q 011249           71 WTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--R-N  147 (490)
Q Consensus        71 ~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~  147 (490)
                      +......+.+.|++++|+..|++..+.  .|+...|..+-.              +|.+.|++++|+..++...+  | +
T Consensus       130 ~k~~G~~~~~~~~~~~Ai~~y~~al~~--~p~~~~~~n~a~--------------~~~~l~~~~~Ai~~~~~al~l~p~~  193 (615)
T TIGR00990       130 LKEKGNKAYRNKDFNKAIKLYSKAIEC--KPDPVYYSNRAA--------------CHNALGDWEKVVEDTTAALELDPDY  193 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHHH--------------HHHHhCCHHHHHHHHHHHHHcCCCC
Confidence            345666778888899999999887765  566554443332              37788888888888888775  3 4


Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHHHhccCC---chhHHHHHHHHHhcCChhHHHHHHhhcCC-----------------
Q 011249          148 VISWSAMVAGYANCGNMKAAKEFYDRMTEKN---SVTWVAMIAGYGKCGEVREAKKVFDEISE-----------------  207 (490)
Q Consensus       148 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----------------  207 (490)
                      ...|..+..++...|++++|+..|......+   ......++...........+...++.-..                 
T Consensus       194 ~~a~~~~a~a~~~lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~  273 (615)
T TIGR00990       194 SKALNRRANAYDGLGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRP  273 (615)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccC
Confidence            5678888888888899888888776554321   11111111111110011112222111110                 


Q ss_pred             ------------CCH---HhHHHHHHHH---HhcCChHHHHHHHHHHHHcC-ccc-ChhhHHHHHHHHhccCChHHHHHH
Q 011249          208 ------------PDA---SCWAAMTVCY---VQNGYAKAAIEMYKVMRQEN-VRI-SEVAMVGAISACTQLGDVEMAAIL  267 (490)
Q Consensus       208 ------------~~~---~~~~~l~~~~---~~~g~~~~A~~~~~~~~~~~-~~p-~~~~~~~l~~~~~~~g~~~~a~~~  267 (490)
                                  .+.   ..+..+...+   ...+++++|++.|++....+ ..| ....+..+...+...|++++|...
T Consensus       274 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~  353 (615)
T TIGR00990       274 KPRPAGLEDSNELDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALAD  353 (615)
T ss_pred             CcchhhhhcccccccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHH
Confidence                        000   0111111111   22468999999999998764 233 345677888888999999999999


Q ss_pred             HHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC
Q 011249          268 AKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP  344 (490)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p  344 (490)
                      ++...+.. |.....|..+..++...|++++|...|+++.+   .+...|..+...+...|++++|...|++.++.  .|
T Consensus       354 ~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l--~P  430 (615)
T TIGR00990       354 LSKSIELD-PRVTQSYIKRASMNLELGDPDKAEEDFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL--DP  430 (615)
T ss_pred             HHHHHHcC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--Cc
Confidence            99998875 45567888899999999999999999998765   36788999999999999999999999999984  55


Q ss_pred             c-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCC-hhhH----
Q 011249          345 N-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD-AGTW----  417 (490)
Q Consensus       345 ~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~-~~~~----  417 (490)
                      + ...+..+...+.+.|++++|+..+++..+  ..+.++..++.+..++...|++++|++.|++.. ..|+ ...+    
T Consensus       431 ~~~~~~~~la~~~~~~g~~~eA~~~~~~al~--~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~  508 (615)
T TIGR00990       431 DFIFSHIQLGVTQYKEGSIASSMATFRRCKK--NFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVL  508 (615)
T ss_pred             cCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--hCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHH
Confidence            4 55777888889999999999999999987  455667888999999999999999999998866 3232 1111    


Q ss_pred             ---HHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          418 ---GALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       418 ---~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                         +.....+...|++++|.++++++++.+|++..++..++.++.+.|++++|.+.+++..+.
T Consensus       509 ~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       509 PLINKALALFQWKQDFIEAENLCEKALIIDPECDIAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence               112222344699999999999999999999999999999999999999999999988765

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.92  E-value=2.7e-20  Score=188.18  Aligned_cols=450  Identities=8%  Similarity=-0.007  Sum_probs=290.3

Q ss_pred             hhhchhhHHHHHHHHhhhcCCC-CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChh
Q 011249            9 RSKTFNQLKQVHSYLLKTLTKP-HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFR   85 (490)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~   85 (490)
                      .-|++..|...+++..+   .. .++.  ++..|...|.+.|+ +++|+..+++..  .|+. ..|..++..+   ++++
T Consensus        56 ~~Gd~~~A~~~l~~Al~---~dP~n~~--~~~~LA~~yl~~g~-~~~A~~~~~kAv~ldP~n-~~~~~~La~i---~~~~  125 (987)
T PRK09782         56 KNNDEATAIREFEYIHQ---QVPDNIP--LTLYLAEAYRHFGH-DDRARLLLEDQLKRHPGD-ARLERSLAAI---PVEV  125 (987)
T ss_pred             hCCCHHHHHHHHHHHHH---hCCCCHH--HHHHHHHHHHHCCC-HHHHHHHHHHHHhcCccc-HHHHHHHHHh---ccCh
Confidence            44788888888888877   55 6677  99999999999999 999999999987  4544 3333333333   8999


Q ss_pred             HHHHHHHHHHhcCCCCCHhhHHHHHHHh------------------------cCCCC---hHHHHHHHHHhcCCHHHHHH
Q 011249           86 QSILLYAKMHRLGVLTSGFTFSSVLNAC------------------------ARVPS---LLEAVICGYTKIGLMDDAQR  138 (490)
Q Consensus        86 ~A~~~~~~m~~~g~~p~~~~~~~ll~~~------------------------~~~~~---~~~~l~~~~~~~g~~~~A~~  138 (490)
                      +|..+|+++.+.  .|+......++...                        ...|.   ....+...|.+.|++++|+.
T Consensus       126 kA~~~ye~l~~~--~P~n~~~~~~la~~~~~~~~l~y~q~eqAl~AL~lr~~~~~~~~~vL~L~~~rlY~~l~dw~~Ai~  203 (987)
T PRK09782        126 KSVTTVEELLAQ--QKACDAVPTLRCRSEVGQNALRLAQLPVARAQLNDATFAASPEGKTLRTDLLQRAIYLKQWSQADT  203 (987)
T ss_pred             hHHHHHHHHHHh--CCCChhHHHHHHHHhhccchhhhhhHHHHHHHHHHhhhCCCCCcHHHHHHHHHHHHHHhCHHHHHH
Confidence            999999999887  44433222222211                        11112   12334677788888888888


Q ss_pred             HHhhcCCC---CHhHHHHHHHHHHh-CCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCC-----C-
Q 011249          139 LFDSMAER---NVISWSAMVAGYAN-CGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISE-----P-  208 (490)
Q Consensus       139 ~~~~~~~~---~~~~~~~l~~~~~~-~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~-  208 (490)
                      +++++.+.   +......|..+|.+ .++ +++..+++...+.|+..+..++..|.+.|+.++|.++++++..     | 
T Consensus       204 lL~~L~k~~pl~~~~~~~L~~ay~q~l~~-~~a~al~~~~lk~d~~l~~ala~~yi~~G~~~~A~~~L~~~~~~~~~~~~  282 (987)
T PRK09782        204 LYNEARQQNTLSAAERRQWFDVLLAGQLD-DRLLALQSQGIFTDPQSRITYATALAYRGEKARLQHYLIENKPLFTTDAQ  282 (987)
T ss_pred             HHHHHHhcCCCCHHHHHHHHHHHHHhhCH-HHHHHHhchhcccCHHHHHHHHHHHHHCCCHHHHHHHHHhCcccccCCCc
Confidence            88777651   22223333334443 233 4444443332233444444444444444444444444444321     0 


Q ss_pred             --------------------------------------------------------------------------------
Q 011249          209 --------------------------------------------------------------------------------  208 (490)
Q Consensus       209 --------------------------------------------------------------------------------  208 (490)
                                                                                                      
T Consensus       283 ~~~~~~~l~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~  362 (987)
T PRK09782        283 EKSWLYLLSKYSANPVQALANYTVQFADNRQYVVGATLPVLLKEGQYDAAQKLLATLPANEMLEERYAVSVATRNKAEAL  362 (987)
T ss_pred             cHHHHHHHHhccCchhhhccchhhhhHHHHHHHHHHHHHHHHhccHHHHHHHHhcCCCcchHHHHHHhhccccCchhHHH
Confidence                                                                                            


Q ss_pred             ------------CHHhHHHHHHHHHhcCChHHHHHHHHHHHHc-C-cc--------------------------------
Q 011249          209 ------------DASCWAAMTVCYVQNGYAKAAIEMYKVMRQE-N-VR--------------------------------  242 (490)
Q Consensus       209 ------------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~-~~--------------------------------  242 (490)
                                  +......+.....+.|+.++|.++|++.... + ..                                
T Consensus       363 ~~~~~~y~~~~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~  442 (987)
T PRK09782        363 RLARLLYQQEPANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYLATPAKVAILSKPL  442 (987)
T ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcccchHHHHHhcccc
Confidence                        0000111111223345555555555544321 0 01                                


Q ss_pred             ------------------------------c--ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 011249          243 ------------------------------I--SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMH  290 (490)
Q Consensus       243 ------------------------------p--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  290 (490)
                                                    +  +...+..+..++.. ++.++|...+.......  |+......+...+
T Consensus       443 ~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~--Pd~~~~L~lA~al  519 (987)
T PRK09782        443 PLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQ--PDAWQHRAVAYQA  519 (987)
T ss_pred             ccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhC--CchHHHHHHHHHH
Confidence                                          1  22333334433333 55566666666555443  3433333445555


Q ss_pred             HhcCChHHHHHHHhcccC--CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcH-HHHHHHHHHhcCCCChHHHHH
Q 011249          291 SKCGYLDLAWREFSRIKN--KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQ-VTFIGVLTACSHGGLVEDGCK  367 (490)
Q Consensus       291 ~~~~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~  367 (490)
                      ...|++++|...|+++..  ++...+..+..++.+.|++++|...+++..+.  .|+. ..+..+.......|++++|..
T Consensus       520 ~~~Gr~eeAi~~~rka~~~~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l--~P~~~~l~~~La~~l~~~Gr~~eAl~  597 (987)
T PRK09782        520 YQVEDYATALAAWQKISLHDMSNEDLLAAANTAQAAGNGAARDRWLQQAEQR--GLGDNALYWWLHAQRYIPGQPELALN  597 (987)
T ss_pred             HHCCCHHHHHHHHHHHhccCCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCccHHHHHHHHHHHHhCCCHHHHHH
Confidence            678888888888887654  44455666777788888999999998888875  3433 333344444556699999999


Q ss_pred             HHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCC
Q 011249          368 QFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGP  445 (490)
Q Consensus       368 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p  445 (490)
                      .+++..+   ..|+...+..+..++.+.|++++|+..+++..  .+.+...+..+..++...|++++|+..++++++..|
T Consensus       598 ~~~~AL~---l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P  674 (987)
T PRK09782        598 DLTRSLN---IAPSANAYVARATIYRQRHNVPAAVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHKGLP  674 (987)
T ss_pred             HHHHHHH---hCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence            9999976   34567888889999999999999999998877  444667888888889999999999999999999999


Q ss_pred             CCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          446 EKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       446 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +++.++..++.++...|++++|+..+++..+..+
T Consensus       675 ~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~P  708 (987)
T PRK09782        675 DDPALIRQLAYVNQRLDDMAATQHYARLVIDDID  708 (987)
T ss_pred             CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            9999999999999999999999999999886654

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.91  E-value=6.4e-22  Score=186.74  Aligned_cols=297  Identities=16%  Similarity=0.139  Sum_probs=175.8

Q ss_pred             HHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCC-CC------HHhHHHHHHHHHhcCC
Q 011249          156 AGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISE-PD------ASCWAAMTVCYVQNGY  225 (490)
Q Consensus       156 ~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~------~~~~~~l~~~~~~~g~  225 (490)
                      ..+...|++++|+..|+++.+.   +..++..++..+...|++++|..+++.+.. ++      ...+..++..|.+.|+
T Consensus        43 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~  122 (389)
T PRK11788         43 LNFLLNEQPDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGL  122 (389)
T ss_pred             HHHHhcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCC
Confidence            3445566666666666666643   233455555555555555555555555443 11      1234455555555555


Q ss_pred             hHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhc
Q 011249          226 AKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSR  305 (490)
Q Consensus       226 ~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  305 (490)
                      +++|+.+|+++.+.. +++..++..++..+.+.|++++|...++.+.+.+..+....                       
T Consensus       123 ~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~-----------------------  178 (389)
T PRK11788        123 LDRAEELFLQLVDEG-DFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVE-----------------------  178 (389)
T ss_pred             HHHHHHHHHHHHcCC-cchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHH-----------------------
Confidence            555555555555432 22344455555555555555555555555544331111000                       


Q ss_pred             ccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchH
Q 011249          306 IKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEH  384 (490)
Q Consensus       306 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  384 (490)
                          ....+..++..+...|++++|...++++.+.  .|+ ...+..+...+...|++++|.++++++... ........
T Consensus       179 ----~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~-~p~~~~~~  251 (389)
T PRK11788        179 ----IAHFYCELAQQALARGDLDAARALLKKALAA--DPQCVRASILLGDLALAQGDYAAAIEALERVEEQ-DPEYLSEV  251 (389)
T ss_pred             ----HHHHHHHHHHHHHhCCCHHHHHHHHHHHHhH--CcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH-ChhhHHHH
Confidence                0112344555666777777777777777663  233 345666667777777777777777777653 21112345


Q ss_pred             HHHHHHHHhhcCChHHHHHHHHhcc-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH-h--
Q 011249          385 LTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA-S--  460 (490)
Q Consensus       385 ~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~-~--  460 (490)
                      +..++.+|...|++++|.+.++++. ..|+...+..++..+...|++++|..+++++++..|+++... .+...+. .  
T Consensus       252 ~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~~P~~~~~~-~l~~~~~~~~~  330 (389)
T PRK11788        252 LPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRRHPSLRGFH-RLLDYHLAEAE  330 (389)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHhCcCHHHHH-HHHHHhhhccC
Confidence            6667777777788888887777765 445656667777777888888888888888888888766433 3333333 2  


Q ss_pred             cCCcchHHHHHHHhhhcccccCCC
Q 011249          461 MGKWKDSEIVKMMISETEKKKSPG  484 (490)
Q Consensus       461 ~g~~~~A~~~~~~~~~~~~~~~~~  484 (490)
                      .|+.+++..++++|.+++++++|.
T Consensus       331 ~g~~~~a~~~~~~~~~~~~~~~p~  354 (389)
T PRK11788        331 EGRAKESLLLLRDLVGEQLKRKPR  354 (389)
T ss_pred             CccchhHHHHHHHHHHHHHhCCCC
Confidence            457788888888888877777776

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.91  E-value=7.4e-20  Score=185.05  Aligned_cols=455  Identities=11%  Similarity=0.013  Sum_probs=316.1

Q ss_pred             hhhhchhhHHHHHHHHhhhcCCC-CchhHhHHHHHHHH--------HhcCCCCHHHHHHHhccCCCC--CCceehHHHHH
Q 011249            8 PRSKTFNQLKQVHSYLLKTLTKP-HDQYHYYAQFLIRL--------LQLPGDNLSYARQVFDQIPKC--KTQFLWTSLIR   76 (490)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~--------~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~l~~   76 (490)
                      ...+++..+..+++.+.+   .. .++.  ++..+...        |.+.+. ..++++  .+...|  ++....-.+..
T Consensus       119 a~i~~~~kA~~~ye~l~~---~~P~n~~--~~~~la~~~~~~~~l~y~q~eq-Al~AL~--lr~~~~~~~~~vL~L~~~r  190 (987)
T PRK09782        119 AAIPVEVKSVTTVEELLA---QQKACDA--VPTLRCRSEVGQNALRLAQLPV-ARAQLN--DATFAASPEGKTLRTDLLQ  190 (987)
T ss_pred             HHhccChhHHHHHHHHHH---hCCCChh--HHHHHHHHhhccchhhhhhHHH-HHHHHH--HhhhCCCCCcHHHHHHHHH
Confidence            334677777788888877   66 6677  77777776        788777 777777  333333  34123444488


Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCC-----------CCh------HHHHHHHHHhcCCHHHHHHH
Q 011249           77 NHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARV-----------PSL------LEAVICGYTKIGLMDDAQRL  139 (490)
Q Consensus        77 ~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~-----------~~~------~~~l~~~~~~~g~~~~A~~~  139 (490)
                      .|.+.|++++|+.++.++.+.+..... -...+-.++...           +..      ..+++..|.+.|+.++|.++
T Consensus       191 lY~~l~dw~~Ai~lL~~L~k~~pl~~~-~~~~L~~ay~q~l~~~~a~al~~~~lk~d~~l~~ala~~yi~~G~~~~A~~~  269 (987)
T PRK09782        191 RAIYLKQWSQADTLYNEARQQNTLSAA-ERRQWFDVLLAGQLDDRLLALQSQGIFTDPQSRITYATALAYRGEKARLQHY  269 (987)
T ss_pred             HHHHHhCHHHHHHHHHHHHhcCCCCHH-HHHHHHHHHHHhhCHHHHHHHhchhcccCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            999999999999999999998543322 122222222110           111      14677788888888888888


Q ss_pred             HhhcCC-----CCHhH------------------------------HHHHHHHHHhCCChHHHHHHH-------------
Q 011249          140 FDSMAE-----RNVIS------------------------------WSAMVAGYANCGNMKAAKEFY-------------  171 (490)
Q Consensus       140 ~~~~~~-----~~~~~------------------------------~~~l~~~~~~~~~~~~a~~~~-------------  171 (490)
                      ++++..     |+..+                              .-.++..+.+.++++.+.++.             
T Consensus       270 L~~~~~~~~~~~~~~~~~~~l~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~  349 (987)
T PRK09782        270 LIENKPLFTTDAQEKSWLYLLSKYSANPVQALANYTVQFADNRQYVVGATLPVLLKEGQYDAAQKLLATLPANEMLEERY  349 (987)
T ss_pred             HHhCcccccCCCccHHHHHHHHhccCchhhhccchhhhhHHHHHHHHHHHHHHHHhccHHHHHHHHhcCCCcchHHHHHH
Confidence            887752     11111                              111133334444444333332             


Q ss_pred             --------------------------------------------------HHhcc-C-C----chhHHHHHHHHHhcCC-
Q 011249          172 --------------------------------------------------DRMTE-K-N----SVTWVAMIAGYGKCGE-  194 (490)
Q Consensus       172 --------------------------------------------------~~~~~-~-~----~~~~~~l~~~~~~~~~-  194 (490)
                                                                        +.... + +    .....-++..|.+.+. 
T Consensus       350 ~~~~~~~~~~~~~~~~~~~y~~~~~~~~~l~q~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~  429 (987)
T PRK09782        350 AVSVATRNKAEALRLARLLYQQEPANLTRLDQLTWQLMQNGQSREAADLLLQRYPFQGDARLSQTLMARLASLLESHPYL  429 (987)
T ss_pred             hhccccCchhHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcccHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHhCCcc
Confidence                                                              11111 0 0    0011234444444443 


Q ss_pred             --hhHHHHH-------------------------HhhcCC---C--CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcc
Q 011249          195 --VREAKKV-------------------------FDEISE---P--DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVR  242 (490)
Q Consensus       195 --~~~A~~~-------------------------~~~~~~---~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  242 (490)
                        ..++..+                         +.....   +  +...|..+..++.. +++++|+..+.+....  .
T Consensus       430 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~~p~~~~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~  506 (987)
T PRK09782        430 ATPAKVAILSKPLPLAEQRQWQSQLPGIADNCPAIVRLLGDMSPSYDAAAWNRLAKCYRD-TLPGVALYAWLQAEQR--Q  506 (987)
T ss_pred             cchHHHHHhccccccchhHHHHhhhhhhhhhHHHHHHhcccCCCCCCHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh--C
Confidence              1122111                         011110   2  45566777777766 7888899988887765  4


Q ss_pred             cChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHH---HHHH
Q 011249          243 ISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYS---SMIT  319 (490)
Q Consensus       243 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~---~l~~  319 (490)
                      |+......+..++...|++++|...++.+...  +|+...+..+..++.+.|++++|...+++..+.++....   .+..
T Consensus       507 Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~all~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~  584 (987)
T PRK09782        507 PDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAANTAQAAGNGAARDRWLQQAEQRGLGDNALYWWLHA  584 (987)
T ss_pred             CchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCccHHHHHHHHH
Confidence            66655555566667999999999999998665  344455667788899999999999999988774333232   3333


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChH
Q 011249          320 AFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLE  399 (490)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  399 (490)
                      .....|++++|...+++..+  ..|+...+..+..++.+.|+.++|...+++...  ..|.+...+..+..++...|+++
T Consensus       585 ~l~~~Gr~~eAl~~~~~AL~--l~P~~~a~~~LA~~l~~lG~~deA~~~l~~AL~--l~Pd~~~a~~nLG~aL~~~G~~e  660 (987)
T PRK09782        585 QRYIPGQPELALNDLTRSLN--IAPSANAYVARATIYRQRHNVPAAVSDLRAALE--LEPNNSNYQAALGYALWDSGDIA  660 (987)
T ss_pred             HHHhCCCHHHHHHHHHHHHH--hCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHCCCHH
Confidence            44456999999999999998  467888899999999999999999999999987  45556778888999999999999


Q ss_pred             HHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          400 KAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       400 ~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      +|+..+++..  .+.++..+..+..++...|++++|+..++++++..|++..+....++...+..+++.|.+.+++....
T Consensus       661 eAi~~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~P~~a~i~~~~g~~~~~~~~~~~a~~~~~r~~~~  740 (987)
T PRK09782        661 QSREMLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLVIDDIDNQALITPLTPEQNQQRFNFRRLHEEVGRRWTF  740 (987)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCchhhhhhhHHHHHHHHHHHHHHHHHHHhhc
Confidence            9999998876  34567789999999999999999999999999999999999999999999999999999988876655


Q ss_pred             ccc
Q 011249          478 EKK  480 (490)
Q Consensus       478 ~~~  480 (490)
                      ++.
T Consensus       741 ~~~  743 (987)
T PRK09782        741 SFD  743 (987)
T ss_pred             Ccc
Confidence            443

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.91  E-value=1.3e-20  Score=186.41  Aligned_cols=317  Identities=10%  Similarity=-0.033  Sum_probs=260.9

Q ss_pred             HHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhHHH
Q 011249          126 GYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVREAK  199 (490)
Q Consensus       126 ~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~A~  199 (490)
                      .+.+.|++++|..+++....  | +...+..++.+....|++++|+..|+++.+  | +...+..+...+...|++++|.
T Consensus        51 ~~~~~g~~~~A~~l~~~~l~~~p~~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~P~~~~a~~~la~~l~~~g~~~~Ai  130 (656)
T PRK15174         51 ACLRKDETDVGLTLLSDRVLTAKNGRDLLRRWVISPLASSQPDAVLQVVNKLLAVNVCQPEDVLLVASVLLKSKQYATVA  130 (656)
T ss_pred             HHHhcCCcchhHHHhHHHHHhCCCchhHHHHHhhhHhhcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHH
Confidence            47889999999999998875  3 556677777888889999999999999985  4 6678889999999999999999


Q ss_pred             HHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCC
Q 011249          200 KVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCC  276 (490)
Q Consensus       200 ~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  276 (490)
                      ..+++..+   .+...+..++.++...|++++|...++.+......+ ...+..+ ..+...|++++|...++.+.+...
T Consensus       131 ~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~-~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~  208 (656)
T PRK15174        131 DLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPPR-GDMIATC-LSFLNKSRLPEDHDLARALLPFFA  208 (656)
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCC-HHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCC
Confidence            99999875   456788899999999999999999999887664332 2333333 347889999999999999887753


Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHH----HHHHHHHHHHcCCCCc-HHH
Q 011249          277 DRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQE----ALDMFLKMRNEGIEPN-QVT  348 (490)
Q Consensus       277 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~----a~~~~~~~~~~~~~p~-~~~  348 (490)
                      .++......+..++...|++++|+..|+++..   .+...+..+...+...|++++    |...++++.+.  .|+ ...
T Consensus       209 ~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l--~P~~~~a  286 (656)
T PRK15174        209 LERQESAGLAVDTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQF--NSDNVRI  286 (656)
T ss_pred             CcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhh--CCCCHHH
Confidence            44455555667888999999999999998876   356788889999999999986    89999999984  554 558


Q ss_pred             HHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCChh-hHHHHHHHHhh
Q 011249          349 FIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAG-TWGALLGACKV  426 (490)
Q Consensus       349 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~-~~~~l~~~~~~  426 (490)
                      +..+...+...|++++|...++++.+  ..+.+...+..+..++.+.|++++|...|+++. ..|+.. .+..+..++..
T Consensus       287 ~~~lg~~l~~~g~~~eA~~~l~~al~--l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~~P~~~~~~~~~a~al~~  364 (656)
T PRK15174        287 VTLYADALIRTGQNEKAIPLLQQSLA--THPDLPYVRAMYARALRQVGQYTAASDEFVQLAREKGVTSKWNRYAAAALLQ  364 (656)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHH
Confidence            88889999999999999999999987  334456677788999999999999999998877 445543 34445677889


Q ss_pred             hCChHHHHHHHHHHHhcCCCCC
Q 011249          427 HVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       427 ~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      .|+.++|...|+++.+..|++.
T Consensus       365 ~G~~deA~~~l~~al~~~P~~~  386 (656)
T PRK15174        365 AGKTSEAESVFEHYIQARASHL  386 (656)
T ss_pred             CCCHHHHHHHHHHHHHhChhhc
Confidence            9999999999999999998864

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.90  E-value=2.7e-20  Score=184.16  Aligned_cols=348  Identities=10%  Similarity=-0.050  Sum_probs=282.4

Q ss_pred             HHhcCCHHHHHHHHhhcCCC------CHhHHHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhH
Q 011249          127 YTKIGLMDDAQRLFDSMAER------NVISWSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVRE  197 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~~~~~~------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~  197 (490)
                      +.+..+++.---.|....+.      +......++..+.+.|++++|..+++....  | +......++.+....|++++
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~l~~~~l~~~p~~~~~l~~l~~~~l~~g~~~~   94 (656)
T PRK15174         15 LLKQEDWEGLCLYFSQHPEKVRDSAGNEQNIILFAIACLRKDETDVGLTLLSDRVLTAKNGRDLLRRWVISPLASSQPDA   94 (656)
T ss_pred             hhhhhchhhHhHHhhcccHhhhhhcccccCHHHHHHHHHhcCCcchhHHHhHHHHHhCCCchhHHHHHhhhHhhcCCHHH
Confidence            34556676666666655541      233455567888999999999999999885  3 56677777888888999999


Q ss_pred             HHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhc
Q 011249          198 AKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEG  274 (490)
Q Consensus       198 A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  274 (490)
                      |...|+++.+   .+...+..+...+...|++++|+..++++.+.. +.+...+..+..++...|++++|...++.+...
T Consensus        95 A~~~l~~~l~~~P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~-P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~  173 (656)
T PRK15174         95 VLQVVNKLLAVNVCQPEDVLLVASVLLKSKQYATVADLAEQAWLAF-SGNSQIFALHLRTLVLMDKELQAISLARTQAQE  173 (656)
T ss_pred             HHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHh
Confidence            9999999875   456788889999999999999999999999763 225677888999999999999999999988776


Q ss_pred             CCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCC----ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHH
Q 011249          275 CCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK----DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFI  350 (490)
Q Consensus       275 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~  350 (490)
                      . +.+...+..+ ..+...|++++|...++.+.+.    +...+..+..++...|++++|+..++++.+.. +.+...+.
T Consensus       174 ~-P~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~-p~~~~~~~  250 (656)
T PRK15174        174 V-PPRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQTGESALARG-LDGAALRR  250 (656)
T ss_pred             C-CCCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHH
Confidence            5 3334444333 3478899999999999987653    23344556778899999999999999999853 23456777


Q ss_pred             HHHHHhcCCCChHH----HHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHH
Q 011249          351 GVLTACSHGGLVED----GCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGAC  424 (490)
Q Consensus       351 ~l~~~~~~~g~~~~----a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~  424 (490)
                      .+...+...|++++    |...++++.+  ..|.+...+..+...+...|++++|...+++..  .+.+...+..+..++
T Consensus       251 ~Lg~~l~~~G~~~eA~~~A~~~~~~Al~--l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l~P~~~~a~~~La~~l  328 (656)
T PRK15174        251 SLGLAYYQSGRSREAKLQAAEHWRHALQ--FNSDNVRIVTLYADALIRTGQNEKAIPLLQQSLATHPDLPYVRAMYARAL  328 (656)
T ss_pred             HHHHHHHHcCCchhhHHHHHHHHHHHHh--hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            88889999999986    8999999987  345567788899999999999999999998877  344566788888999


Q ss_pred             hhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          425 KVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       425 ~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      ...|++++|+..++++.+.+|+++..+..++.++...|++++|...+++..+..++
T Consensus       329 ~~~G~~~eA~~~l~~al~~~P~~~~~~~~~a~al~~~G~~deA~~~l~~al~~~P~  384 (656)
T PRK15174        329 RQVGQYTAASDEFVQLAREKGVTSKWNRYAAAALLQAGKTSEAESVFEHYIQARAS  384 (656)
T ss_pred             HHCCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhChh
Confidence            99999999999999999999998877777888999999999999999998877554

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.90  E-value=4.9e-21  Score=180.73  Aligned_cols=301  Identities=14%  Similarity=0.071  Sum_probs=159.3

Q ss_pred             HHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHH
Q 011249           44 LLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLE  121 (490)
Q Consensus        44 ~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~  121 (490)
                      .+...|+ +++|...|+++.  .|+....+..+...+...|++++|..+++.+...+..++.......           .
T Consensus        44 ~~~~~~~-~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~-----------~  111 (389)
T PRK11788         44 NFLLNEQ-PDKAIDLFIEMLKVDPETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLAL-----------Q  111 (389)
T ss_pred             HHHhcCC-hHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHH-----------H
Confidence            3344455 555666555554  2333234555555555555666666555555543211111100000           1


Q ss_pred             HHHHHHHhcCCHHHHHHHHhhcCC---CCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHH
Q 011249          122 AVICGYTKIGLMDDAQRLFDSMAE---RNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREA  198 (490)
Q Consensus       122 ~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  198 (490)
                      .++..|.+.|++++|..+|+++.+   .+..+++.++..+.+.|++++|.+.++++.+.++.....              
T Consensus       112 ~La~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~--------------  177 (389)
T PRK11788        112 ELGQDYLKAGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRV--------------  177 (389)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchH--------------
Confidence            122334555555555555555543   233444455555555555555555555444321100000              


Q ss_pred             HHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCC
Q 011249          199 KKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDR  278 (490)
Q Consensus       199 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~  278 (490)
                               .....+..++..+.+.|++++|.+.|+++.+.. +.+...+..+...+.+.|++++|.++++++.+.+...
T Consensus       178 ---------~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~  247 (389)
T PRK11788        178 ---------EIAHFYCELAQQALARGDLDAARALLKKALAAD-PQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEY  247 (389)
T ss_pred             ---------HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhh
Confidence                     001123445555666666666666666666542 1233455556666666666666666666666543222


Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHhcccC--CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHh
Q 011249          279 TNYVSNALIHMHSKCGYLDLAWREFSRIKN--KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTAC  356 (490)
Q Consensus       279 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  356 (490)
                      ...+++.++.+|...|++++|...++++.+  |+...+..++..+.+.|++++|..+++++.+.  .|+..++..++..+
T Consensus       248 ~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~l~~~l~~--~P~~~~~~~l~~~~  325 (389)
T PRK11788        248 LSEVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQALLREQLRR--HPSLRGFHRLLDYH  325 (389)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHHHHHHHHh--CcCHHHHHHHHHHh
Confidence            234455666666666777777666666554  45455566667777777777777777777663  56666666666554


Q ss_pred             cC---CCChHHHHHHHHHHHHHcCCCCCch
Q 011249          357 SH---GGLVEDGCKQFELMTRVFGIKPLTE  383 (490)
Q Consensus       357 ~~---~g~~~~a~~~~~~~~~~~~~~~~~~  383 (490)
                      ..   .|+.+++..+++++.++ ++.|++.
T Consensus       326 ~~~~~~g~~~~a~~~~~~~~~~-~~~~~p~  354 (389)
T PRK11788        326 LAEAEEGRAKESLLLLRDLVGE-QLKRKPR  354 (389)
T ss_pred             hhccCCccchhHHHHHHHHHHH-HHhCCCC
Confidence            42   44677777777777764 5555555

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.89  E-value=1.1e-19  Score=183.57  Aligned_cols=393  Identities=8%  Similarity=-0.029  Sum_probs=209.4

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhc
Q 011249           37 YAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACA  114 (490)
Q Consensus        37 ~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~  114 (490)
                      ...-.+.+....|+ .++|++++++..  .|.....+..+...+...|++++|.++|++..+.  .|+.......+    
T Consensus        17 ~~~d~~~ia~~~g~-~~~A~~~~~~~~~~~~~~a~~~~~lA~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~l----   89 (765)
T PRK10049         17 QIADWLQIALWAGQ-DAEVITVYNRYRVHMQLPARGYAAVAVAYRNLKQWQNSLTLWQKALSL--EPQNDDYQRGL----   89 (765)
T ss_pred             HHHHHHHHHHHcCC-HHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHH----
Confidence            44566667777777 788888877765  2333234777777778888888888888877765  44433322222    


Q ss_pred             CCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHH
Q 011249          115 RVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAG  188 (490)
Q Consensus       115 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~  188 (490)
                               +..+...|+.++|+..++++.+  | +.. +..+..++...|+.++|+..++++.+.   +...+..++.+
T Consensus        90 ---------a~~l~~~g~~~eA~~~l~~~l~~~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~  159 (765)
T PRK10049         90 ---------ILTLADAGQYDEALVKAKQLVSGAPDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQA  159 (765)
T ss_pred             ---------HHHHHHCCCHHHHHHHHHHHHHhCCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence                     2236777888888888877764  3 445 667777777788888888888777753   44455666677


Q ss_pred             HHhcCChhHHHHHHhhcCC-CCH------HhHHHHHHHHHh-----cCCh---HHHHHHHHHHHHc-CcccChh-hHH--
Q 011249          189 YGKCGEVREAKKVFDEISE-PDA------SCWAAMTVCYVQ-----NGYA---KAAIEMYKVMRQE-NVRISEV-AMV--  249 (490)
Q Consensus       189 ~~~~~~~~~A~~~~~~~~~-~~~------~~~~~l~~~~~~-----~g~~---~~A~~~~~~~~~~-~~~p~~~-~~~--  249 (490)
                      +...+..+.|++.++.... |+.      .....++.....     .+++   ++|++.++.+.+. ...|+.. .+.  
T Consensus       160 l~~~~~~e~Al~~l~~~~~~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a  239 (765)
T PRK10049        160 LRNNRLSAPALGAIDDANLTPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRA  239 (765)
T ss_pred             HHHCCChHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHH
Confidence            7777777777777776665 211      011122222211     1223   5566666666542 1122221 111  


Q ss_pred             --HHHHHHhccCChHHHHHHHHHHHhcCCC-CchhHHHHHHHHHHhcCChHHHHHHHhcccCCC-------hhHHHHHHH
Q 011249          250 --GAISACTQLGDVEMAAILAKHVDEGCCD-RTNYVSNALIHMHSKCGYLDLAWREFSRIKNKD-------VISYSSMIT  319 (490)
Q Consensus       250 --~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-------~~~~~~l~~  319 (490)
                        ..+.++...|++++|...|+.+.+.+.+ |+. ....+..+|...|++++|+..|+++...+       ......+..
T Consensus       240 ~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~-a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~  318 (765)
T PRK10049        240 RIDRLGALLARDRYKDVISEYQRLKAEGQIIPPW-AQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFY  318 (765)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHH-HHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHH
Confidence              1122334456666666666666555421 111 11123455566666666666666554311       122334444


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCC-----------CCcH---HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHH
Q 011249          320 AFADHGKSQEALDMFLKMRNEGI-----------EPNQ---VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHL  385 (490)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~~-----------~p~~---~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~  385 (490)
                      ++...|++++|..+++++.+...           .|+.   ..+..+...+...|+.++|++.++++..  ..|.+...+
T Consensus       319 a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~--~~P~n~~l~  396 (765)
T PRK10049        319 SLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAY--NAPGNQGLR  396 (765)
T ss_pred             HHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCCCHHHH
Confidence            55556666666666666554310           0111   1223334444455555555555555544  233334444


Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                      ..++..+...|++++|++.+++.. ..| +...+...+..+...|++++|+.+++++++..|+++.
T Consensus       397 ~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~Pd~~~  462 (765)
T PRK10049        397 IDYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDDVVAREPQDPG  462 (765)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCHH
Confidence            555555555555555555555444 222 2334444444445555555555555555555555443

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.89  E-value=6.3e-19  Score=178.19  Aligned_cols=391  Identities=8%  Similarity=0.022  Sum_probs=295.5

Q ss_pred             ehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--C-
Q 011249           70 LWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--R-  146 (490)
Q Consensus        70 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-  146 (490)
                      --.-.+......|+.++|++++.+..... +.+...+..+-.              .+.+.|++++|..++++..+  | 
T Consensus        17 ~~~d~~~ia~~~g~~~~A~~~~~~~~~~~-~~~a~~~~~lA~--------------~~~~~g~~~~A~~~~~~al~~~P~   81 (765)
T PRK10049         17 QIADWLQIALWAGQDAEVITVYNRYRVHM-QLPARGYAAVAV--------------AYRNLKQWQNSLTLWQKALSLEPQ   81 (765)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHH--------------HHHHcCCHHHHHHHHHHHHHhCCC
Confidence            34455666788999999999999987632 223333433333              47889999999999999754  3 


Q ss_pred             CHhHHHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHH
Q 011249          147 NVISWSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCY  220 (490)
Q Consensus       147 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~  220 (490)
                      +...+..++..+...|++++|+..++++.+  | +.. +..+..++...|+.++|+..++++.+   .+...+..+..++
T Consensus        82 ~~~a~~~la~~l~~~g~~~eA~~~l~~~l~~~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~P~~~~~~~~la~~l  160 (765)
T PRK10049         82 NDDYQRGLILTLADAGQYDEALVKAKQLVSGAPDKAN-LLALAYVYKRAGRHWDELRAMTQALPRAPQTQQYPTEYVQAL  160 (765)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            567788889999999999999999999985  3 555 88889999999999999999999876   3556677788888


Q ss_pred             HhcCChHHHHHHHHHHHHcCcccCh------hhHHHHHHHHh-----ccCCh---HHHHHHHHHHHhc-CCCCchh-HH-
Q 011249          221 VQNGYAKAAIEMYKVMRQENVRISE------VAMVGAISACT-----QLGDV---EMAAILAKHVDEG-CCDRTNY-VS-  283 (490)
Q Consensus       221 ~~~g~~~~A~~~~~~~~~~~~~p~~------~~~~~l~~~~~-----~~g~~---~~a~~~~~~~~~~-~~~~~~~-~~-  283 (490)
                      ...+..++|++.++....   .|+.      .....++....     ..+++   ++|...++.+.+. ...|+.. .+ 
T Consensus       161 ~~~~~~e~Al~~l~~~~~---~p~~~~~l~~~~~~~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~  237 (765)
T PRK10049        161 RNNRLSAPALGAIDDANL---TPAEKRDLEADAAAELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQ  237 (765)
T ss_pred             HHCCChHHHHHHHHhCCC---CHHHHHHHHHHHHHHHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHH
Confidence            899999999999886654   2221      11222233222     22334   7788888888754 1222221 11 


Q ss_pred             ---HHHHHHHHhcCChHHHHHHHhcccCCC---h-hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC---cHHHHHHHH
Q 011249          284 ---NALIHMHSKCGYLDLAWREFSRIKNKD---V-ISYSSMITAFADHGKSQEALDMFLKMRNEGIEP---NQVTFIGVL  353 (490)
Q Consensus       284 ---~~l~~~~~~~~~~~~A~~~~~~~~~~~---~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p---~~~~~~~l~  353 (490)
                         ...+.++...|++++|+..|+.+.+.+   + .....+..+|...|++++|+..|+++.+.....   .......+.
T Consensus       238 ~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~~a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~  317 (765)
T PRK10049        238 RARIDRLGALLARDRYKDVISEYQRLKAEGQIIPPWAQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLF  317 (765)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHH
Confidence               111334567799999999999988732   2 122335778999999999999999988642111   134566677


Q ss_pred             HHhcCCCChHHHHHHHHHHHHHcC----------CCCC---chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHH
Q 011249          354 TACSHGGLVEDGCKQFELMTRVFG----------IKPL---TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWG  418 (490)
Q Consensus       354 ~~~~~~g~~~~a~~~~~~~~~~~~----------~~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~  418 (490)
                      .++...|++++|...++.+.....          ..|+   ...+..++..+...|++++|++.++++.  .+.+...+.
T Consensus       318 ~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~  397 (765)
T PRK10049        318 YSLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRI  397 (765)
T ss_pred             HHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHH
Confidence            788999999999999999987310          0122   2345677888999999999999999877  455677889


Q ss_pred             HHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          419 ALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       419 ~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .++..+...|++++|++.++++++.+|+++.++..++..+...|++++|+.+++++.+..+
T Consensus       398 ~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~~a~~al~~~~~~~A~~~~~~ll~~~P  458 (765)
T PRK10049        398 DYASVLQARGWPRAAENELKKAEVLEPRNINLEVEQAWTALDLQEWRQMDVLTDDVVAREP  458 (765)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCC
Confidence            9999999999999999999999999999999999999999999999999999999987644

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

Probab=99.89  E-value=5.7e-20  Score=174.63  Aligned_cols=443  Identities=12%  Similarity=0.075  Sum_probs=336.0

Q ss_pred             hhHHHHHHHHhhhcCCCCchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCC-----CCCceehHHHHHHHHhcCChhHHH
Q 011249           14 NQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPK-----CKTQFLWTSLIRNHVLHAHFRQSI   88 (490)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~-----~~~~~~~~~l~~~~~~~g~~~~A~   88 (490)
                      ..+.++.....+  +.+.||+  +.+.|.+-|--.++ ...++.+...+..     +-.+.+|..+..++...|++++|.
T Consensus       253 ~~~~~ll~~ay~--~n~~nP~--~l~~LAn~fyfK~d-y~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~  327 (1018)
T KOG2002|consen  253 KKGVQLLQRAYK--ENNENPV--ALNHLANHFYFKKD-YERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAF  327 (1018)
T ss_pred             HHHHHHHHHHHh--hcCCCcH--HHHHHHHHHhhccc-HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHH
Confidence            345555555554  1338999  99999999999999 9999998877642     223356999999999999999999


Q ss_pred             HHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCC---
Q 011249           89 LLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCG---  162 (490)
Q Consensus        89 ~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~---  162 (490)
                      ..|-+..+.  .|+..+++.+            .+..+|.+.|+.+.+...|+.+.+  | +..+...|...|...+   
T Consensus       328 ~yY~~s~k~--~~d~~~l~~~------------GlgQm~i~~~dle~s~~~fEkv~k~~p~~~etm~iLG~Lya~~~~~~  393 (1018)
T KOG2002|consen  328 KYYMESLKA--DNDNFVLPLV------------GLGQMYIKRGDLEESKFCFEKVLKQLPNNYETMKILGCLYAHSAKKQ  393 (1018)
T ss_pred             HHHHHHHcc--CCCCcccccc------------chhHHHHHhchHHHHHHHHHHHHHhCcchHHHHHHHHhHHHhhhhhh
Confidence            999776654  5666444321            255679999999999999999986  4 4556666777776664   


Q ss_pred             -ChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcC--------CCCHHhHHHHHHHHHhcCChHHHH
Q 011249          163 -NMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEIS--------EPDASCWAAMTVCYVQNGYAKAAI  230 (490)
Q Consensus       163 -~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~--------~~~~~~~~~l~~~~~~~g~~~~A~  230 (490)
                       ..+.|..++.+..++   |...|..+..++....-+.. +.+|..+.        ...+...|.+...+...|+++.|.
T Consensus       394 ~~~d~a~~~l~K~~~~~~~d~~a~l~laql~e~~d~~~s-L~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~  472 (1018)
T KOG2002|consen  394 EKRDKASNVLGKVLEQTPVDSEAWLELAQLLEQTDPWAS-LDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKAL  472 (1018)
T ss_pred             HHHHHHHHHHHHHHhcccccHHHHHHHHHHHHhcChHHH-HHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHH
Confidence             567788888887765   67788888877766544333 44443332        367788999999999999999999


Q ss_pred             HHHHHHHHc---CcccCh------hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHH
Q 011249          231 EMYKVMRQE---NVRISE------VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWR  301 (490)
Q Consensus       231 ~~~~~~~~~---~~~p~~------~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~  301 (490)
                      ..|.+....   ...++.      .+-..+....-..++.+.|.+.|..+.+.. |.=+..|.-++.+....++..+|..
T Consensus       473 ~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkeh-p~YId~ylRl~~ma~~k~~~~ea~~  551 (1018)
T KOG2002|consen  473 EHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEH-PGYIDAYLRLGCMARDKNNLYEASL  551 (1018)
T ss_pred             HHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHC-chhHHHHHHhhHHHHhccCcHHHHH
Confidence            999988754   122232      244556677778889999999999998874 3334445555544455578889999


Q ss_pred             HHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCcHHHHHHHHHHhcC------------CCChHHH
Q 011249          302 EFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEG-IEPNQVTFIGVLTACSH------------GGLVEDG  365 (490)
Q Consensus       302 ~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~~~~~~l~~~~~~------------~g~~~~a  365 (490)
                      .++++..   .++..+..+...+.+...+..|.+-|+...+.- ..+|.+....|.+.|..            .+..++|
T Consensus       552 ~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KA  631 (1018)
T KOG2002|consen  552 LLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKA  631 (1018)
T ss_pred             HHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHH
Confidence            9998876   577888888889999999999998777776532 23577777777765532            2356788


Q ss_pred             HHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhc
Q 011249          366 CKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLEL  443 (490)
Q Consensus       366 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  443 (490)
                      +++|.++.+  ..|.+...-+.+.-+++..|++.+|..+|.++.  ......+|..+..+|...|++-.|++.|+...+.
T Consensus       632 lq~y~kvL~--~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkk  709 (1018)
T KOG2002|consen  632 LQLYGKVLR--NDPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKK  709 (1018)
T ss_pred             HHHHHHHHh--cCcchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            888888887  566777888889999999999999999999888  2345678999999999999999999999999885


Q ss_pred             C--CCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          444 G--PEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       444 ~--p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .  .+++.+...|++++.+.|++.+|.+.........+
T Consensus       710 f~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~~p  747 (1018)
T KOG2002|consen  710 FYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHLAP  747 (1018)
T ss_pred             hcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCC
Confidence            4  46788999999999999999999999887765544

>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=99.88  E-value=1.3e-18  Score=172.86  Aligned_cols=387  Identities=10%  Similarity=-0.006  Sum_probs=269.1

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCH-hhHHHHHHHh
Q 011249           37 YAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSG-FTFSSVLNAC  113 (490)
Q Consensus        37 ~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~-~~~~~ll~~~  113 (490)
                      .+......+.+.|+ +++|+..|++..  .|+. ..|..+..+|.+.|++++|+..++...+.  .|+. ..+..+-.  
T Consensus       129 ~~k~~G~~~~~~~~-~~~Ai~~y~~al~~~p~~-~~~~n~a~~~~~l~~~~~Ai~~~~~al~l--~p~~~~a~~~~a~--  202 (615)
T TIGR00990       129 KLKEKGNKAYRNKD-FNKAIKLYSKAIECKPDP-VYYSNRAACHNALGDWEKVVEDTTAALEL--DPDYSKALNRRAN--  202 (615)
T ss_pred             HHHHHHHHHHHcCC-HHHHHHHHHHHHhcCCch-HHHHHHHHHHHHhCCHHHHHHHHHHHHHc--CCCCHHHHHHHHH--
Confidence            45566777777787 888888887764  4554 66777777788888888888888877765  3433 23333222  


Q ss_pred             cCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCC---CHhHHHHHHHHHHhCCChHHHHHH--------------------
Q 011249          114 ARVPSLLEAVICGYTKIGLMDDAQRLFDSMAER---NVISWSAMVAGYANCGNMKAAKEF--------------------  170 (490)
Q Consensus       114 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~--------------------  170 (490)
                                  +|...|++++|+..|..+...   +......++..+........+...                    
T Consensus       203 ------------a~~~lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~  270 (615)
T TIGR00990       203 ------------AYDGLGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQS  270 (615)
T ss_pred             ------------HHHHcCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence                        366777777777666544321   111111111100000000111111                    


Q ss_pred             ---------HHHhccCCc---hhHHHHHHHH---HhcCChhHHHHHHhhcCC------CCHHhHHHHHHHHHhcCChHHH
Q 011249          171 ---------YDRMTEKNS---VTWVAMIAGY---GKCGEVREAKKVFDEISE------PDASCWAAMTVCYVQNGYAKAA  229 (490)
Q Consensus       171 ---------~~~~~~~~~---~~~~~l~~~~---~~~~~~~~A~~~~~~~~~------~~~~~~~~l~~~~~~~g~~~~A  229 (490)
                               +....+.+.   ..+..+...+   ...+++++|.+.|+...+      .....|+.+..++...|++++|
T Consensus       271 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA  350 (615)
T TIGR00990       271 FRPKPRPAGLEDSNELDEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEA  350 (615)
T ss_pred             ccCCcchhhhhcccccccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHH
Confidence                     111111011   1111111111   224678999999988764      2345788888999999999999


Q ss_pred             HHHHHHHHHcCcccC-hhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC
Q 011249          230 IEMYKVMRQENVRIS-EVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN  308 (490)
Q Consensus       230 ~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  308 (490)
                      +..|++.....  |+ ...|..+..++...|++++|...++.+.+.. +.+..++..+...+...|++++|...|++..+
T Consensus       351 ~~~~~kal~l~--P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~  427 (615)
T TIGR00990       351 LADLSKSIELD--PRVTQSYIKRASMNLELGDPDKAEEDFDKALKLN-SEDPDIYYHRAQLHFIKGEFAQAGKDYQKSID  427 (615)
T ss_pred             HHHHHHHHHcC--CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            99999998763  44 5678888889999999999999999998875 66788889999999999999999999999876


Q ss_pred             --C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC-ch
Q 011249          309 --K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL-TE  383 (490)
Q Consensus       309 --~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~  383 (490)
                        | +...+..+..++.+.|++++|+..|++..+.  .| +...+..+...+...|++++|...|++....   .|+ ..
T Consensus       428 l~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l---~p~~~~  502 (615)
T TIGR00990       428 LDPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKN--FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIEL---EKETKP  502 (615)
T ss_pred             cCccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhc---CCcccc
Confidence              3 5667888888999999999999999999874  44 4668888899999999999999999998863   222 11


Q ss_pred             H-------HHHHHHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          384 H-------LTCMVDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       384 ~-------~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                      .       ++.....+...|++++|.+++++.. ..| +...+..++..+...|++++|++.|+++.++.+....
T Consensus       503 ~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p~~~~a~~~la~~~~~~g~~~eAi~~~e~A~~l~~~~~e  577 (615)
T TIGR00990       503 MYMNVLPLINKALALFQWKQDFIEAENLCEKALIIDPECDIAVATMAQLLLQQGDVDEALKLFERAAELARTEGE  577 (615)
T ss_pred             ccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHhccHHH
Confidence            1       1222233445799999999998865 334 4557888999999999999999999999998776443

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.86  E-value=3.1e-17  Score=162.88  Aligned_cols=417  Identities=9%  Similarity=-0.017  Sum_probs=256.5

Q ss_pred             hhhchhhHHHHHHHHhhhcCCCCc--hhHhHHHHHHHHHhcCCCCHHHHHHHhccCCCCCCceehHHH--HHHHHhcCCh
Q 011249            9 RSKTFNQLKQVHSYLLKTLTKPHD--QYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSL--IRNHVLHAHF   84 (490)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~l--~~~~~~~g~~   84 (490)
                      ..|++..|...++++.+   ..|+  +.  ++ .++.++...|+ .++|+..+++...|++...+..+  ...+...|++
T Consensus        46 r~Gd~~~Al~~L~qaL~---~~P~~~~a--v~-dll~l~~~~G~-~~~A~~~~eka~~p~n~~~~~llalA~ly~~~gdy  118 (822)
T PRK14574         46 RAGDTAPVLDYLQEESK---AGPLQSGQ--VD-DWLQIAGWAGR-DQEVIDVYERYQSSMNISSRGLASAARAYRNEKRW  118 (822)
T ss_pred             hCCCHHHHHHHHHHHHh---hCccchhh--HH-HHHHHHHHcCC-cHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCH
Confidence            44666667766666665   4433  23  33 77777777777 78888888877766552333333  3356666888


Q ss_pred             hHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--CCHhHHHHHHHHHHhCC
Q 011249           85 RQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--RNVISWSAMVAGYANCG  162 (490)
Q Consensus        85 ~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~  162 (490)
                      ++|+++|+++.+.  .|+.......             ++..+...++.++|++.++++.+  |+...+..++..+...+
T Consensus       119 d~Aiely~kaL~~--dP~n~~~l~g-------------La~~y~~~~q~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~  183 (822)
T PRK14574        119 DQALALWQSSLKK--DPTNPDLISG-------------MIMTQADAGRGGVVLKQATELAERDPTVQNYMTLSYLNRATD  183 (822)
T ss_pred             HHHHHHHHHHHhh--CCCCHHHHHH-------------HHHHHhhcCCHHHHHHHHHHhcccCcchHHHHHHHHHHHhcc
Confidence            8888888887776  4443222111             22346777888888888887776  34334433333333345


Q ss_pred             ChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhHHHHHHhhcCC-CCHHhH--------HHHHHHH-----HhcCC
Q 011249          163 NMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVREAKKVFDEISE-PDASCW--------AAMTVCY-----VQNGY  225 (490)
Q Consensus       163 ~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~~~~~--------~~l~~~~-----~~~g~  225 (490)
                      +..+|++.++++.+  | +...+..+..+..+.|-...|.++..+-+. -+...+        ..+++.-     ...++
T Consensus       184 ~~~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r  263 (822)
T PRK14574        184 RNYDALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETER  263 (822)
T ss_pred             hHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhh
Confidence            55557888877774  3 555667777777777777777777766553 111110        1111110     01122


Q ss_pred             h---HHHHHHHHHHHH-cCcccChh-----hHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCh
Q 011249          226 A---KAAIEMYKVMRQ-ENVRISEV-----AMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYL  296 (490)
Q Consensus       226 ~---~~A~~~~~~~~~-~~~~p~~~-----~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  296 (490)
                      +   +.|+.-++.+.. .+..|...     ...-.+-++...|+..++++.|+.+...+.+....+-.++.++|...+++
T Consensus       264 ~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P  343 (822)
T PRK14574        264 FDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLP  343 (822)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCc
Confidence            2   334445555443 12223221     12233445667777888888888887776555556667777888888888


Q ss_pred             HHHHHHHhcccCC---------ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCC-----------CCcH--H-HHHHHH
Q 011249          297 DLAWREFSRIKNK---------DVISYSSMITAFADHGKSQEALDMFLKMRNEGI-----------EPNQ--V-TFIGVL  353 (490)
Q Consensus       297 ~~A~~~~~~~~~~---------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-----------~p~~--~-~~~~l~  353 (490)
                      ++|+.+|+.+..+         +......|.-+|...+++++|..+++++.+...           .|++  . .+..++
T Consensus       344 ~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a  423 (822)
T PRK14574        344 EKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLV  423 (822)
T ss_pred             HHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHH
Confidence            8888888776441         222245667777778888888888887776311           1222  1 333445


Q ss_pred             HHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChH
Q 011249          354 TACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAE  431 (490)
Q Consensus       354 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~  431 (490)
                      ..+...|+..+|++.++++..  .-|-|......+.+.+...|.+.+|.+.++...  .+.+..+....+.++...|++.
T Consensus       424 ~~~~~~gdl~~Ae~~le~l~~--~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~~  501 (822)
T PRK14574        424 QSLVALNDLPTAQKKLEDLSS--TAPANQNLRIALASIYLARDLPRKAEQELKAVESLAPRSLILERAQAETAMALQEWH  501 (822)
T ss_pred             HHHHHcCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhhHH
Confidence            556677788888888888766  456667777777777888888888888776654  3334556666777777778888


Q ss_pred             HHHHHHHHHHhcCCCCCc
Q 011249          432 LGEIAARHLLELGPEKTG  449 (490)
Q Consensus       432 ~a~~~~~~~~~~~p~~~~  449 (490)
                      +|..+.+.+.+..|+++.
T Consensus       502 ~A~~~~~~l~~~~Pe~~~  519 (822)
T PRK14574        502 QMELLTDDVISRSPEDIP  519 (822)
T ss_pred             HHHHHHHHHHhhCCCchh
Confidence            888888888888887764

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.86  E-value=3.4e-17  Score=162.61  Aligned_cols=424  Identities=10%  Similarity=0.026  Sum_probs=306.5

Q ss_pred             HHHHHHHhcCCCCHHHHHHHhccCCC--CCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCC
Q 011249           39 QFLIRLLQLPGDNLSYARQVFDQIPK--CKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARV  116 (490)
Q Consensus        39 ~~l~~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~  116 (490)
                      ..-+-...+.|+ ++.|+..|++..+  |+.......++..+...|+.++|+..+++..    .|+...+..++.     
T Consensus        38 y~~aii~~r~Gd-~~~Al~~L~qaL~~~P~~~~av~dll~l~~~~G~~~~A~~~~eka~----~p~n~~~~~lla-----  107 (822)
T PRK14574         38 YDSLIIRARAGD-TAPVLDYLQEESKAGPLQSGQVDDWLQIAGWAGRDQEVIDVYERYQ----SSMNISSRGLAS-----  107 (822)
T ss_pred             HHHHHHHHhCCC-HHHHHHHHHHHHhhCccchhhHHHHHHHHHHcCCcHHHHHHHHHhc----cCCCCCHHHHHH-----
Confidence            344445568888 9999999999874  3321123388888888899999999999887    454444544432     


Q ss_pred             CChHHHHHHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCCChHHHHHHHHHhccCCch--hHHHHHHHHHh
Q 011249          117 PSLLEAVICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSV--TWVAMIAGYGK  191 (490)
Q Consensus       117 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--~~~~l~~~~~~  191 (490)
                            +...|...|++++|+++|+++.+  | +...+..++..+...++.++|++.++++...++.  .+..++..+..
T Consensus       108 ------lA~ly~~~gdyd~Aiely~kaL~~dP~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~dp~~~~~l~layL~~~  181 (822)
T PRK14574        108 ------AARAYRNEKRWDQALALWQSSLKKDPTNPDLISGMIMTQADAGRGGVVLKQATELAERDPTVQNYMTLSYLNRA  181 (822)
T ss_pred             ------HHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHhhcCCHHHHHHHHHHhcccCcchHHHHHHHHHHHh
Confidence                  23357888999999999999986  3 5566777888899999999999999999875443  44444444444


Q ss_pred             cCChhHHHHHHhhcCC--C-CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhH------HHHHHHH-----hc
Q 011249          192 CGEVREAKKVFDEISE--P-DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAM------VGAISAC-----TQ  257 (490)
Q Consensus       192 ~~~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~------~~l~~~~-----~~  257 (490)
                      .++..+|++.++++.+  | +...+..+..+..+.|-...|+++.++-... +.+.....      ...++--     ..
T Consensus       182 ~~~~~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~-f~~~~~~~l~~~~~a~~vr~a~~~~~~~  260 (822)
T PRK14574        182 TDRNYDALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLAKENPNL-VSAEHYRQLERDAAAEQVRMAVLPTRSE  260 (822)
T ss_pred             cchHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccc-cCHHHHHHHHHHHHHHHHhhcccccccc
Confidence            5666669999998875  4 5677788889999999999988776653211 11111100      1111100     01


Q ss_pred             cCCh---HHHHHHHHHHHhc-C-CCCchhHH----HHHHHHHHhcCChHHHHHHHhcccCC----ChhHHHHHHHHHHhc
Q 011249          258 LGDV---EMAAILAKHVDEG-C-CDRTNYVS----NALIHMHSKCGYLDLAWREFSRIKNK----DVISYSSMITAFADH  324 (490)
Q Consensus       258 ~g~~---~~a~~~~~~~~~~-~-~~~~~~~~----~~l~~~~~~~~~~~~A~~~~~~~~~~----~~~~~~~l~~~~~~~  324 (490)
                      ..++   +.|..-++.+... + .|+....|    .-.+-++...|++.++++.|+.+..+    ...+-..+.++|...
T Consensus       261 ~~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~  340 (822)
T PRK14574        261 TERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDR  340 (822)
T ss_pred             hhhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhc
Confidence            2233   3344444444432 1 12222222    22355678889999999999999852    345677889999999


Q ss_pred             CChHHHHHHHHHHHHcC-----CCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcC----------CCCC---chHHH
Q 011249          325 GKSQEALDMFLKMRNEG-----IEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFG----------IKPL---TEHLT  386 (490)
Q Consensus       325 ~~~~~a~~~~~~~~~~~-----~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~----------~~~~---~~~~~  386 (490)
                      +++++|+.+|+.+....     ..++......|.-++...+++++|..+++.+.+...          -.|+   ...+.
T Consensus       341 ~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~  420 (822)
T PRK14574        341 RLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQT  420 (822)
T ss_pred             CCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHH
Confidence            99999999999997643     122334457888999999999999999999987311          0122   22334


Q ss_pred             HHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCc
Q 011249          387 CMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKW  464 (490)
Q Consensus       387 ~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  464 (490)
                      .++..+.-.|++.+|++.++++.  .+-|......+...+...|.+.+|++.++.+...+|++..+....+.++...|+|
T Consensus       421 l~a~~~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l~P~~~~~~~~~~~~al~l~e~  500 (822)
T PRK14574        421 LLVQSLVALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKAEQELKAVESLAPRSLILERAQAETAMALQEW  500 (822)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhhCCccHHHHHHHHHHHHhhhhH
Confidence            56778899999999999999987  4557889999999999999999999999999999999999999999999999999


Q ss_pred             chHHHHHHHhhhccc
Q 011249          465 KDSEIVKMMISETEK  479 (490)
Q Consensus       465 ~~A~~~~~~~~~~~~  479 (490)
                      ++|..+.+++.+..+
T Consensus       501 ~~A~~~~~~l~~~~P  515 (822)
T PRK14574        501 HQMELLTDDVISRSP  515 (822)
T ss_pred             HHHHHHHHHHHhhCC
Confidence            999999988766544

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

Probab=99.85  E-value=3e-18  Score=149.83  Aligned_cols=412  Identities=16%  Similarity=0.128  Sum_probs=282.1

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHhccCC----CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHH
Q 011249           37 YAQFLIRLLQLPGDNLSYARQVFDQIP----KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNA  112 (490)
Q Consensus        37 ~~~~l~~~~~~~~~~~~~A~~~~~~~~----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~  112 (490)
                      ++.-|..-|..+.. ..+|+..++-+.    .|+....--.+...+.++..+.+|++.|+-....-...+-.+-.-+++-
T Consensus       203 vl~nlaqqy~~ndm-~~ealntyeiivknkmf~nag~lkmnigni~~kkr~fskaikfyrmaldqvpsink~~rikil~n  281 (840)
T KOG2003|consen  203 VLFNLAQQYEANDM-TAEALNTYEIIVKNKMFPNAGILKMNIGNIHFKKREFSKAIKFYRMALDQVPSINKDMRIKILNN  281 (840)
T ss_pred             HHHHHHHHhhhhHH-HHHHhhhhhhhhcccccCCCceeeeeecceeeehhhHHHHHHHHHHHHhhccccchhhHHHHHhh
Confidence            44455566777788 889999988775    2443233334556677889999999999877765222222232223322


Q ss_pred             hcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--CCHhHHHHHHHHHHhCCChHHHHHHHHHhcc----C---------
Q 011249          113 CARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--RNVISWSAMVAGYANCGNMKAAKEFYDRMTE----K---------  177 (490)
Q Consensus       113 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~---------  177 (490)
                                +.-.+.+.|+++.|+..|+...+  ||..+--.|+-++..-|+.++..+.|.+|..    +         
T Consensus       282 ----------igvtfiq~gqy~dainsfdh~m~~~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddkyi~~~  351 (840)
T KOG2003|consen  282 ----------IGVTFIQAGQYDDAINSFDHCMEEAPNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDKYIKEK  351 (840)
T ss_pred             ----------cCeeEEecccchhhHhhHHHHHHhCccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCcccccCCc
Confidence                      22247888999999999998876  7777655666677778999999999999973    1         


Q ss_pred             -Cc--hhHH-----HHHHHHHhcC--ChhHHHHHHhhcC----CCCHH-------------hHH--------HHHHHHHh
Q 011249          178 -NS--VTWV-----AMIAGYGKCG--EVREAKKVFDEIS----EPDAS-------------CWA--------AMTVCYVQ  222 (490)
Q Consensus       178 -~~--~~~~-----~l~~~~~~~~--~~~~A~~~~~~~~----~~~~~-------------~~~--------~l~~~~~~  222 (490)
                       |+  ...+     -.+.-.-+.+  +.++++-.--++.    .|+-.             .+.        .-...+.+
T Consensus       352 ddp~~~ll~eai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka~~~lk  431 (840)
T KOG2003|consen  352 DDPDDNLLNEAIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAIDLEINKAGELLK  431 (840)
T ss_pred             CCcchHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHHHHHHh
Confidence             11  1111     1111111111  1222221111111    12210             011        11234677


Q ss_pred             cCChHHHHHHHHHHHHcCcccChhhHH------------------------------------HHHHHHhccCChHHHHH
Q 011249          223 NGYAKAAIEMYKVMRQENVRISEVAMV------------------------------------GAISACTQLGDVEMAAI  266 (490)
Q Consensus       223 ~g~~~~A~~~~~~~~~~~~~p~~~~~~------------------------------------~l~~~~~~~g~~~~a~~  266 (490)
                      .|+++.|+++++-+.+..-+.-...-+                                    .-.+.....|++++|..
T Consensus       432 ~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~dryn~~a~~nkgn~~f~ngd~dka~~  511 (840)
T KOG2003|consen  432 NGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAFANGDLDKAAE  511 (840)
T ss_pred             ccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhcccccCHHHhhcCCceeeecCcHHHHHH
Confidence            788888888777765432221111111                                    11111123578888888


Q ss_pred             HHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 011249          267 LAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIE  343 (490)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  343 (490)
                      .|++.....-.-....|| +.-.+...|++++|+..|-++..   .+..+...+...|-...++.+|++++.+.... ++
T Consensus       512 ~ykeal~ndasc~ealfn-iglt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~~q~~sl-ip  589 (840)
T KOG2003|consen  512 FYKEALNNDASCTEALFN-IGLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELLMQANSL-IP  589 (840)
T ss_pred             HHHHHHcCchHHHHHHHH-hcccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhccc-CC
Confidence            888887655333333444 44567788999999999877654   67778888888898899999999999877663 44


Q ss_pred             CcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCChhhHHHHHH
Q 011249          344 PNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAGTWGALLG  422 (490)
Q Consensus       344 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~~~~~l~~  422 (490)
                      .|+..+..|...|-+.|+-..|.+.+-.--+  -++.+.++...|..-|....-+++|+.+|++.. .+|+..-|..++.
T Consensus       590 ~dp~ilskl~dlydqegdksqafq~~ydsyr--yfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwqlmia  667 (840)
T KOG2003|consen  590 NDPAILSKLADLYDQEGDKSQAFQCHYDSYR--YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQLMIA  667 (840)
T ss_pred             CCHHHHHHHHHHhhcccchhhhhhhhhhccc--ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHHHHHH
Confidence            4677899999999999999999988776655  677888999999999999999999999998876 7899999998887


Q ss_pred             HH-hhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCC
Q 011249          423 AC-KVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGK  463 (490)
Q Consensus       423 ~~-~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  463 (490)
                      .| .+.|++++|.++|+......|.+...+..|++++...|.
T Consensus       668 sc~rrsgnyqka~d~yk~~hrkfpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  668 SCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             HHHHhcccHHHHHHHHHHHHHhCccchHHHHHHHHHhccccc
Confidence            76 568999999999999999999999999999999888775

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

Probab=99.82  E-value=1.3e-16  Score=152.17  Aligned_cols=442  Identities=14%  Similarity=0.111  Sum_probs=335.2

Q ss_pred             hchhhHHHHHHHHhhhcCCC----CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCC--CCC-ceehHHHHHHHHhcCC
Q 011249           11 KTFNQLKQVHSYLLKTLTKP----HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPK--CKT-QFLWTSLIRNHVLHAH   83 (490)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~--~~~-~~~~~~l~~~~~~~g~   83 (490)
                      ++++.+..+....++   .-    --..  .+..+.++|...|+ +++|...|-+...  ++. ...+--|.+.+...|+
T Consensus       284 ~dy~~v~~la~~ai~---~t~~~~~~ae--s~Y~~gRs~Ha~Gd-~ekA~~yY~~s~k~~~d~~~l~~~GlgQm~i~~~d  357 (1018)
T KOG2002|consen  284 KDYERVWHLAEHAIK---NTENKSIKAE--SFYQLGRSYHAQGD-FEKAFKYYMESLKADNDNFVLPLVGLGQMYIKRGD  357 (1018)
T ss_pred             ccHHHHHHHHHHHHH---hhhhhHHHHH--HHHHHHHHHHhhcc-HHHHHHHHHHHHccCCCCccccccchhHHHHHhch
Confidence            466666666666666   33    2223  47889999999999 9999999987753  333 2445668889999999


Q ss_pred             hhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcC----CHHHHHHHHhhcCCC---CHhHHHHHHH
Q 011249           84 FRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIG----LMDDAQRLFDSMAER---NVISWSAMVA  156 (490)
Q Consensus        84 ~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g----~~~~A~~~~~~~~~~---~~~~~~~l~~  156 (490)
                      .+.+...|+...+.  .|+...-..++..             .|...+    ..+.|..++.+..++   |...|-.+..
T Consensus       358 le~s~~~fEkv~k~--~p~~~etm~iLG~-------------Lya~~~~~~~~~d~a~~~l~K~~~~~~~d~~a~l~laq  422 (1018)
T KOG2002|consen  358 LEESKFCFEKVLKQ--LPNNYETMKILGC-------------LYAHSAKKQEKRDKASNVLGKVLEQTPVDSEAWLELAQ  422 (1018)
T ss_pred             HHHHHHHHHHHHHh--CcchHHHHHHHHh-------------HHHhhhhhhHHHHHHHHHHHHHHhcccccHHHHHHHHH
Confidence            99999999999886  6766655555554             244443    567888888888764   5667777777


Q ss_pred             HHHhCCChHHHHHHHHHhc--------cCCchhHHHHHHHHHhcCChhHHHHHHhhcCC-------CCH------HhHHH
Q 011249          157 GYANCGNMKAAKEFYDRMT--------EKNSVTWVAMIAGYGKCGEVREAKKVFDEISE-------PDA------SCWAA  215 (490)
Q Consensus       157 ~~~~~~~~~~a~~~~~~~~--------~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-------~~~------~~~~~  215 (490)
                      .+... ++..++.+|..+.        ..-+...|.+...+...|++++|...|.....       ++.      .+-..
T Consensus       423 l~e~~-d~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YN  501 (1018)
T KOG2002|consen  423 LLEQT-DPWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYN  501 (1018)
T ss_pred             HHHhc-ChHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHH
Confidence            66554 4444466666655        23677889999999999999999999987643       222      23445


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCcccC-hhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcC
Q 011249          216 MTVCYVQNGYAKAAIEMYKVMRQENVRIS-EVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCG  294 (490)
Q Consensus       216 l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  294 (490)
                      +..+.-..++++.|.+.|..+.+.  .|. ...|..++......+...+|...++++.... ..++..+..+...|.+..
T Consensus       502 larl~E~l~~~~~A~e~Yk~Ilke--hp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d-~~np~arsl~G~~~l~k~  578 (1018)
T KOG2002|consen  502 LARLLEELHDTEVAEEMYKSILKE--HPGYIDAYLRLGCMARDKNNLYEASLLLKDALNID-SSNPNARSLLGNLHLKKS  578 (1018)
T ss_pred             HHHHHHhhhhhhHHHHHHHHHHHH--CchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcc-cCCcHHHHHHHHHHHhhh
Confidence            777888889999999999999986  344 3455555544456688999999999998775 667777777888999999


Q ss_pred             ChHHHHHHHhcccC-----CChhHHHHHHHHHHh------------cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhc
Q 011249          295 YLDLAWREFSRIKN-----KDVISYSSMITAFAD------------HGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACS  357 (490)
Q Consensus       295 ~~~~A~~~~~~~~~-----~~~~~~~~l~~~~~~------------~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~  357 (490)
                      .+..|.+-|+.+.+     +|+.+.-+|...|.+            .+..++|+++|.+.++.. +.|...-+.+.-+++
T Consensus       579 ~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~~d-pkN~yAANGIgiVLA  657 (1018)
T KOG2002|consen  579 EWKPAKKKFETILKKTSTKTDAYSLIALGNVYIQALHNPSRNPEKEKKHQEKALQLYGKVLRND-PKNMYAANGIGIVLA  657 (1018)
T ss_pred             hhcccccHHHHHHhhhccCCchhHHHHhhHHHHHHhcccccChHHHHHHHHHHHHHHHHHHhcC-cchhhhccchhhhhh
Confidence            99888886665543     466666666665542            345788999999988852 336667788888899


Q ss_pred             CCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc----CCCChhhHHHHHHHHhhhCChHHH
Q 011249          358 HGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK----DFCDAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       358 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      ..|++.+|..+|.++.+.  ......+|-.+..+|..+|++..|+++|+...    ...+..+...|..++...|.+.+|
T Consensus       658 ~kg~~~~A~dIFsqVrEa--~~~~~dv~lNlah~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~ea  735 (1018)
T KOG2002|consen  658 EKGRFSEARDIFSQVREA--TSDFEDVWLNLAHCYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEA  735 (1018)
T ss_pred             hccCchHHHHHHHHHHHH--HhhCCceeeeHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHH
Confidence            999999999999999984  44566788889999999999999999998765    446788999999999999999999


Q ss_pred             HHHHHHHHhcCCCCCchHHHHHHHHHhc-------------------CCcchHHHHHHHhhhcccc
Q 011249          434 EIAARHLLELGPEKTGNSALLANIYASM-------------------GKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       434 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~-------------------g~~~~A~~~~~~~~~~~~~  480 (490)
                      .+.+..+....|.++.+..+++.+..+.                   +..+.|.++|..|...+-.
T Consensus       736 k~~ll~a~~~~p~~~~v~FN~a~v~kkla~s~lr~~k~t~eev~~a~~~le~a~r~F~~ls~~~d~  801 (1018)
T KOG2002|consen  736 KEALLKARHLAPSNTSVKFNLALVLKKLAESILRLEKRTLEEVLEAVKELEEARRLFTELSKNGDK  801 (1018)
T ss_pred             HHHHHHHHHhCCccchHHhHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence            9999999999999999888877665532                   3456777788777766543

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

Probab=99.79  E-value=2.1e-14  Score=131.56  Aligned_cols=434  Identities=12%  Similarity=0.095  Sum_probs=330.3

Q ss_pred             HhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHH----HhcCCCCCHhhHHHHHHHhcCCCC
Q 011249           45 LQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKM----HRLGVLTSGFTFSSVLNACARVPS  118 (490)
Q Consensus        45 ~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m----~~~g~~p~~~~~~~ll~~~~~~~~  118 (490)
                      |++... ++.|.+++++..  -|.....|-+-...--.+|+.+...+++.+.    ...|+..+...|-.=-..|-..|.
T Consensus       416 larLet-YenAkkvLNkaRe~iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~e~ags  494 (913)
T KOG0495|consen  416 LARLET-YENAKKVLNKAREIIPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEACEDAGS  494 (913)
T ss_pred             HHHHHH-HHHHHHHHHHHHhhCCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHHhhcCC
Confidence            344444 666666666654  2333366666666666778888887777653    345655555444333333333332


Q ss_pred             hH-----------------------HHHHHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCCChHHHHHHHH
Q 011249          119 LL-----------------------EAVICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCGNMKAAKEFYD  172 (490)
Q Consensus       119 ~~-----------------------~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~  172 (490)
                      ..                       ..-...|.+.+.++-|+.+|....+  | +...|......--..|..+....+|+
T Consensus       495 v~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqvfp~k~slWlra~~~ek~hgt~Esl~Allq  574 (913)
T KOG0495|consen  495 VITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQVFPCKKSLWLRAAMFEKSHGTRESLEALLQ  574 (913)
T ss_pred             hhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhhccchhHHHHHHHHHHHhcCcHHHHHHHHH
Confidence            22                       3345556677777778888877776  3 55667777766667788888888888


Q ss_pred             HhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChh
Q 011249          173 RMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEV  246 (490)
Q Consensus       173 ~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~  246 (490)
                      +....   ....|...+.-+...||+..|..++..+.+   .+...|..-+.....+.++++|..+|.+....  .|+..
T Consensus       575 kav~~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar~~--sgTeR  652 (913)
T KOG0495|consen  575 KAVEQCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKARSI--SGTER  652 (913)
T ss_pred             HHHHhCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHhcc--CCcch
Confidence            88853   555667777778888999999999888765   46678888888889999999999999888764  56777


Q ss_pred             hHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-ChhHHHHHHHHHHh
Q 011249          247 AMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-DVISYSSMITAFAD  323 (490)
Q Consensus       247 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~  323 (490)
                      .|.--+..---.++.++|.++++...+.- +.-...|..+.+.+.+.++++.|...|..-.+  | .+..|-.+...--+
T Consensus       653 v~mKs~~~er~ld~~eeA~rllEe~lk~f-p~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllLakleEk  731 (913)
T KOG0495|consen  653 VWMKSANLERYLDNVEEALRLLEEALKSF-PDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLLAKLEEK  731 (913)
T ss_pred             hhHHHhHHHHHhhhHHHHHHHHHHHHHhC-CchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHHHHHHHH
Confidence            77776766677889999999998888774 66677888889999999999999999988776  4 45578888878888


Q ss_pred             cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHH
Q 011249          324 HGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHS  403 (490)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  403 (490)
                      .|++-.|..++++..-.+ +-+...|...|+.-.+.|..+.|..++.+..+  ..+.+...|..-|.+..+.++-..+..
T Consensus       732 ~~~~~rAR~ildrarlkN-Pk~~~lwle~Ir~ElR~gn~~~a~~lmakALQ--ecp~sg~LWaEaI~le~~~~rkTks~D  808 (913)
T KOG0495|consen  732 DGQLVRARSILDRARLKN-PKNALLWLESIRMELRAGNKEQAELLMAKALQ--ECPSSGLLWAEAIWLEPRPQRKTKSID  808 (913)
T ss_pred             hcchhhHHHHHHHHHhcC-CCcchhHHHHHHHHHHcCCHHHHHHHHHHHHH--hCCccchhHHHHHHhccCcccchHHHH
Confidence            889999999999988753 33566888889988899999999999999988  577777788888888778777777777


Q ss_pred             HHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccccCC
Q 011249          404 LIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSP  483 (490)
Q Consensus       404 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  483 (490)
                      .+++..  .|+.+...+...+.....+++|.+-|.++++.+|++-.++..+...+.+.|.-++-.+++++...  .+|.-
T Consensus       809 ALkkce--~dphVllaia~lfw~e~k~~kar~Wf~Ravk~d~d~GD~wa~fykfel~hG~eed~kev~~~c~~--~EP~h  884 (913)
T KOG0495|consen  809 ALKKCE--HDPHVLLAIAKLFWSEKKIEKAREWFERAVKKDPDNGDAWAWFYKFELRHGTEEDQKEVLKKCET--AEPTH  884 (913)
T ss_pred             HHHhcc--CCchhHHHHHHHHHHHHHHHHHHHHHHHHHccCCccchHHHHHHHHHHHhCCHHHHHHHHHHHhc--cCCCC
Confidence            776654  67777888888888899999999999999999999999999999999999999999999988765  46777


Q ss_pred             CccccC
Q 011249          484 GCSWIS  489 (490)
Q Consensus       484 ~~~~~~  489 (490)
                      |..|..
T Consensus       885 G~~W~a  890 (913)
T KOG0495|consen  885 GELWQA  890 (913)
T ss_pred             CcHHHH
Confidence            888864

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

Probab=99.78  E-value=1.4e-18  Score=155.30  Aligned_cols=258  Identities=14%  Similarity=0.065  Sum_probs=115.2

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCccc-ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc
Q 011249          215 AMTVCYVQNGYAKAAIEMYKVMRQENVRI-SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC  293 (490)
Q Consensus       215 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  293 (490)
                      .+...+.+.|++++|++++++.......| +...+..+...+...++++.|...++++...+ +.++..+..++.. ...
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~-~~~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASD-KANPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccc-ccc
Confidence            45777888899999999997655443223 34444555556677889999999999988776 4466677777777 688


Q ss_pred             CChHHHHHHHhcccC--CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCcHHHHHHHHHHhcCCCChHHHHHHHH
Q 011249          294 GYLDLAWREFSRIKN--KDVISYSSMITAFADHGKSQEALDMFLKMRNEG-IEPNQVTFIGVLTACSHGGLVEDGCKQFE  370 (490)
Q Consensus       294 ~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~~~~~~l~~~~~~~g~~~~a~~~~~  370 (490)
                      +++++|.++++..-+  +++..+..++..+...++++++..+++.+.... ..++...|..+...+.+.|+.++|++.++
T Consensus        91 ~~~~~A~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~  170 (280)
T PF13429_consen   91 GDPEEALKLAEKAYERDGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDYR  170 (280)
T ss_dssp             ---------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHHH
T ss_pred             ccccccccccccccccccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            999999988877644  566777888888999999999999999987643 34566788888889999999999999999


Q ss_pred             HHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC
Q 011249          371 LMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       371 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      ++.+.  .|.+......++..+...|+.+++.++++...  .+.++..+..+..++...|+.++|...++++.+..|+|+
T Consensus       171 ~al~~--~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d~  248 (280)
T PF13429_consen  171 KALEL--DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDDP  248 (280)
T ss_dssp             HHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-H
T ss_pred             HHHHc--CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhcccccccccccccccccccccccc
Confidence            99883  44457788889999999999999888887776  356777889999999999999999999999999999999


Q ss_pred             chHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          449 GNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       449 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      .....++.++...|+.++|.++.+++.+
T Consensus       249 ~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  249 LWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             HHHHHHHHHHT-----------------
T ss_pred             cccccccccccccccccccccccccccc
Confidence            9999999999999999999999887653

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

Probab=99.77  E-value=1.7e-15  Score=143.66  Aligned_cols=336  Identities=15%  Similarity=0.131  Sum_probs=255.3

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhc---CCCCHHhHHHHHHHHHhcC
Q 011249          151 WSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEI---SEPDASCWAAMTVCYVQNG  224 (490)
Q Consensus       151 ~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~---~~~~~~~~~~l~~~~~~~g  224 (490)
                      .-...+.....|++++|.+++.++++.   +...|.+|..+|-..|+.+++...+-.+   .+.|...|..+.....+.|
T Consensus       142 ll~eAN~lfarg~~eeA~~i~~EvIkqdp~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~p~d~e~W~~ladls~~~~  221 (895)
T KOG2076|consen  142 LLGEANNLFARGDLEEAEEILMEVIKQDPRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLNPKDYELWKRLADLSEQLG  221 (895)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhCccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcCCCChHHHHHHHHHHHhcc
Confidence            333445555669999999999999864   6678999999999999999988776443   3467788999999999999


Q ss_pred             ChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHH----HHHHHHHHhcCChHHHH
Q 011249          225 YAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVS----NALIHMHSKCGYLDLAW  300 (490)
Q Consensus       225 ~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~----~~l~~~~~~~~~~~~A~  300 (490)
                      ++++|.-.|.+.++.. +++...+-.-...|.+.|+...|...|.++.....+.|..-+    -..++.+...++-+.|.
T Consensus       222 ~i~qA~~cy~rAI~~~-p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~  300 (895)
T KOG2076|consen  222 NINQARYCYSRAIQAN-PSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAA  300 (895)
T ss_pred             cHHHHHHHHHHHHhcC-CcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            9999999999998874 345556666667788899999999999998887643333222    22455666777778888


Q ss_pred             HHHhcccC-----CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHH--------------------------
Q 011249          301 REFSRIKN-----KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTF--------------------------  349 (490)
Q Consensus       301 ~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~--------------------------  349 (490)
                      +.++....     -+...++.++..|.+...++.+......+......+|...+                          
T Consensus       301 ~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v  380 (895)
T KOG2076|consen  301 KALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRV  380 (895)
T ss_pred             HHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchh
Confidence            88877665     24457888888899999999998888887762222222111                          


Q ss_pred             HHHHHHhcCCCChHHHHHHHHHHHHHcC--CCCCchHHHHHHHHHhhcCChHHHHHHHHhccCC---CChhhHHHHHHHH
Q 011249          350 IGVLTACSHGGLVEDGCKQFELMTRVFG--IKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDF---CDAGTWGALLGAC  424 (490)
Q Consensus       350 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~~~~~~l~~~~  424 (490)
                      ..++-++.+....+....+....... .  ...+...|..+.++|...|++.+|+.+|..+...   .+...|..+...+
T Consensus       381 ~rl~icL~~L~~~e~~e~ll~~l~~~-n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~  459 (895)
T KOG2076|consen  381 IRLMICLVHLKERELLEALLHFLVED-NVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCY  459 (895)
T ss_pred             HhHhhhhhcccccchHHHHHHHHHHh-cCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHH
Confidence            12222334444444444555555553 5  3345778899999999999999999999998833   2456899999999


Q ss_pred             hhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccccCCCcccc
Q 011249          425 KVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI  488 (490)
Q Consensus       425 ~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  488 (490)
                      ...|.+++|.+.|++++...|++..+..+|+.++.+.|+.++|.+++..+...+.+..+++.|-
T Consensus       460 ~~l~e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~~  523 (895)
T KOG2076|consen  460 MELGEYEEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQIINPDGRNAEACAWE  523 (895)
T ss_pred             HHHhhHHHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhcccCCCccchhhcccc
Confidence            9999999999999999999999999999999999999999999999999886666666777773

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

Probab=99.75  E-value=1.4e-13  Score=121.62  Aligned_cols=438  Identities=11%  Similarity=0.059  Sum_probs=327.0

Q ss_pred             hchhhHHHHHHHHhhhcCCC-CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHH
Q 011249           11 KTFNQLKQVHSYLLKTLTKP-HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQS   87 (490)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A   87 (490)
                      ++...|.++++....   .+ ++..  +|-..+++-.++.. +..|+.+|++..  -|.+...|..-+..--..|+...|
T Consensus        87 ~e~~RARSv~ERALd---vd~r~it--LWlkYae~Emknk~-vNhARNv~dRAvt~lPRVdqlWyKY~ymEE~LgNi~ga  160 (677)
T KOG1915|consen   87 KEIQRARSVFERALD---VDYRNIT--LWLKYAEFEMKNKQ-VNHARNVWDRAVTILPRVDQLWYKYIYMEEMLGNIAGA  160 (677)
T ss_pred             HHHHHHHHHHHHHHh---cccccch--HHHHHHHHHHhhhh-HhHHHHHHHHHHHhcchHHHHHHHHHHHHHHhcccHHH
Confidence            456678888888887   66 8888  99999999999999 999999999876  344435677777777778999999


Q ss_pred             HHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcC--CCCHhHHHHHHHHHHhCCChH
Q 011249           88 ILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMA--ERNVISWSAMVAGYANCGNMK  165 (490)
Q Consensus        88 ~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~  165 (490)
                      .++|++..+.  .|+...|.+.|+-              =.+...++.|+.++++..  .|++.+|-....--.+.|+..
T Consensus       161 RqiferW~~w--~P~eqaW~sfI~f--------------ElRykeieraR~IYerfV~~HP~v~~wikyarFE~k~g~~~  224 (677)
T KOG1915|consen  161 RQIFERWMEW--EPDEQAWLSFIKF--------------ELRYKEIERARSIYERFVLVHPKVSNWIKYARFEEKHGNVA  224 (677)
T ss_pred             HHHHHHHHcC--CCcHHHHHHHHHH--------------HHHhhHHHHHHHHHHHHheecccHHHHHHHHHHHHhcCcHH
Confidence            9999998876  8999999988874              577889999999999876  499999999999999999999


Q ss_pred             HHHHHHHHhccC------CchhHHHHHHHHHhcCChhHHHHHHhhcCC-----CCHHhHHHHHHHHHhcCChHHHHH---
Q 011249          166 AAKEFYDRMTEK------NSVTWVAMIAGYGKCGEVREAKKVFDEISE-----PDASCWAAMTVCYVQNGYAKAAIE---  231 (490)
Q Consensus       166 ~a~~~~~~~~~~------~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~~~~~~~l~~~~~~~g~~~~A~~---  231 (490)
                      .|.++|+...+-      +...+.+...--.++..++.|.-+|.-...     .....|..+...--+-|+......   
T Consensus       225 ~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv  304 (677)
T KOG1915|consen  225 LARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIV  304 (677)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHh
Confidence            999999988853      444566666666677788888888765543     224456656555555666544333   


Q ss_pred             -----HHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchh------HHH---HHHHHHHhcCChH
Q 011249          232 -----MYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNY------VSN---ALIHMHSKCGYLD  297 (490)
Q Consensus       232 -----~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~------~~~---~l~~~~~~~~~~~  297 (490)
                           -|+.+.+.+ +.|-.++...+..-...|+.+...++|+.+...-.|.+..      +|.   -.+-.-....+.+
T Consensus       305 ~KRk~qYE~~v~~n-p~nYDsWfdylrL~e~~g~~~~Ire~yErAIanvpp~~ekr~W~RYIYLWinYalyeEle~ed~e  383 (677)
T KOG1915|consen  305 GKRKFQYEKEVSKN-PYNYDSWFDYLRLEESVGDKDRIRETYERAIANVPPASEKRYWRRYIYLWINYALYEELEAEDVE  383 (677)
T ss_pred             hhhhhHHHHHHHhC-CCCchHHHHHHHHHHhcCCHHHHHHHHHHHHccCCchhHHHHHHHHHHHHHHHHHHHHHHhhhHH
Confidence                 244445443 3466777778888888899999999999998765332211      111   1112223567888


Q ss_pred             HHHHHHhcccC--C-ChhH----HHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHH
Q 011249          298 LAWREFSRIKN--K-DVIS----YSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFE  370 (490)
Q Consensus       298 ~A~~~~~~~~~--~-~~~~----~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~  370 (490)
                      .+.++|+...+  | ...|    |........++.+...|.+++...+  |.-|...+|...|..-.+.++++.+..+++
T Consensus       384 rtr~vyq~~l~lIPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI--G~cPK~KlFk~YIelElqL~efDRcRkLYE  461 (677)
T KOG1915|consen  384 RTRQVYQACLDLIPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI--GKCPKDKLFKGYIELELQLREFDRCRKLYE  461 (677)
T ss_pred             HHHHHHHHHHhhcCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh--ccCCchhHHHHHHHHHHHHhhHHHHHHHHH
Confidence            88888877665  3 2333    4444445567889999999998876  468999999999998889999999999999


Q ss_pred             HHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCCh----hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          371 LMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDA----GTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       371 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      +..+  -.|-+..+|......-...|+.+.|..+|+-...+|..    ..|.+.|.--...|.+++|..+|+++++..+.
T Consensus       462 kfle--~~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ekaR~LYerlL~rt~h  539 (677)
T KOG1915|consen  462 KFLE--FSPENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEKARALYERLLDRTQH  539 (677)
T ss_pred             HHHh--cChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHHHHHHHHHHHHhccc
Confidence            9987  44556788888888888899999999999888766643    35666666667889999999999999998776


Q ss_pred             CCchHHHHHHHHH-----hcC-----------CcchHHHHHHHhhh
Q 011249          447 KTGNSALLANIYA-----SMG-----------KWKDSEIVKMMISE  476 (490)
Q Consensus       447 ~~~~~~~l~~~~~-----~~g-----------~~~~A~~~~~~~~~  476 (490)
                      .. ++...+..-.     +.|           ....|..+|++...
T Consensus       540 ~k-vWisFA~fe~s~~~~~~~~~~~~~e~~~~~~~~AR~iferAn~  584 (677)
T KOG1915|consen  540 VK-VWISFAKFEASASEGQEDEDLAELEITDENIKRARKIFERANT  584 (677)
T ss_pred             ch-HHHhHHHHhccccccccccchhhhhcchhHHHHHHHHHHHHHH
Confidence            44 5666654433     233           44567777776543

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.74  E-value=1.4e-13  Score=120.02  Aligned_cols=405  Identities=15%  Similarity=0.112  Sum_probs=282.7

Q ss_pred             eehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCC--ChH----HHHHHH---------HHhcCCH
Q 011249           69 FLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVP--SLL----EAVICG---------YTKIGLM  133 (490)
Q Consensus        69 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~--~~~----~~l~~~---------~~~~g~~  133 (490)
                      .+=|.|+. +...|...++.-+|+.|.+.|++.+...-..++...+-..  +..    .-.+..         -.+.|.+
T Consensus       117 ~~E~nL~k-mIS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~v  195 (625)
T KOG4422|consen  117 ETENNLLK-MISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGAV  195 (625)
T ss_pred             cchhHHHH-HHhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhccccccccccccccccH
Confidence            44556665 4467899999999999999999888877777666322111  110    000000         0011111


Q ss_pred             HHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccC----CchhHHHHHHHHHhcCChhHHHHHHhhcCC--
Q 011249          134 DDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEK----NSVTWVAMIAGYGKCGEVREAKKVFDEISE--  207 (490)
Q Consensus       134 ~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--  207 (490)
                        |. ++-+...++..+|..+|.++++-...+.|.++|++..+.    +..+||.+|.+-.-..+    .+++.+|..  
T Consensus       196 --Ad-L~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~~----K~Lv~EMisqk  268 (625)
T KOG4422|consen  196 --AD-LLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSVG----KKLVAEMISQK  268 (625)
T ss_pred             --HH-HHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhcc----HHHHHHHHHhh
Confidence              22 444444457789999999999999999999999998854    77888988877554433    566666653  


Q ss_pred             --CCHHhHHHHHHHHHhcCChHH----HHHHHHHHHHcCcccChhhHHHHHHHHhccCChHH-HHHHHHHHHh----cCC
Q 011249          208 --PDASCWAAMTVCYVQNGYAKA----AIEMYKVMRQENVRISEVAMVGAISACTQLGDVEM-AAILAKHVDE----GCC  276 (490)
Q Consensus       208 --~~~~~~~~l~~~~~~~g~~~~----A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~-a~~~~~~~~~----~~~  276 (490)
                        ||..|+|+++.+..+.|+++.    |++++.+|++.|+.|+..+|..++..+.+.++..+ +..+..++..    ..+
T Consensus       269 m~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~f  348 (625)
T KOG4422|consen  269 MTPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTF  348 (625)
T ss_pred             cCCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcc
Confidence              999999999999999998865    57788999999999999999999999988887644 4455555432    222


Q ss_pred             ----CCchhHHHHHHHHHHhcCChHHHHHHHhcccC--------C---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 011249          277 ----DRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--------K---DVISYSSMITAFADHGKSQEALDMFLKMRNEG  341 (490)
Q Consensus       277 ----~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--------~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  341 (490)
                          +.+...|...+..|.+..+.+-|.++-.-...        +   ...-|..+....++....+.-+..|+.|+-.-
T Consensus       349 kp~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~  428 (625)
T KOG4422|consen  349 KPITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSA  428 (625)
T ss_pred             cCCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccce
Confidence                33456677788888899999888887665543        1   22346667778888889999999999999887


Q ss_pred             CCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcC-Ch--------HH-----HHHHHHh
Q 011249          342 IEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSG-QL--------EK-----AHSLIMD  407 (490)
Q Consensus       342 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~--------~~-----A~~~~~~  407 (490)
                      +-|+..+...++++....|.++-.-++|..+.. +|...+...-..+...+++.. +.        ..     |..+++.
T Consensus       429 y~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~-~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~  507 (625)
T KOG4422|consen  429 YFPHSQTMIHLLRALDVANRLEVIPRIWKDSKE-YGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEA  507 (625)
T ss_pred             ecCCchhHHHHHHHHhhcCcchhHHHHHHHHHH-hhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence            889999999999999999999999999999888 465555444444444444433 11        11     1111111


Q ss_pred             -------cc-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC---CCCCc--hHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          408 -------YK-DFCDAGTWGALLGACKVHVNAELGEIAARHLLELG---PEKTG--NSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       408 -------~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~---p~~~~--~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                             +. ..-.+...+..+-.+.+.|..++|-+++.-..+.+   |..|.  +...+...-.+.+....|..+++-|
T Consensus       508 ~e~~~~R~r~~~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~~~spsqA~~~lQ~a  587 (625)
T KOG4422|consen  508 YESQPIRQRAQDWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQAIEVLQLA  587 (625)
T ss_pred             HHhhHHHHHhccCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHhcCCHHHHHHHHHHH
Confidence                   11 23345566667777888999999999998886533   55443  2234455556667788888888888


Q ss_pred             hhcccccC
Q 011249          475 SETEKKKS  482 (490)
Q Consensus       475 ~~~~~~~~  482 (490)
                      ...+..+.
T Consensus       588 ~~~n~~~~  595 (625)
T KOG4422|consen  588 SAFNLPIC  595 (625)
T ss_pred             HHcCchhh
Confidence            77665443

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

Probab=99.74  E-value=6e-15  Score=130.60  Aligned_cols=384  Identities=16%  Similarity=0.075  Sum_probs=253.5

Q ss_pred             hHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCCH--
Q 011249           71 WTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNV--  148 (490)
Q Consensus        71 ~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--  148 (490)
                      +-....-|.++|.+++|++.|.+.++.  .||..+|-.-..+|             |...|++++..+--.+.++-++  
T Consensus       118 lK~~GN~~f~~kkY~eAIkyY~~AI~l--~p~epiFYsNraAc-------------Y~~lgd~~~Vied~TkALEl~P~Y  182 (606)
T KOG0547|consen  118 LKTKGNKFFRNKKYDEAIKYYTQAIEL--CPDEPIFYSNRAAC-------------YESLGDWEKVIEDCTKALELNPDY  182 (606)
T ss_pred             HHhhhhhhhhcccHHHHHHHHHHHHhc--CCCCchhhhhHHHH-------------HHHHhhHHHHHHHHHHHhhcCcHH
Confidence            334556677889999999999999886  77855555555554             8888999988888777776333  


Q ss_pred             -hHHHHHHHHHHhCCChHHHHHHHHHhc--c-CCchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHH------
Q 011249          149 -ISWSAMVAGYANCGNMKAAKEFYDRMT--E-KNSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAA------  215 (490)
Q Consensus       149 -~~~~~l~~~~~~~~~~~~a~~~~~~~~--~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~------  215 (490)
                       ..+..-..++-..|++++|+.-..-.-  + -+......++.--.+.--...+.+-+.+-..   |+.....+      
T Consensus       183 ~KAl~RRA~A~E~lg~~~eal~D~tv~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~  262 (606)
T KOG0547|consen  183 VKALLRRASAHEQLGKFDEALFDVTVLCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFH  262 (606)
T ss_pred             HHHHHHHHHHHHhhccHHHHHHhhhHHHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhcc
Confidence             355555667777777777654322110  0 0000000111100110011122222221011   22222222      


Q ss_pred             -----------------HHHHHHh--cC---ChHHHHHHHHHHHHc-CcccCh-----------hhHHHHHHHHhccCCh
Q 011249          216 -----------------MTVCYVQ--NG---YAKAAIEMYKVMRQE-NVRISE-----------VAMVGAISACTQLGDV  261 (490)
Q Consensus       216 -----------------l~~~~~~--~g---~~~~A~~~~~~~~~~-~~~p~~-----------~~~~~l~~~~~~~g~~  261 (490)
                                       +..++..  .+   .+..|...+.+-... -..++.           .+.......+.-.|+.
T Consensus       263 ~~~~~~~~~~~~ksDa~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~  342 (606)
T KOG0547|consen  263 ADPKPLFDNKSDKSDAALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDS  342 (606)
T ss_pred             ccccccccCCCccchhhHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCc
Confidence                             1111111  11   233333333221110 011111           1122222223456888


Q ss_pred             HHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHH
Q 011249          262 EMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMR  338 (490)
Q Consensus       262 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  338 (490)
                      -.+..-++..++.. +.+...|--+..+|....+.++.++.|.+..+   .++.+|..-.+.+.-.+++++|..-|++.+
T Consensus       343 ~~a~~d~~~~I~l~-~~~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai  421 (606)
T KOG0547|consen  343 LGAQEDFDAAIKLD-PAFNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIADFQKAI  421 (606)
T ss_pred             hhhhhhHHHHHhcC-cccchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999998876 33444477788889999999999999998775   467788888888888899999999999999


Q ss_pred             HcCCCCcH-HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCC---
Q 011249          339 NEGIEPNQ-VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD---  413 (490)
Q Consensus       339 ~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~---  413 (490)
                      .  +.|+. ..|..+..+..+.+.++++...|++..+  .+|..+++|+.....+...+++++|.+.|+... ..|.   
T Consensus       422 ~--L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kk--kFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~LE~~~~~  497 (606)
T KOG0547|consen  422 S--LDPENAYAYIQLCCALYRQHKIAESMKTFEEAKK--KFPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIELEPREHL  497 (606)
T ss_pred             h--cChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hCCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhhcccccc
Confidence            8  56654 4777777777889999999999999998  678888999999999999999999999998765 2222   


Q ss_pred             ------hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          414 ------AGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       414 ------~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                            +.+...++.. .-.+++..|+.+++++.+++|....+|..|+.+..++|+.++|+++|++..
T Consensus       498 ~~v~~~plV~Ka~l~~-qwk~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  498 IIVNAAPLVHKALLVL-QWKEDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             ccccchhhhhhhHhhh-chhhhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence                  2222233322 234899999999999999999999999999999999999999999998753

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

Probab=99.74  E-value=1.1e-15  Score=134.04  Aligned_cols=394  Identities=14%  Similarity=0.101  Sum_probs=275.1

Q ss_pred             ehHH---HHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC-
Q 011249           70 LWTS---LIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE-  145 (490)
Q Consensus        70 ~~~~---l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-  145 (490)
                      +|+.   |.+-|..+....+|+..|+-+.+....|+.-....-             +...+.+.+.+.+|++.+.-... 
T Consensus       200 tfsvl~nlaqqy~~ndm~~ealntyeiivknkmf~nag~lkmn-------------igni~~kkr~fskaikfyrmaldq  266 (840)
T KOG2003|consen  200 TFSVLFNLAQQYEANDMTAEALNTYEIIVKNKMFPNAGILKMN-------------IGNIHFKKREFSKAIKFYRMALDQ  266 (840)
T ss_pred             hHHHHHHHHHHhhhhHHHHHHhhhhhhhhcccccCCCceeeee-------------ecceeeehhhHHHHHHHHHHHHhh
Confidence            4554   445566678899999999999988888876544322             23357888899999999887664 


Q ss_pred             -CC------HhHHHHHHHHHHhCCChHHHHHHHHHhcc--CCchhHHHHHHHHHhcCChhHHHHHHhhcCC---------
Q 011249          146 -RN------VISWSAMVAGYANCGNMKAAKEFYDRMTE--KNSVTWVAMIAGYGKCGEVREAKKVFDEISE---------  207 (490)
Q Consensus       146 -~~------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---------  207 (490)
                       |+      +...+.+...+.+.|+++.|+..|+...+  ||..+-..|+-++...|+.++..+.|.++..         
T Consensus       267 vpsink~~rikil~nigvtfiq~gqy~dainsfdh~m~~~pn~~a~~nl~i~~f~i~d~ekmkeaf~kli~ip~~~dddk  346 (840)
T KOG2003|consen  267 VPSINKDMRIKILNNIGVTFIQAGQYDDAINSFDHCMEEAPNFIAALNLIICAFAIGDAEKMKEAFQKLIDIPGEIDDDK  346 (840)
T ss_pred             ccccchhhHHHHHhhcCeeEEecccchhhHhhHHHHHHhCccHHhhhhhhhhheecCcHHHHHHHHHHHhcCCCCCCccc
Confidence             32      34567777789999999999999999885  5766666777778888999999999988863         


Q ss_pred             -------CCHHhHHHHH-----HHHHhcC--ChHHHHHHHHHHHHcCcccChh-hHH--------------------HHH
Q 011249          208 -------PDASCWAAMT-----VCYVQNG--YAKAAIEMYKVMRQENVRISEV-AMV--------------------GAI  252 (490)
Q Consensus       208 -------~~~~~~~~l~-----~~~~~~g--~~~~A~~~~~~~~~~~~~p~~~-~~~--------------------~l~  252 (490)
                             |+....+.-+     .-+-+.+  +.++++-.--+++.--+.|+-. .+.                    .-.
T Consensus       347 yi~~~ddp~~~ll~eai~nd~lk~~ek~~ka~aek~i~ta~kiiapvi~~~fa~g~dwcle~lk~s~~~~la~dlei~ka  426 (840)
T KOG2003|consen  347 YIKEKDDPDDNLLNEAIKNDHLKNMEKENKADAEKAIITAAKIIAPVIAPDFAAGCDWCLESLKASQHAELAIDLEINKA  426 (840)
T ss_pred             ccCCcCCcchHHHHHHHhhHHHHHHHHhhhhhHHHHHHHHHHHhccccccchhcccHHHHHHHHHhhhhhhhhhhhhhHH
Confidence                   2322222222     2222222  1223333333333323333321 010                    112


Q ss_pred             HHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHH------------------------------------HHhcCCh
Q 011249          253 SACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHM------------------------------------HSKCGYL  296 (490)
Q Consensus       253 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~------------------------------------~~~~~~~  296 (490)
                      ..+.+.|+++.|.++++-+.+..-..-...-+.|-..                                    -...|++
T Consensus       427 ~~~lk~~d~~~aieilkv~~~kdnk~~saaa~nl~~l~flqggk~~~~aqqyad~aln~dryn~~a~~nkgn~~f~ngd~  506 (840)
T KOG2003|consen  427 GELLKNGDIEGAIEILKVFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAFANGDL  506 (840)
T ss_pred             HHHHhccCHHHHHHHHHHHHhccchhhHHHhhhhHHHHHHhcccchhHHHHHHHHHhcccccCHHHhhcCCceeeecCcH
Confidence            2356789999999999887654322211111111100                                    1124678


Q ss_pred             HHHHHHHhcccCCChhHHHHHH---HHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHH
Q 011249          297 DLAWREFSRIKNKDVISYSSMI---TAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMT  373 (490)
Q Consensus       297 ~~A~~~~~~~~~~~~~~~~~l~---~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  373 (490)
                      ++|.+.|++....|...-.+|.   -.+-..|+.++|+..|-++..- +.-+...+..+...|....+...|++++.+..
T Consensus       507 dka~~~ykeal~ndasc~ealfniglt~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~~~q~~  585 (840)
T KOG2003|consen  507 DKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIELLMQAN  585 (840)
T ss_pred             HHHHHHHHHHHcCchHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHHHHHhc
Confidence            8888888888876665444433   3566789999999999887653 23455677788888988899999999998886


Q ss_pred             HHcCCCCCchHHHHHHHHHhhcCChHHHHHHH-Hhcc-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchH
Q 011249          374 RVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLI-MDYK-DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       374 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~-~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                      .  -++.|+.....|.+.|-+.|+-.+|.+.+ +... .+.+..+..-|..-|....-+++++.+|+++.-+.|+-..--
T Consensus       586 s--lip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~~kwq  663 (840)
T KOG2003|consen  586 S--LIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQSKWQ  663 (840)
T ss_pred             c--cCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccHHHHH
Confidence            5  67778999999999999999999999875 5555 566888888888888888889999999999999999855544


Q ss_pred             HHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          452 ALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       452 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ..++.++.+.|+|++|.++++.+..+-+
T Consensus       664 lmiasc~rrsgnyqka~d~yk~~hrkfp  691 (840)
T KOG2003|consen  664 LMIASCFRRSGNYQKAFDLYKDIHRKFP  691 (840)
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHHHhCc
Confidence            4556777789999999999998876543

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

Probab=99.72  E-value=1.2e-12  Score=120.20  Aligned_cols=359  Identities=12%  Similarity=0.097  Sum_probs=279.8

Q ss_pred             HHHHHHhcCCHHHHHHHHhhcCC---CCHhHHHHHHHHHHhCCChHHHHHHHHHhcc--------CCchhHHHHHHHHHh
Q 011249          123 VICGYTKIGLMDDAQRLFDSMAE---RNVISWSAMVAGYANCGNMKAAKEFYDRMTE--------KNSVTWVAMIAGYGK  191 (490)
Q Consensus       123 l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--------~~~~~~~~l~~~~~~  191 (490)
                      |-.+|.+..-++.|..++++..+   .+...|-+-...--++|+.+.+.++..+...        -+...|..=...|-.
T Consensus       412 LwlAlarLetYenAkkvLNkaRe~iptd~~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~e~  491 (913)
T KOG0495|consen  412 LWLALARLETYENAKKVLNKAREIIPTDREIWITAAKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEACED  491 (913)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCCCChhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHHhh
Confidence            44556666777777777776655   3666777766666777777777777766552        144555555566666


Q ss_pred             cCChhHHHHHHhhcCC------CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHH
Q 011249          192 CGEVREAKKVFDEISE------PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAA  265 (490)
Q Consensus       192 ~~~~~~A~~~~~~~~~------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~  265 (490)
                      .|..-.+..+......      .-..+|..-...|.+.+.++-|..+|....+.- +-+...|......--..|..+...
T Consensus       492 agsv~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqvf-p~k~slWlra~~~ek~hgt~Esl~  570 (913)
T KOG0495|consen  492 AGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQVF-PCKKSLWLRAAMFEKSHGTRESLE  570 (913)
T ss_pred             cCChhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhhc-cchhHHHHHHHHHHHhcCcHHHHH
Confidence            6666666666555432      334578888888899999999999998888753 335567777777667788999999


Q ss_pred             HHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 011249          266 ILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGI  342 (490)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  342 (490)
                      .+++++.... |.....+......+-..|++..|..++..+-+  | +...|..-+.......+++.|..+|.+...  .
T Consensus       571 Allqkav~~~-pkae~lwlM~ake~w~agdv~~ar~il~~af~~~pnseeiwlaavKle~en~e~eraR~llakar~--~  647 (913)
T KOG0495|consen  571 ALLQKAVEQC-PKAEILWLMYAKEKWKAGDVPAARVILDQAFEANPNSEEIWLAAVKLEFENDELERARDLLAKARS--I  647 (913)
T ss_pred             HHHHHHHHhC-CcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccccHHHHHHHHHHHhc--c
Confidence            9999998875 66677787888888889999999999988765  3 556888888888999999999999999887  4


Q ss_pred             CCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHH
Q 011249          343 EPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGAL  420 (490)
Q Consensus       343 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l  420 (490)
                      .|+...|..-+..-...++.++|.+++++..+  .++.-...|..+.+.+.+.++.+.|.+.|..-. ..| .+..|..+
T Consensus       648 sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk--~fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipLWllL  725 (913)
T KOG0495|consen  648 SGTERVWMKSANLERYLDNVEEALRLLEEALK--SFPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPLWLLL  725 (913)
T ss_pred             CCcchhhHHHhHHHHHhhhHHHHHHHHHHHHH--hCCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchHHHHH
Confidence            67777776666666668999999999999998  566667788889999999999999999886655 334 56788888


Q ss_pred             HHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccccCCCccccC
Q 011249          421 LGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWIS  489 (490)
Q Consensus       421 ~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  489 (490)
                      ...-.+.|..-+|..+++++.-.+|.++..|...+.+-.+.|+.+.|..++.+..+.  -+..|.=|.+
T Consensus       726 akleEk~~~~~rAR~ildrarlkNPk~~~lwle~Ir~ElR~gn~~~a~~lmakALQe--cp~sg~LWaE  792 (913)
T KOG0495|consen  726 AKLEEKDGQLVRARSILDRARLKNPKNALLWLESIRMELRAGNKEQAELLMAKALQE--CPSSGLLWAE  792 (913)
T ss_pred             HHHHHHhcchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCccchhHHH
Confidence            888888999999999999999999999999999999999999999999999888765  3455655543

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

Probab=99.71  E-value=2.2e-13  Score=120.10  Aligned_cols=392  Identities=8%  Similarity=0.000  Sum_probs=278.2

Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCC--CCh--HHHHHHHHHhcCCHHHHHHHHhhcCC--
Q 011249           72 TSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARV--PSL--LEAVICGYTKIGLMDDAQRLFDSMAE--  145 (490)
Q Consensus        72 ~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~--~~~--~~~l~~~~~~~g~~~~A~~~~~~~~~--  145 (490)
                      ..+..++.....++.|.-.++.....        ....+..+++.  +..  .........+.+....-.+.|..+.+  
T Consensus        82 y~laks~fd~kEf~Raa~fL~~~~s~--------k~~FL~lysk~La~~kk~~e~~~~~l~~~~~~~~~~~~l~~L~~~l  153 (559)
T KOG1155|consen   82 YLLAKSYFDCKEFERAAFFLQNCKSK--------KSAFLRLYSKYLAGEKKSEEEMAELLGRLESFSRINSELIELNKPL  153 (559)
T ss_pred             hhhHhhhhhhHHHHHHHHHHHhcchH--------HHHHHHHHHHHHhhhHHHHHHHHHhhccchhhhhhhhHHHHHhhHH
Confidence            35667777788888888777765442        12222222111  000  01222222233333333333333322  


Q ss_pred             --------CCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCH-HhHHHH
Q 011249          146 --------RNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDA-SCWAAM  216 (490)
Q Consensus       146 --------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~l  216 (490)
                              .|...+-.....+.+.|....|+..|......-+..|.+.+....-..+.+.+..+.......+. ..=-.+
T Consensus       154 e~~~~~~~~D~fllYL~Gvv~k~~~~~s~A~~sfv~~v~~~P~~W~AWleL~~lit~~e~~~~l~~~l~~~~h~M~~~F~  233 (559)
T KOG1155|consen  154 ESKHCGGEKDEFLLYLYGVVLKELGLLSLAIDSFVEVVNRYPWFWSAWLELSELITDIEILSILVVGLPSDMHWMKKFFL  233 (559)
T ss_pred             HHHHhcccchhHHHHHHHHHHHhhchHHHHHHHHHHHHhcCCcchHHHHHHHHhhchHHHHHHHHhcCcccchHHHHHHH
Confidence                    34444444556677788899999999888877677777776666666666666555544443221 122234


Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCC---chhHHHHHHHHHHhc
Q 011249          217 TVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDR---TNYVSNALIHMHSKC  293 (490)
Q Consensus       217 ~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~  293 (490)
                      ..++....+.+++++-.+.....|+..+...-+....+.-...|+++|+.+|+++.+.. |-   |..+|..++-+-...
T Consensus       234 ~~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knD-PYRl~dmdlySN~LYv~~~~  312 (559)
T KOG1155|consen  234 KKAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKND-PYRLDDMDLYSNVLYVKNDK  312 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcC-CCcchhHHHHhHHHHHHhhh
Confidence            56677777889999988888888877666555566666778899999999999999884 33   455666555443332


Q ss_pred             CChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcH-HHHHHHHHHhcCCCChHHHHHHHHHH
Q 011249          294 GYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQ-VTFIGVLTACSHGGLVEDGCKQFELM  372 (490)
Q Consensus       294 ~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~  372 (490)
                      .++.---.....+.+-.+.|...+..-|.-.++.++|...|++.++  +.|.. ..|+.+..-|....+...|..-++.+
T Consensus       313 skLs~LA~~v~~idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALk--LNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrA  390 (559)
T KOG1155|consen  313 SKLSYLAQNVSNIDKYRPETCCIIANYYSLRSEHEKAVMYFKRALK--LNPKYLSAWTLMGHEYVEMKNTHAAIESYRRA  390 (559)
T ss_pred             HHHHHHHHHHHHhccCCccceeeehhHHHHHHhHHHHHHHHHHHHh--cCcchhHHHHHhhHHHHHhcccHHHHHHHHHH
Confidence            2222222222233444567788888889999999999999999998  46654 46777777899999999999999999


Q ss_pred             HHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCch
Q 011249          373 TRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGN  450 (490)
Q Consensus       373 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~  450 (490)
                      .+  -.|.|-..|..|.++|.-.+.+.=|+-+|++..  .+.|+..|.+|...|.+.++.++|++.|.++...+-.+..+
T Consensus       391 vd--i~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~  468 (559)
T KOG1155|consen  391 VD--INPRDYRAWYGLGQAYEIMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSA  468 (559)
T ss_pred             Hh--cCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHH
Confidence            98  567788899999999999999999999998887  45678899999999999999999999999999988778899


Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          451 SALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       451 ~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      +..|+++|.+.++.++|...+++-++
T Consensus       469 l~~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  469 LVRLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             HHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            99999999999999999999988765

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.70  E-value=3.2e-14  Score=133.08  Aligned_cols=214  Identities=9%  Similarity=-0.034  Sum_probs=104.8

Q ss_pred             HHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCC---Chh--------HHHHHHHHHH
Q 011249          254 ACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK---DVI--------SYSSMITAFA  322 (490)
Q Consensus       254 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---~~~--------~~~~l~~~~~  322 (490)
                      .+...|+++.|...++.+.+.. |.++.+...+...|.+.|++++|.+++..+.+.   +..        +|..++....
T Consensus       162 l~l~~g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~  240 (398)
T PRK10747        162 IQLARNENHAARHGVDKLLEVA-PRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAM  240 (398)
T ss_pred             HHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            3444444444444444444443 333444444444444445555444444444331   011        1222222222


Q ss_pred             hcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHH
Q 011249          323 DHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAH  402 (490)
Q Consensus       323 ~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  402 (490)
                      ...+.+...++++.+.+. .+.++.....+...+...|+.++|.+++++..+.   +|+....  ++.+....++.+++.
T Consensus       241 ~~~~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~---~~~~~l~--~l~~~l~~~~~~~al  314 (398)
T PRK10747        241 ADQGSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR---QYDERLV--LLIPRLKTNNPEQLE  314 (398)
T ss_pred             HhcCHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---CCCHHHH--HHHhhccCCChHHHH
Confidence            233334444444443322 2234445555566666666666666666655542   3333211  222233446666666


Q ss_pred             HHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          403 SLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       403 ~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      +..+.+.  .+.++..+..+...|...+++++|.+.|+++.+..|++ ..+..++.++.+.|+.++|.+++++-.
T Consensus       315 ~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~-~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        315 KVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDA-YDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             HHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            6665554  22334445566666666666666666666666666663 334556666666666666666666543

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

Probab=99.70  E-value=3.8e-13  Score=128.04  Aligned_cols=313  Identities=12%  Similarity=0.111  Sum_probs=191.0

Q ss_pred             cchhhhhhchhhHHHHHHHHhhhcCCC-CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHh
Q 011249            4 KYLVPRSKTFNQLKQVHSYLLKTLTKP-HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVL   80 (490)
Q Consensus         4 ~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~   80 (490)
                      +..+-+.|+++.|..+...+++   .. .++.  .|..|...|-+.|+ .+++...+=..-  .|.....|-.+.....+
T Consensus       146 AN~lfarg~~eeA~~i~~EvIk---qdp~~~~--ay~tL~~IyEqrGd-~eK~l~~~llAAHL~p~d~e~W~~ladls~~  219 (895)
T KOG2076|consen  146 ANNLFARGDLEEAEEILMEVIK---QDPRNPI--AYYTLGEIYEQRGD-IEKALNFWLLAAHLNPKDYELWKRLADLSEQ  219 (895)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHH---hCccchh--hHHHHHHHHHHccc-HHHHHHHHHHHHhcCCCChHHHHHHHHHHHh
Confidence            4455567999999999999999   77 8888  99999999999999 999998875543  45444789999999999


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--C--CHh----HHH
Q 011249           81 HAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--R--NVI----SWS  152 (490)
Q Consensus        81 ~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~--~~~----~~~  152 (490)
                      .|++++|.-.|.+..+.  .|+..  ..+..           -+..|-+.|+...|...|.++..  |  |..    .--
T Consensus       220 ~~~i~qA~~cy~rAI~~--~p~n~--~~~~e-----------rs~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~  284 (895)
T KOG2076|consen  220 LGNINQARYCYSRAIQA--NPSNW--ELIYE-----------RSSLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIR  284 (895)
T ss_pred             cccHHHHHHHHHHHHhc--CCcch--HHHHH-----------HHHHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHH
Confidence            99999999999999887  34432  22222           12346777888888877777765  2  111    122


Q ss_pred             HHHHHHHhCCChHHHHHHHHHhccC-----CchhHHHHHHHHHhcCChhHHHHHHhhcCC--------------------
Q 011249          153 AMVAGYANCGNMKAAKEFYDRMTEK-----NSVTWVAMIAGYGKCGEVREAKKVFDEISE--------------------  207 (490)
Q Consensus       153 ~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--------------------  207 (490)
                      ..+..+...++-+.|.+.++.....     +...++.++..+.+...++.|.........                    
T Consensus       285 ~~~~~~~~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~  364 (895)
T KOG2076|consen  285 RVAHYFITHNERERAAKALEGALSKEKDEASLEDLNILAELFLKNKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEP  364 (895)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHhHHHHHhhHHHHHHhccccCCChhhhhhhhhccccc
Confidence            2345566666667777777766642     445566677777776666666655543321                    


Q ss_pred             ------CCHHhHH----HHHHHHHhcCChHHHHHHHHHHHHcCc--ccChhhHHHHHHHHhccCChHHHHHHHHHHHhcC
Q 011249          208 ------PDASCWA----AMTVCYVQNGYAKAAIEMYKVMRQENV--RISEVAMVGAISACTQLGDVEMAAILAKHVDEGC  275 (490)
Q Consensus       208 ------~~~~~~~----~l~~~~~~~g~~~~A~~~~~~~~~~~~--~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  275 (490)
                            ++...|.    -++-++.+.+..+....+........+  .-+...|.-+..++.+.|++.+|..++..+....
T Consensus       365 ~~~~~~~~~~s~~l~v~rl~icL~~L~~~e~~e~ll~~l~~~n~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~  444 (895)
T KOG2076|consen  365 NALCEVGKELSYDLRVIRLMICLVHLKERELLEALLHFLVEDNVWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNRE  444 (895)
T ss_pred             cccccCCCCCCccchhHhHhhhhhcccccchHHHHHHHHHHhcCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCc
Confidence                  0001111    122222333333333333333333332  2233455556666666666666666666665554


Q ss_pred             CCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-ChhHHHHHHHHHHhcCChHHHHHHHHHH
Q 011249          276 CDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-DVISYSSMITAFADHGKSQEALDMFLKM  337 (490)
Q Consensus       276 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~  337 (490)
                      ..-+..+|-.+..+|...|.++.|.+.|+++..  | +...--.|...+.+.|++++|.+.++.+
T Consensus       445 ~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D~Ri~Lasl~~~~g~~EkalEtL~~~  509 (895)
T KOG2076|consen  445 GYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDNLDARITLASLYQQLGNHEKALETLEQI  509 (895)
T ss_pred             cccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchhhhhhHHHHHHhcCCHHHHHHHHhcc
Confidence            344455566666666666666666666666554  2 2233334444555666666666666553

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

Probab=99.69  E-value=7.4e-15  Score=135.20  Aligned_cols=277  Identities=14%  Similarity=0.039  Sum_probs=201.5

Q ss_pred             ChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCc--ccChhhHHHHHHHHhccCChHHHHHHH
Q 011249          194 EVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENV--RISEVAMVGAISACTQLGDVEMAAILA  268 (490)
Q Consensus       194 ~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~p~~~~~~~l~~~~~~~g~~~~a~~~~  268 (490)
                      +..+|+..|..+..   ........+..+|...+++++|.++|+.+.+...  .-+...|...+..+.+    +-+..++
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 NCREALNLFEKLPSHHYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQD----EVALSYL  409 (638)
T ss_pred             HHHHHHHHHHhhHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHh----hHHHHHH
Confidence            56777888877554   2334455677888888888888888888876421  1245667766665433    2223333


Q ss_pred             H-HHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCC---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC
Q 011249          269 K-HVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK---DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP  344 (490)
Q Consensus       269 ~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p  344 (490)
                      . .+.+.. +..+.+|.++.+.|.-+++.+.|++.|++...-   ...+|+.+..-+.....+|.|...|+..+.  +.|
T Consensus       410 aq~Li~~~-~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~--~~~  486 (638)
T KOG1126|consen  410 AQDLIDTD-PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALG--VDP  486 (638)
T ss_pred             HHHHHhhC-CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhc--CCc
Confidence            2 333333 667788888888888888888888888887763   456777777777888888888888888775  455


Q ss_pred             cHH-HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHH
Q 011249          345 NQV-TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALL  421 (490)
Q Consensus       345 ~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~  421 (490)
                      ... .|-.+...|.++++++.|+-.|+++.+  --|-+......+...+.+.|+.++|++++++..  ++.++..--.-+
T Consensus       487 rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~--INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~  564 (638)
T KOG1126|consen  487 RHYNAWYGLGTVYLKQEKLEFAEFHFQKAVE--INPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRA  564 (638)
T ss_pred             hhhHHHHhhhhheeccchhhHHHHHHHhhhc--CCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHH
Confidence            443 666777888888999998888888875  233345555667778888889999999988776  444555555556


Q ss_pred             HHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          422 GACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       422 ~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ..+...+++++|.+.++++.+.-|++..++..++.+|.+.|+.+.|+.-|--+.+.++
T Consensus       565 ~il~~~~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldp  622 (638)
T KOG1126|consen  565 SILFSLGRYVEALQELEELKELVPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDP  622 (638)
T ss_pred             HHHHhhcchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCC
Confidence            6677888899999999999999999999999999999999999988888877765544

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

Probab=99.68  E-value=1.8e-12  Score=114.75  Aligned_cols=424  Identities=10%  Similarity=0.088  Sum_probs=301.8

Q ss_pred             CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCC---CCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHH
Q 011249           31 HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPK---CKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFS  107 (490)
Q Consensus        31 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~  107 (490)
                      -+..  .|-.....--..++ ...|+.+|++...   .+. ..|-.-+..-.++.+...|..++++....=...|..-|.
T Consensus        71 ~~~~--~WikYaqwEesq~e-~~RARSv~ERALdvd~r~i-tLWlkYae~Emknk~vNhARNv~dRAvt~lPRVdqlWyK  146 (677)
T KOG1915|consen   71 LNMQ--VWIKYAQWEESQKE-IQRARSVFERALDVDYRNI-TLWLKYAEFEMKNKQVNHARNVWDRAVTILPRVDQLWYK  146 (677)
T ss_pred             HHHH--HHHHHHHHHHhHHH-HHHHHHHHHHHHhcccccc-hHHHHHHHHHHhhhhHhHHHHHHHHHHHhcchHHHHHHH
Confidence            4445  66666666667777 8889999998763   333 557777778888999999999999887752222333332


Q ss_pred             HHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--CCHhHHHHHHHHHHhCCChHHHHHHHHHhc--cCCchhHH
Q 011249          108 SVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--RNVISWSAMVAGYANCGNMKAAKEFYDRMT--EKNSVTWV  183 (490)
Q Consensus       108 ~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~--~~~~~~~~  183 (490)
                      .+.               +=-..|++..|+++|++-.+  |+...|++.++.-.+-+..+.|..+|++..  .|++.+|.
T Consensus       147 Y~y---------------mEE~LgNi~gaRqiferW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV~~HP~v~~wi  211 (677)
T KOG1915|consen  147 YIY---------------MEEMLGNIAGARQIFERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFVLVHPKVSNWI  211 (677)
T ss_pred             HHH---------------HHHHhcccHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHheecccHHHHH
Confidence            222               12345899999999998775  899999999999999999999999999877  68888898


Q ss_pred             HHHHHHHhcCChhHHHHHHhhcCC------CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCccc-ChhhHHHHHHHHh
Q 011249          184 AMIAGYGKCGEVREAKKVFDEISE------PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRI-SEVAMVGAISACT  256 (490)
Q Consensus       184 ~l~~~~~~~~~~~~A~~~~~~~~~------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~  256 (490)
                      ..+..-.+.|....|..+|+...+      .+...+.+....-.+...++.|.-+|+-....=..- ....|......--
T Consensus       212 kyarFE~k~g~~~~aR~VyerAie~~~~d~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEK  291 (677)
T KOG1915|consen  212 KYARFEEKHGNVALARSVYERAIEFLGDDEEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEK  291 (677)
T ss_pred             HHHHHHHhcCcHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHH
Confidence            888888899999999999988765      233445555555566777888888888877652111 1234444444434


Q ss_pred             ccCChHHHHH--------HHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--CCh---hHHHHHHH----
Q 011249          257 QLGDVEMAAI--------LAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KDV---ISYSSMIT----  319 (490)
Q Consensus       257 ~~g~~~~a~~--------~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~---~~~~~l~~----  319 (490)
                      +-|+......        -|+..++.+ +.|-.+|--.+..-...|+.+...++|++...  |..   ..|...|-    
T Consensus       292 qfGd~~gIEd~Iv~KRk~qYE~~v~~n-p~nYDsWfdylrL~e~~g~~~~Ire~yErAIanvpp~~ekr~W~RYIYLWin  370 (677)
T KOG1915|consen  292 QFGDKEGIEDAIVGKRKFQYEKEVSKN-PYNYDSWFDYLRLEESVGDKDRIRETYERAIANVPPASEKRYWRRYIYLWIN  370 (677)
T ss_pred             HhcchhhhHHHHhhhhhhHHHHHHHhC-CCCchHHHHHHHHHHhcCCHHHHHHHHHHHHccCCchhHHHHHHHHHHHHHH
Confidence            4455443322        234444444 66777777788888888999999999988765  211   12222211    


Q ss_pred             ----HHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHH----HhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHH
Q 011249          320 ----AFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLT----ACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVD  390 (490)
Q Consensus       320 ----~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~----~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  390 (490)
                          .-....+.+.+.++|+..++  +.| ...||..+=-    --.++.++..|.+++....   |..|...++...|.
T Consensus       371 YalyeEle~ed~ertr~vyq~~l~--lIPHkkFtFaKiWlmyA~feIRq~~l~~ARkiLG~AI---G~cPK~KlFk~YIe  445 (677)
T KOG1915|consen  371 YALYEELEAEDVERTRQVYQACLD--LIPHKKFTFAKIWLMYAQFEIRQLNLTGARKILGNAI---GKCPKDKLFKGYIE  445 (677)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHh--hcCcccchHHHHHHHHHHHHHHHcccHHHHHHHHHHh---ccCCchhHHHHHHH
Confidence                11346788889999998888  344 3445544432    2356788889999998885   77888889988888


Q ss_pred             HHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC-C-chHHHHHHHHHhcCCcch
Q 011249          391 LLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK-T-GNSALLANIYASMGKWKD  466 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~-~-~~~~~l~~~~~~~g~~~~  466 (490)
                      .-.+.++++.+.++|++..  .+.+-.+|......-...|+.++|..+|+-++.....+ | -.+...+..-...|.++.
T Consensus       446 lElqL~efDRcRkLYEkfle~~Pe~c~~W~kyaElE~~LgdtdRaRaifelAi~qp~ldmpellwkaYIdFEi~~~E~ek  525 (677)
T KOG1915|consen  446 LELQLREFDRCRKLYEKFLEFSPENCYAWSKYAELETSLGDTDRARAIFELAISQPALDMPELLWKAYIDFEIEEGEFEK  525 (677)
T ss_pred             HHHHHhhHHHHHHHHHHHHhcChHhhHHHHHHHHHHHHhhhHHHHHHHHHHHhcCcccccHHHHHHHhhhhhhhcchHHH
Confidence            8889999999999998877  34466788888887888899999999999888754222 2 245556666778899999


Q ss_pred             HHHHHHHhhhccc
Q 011249          467 SEIVKMMISETEK  479 (490)
Q Consensus       467 A~~~~~~~~~~~~  479 (490)
                      |..+++++.+...
T Consensus       526 aR~LYerlL~rt~  538 (677)
T KOG1915|consen  526 ARALYERLLDRTQ  538 (677)
T ss_pred             HHHHHHHHHHhcc
Confidence            9999998887643

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.68  E-value=1.9e-13  Score=127.93  Aligned_cols=276  Identities=12%  Similarity=0.027  Sum_probs=184.7

Q ss_pred             CCChHHHHHHHHHhccC--Cchh-HHHHHHHHHhcCChhHHHHHHhhcCC--CCHHhHH--HHHHHHHhcCChHHHHHHH
Q 011249          161 CGNMKAAKEFYDRMTEK--NSVT-WVAMIAGYGKCGEVREAKKVFDEISE--PDASCWA--AMTVCYVQNGYAKAAIEMY  233 (490)
Q Consensus       161 ~~~~~~a~~~~~~~~~~--~~~~-~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~--~l~~~~~~~g~~~~A~~~~  233 (490)
                      .|++++|.+.+....+.  ++.. |........+.|+++.|.+.+.++.+  |+.....  .....+...|+++.|.+.+
T Consensus        97 eGd~~~A~k~l~~~~~~~~~p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~~~~~~~~~~l~~a~l~l~~g~~~~Al~~l  176 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHAEQPVVNYLLAAEAAQQRGDEARANQHLERAAELADNDQLPVEITRVRIQLARNENHAARHGV  176 (398)
T ss_pred             CCCHHHHHHHHHHHHhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            46666666555554432  1222 22223333566666666666666554  3332222  2245666667777777777


Q ss_pred             HHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCch-------hHHHHHHHHHHhcCChHHHHHHHhcc
Q 011249          234 KVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTN-------YVSNALIHMHSKCGYLDLAWREFSRI  306 (490)
Q Consensus       234 ~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~A~~~~~~~  306 (490)
                      +++.+..+. +......+...+.+.|++++|..++..+.+.+..++.       ..|..++.......+.+...++++.+
T Consensus       177 ~~~~~~~P~-~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~l  255 (398)
T PRK10747        177 DKLLEVAPR-HPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQ  255 (398)
T ss_pred             HHHHhcCCC-CHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhC
Confidence            766665422 4455666666666777777777777776665533221       12223333333444556666666666


Q ss_pred             cC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCch
Q 011249          307 KN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTE  383 (490)
Q Consensus       307 ~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  383 (490)
                      .+   .++.....+...+...|+.++|.+++++..+.  .|+....  ++.+....++.+++.+..+...+  ..|.|+.
T Consensus       256 p~~~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~--~~~~~l~--~l~~~l~~~~~~~al~~~e~~lk--~~P~~~~  329 (398)
T PRK10747        256 SRKTRHQVALQVAMAEHLIECDDHDTAQQIILDGLKR--QYDERLV--LLIPRLKTNNPEQLEKVLRQQIK--QHGDTPL  329 (398)
T ss_pred             CHHHhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCHHHH--HHHhhccCCChHHHHHHHHHHHh--hCCCCHH
Confidence            54   47778888889999999999999999998873  5555322  23334456899999999999987  4566677


Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhc
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAGTWGALLGACKVHVNAELGEIAARHLLEL  443 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  443 (490)
                      .+..+...+.+.|++++|.+.|+... ..|+...+..+..++...|+.++|.+++++.+..
T Consensus       330 l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~  390 (398)
T PRK10747        330 LWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYAWLADALDRLHKPEEAAAMRRDGLML  390 (398)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            78889999999999999999998877 6688888889999999999999999999998764

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

Probab=99.68  E-value=7.4e-15  Score=135.16  Aligned_cols=277  Identities=14%  Similarity=0.090  Sum_probs=223.3

Q ss_pred             ChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCC------CCHHhHHHHHHHHHhcCChHHHHHHH
Q 011249          163 NMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISE------PDASCWAAMTVCYVQNGYAKAAIEMY  233 (490)
Q Consensus       163 ~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~------~~~~~~~~l~~~~~~~g~~~~A~~~~  233 (490)
                      +..+|+..|.+....   .......+..+|...+++++|+++|+.+.+      .+...|.+.+..+-+.    -++..+
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            567888888885432   445667888999999999999999999875      5677888777655332    222222


Q ss_pred             -HHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChh
Q 011249          234 -KVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVI  312 (490)
Q Consensus       234 -~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~  312 (490)
                       +.+.... +-.+.+|..+.++|.-+++.+.|++.|++..+.. +....+|+.+..-+....++|.|...|+.....|+.
T Consensus       410 aq~Li~~~-~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQld-p~faYayTLlGhE~~~~ee~d~a~~~fr~Al~~~~r  487 (638)
T KOG1126|consen  410 AQDLIDTD-PNSPESWCALGNCFSLQKDHDTAIKCFKRAIQLD-PRFAYAYTLLGHESIATEEFDKAMKSFRKALGVDPR  487 (638)
T ss_pred             HHHHHhhC-CCCcHHHHHhcchhhhhhHHHHHHHHHHHhhccC-CccchhhhhcCChhhhhHHHHhHHHHHHhhhcCCch
Confidence             2333332 3467899999999999999999999999999876 557889999999999999999999999999987666


Q ss_pred             HHH---HHHHHHHhcCChHHHHHHHHHHHHcCCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHH
Q 011249          313 SYS---SMITAFADHGKSQEALDMFLKMRNEGIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCM  388 (490)
Q Consensus       313 ~~~---~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l  388 (490)
                      .|+   .+...|.+.++++.|+-.|+++.+  +.|. .+....+...+.+.|+.++|+.+++++..  --+.++..-...
T Consensus       488 hYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~--INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~--ld~kn~l~~~~~  563 (638)
T KOG1126|consen  488 HYNAWYGLGTVYLKQEKLEFAEFHFQKAVE--INPSNSVILCHIGRIQHQLKRKDKALQLYEKAIH--LDPKNPLCKYHR  563 (638)
T ss_pred             hhHHHHhhhhheeccchhhHHHHHHHhhhc--CCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHh--cCCCCchhHHHH
Confidence            555   467789999999999999999998  5664 45677778888999999999999999976  334455555566


Q ss_pred             HHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          389 VDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       389 ~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                      +..+...+++++|+..++++.  .+.+..++..+...|.+.|+.+.|+.-|..+..++|.-..
T Consensus       564 ~~il~~~~~~~eal~~LEeLk~~vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~ldpkg~~  626 (638)
T KOG1126|consen  564 ASILFSLGRYVEALQELEELKELVPQESSVFALLGKIYKRLGNTDLALLHFSWALDLDPKGAQ  626 (638)
T ss_pred             HHHHHhhcchHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHccchHHHHhhHHHhcCCCccch
Confidence            788889999999999999988  3445667888889999999999999999999999987443

>TIGR00540 hemY_coli hemY protein

Probab=99.67  E-value=2.5e-13  Score=127.80  Aligned_cols=116  Identities=12%  Similarity=0.083  Sum_probs=66.3

Q ss_pred             HhCCChHHHHHHHHHhccC--C-chhHHHHHHHHHhcCChhHHHHHHhhcCC--CCH--HhHHHHHHHHHhcCChHHHHH
Q 011249          159 ANCGNMKAAKEFYDRMTEK--N-SVTWVAMIAGYGKCGEVREAKKVFDEISE--PDA--SCWAAMTVCYVQNGYAKAAIE  231 (490)
Q Consensus       159 ~~~~~~~~a~~~~~~~~~~--~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~--~~~~~l~~~~~~~g~~~~A~~  231 (490)
                      ...|+++.|.+.+.+..+.  + ...+.....+....|+.+.|.+.+.+..+  |+.  .........+...|+++.|.+
T Consensus        95 ~~~g~~~~A~~~l~~~~~~~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al~  174 (409)
T TIGR00540        95 LAEGDYAKAEKLIAKNADHAAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAARH  174 (409)
T ss_pred             HhCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHHH
Confidence            3466677777666665542  2 22233444555666666666666666533  332  222334566666666666666


Q ss_pred             HHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcC
Q 011249          232 MYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGC  275 (490)
Q Consensus       232 ~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  275 (490)
                      .++.+.+..+. +...+..+...+...|++++|.+.+..+.+.+
T Consensus       175 ~l~~l~~~~P~-~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~  217 (409)
T TIGR00540       175 GVDKLLEMAPR-HKEVLKLAEEAYIRSGAWQALDDIIDNMAKAG  217 (409)
T ss_pred             HHHHHHHhCCC-CHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcC
Confidence            66666665422 44455566666666666666666666666665

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.

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.66  E-value=1.3e-12  Score=118.18  Aligned_cols=447  Identities=11%  Similarity=0.011  Sum_probs=284.3

Q ss_pred             chhhHHHHHHHHhhhcCCCCchhHhHHHHHHHHHhcCCCCHHHHHHHhcc--CCCCCCceehHHHHHHHHhcCChhHHHH
Q 011249           12 TFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQ--IPKCKTQFLWTSLIRNHVLHAHFRQSIL   89 (490)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~--~~~~~~~~~~~~l~~~~~~~g~~~~A~~   89 (490)
                      ++..|..+-+.+..   .+.+|.  --.-+.+.+.-.+. .+.|..+...  +...+. .+.......+.+..++++|..
T Consensus        31 ~y~~a~f~adkV~~---l~~dp~--d~~~~aq~l~~~~~-y~ra~~lit~~~le~~d~-~cryL~~~~l~~lk~~~~al~  103 (611)
T KOG1173|consen   31 RYKTALFWADKVAG---LTNDPA--DIYWLAQVLYLGRQ-YERAAHLITTYKLEKRDI-ACRYLAAKCLVKLKEWDQALL  103 (611)
T ss_pred             hhhHHHHHHHHHHh---ccCChH--HHHHHHHHHHhhhH-HHHHHHHHHHhhhhhhhH-HHHHHHHHHHHHHHHHHHHHH
Confidence            45556666666655   444444  44566777777777 7777777654  345555 677777788888999999999


Q ss_pred             HHHHH----HhcC---------CCCCHhh----HHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCCHhHHH
Q 011249           90 LYAKM----HRLG---------VLTSGFT----FSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWS  152 (490)
Q Consensus        90 ~~~~m----~~~g---------~~p~~~~----~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  152 (490)
                      ++...    ....         +.+|...    -+.-...|...|.       .|......++|...|.+....|+..+.
T Consensus       104 vl~~~~~~~~~f~yy~~~~~~~l~~n~~~~~~~~~~essic~lRgk-------~y~al~n~~~ar~~Y~~Al~~D~~c~E  176 (611)
T KOG1173|consen  104 VLGRGHVETNPFSYYEKDAANTLELNSAGEDLMINLESSICYLRGK-------VYVALDNREEARDKYKEALLADAKCFE  176 (611)
T ss_pred             HhcccchhhcchhhcchhhhceeccCcccccccccchhceeeeeee-------hhhhhccHHHHHHHHHHHHhcchhhHH
Confidence            98832    1110         1111111    0111111211111       244455677777777776665655544


Q ss_pred             HHHHHHHhC-CChHHHHHHHHHhc-----cCCchhHHHHHHHHHhcCChhHHHHHH--hhcC--CCCHHhHHHHHHHHHh
Q 011249          153 AMVAGYANC-GNMKAAKEFYDRMT-----EKNSVTWVAMIAGYGKCGEVREAKKVF--DEIS--EPDASCWAAMTVCYVQ  222 (490)
Q Consensus       153 ~l~~~~~~~-~~~~~a~~~~~~~~-----~~~~~~~~~l~~~~~~~~~~~~A~~~~--~~~~--~~~~~~~~~l~~~~~~  222 (490)
                      .+...-... --.++-..+++...     ..+......+.........-++....-  +.+.  +.++........-+..
T Consensus       177 a~~~lvs~~mlt~~Ee~~ll~~l~~a~~~~ed~e~l~~lyel~~~k~~n~~~~~r~~~~sl~~l~~~~dll~~~ad~~y~  256 (611)
T KOG1173|consen  177 AFEKLVSAHMLTAQEEFELLESLDLAMLTKEDVERLEILYELKLCKNRNEESLTRNEDESLIGLAENLDLLAEKADRLYY  256 (611)
T ss_pred             HHHHHHHHHhcchhHHHHHHhcccHHhhhhhHHHHHHHHHHhhhhhhccccccccCchhhhhhhhhcHHHHHHHHHHHHH
Confidence            433221110 00111122222110     111211112211110000000000000  0011  1455556666677778


Q ss_pred             cCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHH
Q 011249          223 NGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWRE  302 (490)
Q Consensus       223 ~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  302 (490)
                      .+++.+..++.+...+.. ++....+..-|.++...|+..+-.-+-.++.+.- |..+.+|-++.--|.-.|+.++|++.
T Consensus       257 ~c~f~~c~kit~~lle~d-pfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y-P~~a~sW~aVg~YYl~i~k~seARry  334 (611)
T KOG1173|consen  257 GCRFKECLKITEELLEKD-PFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY-PSKALSWFAVGCYYLMIGKYSEARRY  334 (611)
T ss_pred             cChHHHHHHHhHHHHhhC-CCCcchHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCCcchhhHHHHHHHhcCcHHHHHH
Confidence            889999999998888653 4455555666667888888777777777777764 67778888888888888999999999


Q ss_pred             HhcccCCC---hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCC
Q 011249          303 FSRIKNKD---VISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIK  379 (490)
Q Consensus       303 ~~~~~~~~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~  379 (490)
                      |.+...-|   ...|-.....|.-.|..|+|+..+..+-+. ++-....+.-+..-|.+.++.+.|.++|.....  -.|
T Consensus       335 ~SKat~lD~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl-~~G~hlP~LYlgmey~~t~n~kLAe~Ff~~A~a--i~P  411 (611)
T KOG1173|consen  335 FSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARL-MPGCHLPSLYLGMEYMRTNNLKLAEKFFKQALA--IAP  411 (611)
T ss_pred             HHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHh-ccCCcchHHHHHHHHHHhccHHHHHHHHHHHHh--cCC
Confidence            98876532   357888888999999999999988887763 121222344455557788899999999988875  445


Q ss_pred             CCchHHHHHHHHHhhcCChHHHHHHHHhcc--------CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCch
Q 011249          380 PLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--------DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGN  450 (490)
Q Consensus       380 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--------~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~  450 (490)
                      .|+...+-+.-.....+.+.+|..+|+...        ..+ -.++++.|..+|.+.+.+++|+..+++++.+.|.++.+
T Consensus       412 ~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~q~aL~l~~k~~~~  491 (611)
T KOG1173|consen  412 SDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYYQKALLLSPKDAST  491 (611)
T ss_pred             CcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHHHHHHHcCCCchhH
Confidence            567777777777778888999999887654        111 34567888889999999999999999999999999999


Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          451 SALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       451 ~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      +..++.+|...|+.+.|.+.|.+..-.
T Consensus       492 ~asig~iy~llgnld~Aid~fhKaL~l  518 (611)
T KOG1173|consen  492 HASIGYIYHLLGNLDKAIDHFHKALAL  518 (611)
T ss_pred             HHHHHHHHHHhcChHHHHHHHHHHHhc
Confidence            999999999999999999999877644

>TIGR00540 hemY_coli hemY protein

Probab=99.65  E-value=6.8e-13  Score=124.90  Aligned_cols=280  Identities=11%  Similarity=-0.012  Sum_probs=116.3

Q ss_pred             hcCChhHHHHHHhhcCC--CCH-HhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHH
Q 011249          191 KCGEVREAKKVFDEISE--PDA-SCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAIL  267 (490)
Q Consensus       191 ~~~~~~~A~~~~~~~~~--~~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~  267 (490)
                      ..|+++.|.+.+.+..+  |++ ..+-....+..+.|+++.|.+.+++..+....+...........+...|+++.|...
T Consensus        96 ~~g~~~~A~~~l~~~~~~~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~l~~~~~~~Al~~  175 (409)
T TIGR00540        96 AEGDYAKAEKLIAKNADHAAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRILLAQNELHAARHG  175 (409)
T ss_pred             hCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHHHHCCCHHHHHHH
Confidence            34555555555544433  221 122223344444455555555555544321111111222224444445555555555


Q ss_pred             HHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHH----HHHHHHHhcCChHHHHHHHHHHHHc
Q 011249          268 AKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYS----SMITAFADHGKSQEALDMFLKMRNE  340 (490)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~----~l~~~~~~~~~~~~a~~~~~~~~~~  340 (490)
                      ++.+.+.. |.++.+...+..++...|++++|.+.+..+.+   .+...+.    .........+..+++...+..+.+.
T Consensus       176 l~~l~~~~-P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~  254 (409)
T TIGR00540       176 VDKLLEMA-PRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKN  254 (409)
T ss_pred             HHHHHHhC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHH
Confidence            55554443 33444444455555555555555555544442   1111111    0001111122222222233333322


Q ss_pred             CC---CCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchH--HHHHHHHHhhcCChHHHHHHHHhcc-CCC-C
Q 011249          341 GI---EPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEH--LTCMVDLLGRSGQLEKAHSLIMDYK-DFC-D  413 (490)
Q Consensus       341 ~~---~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~--~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~  413 (490)
                      ..   +.+...+..+...+...|+.++|.+.+++..+.  .+++...  ...........++.+.+.+.+++.. ..| +
T Consensus       255 ~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~--~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~  332 (409)
T TIGR00540       255 QPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKK--LGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVDDK  332 (409)
T ss_pred             CCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhh--CCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhCCCC
Confidence            10   013344444445555555555555555555442  1111110  0111111122344455555554443 122 2


Q ss_pred             h--hhHHHHHHHHhhhCChHHHHHHHH--HHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          414 A--GTWGALLGACKVHVNAELGEIAAR--HLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       414 ~--~~~~~l~~~~~~~g~~~~a~~~~~--~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      +  ....++...|.+.|++++|.+.|+  .+.+..|++. .+..++.++.+.|+.++|.+++++.
T Consensus       333 ~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~-~~~~La~ll~~~g~~~~A~~~~~~~  396 (409)
T TIGR00540       333 PKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDAN-DLAMAADAFDQAGDKAEAAAMRQDS  396 (409)
T ss_pred             hhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHH-HHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3  344455555566666666666666  3444445432 2445566666666666666665543

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.

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

Probab=99.65  E-value=1.1e-15  Score=136.69  Aligned_cols=251  Identities=14%  Similarity=0.089  Sum_probs=107.2

Q ss_pred             HHHHHHHhcCChhHHHHHHhhc-CC----CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhcc
Q 011249          184 AMIAGYGKCGEVREAKKVFDEI-SE----PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQL  258 (490)
Q Consensus       184 ~l~~~~~~~~~~~~A~~~~~~~-~~----~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  258 (490)
                      .+...+.+.|++++|++++++. ..    .+...|..+.......++++.|.+.|+++...+.. ++..+..++.. ...
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~-~~~~~~~l~~l-~~~   90 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKA-NPQDYERLIQL-LQD   90 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccc-ccc
Confidence            3466677777777777777432 22    34555666666777778888888888888765433 45556666665 677


Q ss_pred             CChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC-----CChhHHHHHHHHHHhcCChHHHHHH
Q 011249          259 GDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN-----KDVISYSSMITAFADHGKSQEALDM  333 (490)
Q Consensus       259 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~  333 (490)
                      +++++|.+++....+..  +++..+..++..+...++++++..+++.+..     +++..|..+...+.+.|++++|+..
T Consensus        91 ~~~~~A~~~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~  168 (280)
T PF13429_consen   91 GDPEEALKLAEKAYERD--GDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRD  168 (280)
T ss_dssp             -----------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHH
T ss_pred             ccccccccccccccccc--cccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            88888887777654432  4555566677778888888888888777542     4667788888889999999999999


Q ss_pred             HHHHHHcCCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--C
Q 011249          334 FLKMRNEGIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--D  410 (490)
Q Consensus       334 ~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~  410 (490)
                      +++..+.  .|+ ......++..+...|+.+++.++++...+.  .+.++..+..+..+|...|+.++|..+|++..  .
T Consensus       169 ~~~al~~--~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~--~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~  244 (280)
T PF13429_consen  169 YRKALEL--DPDDPDARNALAWLLIDMGDYDEAREALKRLLKA--APDDPDLWDALAAAYLQLGRYEEALEYLEKALKLN  244 (280)
T ss_dssp             HHHHHHH---TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH---HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHS
T ss_pred             HHHHHHc--CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHH--CcCHHHHHHHHHHHhcccccccccccccccccccc
Confidence            9999984  665 567788888999999999999999998884  36677888899999999999999999998876  4


Q ss_pred             CCChhhHHHHHHHHhhhCChHHHHHHHHHHHh
Q 011249          411 FCDAGTWGALLGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       411 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                      +.|+.....+..++...|+.++|.++.+++.+
T Consensus       245 p~d~~~~~~~a~~l~~~g~~~~A~~~~~~~~~  276 (280)
T PF13429_consen  245 PDDPLWLLAYADALEQAGRKDEALRLRRQALR  276 (280)
T ss_dssp             TT-HHHHHHHHHHHT-----------------
T ss_pred             cccccccccccccccccccccccccccccccc
Confidence            55788888999999999999999999988765

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

Probab=99.62  E-value=6.6e-12  Score=110.97  Aligned_cols=155  Identities=12%  Similarity=0.034  Sum_probs=72.0

Q ss_pred             hHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHh
Q 011249          247 AMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFAD  323 (490)
Q Consensus       247 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~  323 (490)
                      |...+.+-|.-.++.++|..+|++..+.+ |.....|+.+.+-|....+...|.+-|+...+   .|-..|-.+.++|.-
T Consensus       332 TCCiIaNYYSlr~eHEKAv~YFkRALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~p~DyRAWYGLGQaYei  410 (559)
T KOG1155|consen  332 TCCIIANYYSLRSEHEKAVMYFKRALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDINPRDYRAWYGLGQAYEI  410 (559)
T ss_pred             ceeeehhHHHHHHhHHHHHHHHHHHHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcCchhHHHHhhhhHHHHH
Confidence            34444444444444444444444444443 33344444444444444444445444444433   233444445555555


Q ss_pred             cCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHH
Q 011249          324 HGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAH  402 (490)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  402 (490)
                      .+.+.-|+-.|++..+  ..| |...|..|..+|.+.++.++|++.|.....  .-..+...+..|.+.|.+.++.++|.
T Consensus       411 m~Mh~YaLyYfqkA~~--~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~--~~dte~~~l~~LakLye~l~d~~eAa  486 (559)
T KOG1155|consen  411 MKMHFYALYYFQKALE--LKPNDSRLWVALGECYEKLNRLEEAIKCYKRAIL--LGDTEGSALVRLAKLYEELKDLNEAA  486 (559)
T ss_pred             hcchHHHHHHHHHHHh--cCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHh--ccccchHHHHHHHHHHHHHHhHHHHH
Confidence            5555555555554444  233 333445555555555555555555554444  22223344444555555555555554


Q ss_pred             HHHH
Q 011249          403 SLIM  406 (490)
Q Consensus       403 ~~~~  406 (490)
                      ..|+
T Consensus       487 ~~ye  490 (559)
T KOG1155|consen  487 QYYE  490 (559)
T ss_pred             HHHH
Confidence            4443

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=99.61  E-value=1.3e-12  Score=110.09  Aligned_cols=260  Identities=13%  Similarity=0.118  Sum_probs=160.0

Q ss_pred             CCChHHHHHHHHHhccCCchhH---HHHHHHHHhcCChhHHHHHHhhcCC-CCH------HhHHHHHHHHHhcCChHHHH
Q 011249          161 CGNMKAAKEFYDRMTEKNSVTW---VAMIAGYGKCGEVREAKKVFDEISE-PDA------SCWAAMTVCYVQNGYAKAAI  230 (490)
Q Consensus       161 ~~~~~~a~~~~~~~~~~~~~~~---~~l~~~~~~~~~~~~A~~~~~~~~~-~~~------~~~~~l~~~~~~~g~~~~A~  230 (490)
                      +++.++|.++|-+|.+.|+.|+   .+|.+.|.+.|..|.|+++...+.+ ||.      .....|..=|...|-++.|+
T Consensus        48 s~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE  127 (389)
T COG2956          48 SNQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAE  127 (389)
T ss_pred             hcCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHH
Confidence            4667777777777776555444   5667777777777777777776654 332      23345666778888888888


Q ss_pred             HHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCc----hhHHHHHHHHHHhcCChHHHHHHHhcc
Q 011249          231 EMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRT----NYVSNALIHMHSKCGYLDLAWREFSRI  306 (490)
Q Consensus       231 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~A~~~~~~~  306 (490)
                      .+|..+...+ ..-......|+..|....+|++|+..-+++.+.+..+.    ...|.-|...+....+.+.|..++.+.
T Consensus       128 ~~f~~L~de~-efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kA  206 (389)
T COG2956         128 DIFNQLVDEG-EFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKA  206 (389)
T ss_pred             HHHHHHhcch-hhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            8888887654 22445677788888888888888888887777664332    234444555555566666666666666


Q ss_pred             cCC---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCch
Q 011249          307 KNK---DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTE  383 (490)
Q Consensus       307 ~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  383 (490)
                      .+.   .+..--.+.+.+...|+++.|.+.|+...+.+..--+.+...|..+|...|+.++....+..+.+.   .+...
T Consensus       207 lqa~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~---~~g~~  283 (389)
T COG2956         207 LQADKKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMET---NTGAD  283 (389)
T ss_pred             HhhCccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHc---cCCcc
Confidence            542   223333445566667777777777777766533333446666666777777777777777666652   23333


Q ss_pred             HHHHHHHHHhhcCChHHHHHHH-HhccCCCChhhHHHHHHHH
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLI-MDYKDFCDAGTWGALLGAC  424 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~-~~~~~~~~~~~~~~l~~~~  424 (490)
                      .-..+.+.-....-.+.|..++ +++..+|+...+..++...
T Consensus       284 ~~l~l~~lie~~~G~~~Aq~~l~~Ql~r~Pt~~gf~rl~~~~  325 (389)
T COG2956         284 AELMLADLIELQEGIDAAQAYLTRQLRRKPTMRGFHRLMDYH  325 (389)
T ss_pred             HHHHHHHHHHHhhChHHHHHHHHHHHhhCCcHHHHHHHHHhh
Confidence            3333444333333344444433 4455566666666666544

>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]

Probab=99.59  E-value=6e-12  Score=106.19  Aligned_cols=277  Identities=13%  Similarity=0.121  Sum_probs=212.5

Q ss_pred             HHhcCCHHHHHHHHhhcCCCCHhH---HHHHHHHHHhCCChHHHHHHHHHhccCCch-------hHHHHHHHHHhcCChh
Q 011249          127 YTKIGLMDDAQRLFDSMAERNVIS---WSAMVAGYANCGNMKAAKEFYDRMTEKNSV-------TWVAMIAGYGKCGEVR  196 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-------~~~~l~~~~~~~~~~~  196 (490)
                      +.-+.+.++|.+.|-+|.+.|..+   .-+|.+.|-+.|..|.|+++.+.+.++...       ....|..-|...|-+|
T Consensus        45 fLLs~Q~dKAvdlF~e~l~~d~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~D  124 (389)
T COG2956          45 FLLSNQPDKAVDLFLEMLQEDPETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLD  124 (389)
T ss_pred             HHhhcCcchHHHHHHHHHhcCchhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhh
Confidence            445689999999999999865554   557889999999999999999998865222       4467778899999999


Q ss_pred             HHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccCh----hhHHHHHHHHhccCChHHHHHHHH
Q 011249          197 EAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISE----VAMVGAISACTQLGDVEMAAILAK  269 (490)
Q Consensus       197 ~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~----~~~~~l~~~~~~~g~~~~a~~~~~  269 (490)
                      .|+.+|..+.+   .-......|+..|....+|++|++.-+++.+.+.++..    ..|.-+...+....+.+.|..+++
T Consensus       125 RAE~~f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~  204 (389)
T COG2956         125 RAEDIFNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLK  204 (389)
T ss_pred             HHHHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            99999999877   34557788999999999999999999999987655543    356666677777889999999999


Q ss_pred             HHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCCh----hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc
Q 011249          270 HVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDV----ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN  345 (490)
Q Consensus       270 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~----~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~  345 (490)
                      +..+.+ +..+..--.+.+.+...|+++.|.+.++.+.+.|+    .+...|..+|...|+.++....+..+.+..  ++
T Consensus       205 kAlqa~-~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~--~g  281 (389)
T COG2956         205 KALQAD-KKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETN--TG  281 (389)
T ss_pred             HHHhhC-ccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHcc--CC
Confidence            998876 55666666788999999999999999999998654    466778889999999999999999999853  33


Q ss_pred             HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh---cCChHHHHHHHHhcc
Q 011249          346 QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR---SGQLEKAHSLIMDYK  409 (490)
Q Consensus       346 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~---~g~~~~A~~~~~~~~  409 (490)
                      ...-..+........-.+.|..++.+-..   -+|+...+..+++.-..   .|...+....++.|.
T Consensus       282 ~~~~l~l~~lie~~~G~~~Aq~~l~~Ql~---r~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mv  345 (389)
T COG2956         282 ADAELMLADLIELQEGIDAAQAYLTRQLR---RKPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMV  345 (389)
T ss_pred             ccHHHHHHHHHHHhhChHHHHHHHHHHHh---hCCcHHHHHHHHHhhhccccccchhhhHHHHHHHH
Confidence            33333444433334444555555544443   37999999888886543   344555555555554

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=99.56  E-value=4.4e-11  Score=104.19  Aligned_cols=275  Identities=14%  Similarity=0.043  Sum_probs=158.5

Q ss_pred             CCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCC----CCHHhHHHHHHHHHhcCChHHHHHHH
Q 011249          161 CGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISE----PDASCWAAMTVCYVQNGYAKAAIEMY  233 (490)
Q Consensus       161 ~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~~~~~~l~~~~~~~g~~~~A~~~~  233 (490)
                      .|++.+|+++..+..+.   ....|..-+.+-...||.+.+-+.+.+..+    ++....-+..+.....|+++.|..-+
T Consensus        97 eG~~~qAEkl~~rnae~~e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~v  176 (400)
T COG3071          97 EGDFQQAEKLLRRNAEHGEQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARENV  176 (400)
T ss_pred             cCcHHHHHHHHHHhhhcCcchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHHH
Confidence            35555555555544332   122233333444445555555555555443    22233444445555555555555555


Q ss_pred             HHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCch-------hHHHHHHHHHHhcCChHHHHHHHhcc
Q 011249          234 KVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTN-------YVSNALIHMHSKCGYLDLAWREFSRI  306 (490)
Q Consensus       234 ~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~~~~~~A~~~~~~~  306 (490)
                      .++.+.+.. ++........+|.+.|++.....++..+.+.+.-.+.       .++..+++-....+..+.-...+++.
T Consensus       177 ~~ll~~~pr-~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~  255 (400)
T COG3071         177 DQLLEMTPR-HPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQ  255 (400)
T ss_pred             HHHHHhCcC-ChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhc
Confidence            555554322 3444555555555566666665555555555543332       23444444444444444444555555


Q ss_pred             cC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCch
Q 011249          307 KN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTE  383 (490)
Q Consensus       307 ~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  383 (490)
                      +.   .++..-.+++.-+.+.|+.++|.++..+..+.+..|+..    ..-.+.+.++.+.-++..++-.+.++  .++.
T Consensus       256 pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~L~----~~~~~l~~~d~~~l~k~~e~~l~~h~--~~p~  329 (400)
T COG3071         256 PRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPRLC----RLIPRLRPGDPEPLIKAAEKWLKQHP--EDPL  329 (400)
T ss_pred             cHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChhHH----HHHhhcCCCCchHHHHHHHHHHHhCC--CChh
Confidence            43   356666667777777788888888777777766666521    12235566777776677776666433  3346


Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHh
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAGTWGALLGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                      .+..|...|.+.+.|.+|.+.|+... ..|+...|..+..++...|+.++|.++.++.+.
T Consensus       330 L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~  389 (400)
T COG3071         330 LLSTLGRLALKNKLWGKASEALEAALKLRPSASDYAELADALDQLGEPEEAEQVRREALL  389 (400)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            66677777777777777777776554 567777777777777777777777777777764

>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]

Probab=99.55  E-value=2.3e-11  Score=105.92  Aligned_cols=279  Identities=12%  Similarity=0.022  Sum_probs=215.5

Q ss_pred             hcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHH
Q 011249          191 KCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAIL  267 (490)
Q Consensus       191 ~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~  267 (490)
                      ..|+|..|++...+..+   .....|..-+.+--+.|+.+.+-.++.+..+....++..............|+.+.|..-
T Consensus        96 ~eG~~~qAEkl~~rnae~~e~p~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~  175 (400)
T COG3071          96 FEGDFQQAEKLLRRNAEHGEQPVLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAAREN  175 (400)
T ss_pred             hcCcHHHHHHHHHHhhhcCcchHHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHH
Confidence            36899999999988655   333455555677778899999999999988764455566677777778889999999999


Q ss_pred             HHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCC----C-------hhHHHHHHHHHHhcCChHHHHHHHHH
Q 011249          268 AKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK----D-------VISYSSMITAFADHGKSQEALDMFLK  336 (490)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~----~-------~~~~~~l~~~~~~~~~~~~a~~~~~~  336 (490)
                      ..++.+.+ +..+.+......+|.+.|++.....++.++.+.    +       ..+|+.+++-....+..+.-...|+.
T Consensus       176 v~~ll~~~-pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~  254 (400)
T COG3071         176 VDQLLEMT-PRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKN  254 (400)
T ss_pred             HHHHHHhC-cCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHh
Confidence            99988887 667778888899999999999999999888773    2       23677777766666666666666666


Q ss_pred             HHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCCh
Q 011249          337 MRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDA  414 (490)
Q Consensus       337 ~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~  414 (490)
                      .-.. .+-++..-..++.-+...|+.++|.++..+..+. +..|+..    ..-...+.++.+.-++..++..  .+.++
T Consensus       255 ~pr~-lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~-~~D~~L~----~~~~~l~~~d~~~l~k~~e~~l~~h~~~p  328 (400)
T COG3071         255 QPRK-LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKR-QWDPRLC----RLIPRLRPGDPEPLIKAAEKWLKQHPEDP  328 (400)
T ss_pred             ccHH-hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHh-ccChhHH----HHHhhcCCCCchHHHHHHHHHHHhCCCCh
Confidence            5543 4455666777788888999999999999998885 6666611    2234456677776666665554  34456


Q ss_pred             hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          415 GTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       415 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      ..+.+|...|.+.+.+.+|.+.|+.+++..|+ .+.|..++.++.+.|+..+|.++.++..-.
T Consensus       329 ~L~~tLG~L~~k~~~w~kA~~~leaAl~~~~s-~~~~~~la~~~~~~g~~~~A~~~r~e~L~~  390 (400)
T COG3071         329 LLLSTLGRLALKNKLWGKASEALEAALKLRPS-ASDYAELADALDQLGEPEEAEQVRREALLL  390 (400)
T ss_pred             hHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCC-hhhHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            78889999999999999999999999998887 778999999999999999999999876643

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.55  E-value=3.3e-10  Score=103.44  Aligned_cols=411  Identities=12%  Similarity=0.077  Sum_probs=248.1

Q ss_pred             HHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCC
Q 011249           39 QFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARV  116 (490)
Q Consensus        39 ~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~  116 (490)
                      -+=++.+..+++ +++|.+..+++.  .|+....+..=+-++.+.+.+++|+.+.+.-...  ..+.. |. +=.+|   
T Consensus        16 ~t~ln~~~~~~e-~e~a~k~~~Kil~~~pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~--~~~~~-~~-fEKAY---   87 (652)
T KOG2376|consen   16 LTDLNRHGKNGE-YEEAVKTANKILSIVPDDEDAIRCKVVALIQLDKYEDALKLIKKNGAL--LVINS-FF-FEKAY---   87 (652)
T ss_pred             HHHHHHhccchH-HHHHHHHHHHHHhcCCCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchh--hhcch-hh-HHHHH---
Confidence            344567778888 999999988885  4666577888888899999999999666543221  11111 10 23333   


Q ss_pred             CChHHHHHHHHHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHH-hcCCh
Q 011249          117 PSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYG-KCGEV  195 (490)
Q Consensus       117 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~-~~~~~  195 (490)
                               +..+.+..|+|+..++-..+.+..+...-...+.+.|++++|+.+|+.+.+.+...+..-+.+-+ ..+-.
T Consensus        88 ---------c~Yrlnk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a~  158 (652)
T KOG2376|consen   88 ---------CEYRLNKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAAA  158 (652)
T ss_pred             ---------HHHHcccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHh
Confidence                     25688999999999996655666677778888999999999999999997664444433322211 11111


Q ss_pred             hHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcC-------------cccCh-hhHHHHHHHHhcc
Q 011249          196 REAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQEN-------------VRISE-VAMVGAISACTQL  258 (490)
Q Consensus       196 ~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-------------~~p~~-~~~~~l~~~~~~~  258 (490)
                      -.+. +.+....   .+-..+......++..|++.+|+++++...+.+             +.-+. ..-..+.-++...
T Consensus       159 l~~~-~~q~v~~v~e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~  237 (652)
T KOG2376|consen  159 LQVQ-LLQSVPEVPEDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQ  237 (652)
T ss_pred             hhHH-HHHhccCCCcchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHh
Confidence            1111 2333332   222333334455666777777777776662211             00000 1122344455666


Q ss_pred             CChHHHHHHHHHHHhcCCCCchhH----HHHHHHHHH-------------------------------------------
Q 011249          259 GDVEMAAILAKHVDEGCCDRTNYV----SNALIHMHS-------------------------------------------  291 (490)
Q Consensus       259 g~~~~a~~~~~~~~~~~~~~~~~~----~~~l~~~~~-------------------------------------------  291 (490)
                      |+-.+|..+|..+.+.. ++|...    .|.|+.+-.                                           
T Consensus       238 Gqt~ea~~iy~~~i~~~-~~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~lL  316 (652)
T KOG2376|consen  238 GQTAEASSIYVDIIKRN-PADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNALL  316 (652)
T ss_pred             cchHHHHHHHHHHHHhc-CCCchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777777776655 333211    111111100                                           


Q ss_pred             --hcCChHHHHHHHhcccCCC-hhHHHHHHHHH--HhcCChHHHHHHHHHHHHcCCCCcH--HHHHHHHHHhcCCCChHH
Q 011249          292 --KCGYLDLAWREFSRIKNKD-VISYSSMITAF--ADHGKSQEALDMFLKMRNEGIEPNQ--VTFIGVLTACSHGGLVED  364 (490)
Q Consensus       292 --~~~~~~~A~~~~~~~~~~~-~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~~~~p~~--~~~~~l~~~~~~~g~~~~  364 (490)
                        ..+..+.+.++...+.... ...+.+++...  ++...+..+..++....+.  .|..  ......+......|+++.
T Consensus       317 ~l~tnk~~q~r~~~a~lp~~~p~~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~~--~p~~s~~v~L~~aQl~is~gn~~~  394 (652)
T KOG2376|consen  317 ALFTNKMDQVRELSASLPGMSPESLFPILLQEATKVREKKHKKAIELLLQFADG--HPEKSKVVLLLRAQLKISQGNPEV  394 (652)
T ss_pred             HHHhhhHHHHHHHHHhCCccCchHHHHHHHHHHHHHHHHHHhhhHHHHHHHhcc--CCchhHHHHHHHHHHHHhcCCHHH
Confidence              1122223333333322211 22333333322  2223467777777777664  4443  345555666788999999


Q ss_pred             HHHHHH--------HHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-----CCCChhhHHHHH----HHHhhh
Q 011249          365 GCKQFE--------LMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-----DFCDAGTWGALL----GACKVH  427 (490)
Q Consensus       365 a~~~~~--------~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~~~~~~~~~l~----~~~~~~  427 (490)
                      |.+++.        .+.+. +.  .+.+...+...+.+.++.+.|..++.+..     ..+.......++    ..-.+.
T Consensus       395 A~~il~~~~~~~~ss~~~~-~~--~P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~  471 (652)
T KOG2376|consen  395 ALEILSLFLESWKSSILEA-KH--LPGTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRH  471 (652)
T ss_pred             HHHHHHHHhhhhhhhhhhh-cc--ChhHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhc
Confidence            999999        45442 33  44556668888888888877777776554     222223333333    334577


Q ss_pred             CChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          428 VNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       428 g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      |+.++|..+++++++.+|++..+...++.+|.+. +.+.|..+-+++
T Consensus       472 G~~~ea~s~leel~k~n~~d~~~l~~lV~a~~~~-d~eka~~l~k~L  517 (652)
T KOG2376|consen  472 GNEEEASSLLEELVKFNPNDTDLLVQLVTAYARL-DPEKAESLSKKL  517 (652)
T ss_pred             CchHHHHHHHHHHHHhCCchHHHHHHHHHHHHhc-CHHHHHHHhhcC
Confidence            9999999999999999999999999999898877 667777776554

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

Probab=99.54  E-value=3.4e-11  Score=107.27  Aligned_cols=377  Identities=11%  Similarity=0.018  Sum_probs=246.9

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhc
Q 011249           37 YAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACA  114 (490)
Q Consensus        37 ~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~  114 (490)
                      .+....+-|-++++ +++|++.+.+..  .|+.+..|.....+|...|+|+++.+--.+..+.  .|+-  --.+++.  
T Consensus       117 ~lK~~GN~~f~~kk-Y~eAIkyY~~AI~l~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl--~P~Y--~KAl~RR--  189 (606)
T KOG0547|consen  117 ALKTKGNKFFRNKK-YDEAIKYYTQAIELCPDEPIFYSNRAACYESLGDWEKVIEDCTKALEL--NPDY--VKALLRR--  189 (606)
T ss_pred             HHHhhhhhhhhccc-HHHHHHHHHHHHhcCCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhc--CcHH--HHHHHHH--
Confidence            34556677788999 999999999986  5663388999999999999999999988887775  4442  2222221  


Q ss_pred             CCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCCh------------HHHHHHHHHhccC---C-
Q 011249          115 RVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNM------------KAAKEFYDRMTEK---N-  178 (490)
Q Consensus       115 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~------------~~a~~~~~~~~~~---~-  178 (490)
                               ..++-..|++++|+.=..         -..+..++....-.            .++.+-+.+=..|   + 
T Consensus       190 ---------A~A~E~lg~~~eal~D~t---------v~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~  251 (606)
T KOG0547|consen  190 ---------ASAHEQLGKFDEALFDVT---------VLCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSA  251 (606)
T ss_pred             ---------HHHHHhhccHHHHHHhhh---------HHHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcH
Confidence                     122444455554432110         00011111000000            0111111100000   0 


Q ss_pred             ----------------------chhHHHHHHHH----Hh-cCChhHHHHHHhhcCC-------C---C------HHhHHH
Q 011249          179 ----------------------SVTWVAMIAGY----GK-CGEVREAKKVFDEISE-------P---D------ASCWAA  215 (490)
Q Consensus       179 ----------------------~~~~~~l~~~~----~~-~~~~~~A~~~~~~~~~-------~---~------~~~~~~  215 (490)
                                            ..+...+...+    .. ...+..|...+.+-..       .   |      ..+...
T Consensus       252 ~fi~syf~sF~~~~~~~~~~~~~ksDa~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~  331 (606)
T KOG0547|consen  252 TFIASYFGSFHADPKPLFDNKSDKSDAALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLL  331 (606)
T ss_pred             HHHHHHHhhccccccccccCCCccchhhHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHH
Confidence                                  00111111111    11 0123333333322111       1   1      122222


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCC
Q 011249          216 MTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGY  295 (490)
Q Consensus       216 l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  295 (490)
                      ..-.+.-.|+.-.|..-|+..++....++. .|.-+...|....+.++..+.|....+.+ +-++.+|..-..++.-.++
T Consensus       332 ~gtF~fL~g~~~~a~~d~~~~I~l~~~~~~-lyI~~a~~y~d~~~~~~~~~~F~~A~~ld-p~n~dvYyHRgQm~flL~q  409 (606)
T KOG0547|consen  332 RGTFHFLKGDSLGAQEDFDAAIKLDPAFNS-LYIKRAAAYADENQSEKMWKDFNKAEDLD-PENPDVYYHRGQMRFLLQQ  409 (606)
T ss_pred             hhhhhhhcCCchhhhhhHHHHHhcCcccch-HHHHHHHHHhhhhccHHHHHHHHHHHhcC-CCCCchhHhHHHHHHHHHH
Confidence            233345578899999999999987544333 37778888999999999999999999987 6778888888888888999


Q ss_pred             hHHHHHHHhcccCC---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHH
Q 011249          296 LDLAWREFSRIKNK---DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELM  372 (490)
Q Consensus       296 ~~~A~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~  372 (490)
                      +++|..-|++...-   ++..|--+..+..+.+++++++..|++.++. ++--+..|+.....+..+++++.|.+.|+..
T Consensus       410 ~e~A~aDF~Kai~L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk-FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~a  488 (606)
T KOG0547|consen  410 YEEAIADFQKAISLDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK-FPNCPEVYNLFAEILTDQQQFDKAVKQYDKA  488 (606)
T ss_pred             HHHHHHHHHHHhhcChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCchHHHHHHHHHhhHHhHHHHHHHHHHH
Confidence            99999999998773   4556666666777889999999999999986 4445678999999999999999999999999


Q ss_pred             HHHcCCCCC---------chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHH
Q 011249          373 TRVFGIKPL---------TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLL  441 (490)
Q Consensus       373 ~~~~~~~~~---------~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  441 (490)
                      .+-   .|+         +.+...++.. .-.+++..|..++++..  ++.....+..|...-.+.|+.++|+++|++..
T Consensus       489 i~L---E~~~~~~~v~~~plV~Ka~l~~-qwk~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  489 IEL---EPREHLIIVNAAPLVHKALLVL-QWKEDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             Hhh---ccccccccccchhhhhhhHhhh-chhhhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            863   332         2222233222 24589999999998887  34456689999999999999999999999988


Q ss_pred             hcCC
Q 011249          442 ELGP  445 (490)
Q Consensus       442 ~~~p  445 (490)
                      .+-.
T Consensus       565 ~lAr  568 (606)
T KOG0547|consen  565 QLAR  568 (606)
T ss_pred             HHHH
Confidence            7543

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.54  E-value=4.3e-11  Score=104.85  Aligned_cols=321  Identities=11%  Similarity=0.123  Sum_probs=163.2

Q ss_pred             eehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcC----
Q 011249           69 FLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMA----  144 (490)
Q Consensus        69 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----  144 (490)
                      .+|..+|.++++--..+.|.++|++..+...+.+..+||.+|.+-            .|..      ..+++.+|.    
T Consensus       208 et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~------------S~~~------~K~Lv~EMisqkm  269 (625)
T KOG4422|consen  208 ETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGAS------------SYSV------GKKLVAEMISQKM  269 (625)
T ss_pred             hhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHH------------Hhhc------cHHHHHHHHHhhc
Confidence            456666666666666666666666665555555666666665542            1111      133444443    


Q ss_pred             CCCHhHHHHHHHHHHhCCChHHHH----HHHHHhc----cCCchhHHHHHHHHHhcCChhH-HHHHHhhcCC--------
Q 011249          145 ERNVISWSAMVAGYANCGNMKAAK----EFYDRMT----EKNSVTWVAMIAGYGKCGEVRE-AKKVFDEISE--------  207 (490)
Q Consensus       145 ~~~~~~~~~l~~~~~~~~~~~~a~----~~~~~~~----~~~~~~~~~l~~~~~~~~~~~~-A~~~~~~~~~--------  207 (490)
                      .||..|+|+++.+..+.|+++.|.    +++.+|+    +|...+|..+|..+.+.++..+ |..++.++..        
T Consensus       270 ~Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fk  349 (625)
T KOG4422|consen  270 TPNLFTFNALLSCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFK  349 (625)
T ss_pred             CCchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCccc
Confidence            266666666666666666554433    3333333    2455556666665555555433 3333332211        


Q ss_pred             ----CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHc---C-cccCh---hhHHHHHHHHhccCChHHHHHHHHHHHhcCC
Q 011249          208 ----PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQE---N-VRISE---VAMVGAISACTQLGDVEMAAILAKHVDEGCC  276 (490)
Q Consensus       208 ----~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~-~~p~~---~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  276 (490)
                          .+...|..-+..|.+..+.+.|.++-.-+...   . +.|+.   .-|..+....++....+....+|+.+.-.-.
T Consensus       350 p~~p~d~~FF~~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y  429 (625)
T KOG4422|consen  350 PITPTDNKFFQSAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAY  429 (625)
T ss_pred             CCCCchhHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccee
Confidence                23334445555555555555555543333211   0 11221   2233444445555555555566666555544


Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHhcccCCC----hhHHHHHHHHHHhcC--------------------C-hHHHH
Q 011249          277 DRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKD----VISYSSMITAFADHG--------------------K-SQEAL  331 (490)
Q Consensus       277 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~----~~~~~~l~~~~~~~~--------------------~-~~~a~  331 (490)
                      -|+..+...++++..-.|.++-.-+++.++..-+    .....-+...+++.+                    + .+...
T Consensus       430 ~p~~~~m~~~lrA~~v~~~~e~ipRiw~D~~~~ght~r~~l~eeil~~L~~~k~hp~tp~r~Ql~~~~ak~aad~~e~~e  509 (625)
T KOG4422|consen  430 FPHSQTMIHLLRALDVANRLEVIPRIWKDSKEYGHTFRSDLREEILMLLARDKLHPLTPEREQLQVAFAKCAADIKEAYE  509 (625)
T ss_pred             cCCchhHHHHHHHHhhcCcchhHHHHHHHHHHhhhhhhHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHHHHH
Confidence            5555555555555555555555555555444311    000011111111111                    1 11112


Q ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHH---HHHHHHhhcCChHHHHHHHHhc
Q 011249          332 DMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLT---CMVDLLGRSGQLEKAHSLIMDY  408 (490)
Q Consensus       332 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~---~l~~~~~~~g~~~~A~~~~~~~  408 (490)
                      ..-.+|.+.  .......+.++..+.+.|+.++|.+++..+.+.++-.|.....+   -+++.-.+..+...|...++-+
T Consensus       510 ~~~~R~r~~--~~~~t~l~~ia~Ll~R~G~~qkA~e~l~l~~~~~~~ip~~p~lnAm~El~d~a~~~~spsqA~~~lQ~a  587 (625)
T KOG4422|consen  510 SQPIRQRAQ--DWPATSLNCIAILLLRAGRTQKAWEMLGLFLRKHNKIPRSPLLNAMAELMDSAKVSNSPSQAIEVLQLA  587 (625)
T ss_pred             hhHHHHHhc--cCChhHHHHHHHHHHHcchHHHHHHHHHHHHhcCCcCCCCcchhhHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            222233433  33445566666677888999999999988866544455555555   4555666778888888888877


Q ss_pred             c
Q 011249          409 K  409 (490)
Q Consensus       409 ~  409 (490)
                      .
T Consensus       588 ~  588 (625)
T KOG4422|consen  588 S  588 (625)
T ss_pred             H
Confidence            5

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.52  E-value=4.6e-12  Score=110.51  Aligned_cols=198  Identities=13%  Similarity=0.044  Sum_probs=156.0

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 011249          279 TNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTA  355 (490)
Q Consensus       279 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~  355 (490)
                      ....+..+...+...|++++|...+++..+   .+...+..+...+...|++++|.+.+++..+.. +.+...+..+...
T Consensus        30 ~~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~  108 (234)
T TIGR02521        30 AAKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTF  108 (234)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHH
Confidence            345566677778888888888888877654   245677778888888899999999998888753 2345567777788


Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHH
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      +...|++++|.+.++++......+.....+..+..++...|++++|...+++..  .+.+...+..+...+...|++++|
T Consensus       109 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  188 (234)
T TIGR02521       109 LCQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDA  188 (234)
T ss_pred             HHHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHH
Confidence            888899999999999887631223334566778888999999999999998776  333466788888889999999999


Q ss_pred             HHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          434 EIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       434 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      ...++++.+..|.++..+..++.++...|+.++|..+.+.+...
T Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       189 RAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            99999999988888888888999999999999999998877643

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.

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.49  E-value=4.4e-10  Score=105.83  Aligned_cols=362  Identities=12%  Similarity=0.055  Sum_probs=250.5

Q ss_pred             HHHHHHHhcCCHHHHHHHHhhcCC---CCHhHHHHHHHHHHhCCChHHHHHHHHHhccC-----CchhHHHHHHHHHh-c
Q 011249          122 AVICGYTKIGLMDDAQRLFDSMAE---RNVISWSAMVAGYANCGNMKAAKEFYDRMTEK-----NSVTWVAMIAGYGK-C  192 (490)
Q Consensus       122 ~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~l~~~~~~-~  192 (490)
                      .+.-+....|+++.+-+.|++...   .....|+.+...+...|.-..|+.++++-..+     |+..+......|.+ .
T Consensus       328 ~Lt~al~~~g~f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lmasklc~e~l  407 (799)
T KOG4162|consen  328 HLTFALSRCGQFEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLMASKLCIERL  407 (799)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHHHHHHHHhch
Confidence            344457888999999999998876   45678999999999999999999999887743     34444444455544 4


Q ss_pred             CChhHHHHHHhhcCC--------CCHHhHHHHHHHHHhc-----------CChHHHHHHHHHHHHcCcccChhhHHHHHH
Q 011249          193 GEVREAKKVFDEISE--------PDASCWAAMTVCYVQN-----------GYAKAAIEMYKVMRQENVRISEVAMVGAIS  253 (490)
Q Consensus       193 ~~~~~A~~~~~~~~~--------~~~~~~~~l~~~~~~~-----------g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~  253 (490)
                      +.+++++.+-.++..        ..+..|..+.-+|...           ....++++.+++..+.+.. |+.....+.-
T Consensus       408 ~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~-dp~~if~lal  486 (799)
T KOG4162|consen  408 KLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPT-DPLVIFYLAL  486 (799)
T ss_pred             hhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCC-CchHHHHHHH
Confidence            556665555544432        3445555555555322           2235678888888765432 3333333444


Q ss_pred             HHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--CC-----------------h---
Q 011249          254 ACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KD-----------------V---  311 (490)
Q Consensus       254 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~-----------------~---  311 (490)
                      -|+..++++.|....++..+.+...++..|..|.-.+...+++.+|+.+.+....  ++                 .   
T Consensus       487 q~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~i~~~~~~~e~~  566 (799)
T KOG4162|consen  487 QYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIHIELTFNDREEA  566 (799)
T ss_pred             HHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhhhhhhcccHHHH
Confidence            5777889999999999999986678888999898899999999999988876553  11                 0   


Q ss_pred             -hHHHHHHHHHH-----------------------hcCChHHHHHHHHHHH--------HcC---------CC--Cc---
Q 011249          312 -ISYSSMITAFA-----------------------DHGKSQEALDMFLKMR--------NEG---------IE--PN---  345 (490)
Q Consensus       312 -~~~~~l~~~~~-----------------------~~~~~~~a~~~~~~~~--------~~~---------~~--p~---  345 (490)
                       .+...++..+-                       ..++..++.+....+.        ..|         +.  |+   
T Consensus       567 l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~~~~~~~~~~  646 (799)
T KOG4162|consen  567 LDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPSSTVLPGPDSLW  646 (799)
T ss_pred             HHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhhhhhcccccccCcccccCCCCchH
Confidence             11111111111                       0111222222211111        011         01  11   


Q ss_pred             ---HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHH
Q 011249          346 ---QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGAL  420 (490)
Q Consensus       346 ---~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l  420 (490)
                         ...|......+...+..++|...+.+...  ..+.....|......+...|.+++|.+.|....  .+.++....++
T Consensus       647 ~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~--~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ldP~hv~s~~Al  724 (799)
T KOG4162|consen  647 YLLQKLWLLAADLFLLSGNDDEARSCLLEASK--IDPLSASVYYLRGLLLEVKGQLEEAKEAFLVALALDPDHVPSMTAL  724 (799)
T ss_pred             HHHHHHHHHHHHHHHhcCCchHHHHHHHHHHh--cchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcCCCCcHHHHHH
Confidence               11334455567788888899888888876  455667778888888999999999999997766  45567799999


Q ss_pred             HHHHhhhCChHHHHH--HHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccccCCCccc
Q 011249          421 LGACKVHVNAELGEI--AARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSW  487 (490)
Q Consensus       421 ~~~~~~~g~~~~a~~--~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~  487 (490)
                      ...+.+.|+...|..  ++..+++.+|.++.+|..++.++.+.|+.++|-+.|+...+... .+|=.+|
T Consensus       725 a~~lle~G~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qLe~-S~PV~pF  792 (799)
T KOG4162|consen  725 AELLLELGSPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAECFQAALQLEE-SNPVLPF  792 (799)
T ss_pred             HHHHHHhCCcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchHHHHHHHHHHHhhcc-CCCcccc
Confidence            999999999998888  99999999999999999999999999999999999998776643 3444443

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.47  E-value=1.7e-12  Score=109.58  Aligned_cols=228  Identities=11%  Similarity=0.013  Sum_probs=127.7

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc
Q 011249          214 AAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC  293 (490)
Q Consensus       214 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  293 (490)
                      +.+.++|.+.|-+.+|.+.++.-.+.  .|-+.||..|..+|.+..+++.|..++.+-.+.- |.++.......+.+.. 
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~f-P~~VT~l~g~ARi~ea-  302 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSF-PFDVTYLLGQARIHEA-  302 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcC-CchhhhhhhhHHHHHH-
Confidence            34556666666666666666655544  3444555556666666666666666655555442 3333333334444444 


Q ss_pred             CChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHH
Q 011249          294 GYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMT  373 (490)
Q Consensus       294 ~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  373 (490)
                                                    .++.++|.++|+...+.. +.+.....++...|.-.++++.|+.+++++.
T Consensus       303 ------------------------------m~~~~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiL  351 (478)
T KOG1129|consen  303 ------------------------------MEQQEDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRIL  351 (478)
T ss_pred             ------------------------------HHhHHHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHH
Confidence                                          444555555555544421 1122344444444555555555555555555


Q ss_pred             HHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc---CCC--ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC
Q 011249          374 RVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK---DFC--DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       374 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---~~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      .. |. .+++.|+.+.-+|.-.+++|-++.-|++..   ..|  ...+|..+.......||+..|.+.|+-++..+|++.
T Consensus       352 qm-G~-~speLf~NigLCC~yaqQ~D~~L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h~  429 (478)
T KOG1129|consen  352 QM-GA-QSPELFCNIGLCCLYAQQIDLVLPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQHG  429 (478)
T ss_pred             Hh-cC-CChHHHhhHHHHHHhhcchhhhHHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcchH
Confidence            52 33 234455555555555555555555554433   112  234666666666667777777777777777777777


Q ss_pred             chHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          449 GNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       449 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      ..+++|+-.-.+.|+.++|..+++......
T Consensus       430 ealnNLavL~~r~G~i~~Arsll~~A~s~~  459 (478)
T KOG1129|consen  430 EALNNLAVLAARSGDILGARSLLNAAKSVM  459 (478)
T ss_pred             HHHHhHHHHHhhcCchHHHHHHHHHhhhhC
Confidence            777777777777777777777777665443

>PRK12370 invasion protein regulator; Provisional

Probab=99.45  E-value=8.7e-11  Score=114.97  Aligned_cols=260  Identities=12%  Similarity=-0.021  Sum_probs=186.6

Q ss_pred             CCHHhHHHHHHHHHh-----cCChHHHHHHHHHHHHcCcccChhhHHHHHHHHh---------ccCChHHHHHHHHHHHh
Q 011249          208 PDASCWAAMTVCYVQ-----NGYAKAAIEMYKVMRQENVRISEVAMVGAISACT---------QLGDVEMAAILAKHVDE  273 (490)
Q Consensus       208 ~~~~~~~~l~~~~~~-----~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~---------~~g~~~~a~~~~~~~~~  273 (490)
                      .+...|...+.+-..     .+.+++|++.|++..+.... +...+..+..++.         ..+++++|...++++.+
T Consensus       254 ~~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~ldP~-~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~  332 (553)
T PRK12370        254 NSIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNMSPN-SIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATE  332 (553)
T ss_pred             CChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhcCCc-cHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHh
Confidence            345555555555322     23467899999999876322 3445555554443         33458899999999998


Q ss_pred             cCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHH-HH
Q 011249          274 GCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV-TF  349 (490)
Q Consensus       274 ~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~-~~  349 (490)
                      .. |.+...+..+..++...|++++|...|++..+  | +...+..+..++...|++++|...++++.+.  .|+.. .+
T Consensus       333 ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l--~P~~~~~~  409 (553)
T PRK12370        333 LD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLSPISADIKYYYGWNLFMAGQLEEALQTINECLKL--DPTRAAAG  409 (553)
T ss_pred             cC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCCChhhH
Confidence            86 66788888889999999999999999999876  4 4567888899999999999999999999984  55432 33


Q ss_pred             HHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCChh-hHHHHHHHHhhh
Q 011249          350 IGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAG-TWGALLGACKVH  427 (490)
Q Consensus       350 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~-~~~~l~~~~~~~  427 (490)
                      ..++..+...|++++|...++++.+. ..+.++..+..+..++...|++++|...++++. ..|+.. ..+.+...+...
T Consensus       410 ~~~~~~~~~~g~~eeA~~~~~~~l~~-~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~  488 (553)
T PRK12370        410 ITKLWITYYHTGIDDAIRLGDELRSQ-HLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQN  488 (553)
T ss_pred             HHHHHHHHhccCHHHHHHHHHHHHHh-ccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhcc
Confidence            33444466688999999999998773 222345557778889999999999999998876 334433 444555556666


Q ss_pred             CChHHHHHHHHHHHhcC---CCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          428 VNAELGEIAARHLLELG---PEKTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       428 g~~~~a~~~~~~~~~~~---p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      |  ++|...++++.+..   |.++..   +..++.-.|+.+.+... +++.+.+
T Consensus       489 g--~~a~~~l~~ll~~~~~~~~~~~~---~~~~~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        489 S--ERALPTIREFLESEQRIDNNPGL---LPLVLVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             H--HHHHHHHHHHHHHhhHhhcCchH---HHHHHHHHhhhHHHHHH-HHhhccc
Confidence            6  58888888877633   444443   66677777887777776 7777654

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.45  E-value=3.2e-09  Score=98.09  Aligned_cols=111  Identities=9%  Similarity=0.122  Sum_probs=68.2

Q ss_pred             CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCCCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcC------CCCCHh
Q 011249           31 HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLG------VLTSGF  104 (490)
Q Consensus        31 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g------~~p~~~  104 (490)
                      .+..  +|...+...-..+- ++.+..++++-..-++ ..-+--|..++..+++++|.+.+.......      .+.+..
T Consensus       136 qH~r--IW~lyl~Fv~~~~l-Pets~rvyrRYLk~~P-~~~eeyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~q  211 (835)
T KOG2047|consen  136 QHDR--IWDLYLKFVESHGL-PETSIRVYRRYLKVAP-EAREEYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQ  211 (835)
T ss_pred             hhcc--chHHHHHHHHhCCC-hHHHHHHHHHHHhcCH-HHHHHHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhh
Confidence            4444  67777777777776 7777777776554444 445666666777777777777776654321      122333


Q ss_pred             hHHHHHHHhcCCCChH------------------------HHHHHHHHhcCCHHHHHHHHhhcCC
Q 011249          105 TFSSVLNACARVPSLL------------------------EAVICGYTKIGLMDDAQRLFDSMAE  145 (490)
Q Consensus       105 ~~~~ll~~~~~~~~~~------------------------~~l~~~~~~~g~~~~A~~~~~~~~~  145 (490)
                      .|..+-...++.++..                        .+|..-|.+.|.+++|..+|++...
T Consensus       212 lw~elcdlis~~p~~~~slnvdaiiR~gi~rftDq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~  276 (835)
T KOG2047|consen  212 LWLELCDLISQNPDKVQSLNVDAIIRGGIRRFTDQLGFLWCSLADYYIRSGLFEKARDVYEEAIQ  276 (835)
T ss_pred             HHHHHHHHHHhCcchhcccCHHHHHHhhcccCcHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            3444433333333222                        6677888888888888888887764

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.44  E-value=2.3e-11  Score=113.45  Aligned_cols=231  Identities=15%  Similarity=0.104  Sum_probs=167.6

Q ss_pred             hhHHHHHHHHhccCChHHHHHHHHHHHhc-----C-CCCchh-HHHHHHHHHHhcCChHHHHHHHhcccC-------C--
Q 011249          246 VAMVGAISACTQLGDVEMAAILAKHVDEG-----C-CDRTNY-VSNALIHMHSKCGYLDLAWREFSRIKN-------K--  309 (490)
Q Consensus       246 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-----~-~~~~~~-~~~~l~~~~~~~~~~~~A~~~~~~~~~-------~--  309 (490)
                      .+...+...|...|+++.|..++++..+.     | ..|... ..+.+...|...+++++|..+|+++..       +  
T Consensus       200 ~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~h  279 (508)
T KOG1840|consen  200 RTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGEDH  279 (508)
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCCC
Confidence            45555777777778888877777776544     1 122222 233466778888888888888877653       1  


Q ss_pred             --ChhHHHHHHHHHHhcCChHHHHHHHHHHHH-----cCCC-CcHH-HHHHHHHHhcCCCChHHHHHHHHHHHHHcC--C
Q 011249          310 --DVISYSSMITAFADHGKSQEALDMFLKMRN-----EGIE-PNQV-TFIGVLTACSHGGLVEDGCKQFELMTRVFG--I  378 (490)
Q Consensus       310 --~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~-p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~  378 (490)
                        -..+++.|..+|.+.|++++|..++++..+     .|.. |... -++.+...|...+++++|..+++...+.+.  .
T Consensus       280 ~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~  359 (508)
T KOG1840|consen  280 PAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAP  359 (508)
T ss_pred             HHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhc
Confidence              234677788888889998888888777654     1222 2222 456667778889999999999988777543  2


Q ss_pred             CCC----chHHHHHHHHHhhcCChHHHHHHHHhcc-------C--CC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHh--
Q 011249          379 KPL----TEHLTCMVDLLGRSGQLEKAHSLIMDYK-------D--FC-DAGTWGALLGACKVHVNAELGEIAARHLLE--  442 (490)
Q Consensus       379 ~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~-------~--~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~--  442 (490)
                      .++    ..+++.|...|...|++++|.++++++.       .  .+ ....++.+...|.+.+.+++|.++|.+...  
T Consensus       360 g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~  439 (508)
T KOG1840|consen  360 GEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIM  439 (508)
T ss_pred             cccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHH
Confidence            222    4568889999999999999999998776       1  12 245778888999999999999999988765  


Q ss_pred             --cCCCC---CchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          443 --LGPEK---TGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       443 --~~p~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                        .+|++   ...|..|+.+|.+.|++++|.++.+.+..
T Consensus       440 ~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~  478 (508)
T KOG1840|consen  440 KLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVLN  478 (508)
T ss_pred             HHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence              34554   45888999999999999999999987763

>KOG1173 consensus Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.44  E-value=7.7e-10  Score=100.64  Aligned_cols=279  Identities=13%  Similarity=0.025  Sum_probs=222.6

Q ss_pred             CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHH
Q 011249          178 NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISA  254 (490)
Q Consensus       178 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~  254 (490)
                      +........+-+...+++.+..++++.+.+   +....+-.-|.++...|+..+-..+=.++++.- +-.+.+|..+.--
T Consensus       243 ~~dll~~~ad~~y~~c~f~~c~kit~~lle~dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~y-P~~a~sW~aVg~Y  321 (611)
T KOG1173|consen  243 NLDLLAEKADRLYYGCRFKECLKITEELLEKDPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDLY-PSKALSWFAVGCY  321 (611)
T ss_pred             cHHHHHHHHHHHHHcChHHHHHHHhHHHHhhCCCCcchHHHHHHHHHHhcccchHHHHHHHHHHhC-CCCCcchhhHHHH
Confidence            666667777888889999999999999876   445566666778889999998888888888764 3367889999988


Q ss_pred             HhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-ChhHHHHHHHHHHhcCChHHHH
Q 011249          255 CTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-DVISYSSMITAFADHGKSQEAL  331 (490)
Q Consensus       255 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~  331 (490)
                      |...|+.++|.++|.+..... +.-...|..+...|.-.|.-++|+..+....+  + .-..+--+.--|.+.++...|.
T Consensus       322 Yl~i~k~seARry~SKat~lD-~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LYlgmey~~t~n~kLAe  400 (611)
T KOG1173|consen  322 YLMIGKYSEARRYFSKATTLD-PTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLYLGMEYMRTNNLKLAE  400 (611)
T ss_pred             HHHhcCcHHHHHHHHHHhhcC-ccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHHHHHHHHHhccHHHHH
Confidence            999999999999999987765 34456788899999999999999998877655  2 2222333444678889999999


Q ss_pred             HHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHc-CC---C-CCchHHHHHHHHHhhcCChHHHHHHH
Q 011249          332 DMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVF-GI---K-PLTEHLTCMVDLLGRSGQLEKAHSLI  405 (490)
Q Consensus       332 ~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-~~---~-~~~~~~~~l~~~~~~~g~~~~A~~~~  405 (490)
                      +.|.+...  +.| |+...+-+.-.....+.+.+|..+|+...... ..   . -...+++.|..+|.+.+++++|+..+
T Consensus       401 ~Ff~~A~a--i~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~~  478 (611)
T KOG1173|consen  401 KFFKQALA--IAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDYY  478 (611)
T ss_pred             HHHHHHHh--cCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHHH
Confidence            99999887  455 55677777777777899999999999887421 01   1 13456788999999999999999999


Q ss_pred             Hhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHh
Q 011249          406 MDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYAS  460 (490)
Q Consensus       406 ~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~  460 (490)
                      ++..  .+.+..++.++.-.+...|+++.|++.|.+++.+.|++..+-..|..+...
T Consensus       479 q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n~~~~~lL~~aie~  535 (611)
T KOG1173|consen  479 QKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDNIFISELLKLAIED  535 (611)
T ss_pred             HHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccHHHHHHHHHHHHh
Confidence            8876  566888999999999999999999999999999999988777777655443

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.44  E-value=8e-09  Score=90.55  Aligned_cols=272  Identities=11%  Similarity=0.010  Sum_probs=210.4

Q ss_pred             CchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHh---HHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHH
Q 011249          178 NSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASC---WAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISA  254 (490)
Q Consensus       178 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~---~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~  254 (490)
                      |+.....+.+++...|+.++|+..|++..-.|+.+   .......+.+.|+.++...+...+.... .-+...|..-+..
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            78888999999999999999999999877644433   3334455677899998888888877542 1233334444444


Q ss_pred             HhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHH
Q 011249          255 CTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEAL  331 (490)
Q Consensus       255 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~  331 (490)
                      ....++++.|..+-++..+.. +.+...+-.-...+...++.++|.-.|+....   -+...|..|+..|...|++.+|.
T Consensus       310 l~~~K~~~rAL~~~eK~I~~~-~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~Lap~rL~~Y~GL~hsYLA~~~~kEA~  388 (564)
T KOG1174|consen  310 LYDEKKFERALNFVEKCIDSE-PRNHEALILKGRLLIALERHTQAVIAFRTAQMLAPYRLEIYRGLFHSYLAQKRFKEAN  388 (564)
T ss_pred             hhhhhhHHHHHHHHHHHhccC-cccchHHHhccHHHHhccchHHHHHHHHHHHhcchhhHHHHHHHHHHHHhhchHHHHH
Confidence            566788999999988887765 45566666667788889999999999987654   37789999999999999999999


Q ss_pred             HHHHHHHHcCCCCcHHHHHHHH-HHhc-CCCChHHHHHHHHHHHHHcCCCCC-chHHHHHHHHHhhcCChHHHHHHHHhc
Q 011249          332 DMFLKMRNEGIEPNQVTFIGVL-TACS-HGGLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDLLGRSGQLEKAHSLIMDY  408 (490)
Q Consensus       332 ~~~~~~~~~~~~p~~~~~~~l~-~~~~-~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~  408 (490)
                      ..-+...+. +.-+..+...+. ..|. ...--++|.+++++..+   +.|+ ....+.+...+...|+.+.++.+++..
T Consensus       389 ~~An~~~~~-~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~---~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~~  464 (564)
T KOG1174|consen  389 ALANWTIRL-FQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLK---INPIYTPAVNLIAELCQVEGPTKDIIKLLEKH  464 (564)
T ss_pred             HHHHHHHHH-hhcchhhhhhhcceeeccCchhHHHHHHHHHhhhc---cCCccHHHHHHHHHHHHhhCccchHHHHHHHH
Confidence            888877664 344555665553 3333 33445789999988865   4554 556677889999999999999999876


Q ss_pred             c-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          409 K-DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       409 ~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      . +.||....+.|...+...+.+++|.+.|..++.++|++-.....|-
T Consensus       465 L~~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~dP~~~~sl~Gl~  512 (564)
T KOG1174|consen  465 LIIFPDVNLHNHLGDIMRAQNEPQKAMEYYYKALRQDPKSKRTLRGLR  512 (564)
T ss_pred             HhhccccHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCccchHHHHHHH
Confidence            6 7899999999999999999999999999999999999887666664

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.44  E-value=5.5e-11  Score=103.70  Aligned_cols=199  Identities=15%  Similarity=0.083  Sum_probs=102.5

Q ss_pred             HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 011249          210 ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHM  289 (490)
Q Consensus       210 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  289 (490)
                      ...+..+...+...|++++|.+.+++..+.. +.+...+..+...+...|++++|...+++..+.. +.+...+..+...
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~  108 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTF  108 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHH
Confidence            4455566666666666666666666665542 1234455555555666666666666666655543 2333344444444


Q ss_pred             HHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHH
Q 011249          290 HSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQ  368 (490)
Q Consensus       290 ~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~  368 (490)
                      +...|+                               +++|...+++..+....| ....+..+...+...|++++|...
T Consensus       109 ~~~~g~-------------------------------~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  157 (234)
T TIGR02521       109 LCQQGK-------------------------------YEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKY  157 (234)
T ss_pred             HHHccc-------------------------------HHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHH
Confidence            444444                               455554444444321111 122334444455555555555555


Q ss_pred             HHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhc
Q 011249          369 FELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLEL  443 (490)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  443 (490)
                      +++..+  ..+.+...+..+...+...|++++|...+++..  .+.++..+..++..+...|+.+.|..+.+.+...
T Consensus       158 ~~~~~~--~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  232 (234)
T TIGR02521       158 LTRALQ--IDPQRPESLLELAELYYLRGQYKDARAYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYGAQLQKL  232 (234)
T ss_pred             HHHHHH--hCcCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhh
Confidence            555554  222234445555555555666666665555443  1223344444455555566666666665555443

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.

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=99.43  E-value=6.3e-09  Score=96.15  Aligned_cols=452  Identities=15%  Similarity=0.172  Sum_probs=283.7

Q ss_pred             hhhhhchhhHHHHHHHHhhhcCCC------CchhHhHHHHHHHHHhcCCCCHHH---HHHHhccCCC--CC-CceehHHH
Q 011249            7 VPRSKTFNQLKQVHSYLLKTLTKP------HDQYHYYAQFLIRLLQLPGDNLSY---ARQVFDQIPK--CK-TQFLWTSL   74 (490)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~l~~~~~~~~~~~~~---A~~~~~~~~~--~~-~~~~~~~l   74 (490)
                      |...++...+.+.+..+.-   .+      ..+.|+.|..+.+...++.+ .-.   .-.+++.+..  +| ....|++|
T Consensus       179 L~~~d~~~eaa~~la~vln---~d~f~sk~gkSn~qlw~elcdlis~~p~-~~~slnvdaiiR~gi~rftDq~g~Lw~SL  254 (835)
T KOG2047|consen  179 LAKSDRLDEAAQRLATVLN---QDEFVSKKGKSNHQLWLELCDLISQNPD-KVQSLNVDAIIRGGIRRFTDQLGFLWCSL  254 (835)
T ss_pred             HHhccchHHHHHHHHHhcC---chhhhhhcccchhhHHHHHHHHHHhCcc-hhcccCHHHHHHhhcccCcHHHHHHHHHH
Confidence            3344455555555544433   22      22223488888888888765 222   2334444432  22 22579999


Q ss_pred             HHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChH-HHHHHHHH--hcC------CHHHHHHHHhhcCC
Q 011249           75 IRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLL-EAVICGYT--KIG------LMDDAQRLFDSMAE  145 (490)
Q Consensus        75 ~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~-~~l~~~~~--~~g------~~~~A~~~~~~~~~  145 (490)
                      ..-|.+.|.+++|.++|++....  ..+...|..+.++++...... .+.+. ..  ..|      +++-....|+.+..
T Consensus       255 AdYYIr~g~~ekarDvyeeai~~--v~tvrDFt~ifd~Ya~FEE~~~~~~me-~a~~~~~n~ed~~dl~~~~a~~e~lm~  331 (835)
T KOG2047|consen  255 ADYYIRSGLFEKARDVYEEAIQT--VMTVRDFTQIFDAYAQFEESCVAAKME-LADEESGNEEDDVDLELHMARFESLMN  331 (835)
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHh--heehhhHHHHHHHHHHHHHHHHHHHHh-hhhhcccChhhhhhHHHHHHHHHHHHh
Confidence            99999999999999999998775  446666777777765543322 12222 11  122      23334455555543


Q ss_pred             --------------C-CHhHHHHHHHHHHhCCChHHHHHHHHHhccC---------CchhHHHHHHHHHhcCChhHHHHH
Q 011249          146 --------------R-NVISWSAMVAGYANCGNMKAAKEFYDRMTEK---------NSVTWVAMIAGYGKCGEVREAKKV  201 (490)
Q Consensus       146 --------------~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---------~~~~~~~l~~~~~~~~~~~~A~~~  201 (490)
                                    | ++..|..-+..  ..|+..+-...|.++.+.         -...|..+.+.|-..|+++.|..+
T Consensus       332 rr~~~lNsVlLRQn~~nV~eW~kRV~l--~e~~~~~~i~tyteAv~~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvi  409 (835)
T KOG2047|consen  332 RRPLLLNSVLLRQNPHNVEEWHKRVKL--YEGNAAEQINTYTEAVKTVDPKKAVGSPGTLWVEFAKLYENNGDLDDARVI  409 (835)
T ss_pred             ccchHHHHHHHhcCCccHHHHHhhhhh--hcCChHHHHHHHHHHHHccCcccCCCChhhHHHHHHHHHHhcCcHHHHHHH
Confidence                          1 34455554443  367788888888887742         234688899999999999999999


Q ss_pred             HhhcCCCC-------HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcc----------c-------ChhhHHHHHHHHhc
Q 011249          202 FDEISEPD-------ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVR----------I-------SEVAMVGAISACTQ  257 (490)
Q Consensus       202 ~~~~~~~~-------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~----------p-------~~~~~~~l~~~~~~  257 (490)
                      |++..+.+       ..+|......-.+..+++.|+++++......-.          |       +...|...+..--.
T Consensus       410 feka~~V~y~~v~dLa~vw~~waemElrh~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs  489 (835)
T KOG2047|consen  410 FEKATKVPYKTVEDLAEVWCAWAEMELRHENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEES  489 (835)
T ss_pred             HHHhhcCCccchHHHHHHHHHHHHHHHhhhhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHH
Confidence            99988722       235555566666778899999988876532111          1       12234444455556


Q ss_pred             cCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC----CCh-hHHHHHHHHHHh---cCChHH
Q 011249          258 LGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN----KDV-ISYSSMITAFAD---HGKSQE  329 (490)
Q Consensus       258 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~-~~~~~l~~~~~~---~~~~~~  329 (490)
                      .|-++....+|+.+.+..+. ++.+.......+....-++++.++|++-..    |++ ..|+.-+.-+.+   ...++.
T Consensus       490 ~gtfestk~vYdriidLria-TPqii~NyAmfLEeh~yfeesFk~YErgI~LFk~p~v~diW~tYLtkfi~rygg~klEr  568 (835)
T KOG2047|consen  490 LGTFESTKAVYDRIIDLRIA-TPQIIINYAMFLEEHKYFEESFKAYERGISLFKWPNVYDIWNTYLTKFIKRYGGTKLER  568 (835)
T ss_pred             hccHHHHHHHHHHHHHHhcC-CHHHHHHHHHHHHhhHHHHHHHHHHHcCCccCCCccHHHHHHHHHHHHHHHhcCCCHHH
Confidence            68888899999999887743 344333345555666778999999998765    444 356665554443   236899


Q ss_pred             HHHHHHHHHHcCCCCcHHHHHHHH--HHhcCCCChHHHHHHHHHHHHHcCCCCC--chHHHHHHHHHhhcCChHHHHHHH
Q 011249          330 ALDMFLKMRNEGIEPNQVTFIGVL--TACSHGGLVEDGCKQFELMTRVFGIKPL--TEHLTCMVDLLGRSGQLEKAHSLI  405 (490)
Q Consensus       330 a~~~~~~~~~~~~~p~~~~~~~l~--~~~~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~  405 (490)
                      |..+|++.++ |.+|...-+..|+  ..-.+.|-...|+.+++++..  ++++.  ...|+..|.--...=-......+|
T Consensus       569 aRdLFEqaL~-~Cpp~~aKtiyLlYA~lEEe~GLar~amsiyerat~--~v~~a~~l~myni~I~kaae~yGv~~TR~iY  645 (835)
T KOG2047|consen  569 ARDLFEQALD-GCPPEHAKTIYLLYAKLEEEHGLARHAMSIYERATS--AVKEAQRLDMYNIYIKKAAEIYGVPRTREIY  645 (835)
T ss_pred             HHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHh--cCCHHHHHHHHHHHHHHHHHHhCCcccHHHH
Confidence            9999999999 6777654333333  223456888899999999876  55554  445666554333322233344455


Q ss_pred             Hhcc-CCCChhhHHH---HHHHHhhhCChHHHHHHHHHHHhcC-CC-CCchHHHHHHHHHhcCCcchHHHHH
Q 011249          406 MDYK-DFCDAGTWGA---LLGACKVHVNAELGEIAARHLLELG-PE-KTGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       406 ~~~~-~~~~~~~~~~---l~~~~~~~g~~~~a~~~~~~~~~~~-p~-~~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      ++.. .-|+...-..   ....-.+.|..++|..++.-..++- |. ++.+|.+.-..-.+.|+-+...+++
T Consensus       646 ekaIe~Lp~~~~r~mclrFAdlEtklGEidRARaIya~~sq~~dPr~~~~fW~twk~FEvrHGnedT~keML  717 (835)
T KOG2047|consen  646 EKAIESLPDSKAREMCLRFADLETKLGEIDRARAIYAHGSQICDPRVTTEFWDTWKEFEVRHGNEDTYKEML  717 (835)
T ss_pred             HHHHHhCChHHHHHHHHHHHHHhhhhhhHHHHHHHHHhhhhcCCCcCChHHHHHHHHHHHhcCCHHHHHHHH
Confidence            4443 2344443332   3344467899999999999888854 53 5678888888888889844444443

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=99.43  E-value=7.6e-12  Score=105.68  Aligned_cols=196  Identities=11%  Similarity=0.043  Sum_probs=165.9

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHhcccC--CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHH-HHHHHH
Q 011249          279 TNYVSNALIHMHSKCGYLDLAWREFSRIKN--KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTF-IGVLTA  355 (490)
Q Consensus       279 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~-~~l~~~  355 (490)
                      |-.--+.+..+|.+.|.+.+|.+.|+...+  |-+.||..|-.+|.+..++..|+.++.+-.+.  .|..+|| ....+.
T Consensus       222 dwwWk~Q~gkCylrLgm~r~AekqlqssL~q~~~~dTfllLskvY~ridQP~~AL~~~~~gld~--fP~~VT~l~g~ARi  299 (478)
T KOG1129|consen  222 DWWWKQQMGKCYLRLGMPRRAEKQLQSSLTQFPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS--FPFDVTYLLGQARI  299 (478)
T ss_pred             hHHHHHHHHHHHHHhcChhhhHHHHHHHhhcCCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc--CCchhhhhhhhHHH
Confidence            333445688899999999999999988765  78889999999999999999999999999884  6766665 456677


Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHH
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      +...++.++|.++++.+.+  ..+.+++...++...|.-.++++-|+.+|+++.  ..-++..|+.+.-.|.-.++++-+
T Consensus       300 ~eam~~~~~a~~lYk~vlk--~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~speLf~NigLCC~yaqQ~D~~  377 (478)
T KOG1129|consen  300 HEAMEQQEDALQLYKLVLK--LHPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQSPELFCNIGLCCLYAQQIDLV  377 (478)
T ss_pred             HHHHHhHHHHHHHHHHHHh--cCCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCCChHHHhhHHHHHHhhcchhhh
Confidence            8888999999999999998  456677777788888899999999999999887  346788999999999999999999


Q ss_pred             HHHHHHHHhcC--CC-CCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          434 EIAARHLLELG--PE-KTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       434 ~~~~~~~~~~~--p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      +..|++++...  |+ -..+|.+++.+....|+..-|.+.|+.....+
T Consensus       378 L~sf~RAlstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d  425 (478)
T KOG1129|consen  378 LPSFQRALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSD  425 (478)
T ss_pred             HHHHHHHHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccC
Confidence            99999999853  43 46799999999999999999999998776554

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=99.43  E-value=4.7e-09  Score=91.92  Aligned_cols=394  Identities=12%  Similarity=0.015  Sum_probs=249.5

Q ss_pred             HhcCChhHHHHHHHHHHhc---CCCCCHhhHHHHHHHhcCCCChH--HHHHHHHHhcCCHHHHHHHHhhcCCC-CHhHHH
Q 011249           79 VLHAHFRQSILLYAKMHRL---GVLTSGFTFSSVLNACARVPSLL--EAVICGYTKIGLMDDAQRLFDSMAER-NVISWS  152 (490)
Q Consensus        79 ~~~g~~~~A~~~~~~m~~~---g~~p~~~~~~~ll~~~~~~~~~~--~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~  152 (490)
                      .....+..|.+-|......   .+.|...+..++=...+..++..  ...+..|-..++-+.|...+...+.. ...--|
T Consensus        54 ~h~r~yr~a~~~~~~~~~~~~s~~r~s~~~~~s~~~S~~~~~~~e~~r~~aecy~~~~n~~~Ai~~l~~~p~t~r~p~in  133 (564)
T KOG1174|consen   54 YKERNYRAALRHFDEIIHKRRLMMRHKNAVLVAIESSYPEFGDAEQRRRAAECYRQIGNTDMAIETLLQVPPTLRSPRIN  133 (564)
T ss_pred             HHHHHHHHHHHHHHHHHHhhHhhccccccccccccccCCCcccHHHHHHHHHHHHHHccchHHHHHHhcCCccccchhHH
Confidence            3445566666666665443   23344444433333344444433  44566788889999999888887763 223333


Q ss_pred             HHHHHHHhCC-ChHHHHHHHHHhcc--------------------------------C-CchhHHHHHHHHHh--cCChh
Q 011249          153 AMVAGYANCG-NMKAAKEFYDRMTE--------------------------------K-NSVTWVAMIAGYGK--CGEVR  196 (490)
Q Consensus       153 ~l~~~~~~~~-~~~~a~~~~~~~~~--------------------------------~-~~~~~~~l~~~~~~--~~~~~  196 (490)
                      .++.-+...| +-.++.--+.+...                                + +..+....+.+++.  .++..
T Consensus       134 lMla~l~~~g~r~~~~vl~ykevvrecp~aL~~i~~ll~l~v~g~e~~S~~m~~~~~~~~~dwls~wika~Aq~~~~~hs  213 (564)
T KOG1174|consen  134 LMLARLQHHGSRHKEAVLAYKEVIRECPMALQVIEALLELGVNGNEINSLVMHAATVPDHFDWLSKWIKALAQMFNFKHS  213 (564)
T ss_pred             HHHHHHHhccccccHHHHhhhHHHHhcchHHHHHHHHHHHhhcchhhhhhhhhheecCCCccHHHHHHHHHHHHHhcccc
Confidence            3333333332 22122211221111                                0 11122223333332  34433


Q ss_pred             HHHHHHhhcC-----CCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccCh-hhHHHHHHHHhccCChHHHHHHHHH
Q 011249          197 EAKKVFDEIS-----EPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISE-VAMVGAISACTQLGDVEMAAILAKH  270 (490)
Q Consensus       197 ~A~~~~~~~~-----~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~  270 (490)
                      .|...+-.+.     ..|+.....+..++...|+.++|+..|++....  .|+. .......-.+...|+.+....+...
T Consensus       214 ~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~--dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~  291 (564)
T KOG1174|consen  214 DASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCA--NPDNVEAMDLYAVLLGQEGGCEQDSALMDY  291 (564)
T ss_pred             hhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhC--ChhhhhhHHHHHHHHHhccCHhhHHHHHHH
Confidence            4433332222     256777888889999999999999988887754  3332 2222223334667777777777776


Q ss_pred             HHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCC---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cH
Q 011249          271 VDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK---DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQ  346 (490)
Q Consensus       271 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~  346 (490)
                      +.... ......|-.-+.......+++.|+.+-++...-   +...+-.-...+...|++++|.-.|+..+.  +.| +.
T Consensus       292 Lf~~~-~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~--Lap~rL  368 (564)
T KOG1174|consen  292 LFAKV-KYTASHWFVHAQLLYDEKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQM--LAPYRL  368 (564)
T ss_pred             HHhhh-hcchhhhhhhhhhhhhhhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHh--cchhhH
Confidence            65443 122222222334445567888888888877653   444555555678889999999999999887  455 56


Q ss_pred             HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHH-HHHh-hcCChHHHHHHHHhcc-CCCC-hhhHHHHHH
Q 011249          347 VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMV-DLLG-RSGQLEKAHSLIMDYK-DFCD-AGTWGALLG  422 (490)
Q Consensus       347 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~-~~~~-~~g~~~~A~~~~~~~~-~~~~-~~~~~~l~~  422 (490)
                      ..|..|+.+|...|++.+|...-....+  -++.+..+...+. ..+. .-..-++|.+++++.. ..|+ ....+.+..
T Consensus       369 ~~Y~GL~hsYLA~~~~kEA~~~An~~~~--~~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~P~Y~~AV~~~AE  446 (564)
T KOG1174|consen  369 EIYRGLFHSYLAQKRFKEANALANWTIR--LFQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKINPIYTPAVNLIAE  446 (564)
T ss_pred             HHHHHHHHHHHhhchHHHHHHHHHHHHH--HhhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccCCccHHHHHHHHH
Confidence            7999999999999999999888877776  4555555555442 2222 2234588999998765 4554 457777888


Q ss_pred             HHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          423 ACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       423 ~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      .|...|..+.++.++++.+...|+ ......|+.++...+.+++|...|......+++
T Consensus       447 L~~~Eg~~~D~i~LLe~~L~~~~D-~~LH~~Lgd~~~A~Ne~Q~am~~y~~ALr~dP~  503 (564)
T KOG1174|consen  447 LCQVEGPTKDIIKLLEKHLIIFPD-VNLHNHLGDIMRAQNEPQKAMEYYYKALRQDPK  503 (564)
T ss_pred             HHHhhCccchHHHHHHHHHhhccc-cHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCcc
Confidence            999999999999999999999998 677899999999999999999999988766554

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

Probab=99.39  E-value=9.2e-10  Score=105.13  Aligned_cols=442  Identities=12%  Similarity=0.018  Sum_probs=256.7

Q ss_pred             HHHHhhhcCCC--CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC----------------------------CCCCce
Q 011249           20 HSYLLKTLTKP--HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP----------------------------KCKTQF   69 (490)
Q Consensus        20 ~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~----------------------------~~~~~~   69 (490)
                      +..++.   .|  |+-+  +|..+|.-||..|+ .+.|- +|..|.                            .|.. .
T Consensus        13 la~~e~---~gi~PnRv--tyqsLiarYc~~gd-ieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpkep~a-D   84 (1088)
T KOG4318|consen   13 LALHEI---SGILPNRV--TYQSLIARYCTKGD-IEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPKEPLA-D   84 (1088)
T ss_pred             HHHHHH---hcCCCchh--hHHHHHHHHcccCC-Ccccc-chhhhhcccccccchhHHHHHhcccccccccCCCCCch-h
Confidence            344444   55  8889  99999999999999 88887 776653                            1222 5


Q ss_pred             ehHHHHHHHHhcCChhH---HHHHHHHH----HhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhh
Q 011249           70 LWTSLIRNHVLHAHFRQ---SILLYAKM----HRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDS  142 (490)
Q Consensus        70 ~~~~l~~~~~~~g~~~~---A~~~~~~m----~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  142 (490)
                      +|+.|..+|...||..-   ..+.++..    ...|+.....-+-..+.+|.+.-.-....+....-.|-++.+++++..
T Consensus        85 tyt~Ll~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~  164 (1088)
T KOG4318|consen   85 TYTNLLKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAK  164 (1088)
T ss_pred             HHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhh
Confidence            67777777777766433   22222221    223444333334344444444333334555556666777777777776


Q ss_pred             cCCC---CHhHHHHHHHHHHhCC-ChHHHHHHHHHhcc-CCchhHHHHHHHHHhcCChhHHHHHHhhcCC----CCHHhH
Q 011249          143 MAER---NVISWSAMVAGYANCG-NMKAAKEFYDRMTE-KNSVTWVAMIAGYGKCGEVREAKKVFDEISE----PDASCW  213 (490)
Q Consensus       143 ~~~~---~~~~~~~l~~~~~~~~-~~~~a~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~~~~  213 (490)
                      ++..   ++...  .++-+.... .+++-....+...+ +++.+|..+++.-...|+.+.|..++.+|.+    -+.+-|
T Consensus       165 ~Pvsa~~~p~~v--fLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~gfpir~HyF  242 (1088)
T KOG4318|consen  165 VPVSAWNAPFQV--FLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEKGFPIRAHYF  242 (1088)
T ss_pred             CCcccccchHHH--HHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHcCCCcccccc
Confidence            6541   11111  233333332 34455555555554 7889999999999999999999999999976    234444


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHH------------------------HHHHHH
Q 011249          214 AAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEM------------------------AAILAK  269 (490)
Q Consensus       214 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~------------------------a~~~~~  269 (490)
                      ..|+-+   .++...+..+++-|...|+.|+..|+...+-.+.+.|....                        |.+.++
T Consensus       243 wpLl~g---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~t~~~~e~sq~~hg~tAavrsaa~rg~~a~k~l~  319 (1088)
T KOG4318|consen  243 WPLLLG---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQTKYGEEGSQLAHGFTAAVRSAACRGLLANKRLR  319 (1088)
T ss_pred             hhhhhc---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchhhhhcccccchhhhhhHHHHHHHhcccHhHHHHH
Confidence            455544   78888888899999999999999888876666555322111                        111111


Q ss_pred             HHH------------hcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCC-------ChhHHHHHHHHHHhcC-----
Q 011249          270 HVD------------EGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK-------DVISYSSMITAFADHG-----  325 (490)
Q Consensus       270 ~~~------------~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-------~~~~~~~l~~~~~~~~-----  325 (490)
                      .-.            =.|+.....+|...+. ...+|.-++.+++-..+..|       ++..|..++.-|.+.-     
T Consensus       320 ~nl~~~v~~s~k~~fLlg~d~~~aiws~c~~-l~hQgk~e~veqlvg~l~npt~r~s~~~V~a~~~~lrqyFrr~e~~~~  398 (1088)
T KOG4318|consen  320 QNLRKSVIGSTKKLFLLGTDILEAIWSMCEK-LRHQGKGEEVEQLVGQLLNPTLRDSGQNVDAFGALLRQYFRRIERHIC  398 (1088)
T ss_pred             HHHHHHHHHHhhHHHHhccccchHHHHHHHH-HHHcCCCchHHHHHhhhcCCccccCcchHHHHHHHHHHHHHHHHhhHH
Confidence            100            0122222233332222 22356666666666555442       3334444443333211     


Q ss_pred             -----------------ChHHHHHHHHHHHHcCCCCcH----------------------------HHHHHHHHHhcCCC
Q 011249          326 -----------------KSQEALDMFLKMRNEGIEPNQ----------------------------VTFIGVLTACSHGG  360 (490)
Q Consensus       326 -----------------~~~~a~~~~~~~~~~~~~p~~----------------------------~~~~~l~~~~~~~g  360 (490)
                                       ...+..++....     .||.                            ..-+.++..|++.-
T Consensus       399 ~~i~~~~qgls~~l~se~tp~vsell~~l-----rkns~lr~lv~Lss~Eler~he~~~~~~h~irdi~~ql~l~l~se~  473 (1088)
T KOG4318|consen  399 SRIYYAGQGLSLNLNSEDTPRVSELLENL-----RKNSFLRQLVGLSSTELERSHEPWPLIAHLIRDIANQLHLTLNSEY  473 (1088)
T ss_pred             HHHHHHHHHHHhhhchhhhHHHHHHHHHh-----CcchHHHHHhhhhHHHHhcccccchhhhhHHHHHHHHHHHHHHHHH
Confidence                             111111111111     2221                            11222333333333


Q ss_pred             ChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-----CCCChhhHHHHHHHHhhhCChHHHHH
Q 011249          361 LVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-----DFCDAGTWGALLGACKVHVNAELGEI  435 (490)
Q Consensus       361 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~~~a~~  435 (490)
                      +..+++..-++.... -+   +..|..|+..+....+.+.|..+.++..     ...+..-+..+.+...+.+....+..
T Consensus       474 n~lK~l~~~ekye~~-lf---~g~ya~Li~l~~~hdkle~Al~~~~e~d~~d~s~~Ld~~~m~~l~dLL~r~~~l~dl~t  549 (1088)
T KOG4318|consen  474 NKLKILCDEEKYEDL-LF---AGLYALLIKLMDLHDKLEYALSFVDEIDTRDESIHLDLPLMTSLQDLLQRLAILYDLST  549 (1088)
T ss_pred             HHHHHHHHHHHHHHH-Hh---hhHHHHHhhhHHHHHHHHHHHhchhhhcccchhhhcccHhHHHHHHHHHHhHHHHHHHH
Confidence            444444333333331 11   2667888888888888999998888876     22355567778888888888999999


Q ss_pred             HHHHHHhc---CCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccccCCCc
Q 011249          436 AARHLLEL---GPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSPGC  485 (490)
Q Consensus       436 ~~~~~~~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  485 (490)
                      +++++.+.   .|........+.+.....|+.+...+..+-+...|+.- +|.
T Consensus       550 iL~e~ks~a~n~~~~a~~~f~~lns~a~agqqe~Lkkl~d~lvslgl~e-tgP  601 (1088)
T KOG4318|consen  550 ILYEDKSSAENEPLVAIILFPLLNSGAPAGQQEKLKKLADILVSLGLSE-TGP  601 (1088)
T ss_pred             HHhhhhHHhhCCchHHHHHHHHHhhhhhccCHHHHHHHHHHHHHhhhhh-ccc
Confidence            99888773   24445566667777788899988888888888777755 343

>PRK12370 invasion protein regulator; Provisional

Probab=99.39  E-value=6.4e-11  Score=115.91  Aligned_cols=211  Identities=9%  Similarity=-0.081  Sum_probs=167.0

Q ss_pred             CChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHh---------cCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCC
Q 011249          259 GDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSK---------CGYLDLAWREFSRIKN---KDVISYSSMITAFADHGK  326 (490)
Q Consensus       259 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---------~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~  326 (490)
                      +++++|..++++..+.. |.+...+..+..+|..         .+++++|...+++..+   .+...+..+...+...|+
T Consensus       275 ~~~~~A~~~~~~Al~ld-P~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~~g~  353 (553)
T PRK12370        275 YSLQQALKLLTQCVNMS-PNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELDHNNPQALGLLGLINTIHSE  353 (553)
T ss_pred             HHHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHccC
Confidence            45689999999998876 4556666666665542         2457899999998876   367788888889999999


Q ss_pred             hHHHHHHHHHHHHcCCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC-chHHHHHHHHHhhcCChHHHHHH
Q 011249          327 SQEALDMFLKMRNEGIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDLLGRSGQLEKAHSL  404 (490)
Q Consensus       327 ~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~  404 (490)
                      +++|...|+++.+.  .|+ ...+..+...+...|++++|...++++.+.   .|+ ...+..++..+...|++++|...
T Consensus       354 ~~~A~~~~~~Al~l--~P~~~~a~~~lg~~l~~~G~~~eAi~~~~~Al~l---~P~~~~~~~~~~~~~~~~g~~eeA~~~  428 (553)
T PRK12370        354 YIVGSLLFKQANLL--SPISADIKYYYGWNLFMAGQLEEALQTINECLKL---DPTRAAAGITKLWITYYHTGIDDAIRL  428 (553)
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc---CCCChhhHHHHHHHHHhccCHHHHHHH
Confidence            99999999999985  565 457778888899999999999999999873   343 33334445567778999999999


Q ss_pred             HHhcc--CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          405 IMDYK--DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       405 ~~~~~--~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      +++..  .+| ++..+..+..++...|+.++|...++++....|.+......++..|...|  ++|...++++.+.
T Consensus       429 ~~~~l~~~~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~  502 (553)
T PRK12370        429 GDELRSQHLQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQNS--ERALPTIREFLES  502 (553)
T ss_pred             HHHHHHhccccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhccH--HHHHHHHHHHHHH
Confidence            98875  234 34456777788889999999999999998888988888888988888888  4888888877654

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.37  E-value=4.5e-10  Score=100.71  Aligned_cols=232  Identities=10%  Similarity=-0.062  Sum_probs=156.9

Q ss_pred             CChHHHHHHHHHHHHcC-cccC--hhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHH
Q 011249          224 GYAKAAIEMYKVMRQEN-VRIS--EVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAW  300 (490)
Q Consensus       224 g~~~~A~~~~~~~~~~~-~~p~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~  300 (490)
                      ++.+.++.-+.++.... ..|+  ...|..+...+...|++++|...|++..+.. |.+...|+.+...+...|++++|.
T Consensus        40 ~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~~~A~  118 (296)
T PRK11189         40 LQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNFDAAY  118 (296)
T ss_pred             hHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            45667777777777432 2222  3457777777888888888888888888876 566788888888899999999999


Q ss_pred             HHHhcccC--C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcC
Q 011249          301 REFSRIKN--K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFG  377 (490)
Q Consensus       301 ~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  377 (490)
                      ..|++..+  | +..+|..+..++...|++++|.+.+++..+.  .|+..........+...++.++|...+.+...  .
T Consensus       119 ~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~--~  194 (296)
T PRK11189        119 EAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRYE--K  194 (296)
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHh--h
Confidence            98888865  3 4567888888888899999999999998874  55433222222234456789999999977655  3


Q ss_pred             CCCCchHHHHHHHHHhhcCChHHH--HHHHHhc-c-----CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCC-CCC
Q 011249          378 IKPLTEHLTCMVDLLGRSGQLEKA--HSLIMDY-K-----DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGP-EKT  448 (490)
Q Consensus       378 ~~~~~~~~~~l~~~~~~~g~~~~A--~~~~~~~-~-----~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p-~~~  448 (490)
                      .+|+...+ .+..  ...|+..++  .+.+.+. .     .+.....|..+...+...|++++|+..|+++++.+| +.+
T Consensus       195 ~~~~~~~~-~~~~--~~lg~~~~~~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~~~~~  271 (296)
T PRK11189        195 LDKEQWGW-NIVE--FYLGKISEETLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNVYNFV  271 (296)
T ss_pred             CCccccHH-HHHH--HHccCCCHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCchHH
Confidence            33433222 2232  334554433  3222221 1     112345788889999999999999999999999996 555


Q ss_pred             chHHHHHHHHHhcCC
Q 011249          449 GNSALLANIYASMGK  463 (490)
Q Consensus       449 ~~~~~l~~~~~~~g~  463 (490)
                      .....++......++
T Consensus       272 e~~~~~~e~~~~~~~  286 (296)
T PRK11189        272 EHRYALLELALLGQD  286 (296)
T ss_pred             HHHHHHHHHHHHHhh
Confidence            555556655444333

>KOG4162 consensus Predicted calmodulin-binding protein [Signal transduction mechanisms]

Probab=99.37  E-value=5e-09  Score=98.95  Aligned_cols=399  Identities=14%  Similarity=0.082  Sum_probs=266.5

Q ss_pred             CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCC--CCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHH
Q 011249           31 HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPK--CKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSS  108 (490)
Q Consensus        31 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~  108 (490)
                      .++.  +|.+|.=+....|+ ++.+.+.|++...  -+....|+.+...+...|.-..|+.+++.-....-+|+..+--.
T Consensus       321 nd~a--i~d~Lt~al~~~g~-f~~lae~fE~~~~~~~~~~e~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~L  397 (799)
T KOG4162|consen  321 NDAA--IFDHLTFALSRCGQ-FEVLAEQFEQALPFSFGEHERWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLL  397 (799)
T ss_pred             chHH--HHHHHHHHHHHHHH-HHHHHHHHHHHhHhhhhhHHHHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHH
Confidence            5888  99999999999999 9999999998752  22226799999999999999999999988655433354333322


Q ss_pred             -HHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--------CCHhHHHHHHHHHHhCC-----------ChHHHH
Q 011249          109 -VLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--------RNVISWSAMVAGYANCG-----------NMKAAK  168 (490)
Q Consensus       109 -ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--------~~~~~~~~l~~~~~~~~-----------~~~~a~  168 (490)
                       .-+.|             +.+.|.+++++..-.++..        -....|..+.-+|...-           ...+++
T Consensus       398 masklc-------------~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~lGi~y~~~A~~a~~~seR~~~h~ksl  464 (799)
T KOG4162|consen  398 MASKLC-------------IERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLFLGIAYGFQARQANLKSERDALHKKSL  464 (799)
T ss_pred             HHHHHH-------------HhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhHhhcCCChHHHHHHHHHHH
Confidence             22333             4455667776666555543        24556666666655421           245678


Q ss_pred             HHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCC----CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCc
Q 011249          169 EFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISE----PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENV  241 (490)
Q Consensus       169 ~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  241 (490)
                      +.+++..+.   |+.+...+.--|+..++++.|.+...+..+    .+...|..|+-++...+++.+|+.+.+.....-.
T Consensus       465 qale~av~~d~~dp~~if~lalq~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd~al~E~~  544 (799)
T KOG4162|consen  465 QALEEAVQFDPTDPLVIFYLALQYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVDAALEEFG  544 (799)
T ss_pred             HHHHHHHhcCCCCchHHHHHHHHHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhh
Confidence            888888653   555555555667788899999888877654    6788999999999999999999999888765311


Q ss_pred             ccChhhHHHHHHHHhccCChHHHHHHHHHHHhc---------------------CC-------CCchhHHHHHHHHHH--
Q 011249          242 RISEVAMVGAISACTQLGDVEMAAILAKHVDEG---------------------CC-------DRTNYVSNALIHMHS--  291 (490)
Q Consensus       242 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~---------------------~~-------~~~~~~~~~l~~~~~--  291 (490)
                      . |-.....-++.-...++.+++.....++...                     |.       ...+.++..+.....  
T Consensus       545 ~-N~~l~~~~~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls~l~a~~  623 (799)
T KOG4162|consen  545 D-NHVLMDGKIHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLSSLVASQ  623 (799)
T ss_pred             h-hhhhchhhhhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHHHHHHhh
Confidence            1 1111111122222345555554443332211                     00       001112222211111  


Q ss_pred             -hcCChHHHHHHHhcccCCC------hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHH
Q 011249          292 -KCGYLDLAWREFSRIKNKD------VISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVED  364 (490)
Q Consensus       292 -~~~~~~~A~~~~~~~~~~~------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~  364 (490)
                       +.-..+.....+.....|+      ...|......+.+.+..++|...+.+.... .......|......+...|.+++
T Consensus       624 ~~~~~se~~Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~~-~~l~~~~~~~~G~~~~~~~~~~E  702 (799)
T KOG4162|consen  624 LKSAGSELKLPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASKI-DPLSASVYYLRGLLLEVKGQLEE  702 (799)
T ss_pred             hhhcccccccCcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHhc-chhhHHHHHHhhHHHHHHHhhHH
Confidence             1111111111122222222      234666777888999999999988888763 23345577777777888999999


Q ss_pred             HHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHH--HHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHH
Q 011249          365 GCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHS--LIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHL  440 (490)
Q Consensus       365 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~--~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  440 (490)
                      |.+.|.....  -.|.++....++..++.+.|+..-|..  ++..+.  ++.++..|..+...+...|+.+.|.+.|.-+
T Consensus       703 A~~af~~Al~--ldP~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa  780 (799)
T KOG4162|consen  703 AKEAFLVALA--LDPDHVPSMTALAELLLELGSPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAECFQAA  780 (799)
T ss_pred             HHHHHHHHHh--cCCCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchHHHHHHHHHH
Confidence            9999998875  334457788899999999998888877  776665  5668889999999999999999999999999


Q ss_pred             HhcCCCCCc
Q 011249          441 LELGPEKTG  449 (490)
Q Consensus       441 ~~~~p~~~~  449 (490)
                      .++++.+|.
T Consensus       781 ~qLe~S~PV  789 (799)
T KOG4162|consen  781 LQLEESNPV  789 (799)
T ss_pred             HhhccCCCc
Confidence            998876663

>PRK11189 lipoprotein NlpI; Provisional

Probab=99.36  E-value=1.3e-10  Score=104.19  Aligned_cols=215  Identities=13%  Similarity=0.077  Sum_probs=157.7

Q ss_pred             cCChHHHHHHHHHHHhcC-CC--CchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHH
Q 011249          258 LGDVEMAAILAKHVDEGC-CD--RTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEAL  331 (490)
Q Consensus       258 ~g~~~~a~~~~~~~~~~~-~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~  331 (490)
                      .+..+.+..-+.++.... ..  .....|..+...|...|+.++|...|++..+   .++..|+.+...+...|++++|.
T Consensus        39 ~~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~  118 (296)
T PRK11189         39 TLQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAY  118 (296)
T ss_pred             chHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHH
Confidence            356677777787777543 12  2245677888899999999999999998876   36789999999999999999999


Q ss_pred             HHHHHHHHcCCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccC
Q 011249          332 DMFLKMRNEGIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKD  410 (490)
Q Consensus       332 ~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  410 (490)
                      ..|++..+  +.|+ ...+..+..++...|++++|.+.+++..+.   .|+..........+...+++++|...|.+...
T Consensus       119 ~~~~~Al~--l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~---~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~  193 (296)
T PRK11189        119 EAFDSVLE--LDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD---DPNDPYRALWLYLAESKLDPKQAKENLKQRYE  193 (296)
T ss_pred             HHHHHHHH--hCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHh
Confidence            99999998  4665 457788888889999999999999999873   34332222222334567889999999966542


Q ss_pred             CCChhhHHHHHHHHhhhCChHHHHHHHHHHH-------hcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          411 FCDAGTWGALLGACKVHVNAELGEIAARHLL-------ELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       411 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-------~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ..++..|. ........|+...+ +.++.+.       +..|..+.+|..++.++.+.|++++|...|++..+.++
T Consensus       194 ~~~~~~~~-~~~~~~~lg~~~~~-~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~  267 (296)
T PRK11189        194 KLDKEQWG-WNIVEFYLGKISEE-TLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNV  267 (296)
T ss_pred             hCCccccH-HHHHHHHccCCCHH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence            21222232 12233345555443 2444443       45567778999999999999999999999999987765

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

Probab=99.34  E-value=3.3e-10  Score=108.05  Aligned_cols=267  Identities=13%  Similarity=0.128  Sum_probs=157.5

Q ss_pred             HHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCC----CHhHHHHHHHHHHhCCCh
Q 011249           89 LLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAER----NVISWSAMVAGYANCGNM  164 (490)
Q Consensus        89 ~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~~~~~l~~~~~~~~~~  164 (490)
                      .++..+...|+.|+..||..+|..              |+..|+++.|- +|.-|.-+    +...++.++.+..+.++.
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiar--------------Yc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~   75 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIAR--------------YCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDA   75 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHH--------------HcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccc
Confidence            466778899999999999999886              78888998887 88877653    445788888888888887


Q ss_pred             HHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHH-HcCccc
Q 011249          165 KAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMR-QENVRI  243 (490)
Q Consensus       165 ~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~p  243 (490)
                      +.+.       +|.+.+|..|..+|...||+..    |+...+    -...+...+...|.-.....++..+. ..+..|
T Consensus        76 Enpk-------ep~aDtyt~Ll~ayr~hGDli~----fe~veq----dLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lp  140 (1088)
T KOG4318|consen   76 ENPK-------EPLADTYTNLLKAYRIHGDLIL----FEVVEQ----DLESINQSFSDHGVGSPERWFLMKIHCCPHSLP  140 (1088)
T ss_pred             cCCC-------CCchhHHHHHHHHHHhccchHH----HHHHHH----HHHHHHhhhhhhccCcHHHHHHhhcccCcccch
Confidence            7765       7788899999999999988655    222211    12233334444444444444443322 122233


Q ss_pred             ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCC-CCchhHHHHHHHHHH-hcCChHHHHHHHhcccC-CChhHHHHHHHH
Q 011249          244 SEVAMVGAISACTQLGDVEMAAILAKHVDEGCC-DRTNYVSNALIHMHS-KCGYLDLAWREFSRIKN-KDVISYSSMITA  320 (490)
Q Consensus       244 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~-~~~~~~~A~~~~~~~~~-~~~~~~~~l~~~  320 (490)
                      |..+.   +......|-++.+.+++..+..... .|..+    +++-+. ....+++-....+...+ +++.+|...+.+
T Consensus       141 da~n~---illlv~eglwaqllkll~~~Pvsa~~~p~~v----fLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~  213 (1088)
T KOG4318|consen  141 DAENA---ILLLVLEGLWAQLLKLLAKVPVSAWNAPFQV----FLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKR  213 (1088)
T ss_pred             hHHHH---HHHHHHHHHHHHHHHHHhhCCcccccchHHH----HHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHH
Confidence            33221   1122233444444444433321110 11111    111111 11223333333333333 677777777777


Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcC
Q 011249          321 FADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSG  396 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  396 (490)
                      -...|+.+.|..++.+|.+.|++.+..-|..|+-+   .++...+..+++-|... |+.|+.+|+...+..+...|
T Consensus       214 alaag~~d~Ak~ll~emke~gfpir~HyFwpLl~g---~~~~q~~e~vlrgmqe~-gv~p~seT~adyvip~l~N~  285 (1088)
T KOG4318|consen  214 ALAAGDVDGAKNLLYEMKEKGFPIRAHYFWPLLLG---INAAQVFEFVLRGMQEK-GVQPGSETQADYVIPQLSNG  285 (1088)
T ss_pred             HHhcCchhhHHHHHHHHHHcCCCcccccchhhhhc---CccchHHHHHHHHHHHh-cCCCCcchhHHHHHhhhcch
Confidence            77777777777777777777777776666666544   56666666666666664 77777777766555555533

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=99.32  E-value=1.4e-10  Score=93.59  Aligned_cols=190  Identities=12%  Similarity=0.023  Sum_probs=101.3

Q ss_pred             HHHHHHHHHhcCChHHHHHHHhcccCC---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc-HHHHHHHHHHhcC
Q 011249          283 SNALIHMHSKCGYLDLAWREFSRIKNK---DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN-QVTFIGVLTACSH  358 (490)
Q Consensus       283 ~~~l~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~  358 (490)
                      ...|.-.|...|+...|..-+++..+.   +..+|..+...|.+.|+.+.|.+-|++...  +.|+ ....|....-+|.
T Consensus        38 rlqLal~YL~~gd~~~A~~nlekAL~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAls--l~p~~GdVLNNYG~FLC~  115 (250)
T COG3063          38 RLQLALGYLQQGDYAQAKKNLEKALEHDPSYYLAHLVRAHYYQKLGENDLADESYRKALS--LAPNNGDVLNNYGAFLCA  115 (250)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHh--cCCCccchhhhhhHHHHh
Confidence            334455556666666666666655542   233555555556666666666666665555  2332 2345555555555


Q ss_pred             CCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHH
Q 011249          359 GGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIA  436 (490)
Q Consensus       359 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~  436 (490)
                      .|++++|...|++....-.......+|..+.-+..+.|+++.|.+.|++..  .+..+.+...+.......|++-.|..+
T Consensus       116 qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~~~~y~~Ar~~  195 (250)
T COG3063         116 QGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELARLHYKAGDYAPARLY  195 (250)
T ss_pred             CCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHHHHHHhcccchHHHHH
Confidence            556666666666555532222234455555555555666666666555444  233344555555555555666666666


Q ss_pred             HHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          437 ARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       437 ~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      +++.....+-....+...+++-.+.|+.+.+-++=..+
T Consensus       196 ~~~~~~~~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL  233 (250)
T COG3063         196 LERYQQRGGAQAESLLLGIRIAKRLGDRAAAQRYQAQL  233 (250)
T ss_pred             HHHHHhcccccHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            65555555544555555555555555555555544433

>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=99.30  E-value=3.2e-09  Score=100.61  Aligned_cols=285  Identities=14%  Similarity=0.057  Sum_probs=160.6

Q ss_pred             HHHHhcCChhHHHHHHhhcCC--CC-HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHh-c-----
Q 011249          187 AGYGKCGEVREAKKVFDEISE--PD-ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACT-Q-----  257 (490)
Q Consensus       187 ~~~~~~~~~~~A~~~~~~~~~--~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~-~-----  257 (490)
                      ..+...|++++|++.++....  .| ..........+.+.|+.++|..+|..+++.+  |+...|...+..+. -     
T Consensus        12 ~il~e~g~~~~AL~~L~~~~~~I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN--Pdn~~Yy~~L~~~~g~~~~~~   89 (517)
T PF12569_consen   12 SILEEAGDYEEALEHLEKNEKQILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN--PDNYDYYRGLEEALGLQLQLS   89 (517)
T ss_pred             HHHHHCCCHHHHHHHHHhhhhhCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCcHHHHHHHHHHHhhhcccc
Confidence            344555666666666655443  23 3334455566666666666666666666653  34433333333332 1     


Q ss_pred             cCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChH-HHHHHHhcccCCC-hhHHHHHHHHHHhcCChHHHHHHHH
Q 011249          258 LGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLD-LAWREFSRIKNKD-VISYSSMITAFADHGKSQEALDMFL  335 (490)
Q Consensus       258 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~-~A~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~  335 (490)
                      ..+.+....+|+.+...-  |.......+.-.+.....+. .+...+.....++ +.+|+.+-..|....+.+-...++.
T Consensus        90 ~~~~~~~~~~y~~l~~~y--p~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~  167 (517)
T PF12569_consen   90 DEDVEKLLELYDELAEKY--PRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVE  167 (517)
T ss_pred             cccHHHHHHHHHHHHHhC--ccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHH
Confidence            123455555666554443  11111111111111111111 1222223333332 2445555555554444444444444


Q ss_pred             HHHHc----C----------CCCcH--HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChH
Q 011249          336 KMRNE----G----------IEPNQ--VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLE  399 (490)
Q Consensus       336 ~~~~~----~----------~~p~~--~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  399 (490)
                      .....    +          -.|+.  .++..+...|...|++++|++++++..+  ..|..+..|..-++.|-+.|+++
T Consensus       168 ~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~--htPt~~ely~~KarilKh~G~~~  245 (517)
T PF12569_consen  168 EYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIE--HTPTLVELYMTKARILKHAGDLK  245 (517)
T ss_pred             HHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHh--cCCCcHHHHHHHHHHHHHCCCHH
Confidence            44321    1          12333  2445566778888899999999988887  33444778888888888999999


Q ss_pred             HHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC--CCC-------CchHHHHHHHHHhcCCcchHH
Q 011249          400 KAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELG--PEK-------TGNSALLANIYASMGKWKDSE  468 (490)
Q Consensus       400 ~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~--p~~-------~~~~~~l~~~~~~~g~~~~A~  468 (490)
                      +|.+.++...  +.-|..+-+-.+..+.+.|++++|.+++....+.+  |..       ..+....+.+|.+.|++..|+
T Consensus       246 ~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~AL  325 (517)
T PF12569_consen  246 EAAEAMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLAL  325 (517)
T ss_pred             HHHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHH
Confidence            9988888777  34455555566677788899999988888876644  221       123355688888999999988


Q ss_pred             HHHHHhhhc
Q 011249          469 IVKMMISET  477 (490)
Q Consensus       469 ~~~~~~~~~  477 (490)
                      +.|..+.+.
T Consensus       326 k~~~~v~k~  334 (517)
T PF12569_consen  326 KRFHAVLKH  334 (517)
T ss_pred             HHHHHHHHH
Confidence            888766543

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=99.30  E-value=3.3e-09  Score=99.30  Aligned_cols=231  Identities=15%  Similarity=0.098  Sum_probs=169.8

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHc-----C-cccChhh-HHHHHHHHhccCChHHHHHHHHHHHhc-----C-CCC
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQE-----N-VRISEVA-MVGAISACTQLGDVEMAAILAKHVDEG-----C-CDR  278 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~-----~-~~p~~~~-~~~l~~~~~~~g~~~~a~~~~~~~~~~-----~-~~~  278 (490)
                      +...+...|...|+++.|+.+++...+.     | ..|...+ ...+...|...+++++|..+|+.+...     | ..|
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            4555888888889999988888887653     2 1334333 334777788889999999988887543     2 111


Q ss_pred             -chhHHHHHHHHHHhcCChHHHHHHHhcccC----------CCh-hHHHHHHHHHHhcCChHHHHHHHHHHHHc---CCC
Q 011249          279 -TNYVSNALIHMHSKCGYLDLAWREFSRIKN----------KDV-ISYSSMITAFADHGKSQEALDMFLKMRNE---GIE  343 (490)
Q Consensus       279 -~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----------~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~  343 (490)
                       -..+++.|..+|.+.|++++|...++...+          +.+ ..++.++..+...+++++|..++++..+.   -+.
T Consensus       281 ~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~~g  360 (508)
T KOG1840|consen  281 AVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDAPG  360 (508)
T ss_pred             HHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhhcc
Confidence             234566677788999999888877776543          122 24566777888999999999999987652   122


Q ss_pred             CcH----HHHHHHHHHhcCCCChHHHHHHHHHHHHHc----C--CCCCchHHHHHHHHHhhcCChHHHHHHHHhcc----
Q 011249          344 PNQ----VTFIGVLTACSHGGLVEDGCKQFELMTRVF----G--IKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK----  409 (490)
Q Consensus       344 p~~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~----~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----  409 (490)
                      ++.    .+++.+...|...|++++|.++++++....    +  ..-....++.|...|.+.+++++|.++|.+..    
T Consensus       361 ~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i~~  440 (508)
T KOG1840|consen  361 EDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDIMK  440 (508)
T ss_pred             ccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHHHH
Confidence            332    488999999999999999999999988752    1  11124456788899999999999999987654    


Q ss_pred             ----CCCC-hhhHHHHHHHHhhhCChHHHHHHHHHHHh
Q 011249          410 ----DFCD-AGTWGALLGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       410 ----~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                          ..|+ ..+|..|+.+|...|+++.|+++.+.+..
T Consensus       441 ~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~~  478 (508)
T KOG1840|consen  441 LCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVLN  478 (508)
T ss_pred             HhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHHH
Confidence                2333 35889999999999999999999998874

>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=99.29  E-value=1.6e-09  Score=102.57  Aligned_cols=258  Identities=10%  Similarity=0.013  Sum_probs=188.0

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCcccCh-hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc-
Q 011249          216 MTVCYVQNGYAKAAIEMYKVMRQENVRISE-VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC-  293 (490)
Q Consensus       216 l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-  293 (490)
                      ....+...|++++|++.++.-.+.  .+|. .........+.+.|+.++|..+|..+.+.+ |.+...|..+..+..-. 
T Consensus        10 ~~~il~e~g~~~~AL~~L~~~~~~--I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rN-Pdn~~Yy~~L~~~~g~~~   86 (517)
T PF12569_consen   10 KNSILEEAGDYEEALEHLEKNEKQ--ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN-PDNYDYYRGLEEALGLQL   86 (517)
T ss_pred             HHHHHHHCCCHHHHHHHHHhhhhh--CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHhhhc
Confidence            345678899999999999886554  4454 556667778899999999999999999998 66677777777766332 


Q ss_pred             ----CChHHHHHHHhcccC--CChhHHHHHHHHHHhcCCh-HHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHH
Q 011249          294 ----GYLDLAWREFSRIKN--KDVISYSSMITAFADHGKS-QEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGC  366 (490)
Q Consensus       294 ----~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~-~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~  366 (490)
                          ...+...++|+++..  |.......+.-.+..-..+ ..+..++..+...|++   .+|..+-..|......+-..
T Consensus        87 ~~~~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvP---slF~~lk~Ly~d~~K~~~i~  163 (517)
T PF12569_consen   87 QLSDEDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVP---SLFSNLKPLYKDPEKAAIIE  163 (517)
T ss_pred             ccccccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCc---hHHHHHHHHHcChhHHHHHH
Confidence                246777888887765  3222222222222221223 3455677777788765   34555555566555555555


Q ss_pred             HHHHHHHHHc-------------CCCCCch--HHHHHHHHHhhcCChHHHHHHHHhcc-CCCC-hhhHHHHHHHHhhhCC
Q 011249          367 KQFELMTRVF-------------GIKPLTE--HLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD-AGTWGALLGACKVHVN  429 (490)
Q Consensus       367 ~~~~~~~~~~-------------~~~~~~~--~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~-~~~~~~l~~~~~~~g~  429 (490)
                      +++.......             .-+|+..  ++..+...|-..|++++|++++++.. ..|+ +..|..-+..+.+.|+
T Consensus       164 ~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~  243 (517)
T PF12569_consen  164 SLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGD  243 (517)
T ss_pred             HHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCC
Confidence            6666654421             1123332  34567888999999999999999776 4454 6788888999999999


Q ss_pred             hHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          430 AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       430 ~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +++|.+.++.+.++++.|..+-+-.+..+.++|+.++|.+++......+.
T Consensus       244 ~~~Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~  293 (517)
T PF12569_consen  244 LKEAAEAMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTASLFTREDV  293 (517)
T ss_pred             HHHHHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCC
Confidence            99999999999999999999999999999999999999999998877765

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 [], [].

>PF13041 PPR_2: PPR repeat family

Probab=99.27  E-value=1.1e-11  Score=77.70  Aligned_cols=50  Identities=16%  Similarity=0.426  Sum_probs=47.2

Q ss_pred             CCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcC
Q 011249           65 CKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACAR  115 (490)
Q Consensus        65 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~  115 (490)
                      ||. .+||++|++|++.|++++|.++|++|.+.|+.||..||+.+|++|++
T Consensus         1 P~~-~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~~~~k   50 (50)
T PF13041_consen    1 PDV-VTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILINGLCK   50 (50)
T ss_pred             Cch-HHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHcC
Confidence            677 89999999999999999999999999999999999999999998753

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.27  E-value=2e-07  Score=86.68  Aligned_cols=418  Identities=11%  Similarity=0.054  Sum_probs=251.7

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHhccCCC--CCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhc
Q 011249           37 YAQFLIRLLQLPGDNLSYARQVFDQIPK--CKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACA  114 (490)
Q Consensus        37 ~~~~l~~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~  114 (490)
                      +.....-.+...|+ .++|....+.-.+  +...+.|..+.-.+-...++++|++.|......  .||....-.=+.   
T Consensus        43 slAmkGL~L~~lg~-~~ea~~~vr~glr~d~~S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~--~~dN~qilrDls---  116 (700)
T KOG1156|consen   43 SLAMKGLTLNCLGK-KEEAYELVRLGLRNDLKSHVCWHVLGLLQRSDKKYDEAIKCYRNALKI--EKDNLQILRDLS---  116 (700)
T ss_pred             hHHhccchhhcccc-hHHHHHHHHHHhccCcccchhHHHHHHHHhhhhhHHHHHHHHHHHHhc--CCCcHHHHHHHH---
Confidence            33444445566677 7888888776543  223267888888888888999999999998775  555432211111   


Q ss_pred             CCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCCChHHHHHHHHHhcc-----CCchhHHH--
Q 011249          115 RVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCGNMKAAKEFYDRMTE-----KNSVTWVA--  184 (490)
Q Consensus       115 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~~~~~--  184 (490)
                                -.-.+.|+++.....-....+  | ....|..+..++.-.|++..|..++++..+     ++...+..  
T Consensus       117 ----------lLQ~QmRd~~~~~~tr~~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se  186 (700)
T KOG1156|consen  117 ----------LLQIQMRDYEGYLETRNQLLQLRPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSE  186 (700)
T ss_pred             ----------HHHHHHHhhhhHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHH
Confidence                      123566777777766666655  3 445788888888889999999998888764     34443322  


Q ss_pred             ----HHHHHHhcCChhHHHHHHhhcCC--CC-HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHh-
Q 011249          185 ----MIAGYGKCGEVREAKKVFDEISE--PD-ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACT-  256 (490)
Q Consensus       185 ----l~~~~~~~~~~~~A~~~~~~~~~--~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~-  256 (490)
                          -.....+.|..++|.+.+.....  .| ...-..-...+.+.++.++|..+|..+...  .||...|...+..+. 
T Consensus       187 ~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~r--nPdn~~Yy~~l~~~lg  264 (700)
T KOG1156|consen  187 LLLYQNQILIEAGSLQKALEHLLDNEKQIVDKLAFEETKADLLMKLGQLEEAVKVYRRLLER--NPDNLDYYEGLEKALG  264 (700)
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHhhhhHHHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhh--CchhHHHHHHHHHHHH
Confidence                22345677888888888877665  22 233345567788899999999999999876  566666655554433 


Q ss_pred             ccCChHHHH-HHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCC-ChhHHHHHHHHHHhcCChHHHHHHH
Q 011249          257 QLGDVEMAA-ILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK-DVISYSSMITAFADHGKSQEALDMF  334 (490)
Q Consensus       257 ~~g~~~~a~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~  334 (490)
                      +..+--++. .+|....+.-....... ..=+.......-.+..-.++....+. -+.++..+...|-.....+-..++.
T Consensus       265 k~~d~~~~lk~ly~~ls~~y~r~e~p~-Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~vf~dl~SLyk~p~k~~~le~Lv  343 (700)
T KOG1156|consen  265 KIKDMLEALKALYAILSEKYPRHECPR-RLPLSVLNGEELKEIVDKYLRPLLSKGVPSVFKDLRSLYKDPEKVAFLEKLV  343 (700)
T ss_pred             HHhhhHHHHHHHHHHHhhcCcccccch-hccHHHhCcchhHHHHHHHHHHHhhcCCCchhhhhHHHHhchhHhHHHHHHH
Confidence            333333333 55555544321111100 00011111111112222333333332 2344555555444332222222222


Q ss_pred             HHHHH----cC----------CCCcHH--HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCCh
Q 011249          335 LKMRN----EG----------IEPNQV--TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQL  398 (490)
Q Consensus       335 ~~~~~----~~----------~~p~~~--~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  398 (490)
                      ..+..    .|          -+|...  ++-.++..+-..|+++.|..+++....  ..|.-++.|..-.+.+...|++
T Consensus       344 t~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g~~~~A~~yId~AId--HTPTliEly~~KaRI~kH~G~l  421 (700)
T KOG1156|consen  344 TSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLGDYEVALEYIDLAID--HTPTLIELYLVKARIFKHAGLL  421 (700)
T ss_pred             HHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHcccHHHHHHHHHHHhc--cCchHHHHHHHHHHHHHhcCCh
Confidence            22221    11          134443  555667778899999999999998875  3333366676777889999999


Q ss_pred             HHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC---------chHHHHHHHHHhcCCcchH
Q 011249          399 EKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT---------GNSALLANIYASMGKWKDS  467 (490)
Q Consensus       399 ~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~---------~~~~~l~~~~~~~g~~~~A  467 (490)
                      ++|..++++..  +.+|...-.--+.-..+.++.++|.++..+..+.+-+-.         .+...=+.+|.+.|++..|
T Consensus       422 ~eAa~~l~ea~elD~aDR~INsKcAKYmLrAn~i~eA~~~~skFTr~~~~~~~~L~~mqcmWf~~E~g~ay~r~~k~g~A  501 (700)
T KOG1156|consen  422 DEAAAWLDEAQELDTADRAINSKCAKYMLRANEIEEAEEVLSKFTREGFGAVNNLAEMQCMWFQLEDGEAYLRQNKLGLA  501 (700)
T ss_pred             HHHHHHHHHHHhccchhHHHHHHHHHHHHHccccHHHHHHHHHhhhcccchhhhHHHhhhHHHhHhhhHHHHHHHHHHHH
Confidence            99999998877  445554444555666788899999998888776542111         1222236678888888777


Q ss_pred             HHHHHHhh
Q 011249          468 EIVKMMIS  475 (490)
Q Consensus       468 ~~~~~~~~  475 (490)
                      ++=+..+.
T Consensus       502 LKkfh~i~  509 (700)
T KOG1156|consen  502 LKKFHEIE  509 (700)
T ss_pred             HHHHhhHH
Confidence            76655443

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.27  E-value=1.2e-07  Score=81.63  Aligned_cols=193  Identities=15%  Similarity=0.083  Sum_probs=124.7

Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHH-----HHHHHHhcCChHHHHHHHhcccC-----CChhHHHHHH
Q 011249          249 VGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNA-----LIHMHSKCGYLDLAWREFSRIKN-----KDVISYSSMI  318 (490)
Q Consensus       249 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~-----l~~~~~~~~~~~~A~~~~~~~~~-----~~~~~~~~l~  318 (490)
                      ..++-.|.+.++..+|..+.+++.-.  .|-......     +..-......+.-|.+.|.-+-+     ..+.-..++.
T Consensus       289 lNL~iYyL~q~dVqeA~~L~Kdl~Pt--tP~EyilKgvv~aalGQe~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmA  366 (557)
T KOG3785|consen  289 LNLIIYYLNQNDVQEAISLCKDLDPT--TPYEYILKGVVFAALGQETGSREHLKIAQQFFQLVGESALECDTIPGRQSMA  366 (557)
T ss_pred             hhheeeecccccHHHHHHHHhhcCCC--ChHHHHHHHHHHHHhhhhcCcHHHHHHHHHHHHHhcccccccccccchHHHH
Confidence            34455577888888888877665321  122222222     22222222345566677765544     2333456677


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHH-HHHHHHHhhcCC
Q 011249          319 TAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHL-TCMVDLLGRSGQ  397 (490)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~g~  397 (490)
                      +.+.-..++++++-.+.....- +.-|...-..+.++++..|++.+|+++|-.+... .++ +..+| ..|.++|.+.++
T Consensus       367 s~fFL~~qFddVl~YlnSi~sY-F~NdD~Fn~N~AQAk~atgny~eaEelf~~is~~-~ik-n~~~Y~s~LArCyi~nkk  443 (557)
T KOG3785|consen  367 SYFFLSFQFDDVLTYLNSIESY-FTNDDDFNLNLAQAKLATGNYVEAEELFIRISGP-EIK-NKILYKSMLARCYIRNKK  443 (557)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH-hcCcchhhhHHHHHHHHhcChHHHHHHHhhhcCh-hhh-hhHHHHHHHHHHHHhcCC
Confidence            7777777888888888777664 3334444445778888889999999998877642 233 33444 467788999999


Q ss_pred             hHHHHHHHHhccCCCChhhHH-HHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          398 LEKAHSLIMDYKDFCDAGTWG-ALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       398 ~~~A~~~~~~~~~~~~~~~~~-~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      ++-|++++-++..+.+..+.. .+.+.|.+.+.+--|-+.|+.+...+|.
T Consensus       444 P~lAW~~~lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~  493 (557)
T KOG3785|consen  444 PQLAWDMMLKTNTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILDPT  493 (557)
T ss_pred             chHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCC
Confidence            999999988877444444443 3446788899998888888888888876

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=99.26  E-value=4.1e-09  Score=85.32  Aligned_cols=195  Identities=14%  Similarity=0.046  Sum_probs=95.0

Q ss_pred             HHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCCh
Q 011249          251 AISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKS  327 (490)
Q Consensus       251 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~  327 (490)
                      |.-.|...|+...|..-+++.++.. |.+..++..+...|.+.|+.+.|.+.|++..+   .+..+.|....-+|..|++
T Consensus        41 Lal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~qg~~  119 (250)
T COG3063          41 LALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCAQGRP  119 (250)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHhCCCh
Confidence            3334444455555555555444443 33444444444555555555555555544433   2334444444445555555


Q ss_pred             HHHHHHHHHHHHcCCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHH
Q 011249          328 QEALDMFLKMRNEGIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIM  406 (490)
Q Consensus       328 ~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  406 (490)
                      ++|...|++....-.-|. ..+|..+.-+..+.|+.+.|...|++..+  ..+..+.....+.......|++-.|..+++
T Consensus       120 ~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~--~dp~~~~~~l~~a~~~~~~~~y~~Ar~~~~  197 (250)
T COG3063         120 EEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALE--LDPQFPPALLELARLHYKAGDYAPARLYLE  197 (250)
T ss_pred             HHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHH--hCcCCChHHHHHHHHHHhcccchHHHHHHH
Confidence            555555555554221121 23455555555555555555555555554  223334444455555555555555555555


Q ss_pred             hcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC
Q 011249          407 DYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       407 ~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      ...  ..++..+..-.|..-...||.+.+-+.=.++.+..|.++
T Consensus       198 ~~~~~~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~fP~s~  241 (250)
T COG3063         198 RYQQRGGAQAESLLLGIRIAKRLGDRAAAQRYQAQLQRLFPYSE  241 (250)
T ss_pred             HHHhcccccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCcH
Confidence            443  223444444444445555666655555555555555544

>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=99.26  E-value=8.6e-10  Score=97.33  Aligned_cols=251  Identities=13%  Similarity=0.027  Sum_probs=158.5

Q ss_pred             HHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHH
Q 011249          188 GYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMA  264 (490)
Q Consensus       188 ~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a  264 (490)
                      -+.-.|++..++.-.+.-..   .+......+.+++...|+++.++   .++.... .|.......+...+...++-+.+
T Consensus        10 n~fy~G~Y~~~i~e~~~~~~~~~~~~e~~~~~~Rs~iAlg~~~~vl---~ei~~~~-~~~l~av~~la~y~~~~~~~e~~   85 (290)
T PF04733_consen   10 NQFYLGNYQQCINEASLKSFSPENKLERDFYQYRSYIALGQYDSVL---SEIKKSS-SPELQAVRLLAEYLSSPSDKESA   85 (290)
T ss_dssp             HHHCTT-HHHHCHHHHCHTSTCHHHHHHHHHHHHHHHHTT-HHHHH---HHS-TTS-SCCCHHHHHHHHHHCTSTTHHCH
T ss_pred             HHHHhhhHHHHHHHhhccCCCchhHHHHHHHHHHHHHHcCChhHHH---HHhccCC-ChhHHHHHHHHHHHhCccchHHH
Confidence            34456777777754441111   22334556677888888877544   3333332 56666665565555544455555


Q ss_pred             HHHHHHHHhcCCC-CchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 011249          265 AILAKHVDEGCCD-RTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIE  343 (490)
Q Consensus       265 ~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  343 (490)
                      ..-++........ .+..+......++...|++++|++++...  .+.......+..|.+.++++.|.+.++.|.+.  .
T Consensus        86 l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~--~  161 (290)
T PF04733_consen   86 LEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG--GSLELLALAVQILLKMNRPDLAEKELKNMQQI--D  161 (290)
T ss_dssp             HHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCC--S
T ss_pred             HHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhc--C
Confidence            4444443333322 23334444455677788999998888776  46677777888899999999999999998863  3


Q ss_pred             CcHHHHHHHHHHh----cCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhH
Q 011249          344 PNQVTFIGVLTAC----SHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTW  417 (490)
Q Consensus       344 p~~~~~~~l~~~~----~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~  417 (490)
                      .|. +...+..++    ...+.+.+|..+|+++..  ..++++.+.+.++.+....|++++|.+++.+..  .+.++.+.
T Consensus       162 eD~-~l~qLa~awv~l~~g~e~~~~A~y~f~El~~--~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~L  238 (290)
T PF04733_consen  162 EDS-ILTQLAEAWVNLATGGEKYQDAFYIFEELSD--KFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTL  238 (290)
T ss_dssp             CCH-HHHHHHHHHHHHHHTTTCCCHHHHHHHHHHC--CS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHH
T ss_pred             CcH-HHHHHHHHHHHHHhCchhHHHHHHHHHHHHh--ccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHH
Confidence            343 333444443    234468899999999876  566778888888888889999999998887765  34456677


Q ss_pred             HHHHHHHhhhCCh-HHHHHHHHHHHhcCCCCCc
Q 011249          418 GALLGACKVHVNA-ELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       418 ~~l~~~~~~~g~~-~~a~~~~~~~~~~~p~~~~  449 (490)
                      ..++......|+. +.+.+.+.++....|+++.
T Consensus       239 aNliv~~~~~gk~~~~~~~~l~qL~~~~p~h~~  271 (290)
T PF04733_consen  239 ANLIVCSLHLGKPTEAAERYLSQLKQSNPNHPL  271 (290)
T ss_dssp             HHHHHHHHHTT-TCHHHHHHHHHCHHHTTTSHH
T ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHhCCCChH
Confidence            7777777777777 6778888888888888553

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.

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.25  E-value=1.2e-09  Score=98.84  Aligned_cols=338  Identities=14%  Similarity=0.053  Sum_probs=177.8

Q ss_pred             HHhcCCHHHHHHHHhhcCC---CCHhHHHHHHHHHHhCCChHHHHHHHHHhccCC---chhHHHHHHHHHhcCChhHHHH
Q 011249          127 YTKIGLMDDAQRLFDSMAE---RNVISWSAMVAGYANCGNMKAAKEFYDRMTEKN---SVTWVAMIAGYGKCGEVREAKK  200 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~l~~~~~~~~~~~~A~~  200 (490)
                      ....|+++.|+..|-+...   +|...|..-..+|...|++++|++--.+-.+-+   +..|.....++.-.|++++|+.
T Consensus        12 a~s~~d~~~ai~~~t~ai~l~p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l~p~w~kgy~r~Gaa~~~lg~~~eA~~   91 (539)
T KOG0548|consen   12 AFSSGDFETAIRLFTEAIMLSPTNHVLYSNRSAAYASLGSYEKALKDATKTRRLNPDWAKGYSRKGAALFGLGDYEEAIL   91 (539)
T ss_pred             hcccccHHHHHHHHHHHHccCCCccchhcchHHHHHHHhhHHHHHHHHHHHHhcCCchhhHHHHhHHHHHhcccHHHHHH
Confidence            4567899999999987764   466778888888899999988888777776543   3478888888888889999988


Q ss_pred             HHhhcCC---CCHHhHHHHHHHHHhcC-----------------C-------------------------------hHHH
Q 011249          201 VFDEISE---PDASCWAAMTVCYVQNG-----------------Y-------------------------------AKAA  229 (490)
Q Consensus       201 ~~~~~~~---~~~~~~~~l~~~~~~~g-----------------~-------------------------------~~~A  229 (490)
                      .|.+-.+   .+...+..+..++....                 +                               .+..
T Consensus        92 ay~~GL~~d~~n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~l~~~~~~p~~l~~~l~d~r~  171 (539)
T KOG0548|consen   92 AYSEGLEKDPSNKQLKTGLAQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKILEIIQKNPTSLKLYLNDPRL  171 (539)
T ss_pred             HHHHHhhcCCchHHHHHhHHHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHHHHHhhcCcHhhhcccccHHH
Confidence            8887654   33444555555441110                 0                               0000


Q ss_pred             HHHHHHHHH--------cC-------ccc---------C-------------hhhHHHHHHHHhccCChHHHHHHHHHHH
Q 011249          230 IEMYKVMRQ--------EN-------VRI---------S-------------EVAMVGAISACTQLGDVEMAAILAKHVD  272 (490)
Q Consensus       230 ~~~~~~~~~--------~~-------~~p---------~-------------~~~~~~l~~~~~~~g~~~~a~~~~~~~~  272 (490)
                      ++..-.+..        .+       ..|         .             ..-...+.++..+..+++.+.+.+....
T Consensus       172 m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lgnaaykkk~f~~a~q~y~~a~  251 (539)
T KOG0548|consen  172 MKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELGNAAYKKKDFETAIQHYAKAL  251 (539)
T ss_pred             HHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            000000000        00       000         0             0011123333333344444444444444


Q ss_pred             hcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCCh---h-------HHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 011249          273 EGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDV---I-------SYSSMITAFADHGKSQEALDMFLKMRNEGI  342 (490)
Q Consensus       273 ~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~---~-------~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  342 (490)
                      +..  .+...++....+|...|.+..+....++..+...   .       .+..+..+|.+.++++.+...|++......
T Consensus       252 el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~rad~klIak~~~r~g~a~~k~~~~~~ai~~~~kaLte~R  329 (539)
T KOG0548|consen  252 ELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRELRADYKLIAKALARLGNAYTKREDYEGAIKYYQKALTEHR  329 (539)
T ss_pred             hHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHHHHHHHHHHHHHHHhhhhhhhHHhHHHHHHHHHHHhhhhc
Confidence            432  3333334444444444444444444333332111   0       111122233344445555555554443222


Q ss_pred             CCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCc-hHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHH
Q 011249          343 EPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLT-EHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGA  419 (490)
Q Consensus       343 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~  419 (490)
                      .|+...         +....+++....+...   -+.|.. .-...-...+.+.|++..|++.|.++.  .+.|...|..
T Consensus       330 t~~~ls---------~lk~~Ek~~k~~e~~a---~~~pe~A~e~r~kGne~Fk~gdy~~Av~~YteAIkr~P~Da~lYsN  397 (539)
T KOG0548|consen  330 TPDLLS---------KLKEAEKALKEAERKA---YINPEKAEEEREKGNEAFKKGDYPEAVKHYTEAIKRDPEDARLYSN  397 (539)
T ss_pred             CHHHHH---------HHHHHHHHHHHHHHHH---hhChhHHHHHHHHHHHHHhccCHHHHHHHHHHHHhcCCchhHHHHH
Confidence            222111         0111111111111111   111111 001112345566777777777777665  4445667777


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      -.-+|.+.|.+..|+.-.+..++++|+.+..|..-+.++....+|++|.+.|++..+.+
T Consensus       398 RAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~eale~d  456 (539)
T KOG0548|consen  398 RAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEALELD  456 (539)
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            77777777777777777777777777777777777777777777777777777666554

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.25  E-value=2.1e-08  Score=86.26  Aligned_cols=412  Identities=10%  Similarity=0.027  Sum_probs=239.6

Q ss_pred             HhcCCCCHHHHHHHhccCCCCC--CceehH-HHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHH
Q 011249           45 LQLPGDNLSYARQVFDQIPKCK--TQFLWT-SLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLE  121 (490)
Q Consensus        45 ~~~~~~~~~~A~~~~~~~~~~~--~~~~~~-~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~  121 (490)
                      +..+.+ +..|+.+++.-...+  .+...+ .+..++.+.|++++|...|+.+....- |+......+ .+         
T Consensus        32 fls~rD-ytGAislLefk~~~~~EEE~~~~lWia~C~fhLgdY~~Al~~Y~~~~~~~~-~~~el~vnL-Ac---------   99 (557)
T KOG3785|consen   32 FLSNRD-YTGAISLLEFKLNLDREEEDSLQLWIAHCYFHLGDYEEALNVYTFLMNKDD-APAELGVNL-AC---------   99 (557)
T ss_pred             HHhccc-chhHHHHHHHhhccchhhhHHHHHHHHHHHHhhccHHHHHHHHHHHhccCC-CCcccchhH-HH---------
Confidence            334445 778888877554221  112333 344566788999999999998877543 333333222 22         


Q ss_pred             HHHHHHHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHH
Q 011249          122 AVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKV  201 (490)
Q Consensus       122 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  201 (490)
                          .+.-.|.+.+|.++-++..+ ++..-..++...-+.|+-++-..+-+.+... ..--.+|.......-.+++|+++
T Consensus       100 ----c~FyLg~Y~eA~~~~~ka~k-~pL~~RLlfhlahklndEk~~~~fh~~LqD~-~EdqLSLAsvhYmR~HYQeAIdv  173 (557)
T KOG3785|consen  100 ----CKFYLGQYIEAKSIAEKAPK-TPLCIRLLFHLAHKLNDEKRILTFHSSLQDT-LEDQLSLASVHYMRMHYQEAIDV  173 (557)
T ss_pred             ----HHHHHHHHHHHHHHHhhCCC-ChHHHHHHHHHHHHhCcHHHHHHHHHHHhhh-HHHHHhHHHHHHHHHHHHHHHHH
Confidence                24556888999888776643 2222334445555666666665555555433 23334555555555678889999


Q ss_pred             HhhcCC--CCHHhHHH-HHHHHHhcCChHHHHHHHHHHHHcCcccCh-hhHHHHHHHHhcc--CChHHHH--H-------
Q 011249          202 FDEISE--PDASCWAA-MTVCYVQNGYAKAAIEMYKVMRQENVRISE-VAMVGAISACTQL--GDVEMAA--I-------  266 (490)
Q Consensus       202 ~~~~~~--~~~~~~~~-l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~--g~~~~a~--~-------  266 (490)
                      +.++..  |+....|. +.-+|.+..-++-+.++++-..+.  .||+ ...+..+....+.  |+..+.+  .       
T Consensus       174 YkrvL~dn~ey~alNVy~ALCyyKlDYydvsqevl~vYL~q--~pdStiA~NLkacn~fRl~ngr~ae~E~k~ladN~~~  251 (557)
T KOG3785|consen  174 YKRVLQDNPEYIALNVYMALCYYKLDYYDVSQEVLKVYLRQ--FPDSTIAKNLKACNLFRLINGRTAEDEKKELADNIDQ  251 (557)
T ss_pred             HHHHHhcChhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHh--CCCcHHHHHHHHHHHhhhhccchhHHHHHHHHhcccc
Confidence            988776  44444443 344666777777777777776654  3343 2333322222221  2211110  0       


Q ss_pred             ---HHHHHHhcCC------------CC-----chhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCC
Q 011249          267 ---LAKHVDEGCC------------DR-----TNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGK  326 (490)
Q Consensus       267 ---~~~~~~~~~~------------~~-----~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~  326 (490)
                         ..+.+.+.+.            -|     -+..-..|+--|.+.+++.+|..+.+++...++.-|-.-.-.+...|+
T Consensus       252 ~~~f~~~l~rHNLVvFrngEgALqVLP~L~~~IPEARlNL~iYyL~q~dVqeA~~L~Kdl~PttP~EyilKgvv~aalGQ  331 (557)
T KOG3785|consen  252 EYPFIEYLCRHNLVVFRNGEGALQVLPSLMKHIPEARLNLIIYYLNQNDVQEAISLCKDLDPTTPYEYILKGVVFAALGQ  331 (557)
T ss_pred             cchhHHHHHHcCeEEEeCCccHHHhchHHHhhChHhhhhheeeecccccHHHHHHHHhhcCCCChHHHHHHHHHHHHhhh
Confidence               1111111110            00     111223355567889999999999988877555544433333444442


Q ss_pred             -------hHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCCh
Q 011249          327 -------SQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQL  398 (490)
Q Consensus       327 -------~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  398 (490)
                             ..-|.+.|+-.-+.+..-|.. ---++..++.-..++++.+.++..+.. +-...|...+ .+..+++..|.+
T Consensus       332 e~gSreHlKiAqqffqlVG~Sa~ecDTIpGRQsmAs~fFL~~qFddVl~YlnSi~s-YF~NdD~Fn~-N~AQAk~atgny  409 (557)
T KOG3785|consen  332 ETGSREHLKIAQQFFQLVGESALECDTIPGRQSMASYFFLSFQFDDVLTYLNSIES-YFTNDDDFNL-NLAQAKLATGNY  409 (557)
T ss_pred             hcCcHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHH-HhcCcchhhh-HHHHHHHHhcCh
Confidence                   344555555443444333332 112233444455678888888888877 3444444443 578999999999


Q ss_pred             HHHHHHHHhccCC--CChhhHHHHH-HHHhhhCChHHHHHHHHHHHhcC-CC-CCchHHHHHHHHHhcCCcchHHHHHHH
Q 011249          399 EKAHSLIMDYKDF--CDAGTWGALL-GACKVHVNAELGEIAARHLLELG-PE-KTGNSALLANIYASMGKWKDSEIVKMM  473 (490)
Q Consensus       399 ~~A~~~~~~~~~~--~~~~~~~~l~-~~~~~~g~~~~a~~~~~~~~~~~-p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~  473 (490)
                      .+|.++|-.+..+  .+..+|.+++ ..|.+.+.++.|..++-   +.+ |. ....+..+++.|.+++++--|-+.|+.
T Consensus       410 ~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~l---k~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~  486 (557)
T KOG3785|consen  410 VEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMML---KTNTPSERFSLLQLIANDCYKANEFYYAAKAFDE  486 (557)
T ss_pred             HHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHHH---hcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence            9999999888722  3556666554 56688888888866554   433 33 344556678889999999888888887


Q ss_pred             hhhccccc
Q 011249          474 ISETEKKK  481 (490)
Q Consensus       474 ~~~~~~~~  481 (490)
                      +...++.+
T Consensus       487 lE~lDP~p  494 (557)
T KOG3785|consen  487 LEILDPTP  494 (557)
T ss_pred             HHccCCCc
Confidence            77655433

>PF13041 PPR_2: PPR repeat family

Probab=99.25  E-value=2.9e-11  Score=75.82  Aligned_cols=50  Identities=30%  Similarity=0.657  Sum_probs=46.0

Q ss_pred             CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcC
Q 011249          309 KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSH  358 (490)
Q Consensus       309 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~  358 (490)
                      ||+.+||+++.+|++.|++++|.++|++|.+.|+.||..||+.++++|++
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            68889999999999999999999999999999999999999999998874

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=99.24  E-value=5.1e-08  Score=88.65  Aligned_cols=403  Identities=12%  Similarity=0.025  Sum_probs=259.5

Q ss_pred             HHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHh-hHHHHHHHhcCCCC
Q 011249           42 IRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGF-TFSSVLNACARVPS  118 (490)
Q Consensus        42 ~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~-~~~~ll~~~~~~~~  118 (490)
                      .++-...|+ +++|...|-...  .|.+...|+.-..+|+..|++++|++=-.+-++.  .|+-. .|+..         
T Consensus         9 gnaa~s~~d-~~~ai~~~t~ai~l~p~nhvlySnrsaa~a~~~~~~~al~da~k~~~l--~p~w~kgy~r~---------   76 (539)
T KOG0548|consen    9 GNAAFSSGD-FETAIRLFTEAIMLSPTNHVLYSNRSAAYASLGSYEKALKDATKTRRL--NPDWAKGYSRK---------   76 (539)
T ss_pred             HHhhccccc-HHHHHHHHHHHHccCCCccchhcchHHHHHHHhhHHHHHHHHHHHHhc--CCchhhHHHHh---------
Confidence            345667888 999999998764  5555477999999999999999998877776665  44422 23222         


Q ss_pred             hHHHHHHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCC---ChHHHHHHHHHhcc-C------CchhHHHH
Q 011249          119 LLEAVICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCG---NMKAAKEFYDRMTE-K------NSVTWVAM  185 (490)
Q Consensus       119 ~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~---~~~~a~~~~~~~~~-~------~~~~~~~l  185 (490)
                           ..++.-.|++++|+..|.+-++  | |...++.+..++....   +.-.--.++..... |      ....|..+
T Consensus        77 -----Gaa~~~lg~~~eA~~ay~~GL~~d~~n~~L~~gl~~a~~~~~~~~~~~~~p~~~~~l~~~p~t~~~~~~~~~~~~  151 (539)
T KOG0548|consen   77 -----GAALFGLGDYEEAILAYSEGLEKDPSNKQLKTGLAQAYLEDYAADQLFTKPYFHEKLANLPLTNYSLSDPAYVKI  151 (539)
T ss_pred             -----HHHHHhcccHHHHHHHHHHHhhcCCchHHHHHhHHHhhhHHHHhhhhccCcHHHHHhhcChhhhhhhccHHHHHH
Confidence                 2235667999999999999886  3 4566777777662110   00000011111110 0      11122222


Q ss_pred             HHHHHh----------cCChhHHHHHHhhcC----------------CC----------------------CHHhHHHHH
Q 011249          186 IAGYGK----------CGEVREAKKVFDEIS----------------EP----------------------DASCWAAMT  217 (490)
Q Consensus       186 ~~~~~~----------~~~~~~A~~~~~~~~----------------~~----------------------~~~~~~~l~  217 (490)
                      +..+-+          ..++..|.-.+....                .|                      -..-...+.
T Consensus       152 l~~~~~~p~~l~~~l~d~r~m~a~~~l~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~d~~ee~~~k~~a~~ek~lg  231 (539)
T KOG0548|consen  152 LEIIQKNPTSLKLYLNDPRLMKADGQLKGVDELLFYASGIEILASMAEPCKQEHNGFPIIEDNTEERRVKEKAHKEKELG  231 (539)
T ss_pred             HHHhhcCcHhhhcccccHHHHHHHHHHhcCccccccccccccCCCCCCcccccCCCCCccchhHHHHHHHHhhhHHHHHH
Confidence            222111          011111211111110                01                      012345577


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHH-------HHHHHH
Q 011249          218 VCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSN-------ALIHMH  290 (490)
Q Consensus       218 ~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~-------~l~~~~  290 (490)
                      +..-+..+++.|++.+.......  -+..-++....++...|.+......-....+.|... ..-|+       .+..+|
T Consensus       232 naaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~-rad~klIak~~~r~g~a~  308 (539)
T KOG0548|consen  232 NAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGREL-RADYKLIAKALARLGNAY  308 (539)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHH-HHHHHHHHHHHHHhhhhh
Confidence            77888889999999999988765  355666677778899998888887777766665221 12222       244467


Q ss_pred             HhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCCChHHHHHHH
Q 011249          291 SKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGGLVEDGCKQF  369 (490)
Q Consensus       291 ~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~  369 (490)
                      .+.++++.|+..|.+...+...     -+...+....+++.+..+...-  +.|... ....-...+.+.|++..|...|
T Consensus       309 ~k~~~~~~ai~~~~kaLte~Rt-----~~~ls~lk~~Ek~~k~~e~~a~--~~pe~A~e~r~kGne~Fk~gdy~~Av~~Y  381 (539)
T KOG0548|consen  309 TKREDYEGAIKYYQKALTEHRT-----PDLLSKLKEAEKALKEAERKAY--INPEKAEEEREKGNEAFKKGDYPEAVKHY  381 (539)
T ss_pred             hhHHhHHHHHHHHHHHhhhhcC-----HHHHHHHHHHHHHHHHHHHHHh--hChhHHHHHHHHHHHHHhccCHHHHHHHH
Confidence            7788899999999886542111     1122333445566655555443  344432 2233366688999999999999


Q ss_pred             HHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC
Q 011249          370 ELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK  447 (490)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~  447 (490)
                      .++++  ..|.|...|....-+|.+.|.+..|++-.+...  .++....|..-..++....++++|.+.|+++++.+|++
T Consensus       382 teAIk--r~P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~eale~dp~~  459 (539)
T KOG0548|consen  382 TEAIK--RDPEDARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEALELDPSN  459 (539)
T ss_pred             HHHHh--cCCchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchh
Confidence            99998  457788999999999999999999999877665  34455677777777788889999999999999999999


Q ss_pred             CchHHHHHHHHHhcCCcchHHHHHHH
Q 011249          448 TGNSALLANIYASMGKWKDSEIVKMM  473 (490)
Q Consensus       448 ~~~~~~l~~~~~~~g~~~~A~~~~~~  473 (490)
                      ..+...+.++.........-.++.++
T Consensus       460 ~e~~~~~~rc~~a~~~~~~~ee~~~r  485 (539)
T KOG0548|consen  460 AEAIDGYRRCVEAQRGDETPEETKRR  485 (539)
T ss_pred             HHHHHHHHHHHHHhhcCCCHHHHHHh
Confidence            99888888877764444444444443

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=99.24  E-value=7.1e-08  Score=89.59  Aligned_cols=384  Identities=12%  Similarity=0.077  Sum_probs=246.9

Q ss_pred             hHHHHHHHHhcCChhHHHHHHHHHHhc-CCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCC---
Q 011249           71 WTSLIRNHVLHAHFRQSILLYAKMHRL-GVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAER---  146 (490)
Q Consensus        71 ~~~l~~~~~~~g~~~~A~~~~~~m~~~-g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---  146 (490)
                      |...+..| ..+++...++..+.+.+. +-.+++...    .            .-.+...|+-++|..........   
T Consensus        11 F~~~lk~y-E~kQYkkgLK~~~~iL~k~~eHgeslAm----k------------GL~L~~lg~~~ea~~~vr~glr~d~~   73 (700)
T KOG1156|consen   11 FRRALKCY-ETKQYKKGLKLIKQILKKFPEHGESLAM----K------------GLTLNCLGKKEEAYELVRLGLRNDLK   73 (700)
T ss_pred             HHHHHHHH-HHHHHHhHHHHHHHHHHhCCccchhHHh----c------------cchhhcccchHHHHHHHHHHhccCcc
Confidence            44444444 445666666666665552 111222221    1            11355678999999988888774   


Q ss_pred             CHhHHHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHH
Q 011249          147 NVISWSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCY  220 (490)
Q Consensus       147 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~  220 (490)
                      +.+.|+.+.-.+....++++|++.|+....-   |...+.-+.-.-++.++++.....-....+   .....|..++.++
T Consensus        74 S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql~~~~ra~w~~~Avs~  153 (700)
T KOG1156|consen   74 SHVCWHVLGLLQRSDKKYDEAIKCYRNALKIEKDNLQILRDLSLLQIQMRDYEGYLETRNQLLQLRPSQRASWIGFAVAQ  153 (700)
T ss_pred             cchhHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhhhHHHHHHHHHHH
Confidence            5578999998888899999999999998853   666777777777778888887777766655   3445688888888


Q ss_pred             HhcCChHHHHHHHHHHHHcC-cccChhhHHHHH------HHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc
Q 011249          221 VQNGYAKAAIEMYKVMRQEN-VRISEVAMVGAI------SACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC  293 (490)
Q Consensus       221 ~~~g~~~~A~~~~~~~~~~~-~~p~~~~~~~l~------~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  293 (490)
                      .-.|+...|..++++..+.. -.|+...+....      ......|..+.|.+.+......- ......-..-...+.+.
T Consensus       154 ~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i-~Dkla~~e~ka~l~~kl  232 (700)
T KOG1156|consen  154 HLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQI-VDKLAFEETKADLLMKL  232 (700)
T ss_pred             HHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHH-HHHHHHhhhHHHHHHHH
Confidence            88999999999999888654 245555444332      23456677777777666554332 22223334456677888


Q ss_pred             CChHHHHHHHhcccC--CChhHHHHHHH-HHHhcCChHHHH-HHHHH---------------------------------
Q 011249          294 GYLDLAWREFSRIKN--KDVISYSSMIT-AFADHGKSQEAL-DMFLK---------------------------------  336 (490)
Q Consensus       294 ~~~~~A~~~~~~~~~--~~~~~~~~l~~-~~~~~~~~~~a~-~~~~~---------------------------------  336 (490)
                      +++++|..++..+..  ||...|..... ++.+-.+.-++. .+|..                                 
T Consensus       233 ~~lEeA~~~y~~Ll~rnPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~  312 (700)
T KOG1156|consen  233 GQLEEAVKVYRRLLERNPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNGEELKEIVDKYLR  312 (700)
T ss_pred             hhHHhHHHHHHHHHhhCchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCcchhHHHHHHHHH
Confidence            899999999888876  44444433332 332222222222 33333                                 


Q ss_pred             -HHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHc-----C------------CCCCchHH--HHHHHHHhhcC
Q 011249          337 -MRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVF-----G------------IKPLTEHL--TCMVDLLGRSG  396 (490)
Q Consensus       337 -~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-----~------------~~~~~~~~--~~l~~~~~~~g  396 (490)
                       +.+.|+++-   +..+...|-.   +... .++++....+     +            -+|.+..|  ..++..+-+.|
T Consensus       313 ~~l~Kg~p~v---f~dl~SLyk~---p~k~-~~le~Lvt~y~~~L~~~~~f~~~D~~~~E~PttllWt~y~laqh~D~~g  385 (700)
T KOG1156|consen  313 PLLSKGVPSV---FKDLRSLYKD---PEKV-AFLEKLVTSYQHSLSGTGMFNFLDDGKQEPPTTLLWTLYFLAQHYDKLG  385 (700)
T ss_pred             HHhhcCCCch---hhhhHHHHhc---hhHh-HHHHHHHHHHHhhcccccCCCcccccccCCchHHHHHHHHHHHHHHHcc
Confidence             333333321   1122221211   1111 1333332211     1            14444444  35778888999


Q ss_pred             ChHHHHHHHHhcc-CCCCh-hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          397 QLEKAHSLIMDYK-DFCDA-GTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       397 ~~~~A~~~~~~~~-~~~~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      +++.|..+++... ..|+. ..|..-.+.+...|+.++|...++++.+++-.|..+-..-+.-..++++.++|.++..+.
T Consensus       386 ~~~~A~~yId~AIdHTPTliEly~~KaRI~kH~G~l~eAa~~l~ea~elD~aDR~INsKcAKYmLrAn~i~eA~~~~skF  465 (700)
T KOG1156|consen  386 DYEVALEYIDLAIDHTPTLIELYLVKARIFKHAGLLDEAAAWLDEAQELDTADRAINSKCAKYMLRANEIEEAEEVLSKF  465 (700)
T ss_pred             cHHHHHHHHHHHhccCchHHHHHHHHHHHHHhcCChHHHHHHHHHHHhccchhHHHHHHHHHHHHHccccHHHHHHHHHh
Confidence            9999999998877 34543 466666688889999999999999999999666766667888899999999999999988


Q ss_pred             hhccc
Q 011249          475 SETEK  479 (490)
Q Consensus       475 ~~~~~  479 (490)
                      .+.|.
T Consensus       466 Tr~~~  470 (700)
T KOG1156|consen  466 TREGF  470 (700)
T ss_pred             hhccc
Confidence            87764

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=99.24  E-value=9.7e-09  Score=87.88  Aligned_cols=298  Identities=13%  Similarity=0.073  Sum_probs=201.6

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHH---HHHHhcCChhHHHHHHhhcCCCCHHhHHH---HHHHHHhcC
Q 011249          151 WSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMI---AGYGKCGEVREAKKVFDEISEPDASCWAA---MTVCYVQNG  224 (490)
Q Consensus       151 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~---~~~~~~~~~~~A~~~~~~~~~~~~~~~~~---l~~~~~~~g  224 (490)
                      .--+...+...|++..|+.-|....+-|+..|.++.   ..|...|+-..|+.-|.+..+..+..+.+   -...+.+.|
T Consensus        41 hlElGk~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlelKpDF~~ARiQRg~vllK~G  120 (504)
T KOG0624|consen   41 HLELGKELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLELKPDFMAARIQRGVVLLKQG  120 (504)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCCccchhhHHHHHhcCccHHHHHHHhchhhhhcc
Confidence            334566667777777777777777766666665543   45666676666666666665422222222   234566777


Q ss_pred             ChHHHHHHHHHHHHcCcccC------------h--hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 011249          225 YAKAAIEMYKVMRQENVRIS------------E--VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMH  290 (490)
Q Consensus       225 ~~~~A~~~~~~~~~~~~~p~------------~--~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  290 (490)
                      .+++|..-|+...+....-.            .  ......+..+...|+...|+....++++.. +-+...+..-..+|
T Consensus       121 ele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~-~Wda~l~~~Rakc~  199 (504)
T KOG0624|consen  121 ELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ-PWDASLRQARAKCY  199 (504)
T ss_pred             cHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC-cchhHHHHHHHHHH
Confidence            77777777777765432100            0  112233445567789999999999998876 67888888888999


Q ss_pred             HhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHH----HHHHH---H------H
Q 011249          291 SKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV----TFIGV---L------T  354 (490)
Q Consensus       291 ~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~----~~~~l---~------~  354 (490)
                      ...|++..|+.-++...+   .+...+--+-..+...|+.+.++...++..+  +.||..    .|..+   .      .
T Consensus       200 i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLK--ldpdHK~Cf~~YKklkKv~K~les~e  277 (504)
T KOG0624|consen  200 IAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEIRECLK--LDPDHKLCFPFYKKLKKVVKSLESAE  277 (504)
T ss_pred             HhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHHHHHHc--cCcchhhHHHHHHHHHHHHHHHHHHH
Confidence            999999999877765544   6777777788888889999999998888887  577653    12111   1      1


Q ss_pred             HhcCCCChHHHHHHHHHHHHHcCCCCC-----chHHHHHHHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHHHhhh
Q 011249          355 ACSHGGLVEDGCKQFELMTRVFGIKPL-----TEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGACKVH  427 (490)
Q Consensus       355 ~~~~~g~~~~a~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~~  427 (490)
                      .....++|.++++..+...+.   .|.     ...+..+-.++...|++.+|++...++. ..| |..++.--..+|.-.
T Consensus       278 ~~ie~~~~t~cle~ge~vlk~---ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~d~~dv~~l~dRAeA~l~d  354 (504)
T KOG0624|consen  278 QAIEEKHWTECLEAGEKVLKN---EPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDIDPDDVQVLCDRAEAYLGD  354 (504)
T ss_pred             HHHhhhhHHHHHHHHHHHHhc---CCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhh
Confidence            234567777777777777663   232     2234455667778888888888887766 334 466777777888888


Q ss_pred             CChHHHHHHHHHHHhcCCCCCchHHHH
Q 011249          428 VNAELGEIAARHLLELGPEKTGNSALL  454 (490)
Q Consensus       428 g~~~~a~~~~~~~~~~~p~~~~~~~~l  454 (490)
                      .+++.|+.-|+++.+.+|++..+-..+
T Consensus       355 E~YD~AI~dye~A~e~n~sn~~~reGl  381 (504)
T KOG0624|consen  355 EMYDDAIHDYEKALELNESNTRAREGL  381 (504)
T ss_pred             HHHHHHHHHHHHHHhcCcccHHHHHHH
Confidence            888888888888888888877655544

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.23  E-value=5.5e-08  Score=81.77  Aligned_cols=401  Identities=11%  Similarity=0.028  Sum_probs=196.5

Q ss_pred             HHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCCh
Q 011249           42 IRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSL  119 (490)
Q Consensus        42 ~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~  119 (490)
                      +..+.+..+ +.+|++++..-.  .|......+.|..+|-...++..|...|+++...  .|...-|..--.        
T Consensus        17 iy~lI~d~r-y~DaI~~l~s~~Er~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql--~P~~~qYrlY~A--------   85 (459)
T KOG4340|consen   17 VYRLIRDAR-YADAIQLLGSELERSPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQL--HPELEQYRLYQA--------   85 (459)
T ss_pred             HHHHHHHhh-HHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--ChHHHHHHHHHH--------
Confidence            333344455 556665554432  2222234555555555566666666666665554  333333321111        


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHhhcCC-CCHhHHHHHH--HHHHhCCChHHHHHHHHHhc-cCCchhHHHHHHHHHhcCCh
Q 011249          120 LEAVICGYTKIGLMDDAQRLFDSMAE-RNVISWSAMV--AGYANCGNMKAAKEFYDRMT-EKNSVTWVAMIAGYGKCGEV  195 (490)
Q Consensus       120 ~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~l~--~~~~~~~~~~~a~~~~~~~~-~~~~~~~~~l~~~~~~~~~~  195 (490)
                           ..+.+.+.+.+|+++...|.. ++...-..-+  ......+++..+..++++.. +.+..+.+...-...+.|++
T Consensus        86 -----QSLY~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqy  160 (459)
T KOG4340|consen   86 -----QSLYKACIYADALRVAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQY  160 (459)
T ss_pred             -----HHHHHhcccHHHHHHHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccH
Confidence                 123444555556655555544 2221111111  12233455555555555554 23444444444444555555


Q ss_pred             hHHHHHHhhcCC----CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhh----HHHHHHHHhccCChHHHHHH
Q 011249          196 REAKKVFDEISE----PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVA----MVGAISACTQLGDVEMAAIL  267 (490)
Q Consensus       196 ~~A~~~~~~~~~----~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~----~~~l~~~~~~~g~~~~a~~~  267 (490)
                      +.|.+-|+...+    .....|+. .-+..+.|+++.|+++..++++.|++-.+..    -+-.+.+ ...|+   ...+
T Consensus       161 EaAvqkFqaAlqvsGyqpllAYni-ALaHy~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDv-rsvgN---t~~l  235 (459)
T KOG4340|consen  161 EAAVQKFQAALQVSGYQPLLAYNL-ALAHYSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDV-RSVGN---TLVL  235 (459)
T ss_pred             HHHHHHHHHHHhhcCCCchhHHHH-HHHHHhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCch-hcccc---hHHH
Confidence            555555555443    22233332 2233344555555555555555554321110    0000000 00000   0000


Q ss_pred             HHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC-----CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 011249          268 AKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN-----KDVISYSSMITAFADHGKSQEALDMFLKMRNEGI  342 (490)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  342 (490)
                      ...       .-+..+|.-...+.+.|+++.|.+.+-+|+.     -|++|...+.-.-. .+++-...+-++-+...+.
T Consensus       236 h~S-------al~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~-~~~p~~g~~KLqFLL~~nP  307 (459)
T KOG4340|consen  236 HQS-------ALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNM-DARPTEGFEKLQFLLQQNP  307 (459)
T ss_pred             HHH-------HHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcc-cCCccccHHHHHHHHhcCC
Confidence            000       0011233334456788999999999999986     37777766654322 3455555555665665422


Q ss_pred             CCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCC-CCchHHHHHHHHHh-hcCChHHHHHHHHhccCCCChhhHHHH
Q 011249          343 EPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIK-PLTEHLTCMVDLLG-RSGQLEKAHSLIMDYKDFCDAGTWGAL  420 (490)
Q Consensus       343 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~-~~~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~~~~~~~~~~l  420 (490)
                       ....||..++-.|++..-++.|-.++.+-... ... .+...|+ +++++. ..-..++|.+-++.+........-..-
T Consensus       308 -fP~ETFANlLllyCKNeyf~lAADvLAEn~~l-Tyk~L~~Yly~-LLdaLIt~qT~pEea~KKL~~La~~l~~kLRklA  384 (459)
T KOG4340|consen  308 -FPPETFANLLLLYCKNEYFDLAADVLAENAHL-TYKFLTPYLYD-LLDALITCQTAPEEAFKKLDGLAGMLTEKLRKLA  384 (459)
T ss_pred             -CChHHHHHHHHHHhhhHHHhHHHHHHhhCcch-hHHHhhHHHHH-HHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence             34568999999999998888888777554321 111 1223333 444443 345677777766555411111111111


Q ss_pred             HHHH-hhhCC----hHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          421 LGAC-KVHVN----AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       421 ~~~~-~~~g~----~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      +..- .+..+    ...+++-+++.+++.   ..+...-++.|++..++..+++.|..-.+-
T Consensus       385 i~vQe~r~~~dd~a~R~ai~~Yd~~LE~Y---LPVlMa~AkiyW~~~Dy~~vEk~Fr~Svef  443 (459)
T KOG4340|consen  385 IQVQEARHNRDDEAIRKAVNEYDETLEKY---LPVLMAQAKIYWNLEDYPMVEKIFRKSVEF  443 (459)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHHHHHHH---HHHHHHHHHhhccccccHHHHHHHHHHHhh
Confidence            1111 11111    223444455555544   123667788999999999999999876553

>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]

Probab=99.19  E-value=1.3e-07  Score=87.01  Aligned_cols=380  Identities=10%  Similarity=0.031  Sum_probs=224.8

Q ss_pred             HHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCC--CHhHHHH
Q 011249           76 RNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAER--NVISWSA  153 (490)
Q Consensus        76 ~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~  153 (490)
                      +-+..+|++++|.+...++...+..+....+.-++.               ..+.+++++|+.+.+.-...  +...+--
T Consensus        20 n~~~~~~e~e~a~k~~~Kil~~~pdd~~a~~cKvVa---------------lIq~~ky~~ALk~ikk~~~~~~~~~~~fE   84 (652)
T KOG2376|consen   20 NRHGKNGEYEEAVKTANKILSIVPDDEDAIRCKVVA---------------LIQLDKYEDALKLIKKNGALLVINSFFFE   84 (652)
T ss_pred             HHhccchHHHHHHHHHHHHHhcCCCcHhhHhhhHhh---------------hhhhhHHHHHHHHHHhcchhhhcchhhHH
Confidence            445567899999999999988752222223333332               57789999999776654431  1111122


Q ss_pred             HHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHH
Q 011249          154 MVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMY  233 (490)
Q Consensus       154 l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  233 (490)
                      -.-+..+.+..++|+..++-..+.+..+...-...+.+.|++++|.++|+.+.+.+...+...+.+-+..--.  +... 
T Consensus        85 KAYc~Yrlnk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~~a--~l~~-  161 (652)
T KOG2376|consen   85 KAYCEYRLNKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAVAA--ALQV-  161 (652)
T ss_pred             HHHHHHHcccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHH--hhhH-
Confidence            3445567899999999999655556667777788899999999999999999775554444443332211100  1111 


Q ss_pred             HHHHHcCcccChhhHHHHH---HHHhccCChHHHHHHHHHHHhcCC-------CCch-------hHHHHHHHHHHhcCCh
Q 011249          234 KVMRQENVRISEVAMVGAI---SACTQLGDVEMAAILAKHVDEGCC-------DRTN-------YVSNALIHMHSKCGYL  296 (490)
Q Consensus       234 ~~~~~~~~~p~~~~~~~l~---~~~~~~g~~~~a~~~~~~~~~~~~-------~~~~-------~~~~~l~~~~~~~~~~  296 (490)
                      +.+......| ..+|..+.   ..+...|++.+|+++++...+.+.       ..+.       ..-.-+..++...|+.
T Consensus       162 ~~~q~v~~v~-e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt  240 (652)
T KOG2376|consen  162 QLLQSVPEVP-EDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQT  240 (652)
T ss_pred             HHHHhccCCC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcch
Confidence            1122222233 33444443   356678999999999998833221       1111       1223455677788999


Q ss_pred             HHHHHHHhcccC---CChh----HHHHHHHHHHh---------------------------------------------c
Q 011249          297 DLAWREFSRIKN---KDVI----SYSSMITAFAD---------------------------------------------H  324 (490)
Q Consensus       297 ~~A~~~~~~~~~---~~~~----~~~~l~~~~~~---------------------------------------------~  324 (490)
                      ++|.+++..+.+   +|..    .-|.++..-..                                             .
T Consensus       241 ~ea~~iy~~~i~~~~~D~~~~Av~~NNLva~~~d~~~~d~~~l~~k~~~~~~l~~~~l~~Ls~~qk~~i~~N~~lL~l~t  320 (652)
T KOG2376|consen  241 AEASSIYVDIIKRNPADEPSLAVAVNNLVALSKDQNYFDGDLLKSKKSQVFKLAEFLLSKLSKKQKQAIYRNNALLALFT  320 (652)
T ss_pred             HHHHHHHHHHHHhcCCCchHHHHHhcchhhhccccccCchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999988764   1211    11111111000                                             0


Q ss_pred             CChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhc--CCCChHHHHHHHHHHHHHcCCCCC-chHHHHHHHHHhhcCChHHH
Q 011249          325 GKSQEALDMFLKMRNEGIEPNQVTFIGVLTACS--HGGLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDLLGRSGQLEKA  401 (490)
Q Consensus       325 ~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~--~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A  401 (490)
                      +..+.+.++-...  .+..|. ..+..++..+.  +......+..++....+  +.+.. ..+...++......|+++.|
T Consensus       321 nk~~q~r~~~a~l--p~~~p~-~~~~~ll~~~t~~~~~~~~ka~e~L~~~~~--~~p~~s~~v~L~~aQl~is~gn~~~A  395 (652)
T KOG2376|consen  321 NKMDQVRELSASL--PGMSPE-SLFPILLQEATKVREKKHKKAIELLLQFAD--GHPEKSKVVLLLRAQLKISQGNPEVA  395 (652)
T ss_pred             hhHHHHHHHHHhC--CccCch-HHHHHHHHHHHHHHHHHHhhhHHHHHHHhc--cCCchhHHHHHHHHHHHHhcCCHHHH
Confidence            0111111111000  011222 23333333322  11245667777777765  33333 34455667788899999999


Q ss_pred             HHHHH--------hcc-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHh----cCCC---CCchHHHHHHHHHhcCCcc
Q 011249          402 HSLIM--------DYK-DFCDAGTWGALLGACKVHVNAELGEIAARHLLE----LGPE---KTGNSALLANIYASMGKWK  465 (490)
Q Consensus       402 ~~~~~--------~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~----~~p~---~~~~~~~l~~~~~~~g~~~  465 (490)
                      .+++.        .+. ....+.+...+...+.+.++.+.|..++..++.    ..+.   -...+..++..-.+.|+-+
T Consensus       396 ~~il~~~~~~~~ss~~~~~~~P~~V~aiv~l~~~~~~~~~a~~vl~~Ai~~~~~~~t~s~~l~~~~~~aa~f~lr~G~~~  475 (652)
T KOG2376|consen  396 LEILSLFLESWKSSILEAKHLPGTVGAIVALYYKIKDNDSASAVLDSAIKWWRKQQTGSIALLSLMREAAEFKLRHGNEE  475 (652)
T ss_pred             HHHHHHHhhhhhhhhhhhccChhHHHHHHHHHHhccCCccHHHHHHHHHHHHHHhcccchHHHhHHHHHhHHHHhcCchH
Confidence            99998        443 334555666677778888888889888888875    2222   2234555666667789999


Q ss_pred             hHHHHHHHhhhccc
Q 011249          466 DSEIVKMMISETEK  479 (490)
Q Consensus       466 ~A~~~~~~~~~~~~  479 (490)
                      +|...++++.+.+.
T Consensus       476 ea~s~leel~k~n~  489 (652)
T KOG2376|consen  476 EASSLLEELVKFNP  489 (652)
T ss_pred             HHHHHHHHHHHhCC
Confidence            99999999987543

>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=99.16  E-value=7.8e-10  Score=97.61  Aligned_cols=252  Identities=13%  Similarity=0.031  Sum_probs=172.4

Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChH
Q 011249          218 VCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLD  297 (490)
Q Consensus       218 ~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  297 (490)
                      +-+.-.|++..++.-.+ ........+......+.+++...|+.+.+   ...+.+.. +|.......+...+...++-+
T Consensus         9 rn~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~v---l~ei~~~~-~~~l~av~~la~y~~~~~~~e   83 (290)
T PF04733_consen    9 RNQFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSV---LSEIKKSS-SPELQAVRLLAEYLSSPSDKE   83 (290)
T ss_dssp             HHHHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHH---HHHS-TTS-SCCCHHHHHHHHHHCTSTTHH
T ss_pred             HHHHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHH---HHHhccCC-ChhHHHHHHHHHHHhCccchH
Confidence            44556789999887665 32222223345666778888888987643   34444444 666666666665555545666


Q ss_pred             HHHHHHhcccC-C----ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHH
Q 011249          298 LAWREFSRIKN-K----DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELM  372 (490)
Q Consensus       298 ~A~~~~~~~~~-~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~  372 (490)
                      .+..-+++... +    +..........+...|++++|++++...      .+.......+..+.+.++++.|.+.++.|
T Consensus        84 ~~l~~l~~~~~~~~~~~~~~~~~~~A~i~~~~~~~~~AL~~l~~~------~~lE~~al~Vqi~L~~~R~dlA~k~l~~~  157 (290)
T PF04733_consen   84 SALEELKELLADQAGESNEIVQLLAATILFHEGDYEEALKLLHKG------GSLELLALAVQILLKMNRPDLAEKELKNM  157 (290)
T ss_dssp             CHHHHHHHCCCTS---CHHHHHHHHHHHHCCCCHHHHHHCCCTTT------TCHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccccccHHHHHHHHHHHHHcCCHHHHHHHHHcc------CcccHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            66666655432 2    2223333334667789999999988652      35566777888999999999999999999


Q ss_pred             HHHcCCCCCchHHHHHHHHHh----hcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          373 TRVFGIKPLTEHLTCMVDLLG----RSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       373 ~~~~~~~~~~~~~~~l~~~~~----~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      .+   +..| .+...++.++.    ..+.+.+|..+|+++.  ..+++.+.+.++.++...|++++|.++++++++.+|.
T Consensus       158 ~~---~~eD-~~l~qLa~awv~l~~g~e~~~~A~y~f~El~~~~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~  233 (290)
T PF04733_consen  158 QQ---IDED-SILTQLAEAWVNLATGGEKYQDAFYIFEELSDKFGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPN  233 (290)
T ss_dssp             HC---CSCC-HHHHHHHHHHHHHHHTTTCCCHHHHHHHHHHCCS--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CC
T ss_pred             Hh---cCCc-HHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccC
Confidence            75   3333 44444555443    2347999999999988  3467888899999999999999999999999999999


Q ss_pred             CCchHHHHHHHHHhcCCc-chHHHHHHHhhhcccccCCCcccc
Q 011249          447 KTGNSALLANIYASMGKW-KDSEIVKMMISETEKKKSPGCSWI  488 (490)
Q Consensus       447 ~~~~~~~l~~~~~~~g~~-~~A~~~~~~~~~~~~~~~~~~~~~  488 (490)
                      ++.++.+++-+....|+. +.+.+++.+++..    .|.+.||
T Consensus       234 ~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~----~p~h~~~  272 (290)
T PF04733_consen  234 DPDTLANLIVCSLHLGKPTEAAERYLSQLKQS----NPNHPLV  272 (290)
T ss_dssp             HHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH----TTTSHHH
T ss_pred             CHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh----CCCChHH
Confidence            999999999888999988 6677888888754    4445444

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.

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=99.16  E-value=6.8e-08  Score=90.89  Aligned_cols=191  Identities=11%  Similarity=0.121  Sum_probs=86.3

Q ss_pred             HHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHH
Q 011249          254 ACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDM  333 (490)
Q Consensus       254 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  333 (490)
                      +......|.+|..+++.+....  .....|..+.+-|...|+++.|.++|.+..     .++-.|..|.+.|+|+.|.++
T Consensus       741 aai~akew~kai~ildniqdqk--~~s~yy~~iadhyan~~dfe~ae~lf~e~~-----~~~dai~my~k~~kw~da~kl  813 (1636)
T KOG3616|consen  741 AAIGAKEWKKAISILDNIQDQK--TASGYYGEIADHYANKGDFEIAEELFTEAD-----LFKDAIDMYGKAGKWEDAFKL  813 (1636)
T ss_pred             HHhhhhhhhhhHhHHHHhhhhc--cccccchHHHHHhccchhHHHHHHHHHhcc-----hhHHHHHHHhccccHHHHHHH
Confidence            3344455555555555554442  222334445555555555555555554322     233344555555555555555


Q ss_pred             HHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCC
Q 011249          334 FLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCD  413 (490)
Q Consensus       334 ~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  413 (490)
                      -.+...  .......|..-..-..+.|++.+|.+++-.+..     |+     ..+.+|-+.|..+..+++.++-....-
T Consensus       814 a~e~~~--~e~t~~~yiakaedldehgkf~eaeqlyiti~~-----p~-----~aiqmydk~~~~ddmirlv~k~h~d~l  881 (1636)
T KOG3616|consen  814 AEECHG--PEATISLYIAKAEDLDEHGKFAEAEQLYITIGE-----PD-----KAIQMYDKHGLDDDMIRLVEKHHGDHL  881 (1636)
T ss_pred             HHHhcC--chhHHHHHHHhHHhHHhhcchhhhhheeEEccC-----ch-----HHHHHHHhhCcchHHHHHHHHhChhhh
Confidence            443321  122223333333334455555555544433211     22     123445555555555555544432222


Q ss_pred             hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHH
Q 011249          414 AGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       414 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      ..+...+..-+...|+...|++.|-++-.        +..-+++|...+.|++|.++-
T Consensus       882 ~dt~~~f~~e~e~~g~lkaae~~flea~d--------~kaavnmyk~s~lw~dayria  931 (1636)
T KOG3616|consen  882 HDTHKHFAKELEAEGDLKAAEEHFLEAGD--------FKAAVNMYKASELWEDAYRIA  931 (1636)
T ss_pred             hHHHHHHHHHHHhccChhHHHHHHHhhhh--------HHHHHHHhhhhhhHHHHHHHH
Confidence            33444444445555555555554443322        333344444445555544443

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.12  E-value=6.4e-07  Score=94.50  Aligned_cols=353  Identities=12%  Similarity=0.056  Sum_probs=216.8

Q ss_pred             HHHhcCCHHHHHHHHhhcCCCCHh--HHHHHHHHHHhCCChHHHHHHHHHhcc----CCchhHHHHHHHHHhcCChhHHH
Q 011249          126 GYTKIGLMDDAQRLFDSMAERNVI--SWSAMVAGYANCGNMKAAKEFYDRMTE----KNSVTWVAMIAGYGKCGEVREAK  199 (490)
Q Consensus       126 ~~~~~g~~~~A~~~~~~~~~~~~~--~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~A~  199 (490)
                      .+...|++.+|..........+..  ............|+++.+...++.+..    .++.........+...|++++|.
T Consensus       350 ~~~~~g~~~~Al~~a~~a~d~~~~~~ll~~~a~~l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~  429 (903)
T PRK04841        350 AWLAQGFPSEAIHHALAAGDAQLLRDILLQHGWSLFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVN  429 (903)
T ss_pred             HHHHCCCHHHHHHHHHHCCCHHHHHHHHHHhHHHHHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHH
Confidence            466677777777766655443221  122223445567788877777776631    23444444555666778888888


Q ss_pred             HHHhhcCC----C----C----HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccCh----hhHHHHHHHHhccCChHH
Q 011249          200 KVFDEISE----P----D----ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISE----VAMVGAISACTQLGDVEM  263 (490)
Q Consensus       200 ~~~~~~~~----~----~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~----~~~~~l~~~~~~~g~~~~  263 (490)
                      ..+.....    .    +    ......+...+...|++++|...+++....-...+.    .....+...+...|++++
T Consensus       430 ~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~  509 (903)
T PRK04841        430 TLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELAR  509 (903)
T ss_pred             HHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHH
Confidence            87765432    1    1    112223345566788999999888887653111121    234455556777899999


Q ss_pred             HHHHHHHHHhcCC---CC--chhHHHHHHHHHHhcCChHHHHHHHhcccC-------C----ChhHHHHHHHHHHhcCCh
Q 011249          264 AAILAKHVDEGCC---DR--TNYVSNALIHMHSKCGYLDLAWREFSRIKN-------K----DVISYSSMITAFADHGKS  327 (490)
Q Consensus       264 a~~~~~~~~~~~~---~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-------~----~~~~~~~l~~~~~~~~~~  327 (490)
                      |...+.+......   .+  .......+...+...|+++.|...+++...       +    ....+..+...+...|++
T Consensus       510 A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~  589 (903)
T PRK04841        510 ALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARL  589 (903)
T ss_pred             HHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCH
Confidence            9888887754311   11  123445566777888999999888776543       1    112344555667778999


Q ss_pred             HHHHHHHHHHHHc--CCCCc--HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHH-----HHHHHHHhhcCCh
Q 011249          328 QEALDMFLKMRNE--GIEPN--QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHL-----TCMVDLLGRSGQL  398 (490)
Q Consensus       328 ~~a~~~~~~~~~~--~~~p~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~-----~~l~~~~~~~g~~  398 (490)
                      ++|...+++....  ...+.  ...+..+...+...|+.+.|...++..............+     ...+..+...|+.
T Consensus       590 ~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  669 (903)
T PRK04841        590 DEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDK  669 (903)
T ss_pred             HHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCH
Confidence            9999888887652  11122  2344445566778899999988888876521111111111     1122444567888


Q ss_pred             HHHHHHHHhccCC--CChh----hHHHHHHHHhhhCChHHHHHHHHHHHhcC------CCCCchHHHHHHHHHhcCCcch
Q 011249          399 EKAHSLIMDYKDF--CDAG----TWGALLGACKVHVNAELGEIAARHLLELG------PEKTGNSALLANIYASMGKWKD  466 (490)
Q Consensus       399 ~~A~~~~~~~~~~--~~~~----~~~~l~~~~~~~g~~~~a~~~~~~~~~~~------p~~~~~~~~l~~~~~~~g~~~~  466 (490)
                      +.|.+++......  ....    .+..+..++...|++++|...++++....      +.....+..++.++.+.|+.++
T Consensus       670 ~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~  749 (903)
T PRK04841        670 EAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSE  749 (903)
T ss_pred             HHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHH
Confidence            9998888765521  1111    13455667788899999999999887742      1223466778888999999999


Q ss_pred             HHHHHHHhhhcc
Q 011249          467 SEIVKMMISETE  478 (490)
Q Consensus       467 A~~~~~~~~~~~  478 (490)
                      |.+.+.+..+..
T Consensus       750 A~~~L~~Al~la  761 (903)
T PRK04841        750 AQRVLLEALKLA  761 (903)
T ss_pred             HHHHHHHHHHHh
Confidence            999988887654

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=99.11  E-value=2.2e-07  Score=86.66  Aligned_cols=194  Identities=10%  Similarity=-0.036  Sum_probs=97.9

Q ss_pred             HHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCC-CCcH--HHHHHHHHHhc
Q 011249          284 NALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGI-EPNQ--VTFIGVLTACS  357 (490)
Q Consensus       284 ~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~p~~--~~~~~l~~~~~  357 (490)
                      ..+...+...|++++|...+++..+   .+...+..+..++...|++++|...+++...... .|+.  ..+..+...+.
T Consensus       118 ~~~a~~~~~~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~  197 (355)
T cd05804         118 GMLAFGLEEAGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYL  197 (355)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHH
Confidence            3444555666666666666666554   2344555566666666666666666666655311 1221  12334555566


Q ss_pred             CCCChHHHHHHHHHHHHHcCCCCCchHH-H--HHHHHHhhcCChHHHHHH--H-Hhcc-C-CCC--hhhHHHHHHHHhhh
Q 011249          358 HGGLVEDGCKQFELMTRVFGIKPLTEHL-T--CMVDLLGRSGQLEKAHSL--I-MDYK-D-FCD--AGTWGALLGACKVH  427 (490)
Q Consensus       358 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~-~--~l~~~~~~~g~~~~A~~~--~-~~~~-~-~~~--~~~~~~l~~~~~~~  427 (490)
                      ..|++++|..++++........+..... +  .++..+...|..+.+.++  + .... . +..  .........++...
T Consensus       198 ~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  277 (355)
T cd05804         198 ERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAGA  277 (355)
T ss_pred             HCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcC
Confidence            6666666666666654310101111111 1  122222333322222222  1 1111 0 101  11112344556667


Q ss_pred             CChHHHHHHHHHHHhcC-C--------CCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          428 VNAELGEIAARHLLELG-P--------EKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       428 g~~~~a~~~~~~~~~~~-p--------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      |+.+.|...++.+.... .        .........+.++...|++++|.+.+......
T Consensus       278 ~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~~  336 (355)
T cd05804         278 GDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRDD  336 (355)
T ss_pred             CCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            77777777777765522 1        12345556677778888888888888776654

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=99.10  E-value=5.7e-09  Score=95.49  Aligned_cols=217  Identities=15%  Similarity=0.078  Sum_probs=172.9

Q ss_pred             HhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHH
Q 011249          255 CTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEAL  331 (490)
Q Consensus       255 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~  331 (490)
                      +.+.|++.+|.-.|+..++.. |-+...|.-|.......++-..|+..+.+..+   .+......|.-.|...|.-..|+
T Consensus       295 lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q~~Al  373 (579)
T KOG1125|consen  295 LMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQNQAL  373 (579)
T ss_pred             HHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhHHHHH
Confidence            457788888888888888876 66778888888888888888888888887766   35567777777888888888999


Q ss_pred             HHHHHHHHcCCCCcHHHHHHHH-----------HHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHH
Q 011249          332 DMFLKMRNEGIEPNQVTFIGVL-----------TACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEK  400 (490)
Q Consensus       332 ~~~~~~~~~~~~p~~~~~~~l~-----------~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  400 (490)
                      +.++.-+...  |...   .+.           ..+.....+....++|-.+....+..+|+.+...|.-.|--.|++++
T Consensus       374 ~~L~~Wi~~~--p~y~---~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdr  448 (579)
T KOG1125|consen  374 KMLDKWIRNK--PKYV---HLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDR  448 (579)
T ss_pred             HHHHHHHHhC--ccch---hccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHH
Confidence            9888876532  1110   000           12223334556667777776655666889999999999999999999


Q ss_pred             HHHHHHhcc-CC-CChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          401 AHSLIMDYK-DF-CDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       401 A~~~~~~~~-~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      |++.|+... .+ .|...||.|...+....+.++|+..|.+++++.|....+.+.|+-.|...|.|++|.+.|=..+..
T Consensus       449 aiDcf~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~m  527 (579)
T KOG1125|consen  449 AVDCFEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALSM  527 (579)
T ss_pred             HHHHHHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHHh
Confidence            999998877 44 467799999999999999999999999999999999999999999999999999999998766554

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=99.08  E-value=4.2e-07  Score=84.78  Aligned_cols=290  Identities=11%  Similarity=0.007  Sum_probs=151.5

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHHHhccC---Cch---hHHHHHHHHHhcCChhHHHHHHhhcCC--C-CHHhHHHHHHHH
Q 011249          150 SWSAMVAGYANCGNMKAAKEFYDRMTEK---NSV---TWVAMIAGYGKCGEVREAKKVFDEISE--P-DASCWAAMTVCY  220 (490)
Q Consensus       150 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~---~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l~~~~  220 (490)
                      .|..+...+...|+.+.+.+.+.+..+.   +..   ........+...|++++|.+.+++..+  | +...+.. ...+
T Consensus         8 a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~-~~~~   86 (355)
T cd05804           8 GHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDYPRDLLALKL-HLGA   86 (355)
T ss_pred             HHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHH-hHHH
Confidence            4445555555566666655555544321   111   112223344556677777776666543  2 2223331 1122


Q ss_pred             Hh----cCChHHHHHHHHHHHHcCcccCh-hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCC
Q 011249          221 VQ----NGYAKAAIEMYKVMRQENVRISE-VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGY  295 (490)
Q Consensus       221 ~~----~g~~~~A~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  295 (490)
                      ..    .+..+.+.+.+..  .....|+. .....+...+...|++++|...+++..+.. +.+...+..+..++...|+
T Consensus        87 ~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~  163 (355)
T cd05804          87 FGLGDFSGMRDHVARVLPL--WAPENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGR  163 (355)
T ss_pred             HHhcccccCchhHHHHHhc--cCcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCC
Confidence            22    3344444444433  11112222 233345556677777777777777777765 4556666777777777788


Q ss_pred             hHHHHHHHhcccC--C---Ch--hHHHHHHHHHHhcCChHHHHHHHHHHHHcCC-CCcHHHH-H--HHHHHhcCCCChHH
Q 011249          296 LDLAWREFSRIKN--K---DV--ISYSSMITAFADHGKSQEALDMFLKMRNEGI-EPNQVTF-I--GVLTACSHGGLVED  364 (490)
Q Consensus       296 ~~~A~~~~~~~~~--~---~~--~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~p~~~~~-~--~l~~~~~~~g~~~~  364 (490)
                      +++|...+++..+  |   +.  ..|..+...+...|++++|..++++...... .+..... .  .++.-+...|....
T Consensus       164 ~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~  243 (355)
T cd05804         164 FKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDV  243 (355)
T ss_pred             HHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCCh
Confidence            8888777776654  1   11  2344566777788888888888888754321 1111111 1  22222333343332


Q ss_pred             HHHHHHHHHHHc--CCCCC--chHHHHHHHHHhhcCChHHHHHHHHhccC--CC---C------hhhHHHHHHHHhhhCC
Q 011249          365 GCKQFELMTRVF--GIKPL--TEHLTCMVDLLGRSGQLEKAHSLIMDYKD--FC---D------AGTWGALLGACKVHVN  429 (490)
Q Consensus       365 a~~~~~~~~~~~--~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~---~------~~~~~~l~~~~~~~g~  429 (490)
                      +... +.+....  ..+..  .........++...|+.++|..+++.+..  ..   .      .........++...|+
T Consensus       244 ~~~w-~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~  322 (355)
T cd05804         244 GDRW-EDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGN  322 (355)
T ss_pred             HHHH-HHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCC
Confidence            2222 2221100  11111  11122456677788888888888877651  11   1      1112222344568899


Q ss_pred             hHHHHHHHHHHHhcC
Q 011249          430 AELGEIAARHLLELG  444 (490)
Q Consensus       430 ~~~a~~~~~~~~~~~  444 (490)
                      .++|.+.+..++...
T Consensus       323 ~~~A~~~L~~al~~a  337 (355)
T cd05804         323 YATALELLGPVRDDL  337 (355)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999999998887643

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.

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=99.04  E-value=2.1e-08  Score=83.68  Aligned_cols=150  Identities=10%  Similarity=-0.004  Sum_probs=106.2

Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCCh
Q 011249          319 TAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQL  398 (490)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  398 (490)
                      ..|...|+++.+....+.+..    |.        ..+...++.+++...++...+  ..+.+...|..+...|...|++
T Consensus        24 ~~Y~~~g~~~~v~~~~~~~~~----~~--------~~~~~~~~~~~~i~~l~~~L~--~~P~~~~~w~~Lg~~~~~~g~~   89 (198)
T PRK10370         24 GSYLLSPKWQAVRAEYQRLAD----PL--------HQFASQQTPEAQLQALQDKIR--ANPQNSEQWALLGEYYLWRNDY   89 (198)
T ss_pred             HHHHHcchHHHHHHHHHHHhC----cc--------ccccCchhHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHHCCCH
Confidence            356777777776444322211    11        012235666777777777776  4566777888888888888888


Q ss_pred             HHHHHHHHhcc--CCCChhhHHHHHHHH-hhhCC--hHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHH
Q 011249          399 EKAHSLIMDYK--DFCDAGTWGALLGAC-KVHVN--AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMM  473 (490)
Q Consensus       399 ~~A~~~~~~~~--~~~~~~~~~~l~~~~-~~~g~--~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~  473 (490)
                      ++|...|++..  .+.+...+..+..++ ...|+  .++|.++++++++.+|+++.++..++..+.+.|++++|...+++
T Consensus        90 ~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~  169 (198)
T PRK10370         90 DNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDANEVTALMLLASDAFMQADYAQAIELWQK  169 (198)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            88888887766  344666777777754 56666  48888888888888888888888888888888888888888888


Q ss_pred             hhhcccccC
Q 011249          474 ISETEKKKS  482 (490)
Q Consensus       474 ~~~~~~~~~  482 (490)
                      +.+.....+
T Consensus       170 aL~l~~~~~  178 (198)
T PRK10370        170 VLDLNSPRV  178 (198)
T ss_pred             HHhhCCCCc
Confidence            877655433

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=99.03  E-value=4e-06  Score=80.38  Aligned_cols=308  Identities=13%  Similarity=0.155  Sum_probs=179.0

Q ss_pred             CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCC-----------CCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCC
Q 011249           31 HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPK-----------CKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGV   99 (490)
Q Consensus        31 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~-----------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~   99 (490)
                      .+..  +|..+.++|.+..+ ++-|.-.+-.|..           .+....=..........|..++|..+|.+-.+.. 
T Consensus       755 kS~~--vW~nmA~McVkT~R-LDVAkVClGhm~~aRgaRAlR~a~q~~~e~eakvAvLAieLgMlEeA~~lYr~ckR~D-  830 (1416)
T KOG3617|consen  755 KSDS--VWDNMASMCVKTRR-LDVAKVCLGHMKNARGARALRRAQQNGEEDEAKVAVLAIELGMLEEALILYRQCKRYD-  830 (1416)
T ss_pred             hhhH--HHHHHHHHhhhhcc-ccHHHHhhhhhhhhhhHHHHHHHHhCCcchhhHHHHHHHHHhhHHHHHHHHHHHHHHH-
Confidence            3455  89999999999998 8888877766641           1111222233334456799999999999887741 


Q ss_pred             CCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCC-HhHHHHHHHHHHhCCChHHHHHHHHHhcc--
Q 011249          100 LTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERN-VISWSAMVAGYANCGNMKAAKEFYDRMTE--  176 (490)
Q Consensus       100 ~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--  176 (490)
                               +++             ..|-..|.+++|.++-+.-.+-. ..||......+-..+|.+.|++.|++...  
T Consensus       831 ---------LlN-------------KlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear~Di~~AleyyEK~~~ha  888 (1416)
T KOG3617|consen  831 ---------LLN-------------KLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEARRDIEAALEYYEKAGVHA  888 (1416)
T ss_pred             ---------HHH-------------HHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhhccHHHHHHHHHhcCChH
Confidence                     222             23677899999988876554422 24666677777788888888888887642  


Q ss_pred             ---------------------CCchhHHHHHHHHHhcCChhHHHHHHhhcCC------------------------CCHH
Q 011249          177 ---------------------KNSVTWVAMIAGYGKCGEVREAKKVFDEISE------------------------PDAS  211 (490)
Q Consensus       177 ---------------------~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~------------------------~~~~  211 (490)
                                           +|...|......+-..|+.|.|+.+|.....                        .|..
T Consensus       889 fev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D~fs~VrI~C~qGk~~kAa~iA~esgd~A  968 (1416)
T KOG3617|consen  889 FEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKDYFSMVRIKCIQGKTDKAARIAEESGDKA  968 (1416)
T ss_pred             HHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhhhhhheeeEeeccCchHHHHHHHhcccHH
Confidence                                 1555666677777778888888888876542                        3445


Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcC--ccc--ChhhHHHHHHHHhcc--CChHHHHHHHHHHHhcCCCCchhHHHH
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQEN--VRI--SEVAMVGAISACTQL--GDVEMAAILAKHVDEGCCDRTNYVSNA  285 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~p--~~~~~~~l~~~~~~~--g~~~~a~~~~~~~~~~~~~~~~~~~~~  285 (490)
                      ....|.+.|-..|++.+|..+|.+.+.-.  ++.  ....-..|.+.+...  .+.-.|-.+|++.   |.     -...
T Consensus       969 AcYhlaR~YEn~g~v~~Av~FfTrAqafsnAIRlcKEnd~~d~L~nlal~s~~~d~v~aArYyEe~---g~-----~~~~ 1040 (1416)
T KOG3617|consen  969 ACYHLARMYENDGDVVKAVKFFTRAQAFSNAIRLCKENDMKDRLANLALMSGGSDLVSAARYYEEL---GG-----YAHK 1040 (1416)
T ss_pred             HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhhcCchhHHHHHHHHHHc---ch-----hhhH
Confidence            55567777777777777777776654210  000  000011112222111  1222333333332   10     1112


Q ss_pred             HHHHHHhcCChHHHHHHHhccc---------C-----CChhHHHHHHHHHHhcCChHHHHHHHHHHHHc----------C
Q 011249          286 LIHMHSKCGYLDLAWREFSRIK---------N-----KDVISYSSMITAFADHGKSQEALDMFLKMRNE----------G  341 (490)
Q Consensus       286 l~~~~~~~~~~~~A~~~~~~~~---------~-----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----------~  341 (490)
                      .+..|-+.|.+.+|+++--.-.         +     .|+...+.-.+.+....++++|..++-...+.          |
T Consensus      1041 AVmLYHkAGm~~kALelAF~tqQf~aL~lIa~DLd~~sDp~ll~RcadFF~~~~qyekAV~lL~~ar~~~~AlqlC~~~n 1120 (1416)
T KOG3617|consen 1041 AVMLYHKAGMIGKALELAFRTQQFSALDLIAKDLDAGSDPKLLRRCADFFENNQQYEKAVNLLCLAREFSGALQLCKNRN 1120 (1416)
T ss_pred             HHHHHHhhcchHHHHHHHHhhcccHHHHHHHHhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            3445666676666655421111         1     36666666666666667777776655443321          1


Q ss_pred             ----------------CCCcH----HHHHHHHHHhcCCCChHHHHHHHHHH
Q 011249          342 ----------------IEPNQ----VTFIGVLTACSHGGLVEDGCKQFELM  372 (490)
Q Consensus       342 ----------------~~p~~----~~~~~l~~~~~~~g~~~~a~~~~~~~  372 (490)
                                      -.|+.    .....+...|.++|.+..|-+-|.+.
T Consensus      1121 v~vtee~aE~mTp~Kd~~~~e~~R~~vLeqvae~c~qQG~Yh~AtKKfTQA 1171 (1416)
T KOG3617|consen 1121 VRVTEEFAELMTPTKDDMPNEQERKQVLEQVAELCLQQGAYHAATKKFTQA 1171 (1416)
T ss_pred             CchhHHHHHhcCcCcCCCccHHHHHHHHHHHHHHHHhccchHHHHHHHhhh
Confidence                            11222    24555666677777777776666555

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=99.03  E-value=4.6e-07  Score=77.90  Aligned_cols=281  Identities=15%  Similarity=0.080  Sum_probs=207.5

Q ss_pred             HHHHhcCCHHHHHHHHhhcCCCCHhHHHHHH---HHHHhCCChHHHHHHHHHhccCCchhHH---HHHHHHHhcCChhHH
Q 011249          125 CGYTKIGLMDDAQRLFDSMAERNVISWSAMV---AGYANCGNMKAAKEFYDRMTEKNSVTWV---AMIAGYGKCGEVREA  198 (490)
Q Consensus       125 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~---~~~~~~~~~~~a~~~~~~~~~~~~~~~~---~l~~~~~~~~~~~~A  198 (490)
                      ..+...|++.+|+.-|....+-|+..|.++.   ..|...|+-..|+.-+.+.++..+..+.   .-...+.+.|.++.|
T Consensus        46 k~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVlelKpDF~~ARiQRg~vllK~Gele~A  125 (504)
T KOG0624|consen   46 KELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLELKPDFMAARIQRGVVLLKQGELEQA  125 (504)
T ss_pred             HHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCCccchhhHHHHHhcCccHHHHHHHhchhhhhcccHHHH
Confidence            3466779999999999999987777776654   5688899999999999988864433333   334578899999999


Q ss_pred             HHHHhhcCC--CC--------------HHhH--HHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCC
Q 011249          199 KKVFDEISE--PD--------------ASCW--AAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGD  260 (490)
Q Consensus       199 ~~~~~~~~~--~~--------------~~~~--~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  260 (490)
                      ..-|+.+.+  |+              ...|  ...+..+...|+...|+.....+.+.. +-|...+..-..+|...|+
T Consensus       126 ~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~-~Wda~l~~~Rakc~i~~~e  204 (504)
T KOG0624|consen  126 EADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ-PWDASLRQARAKCYIAEGE  204 (504)
T ss_pred             HHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC-cchhHHHHHHHHHHHhcCc
Confidence            999998865  21              1112  223445667899999999999998753 3377788888889999999


Q ss_pred             hHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--CChh----HHHHH---------HHHHHhcC
Q 011249          261 VEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KDVI----SYSSM---------ITAFADHG  325 (490)
Q Consensus       261 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~----~~~~l---------~~~~~~~~  325 (490)
                      +..|+.-++.+.+.. ..+...+--+...+...|+.+.++...++-.+  ||-.    .|..+         +......+
T Consensus       205 ~k~AI~Dlk~askLs-~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLKldpdHK~Cf~~YKklkKv~K~les~e~~ie~~  283 (504)
T KOG0624|consen  205 PKKAIHDLKQASKLS-QDNTEGHYKISQLLYTVGDAENSLKEIRECLKLDPDHKLCFPFYKKLKKVVKSLESAEQAIEEK  283 (504)
T ss_pred             HHHHHHHHHHHHhcc-ccchHHHHHHHHHHHhhhhHHHHHHHHHHHHccCcchhhHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            999999998888776 44555555677888888999999888887766  3221    12211         12344567


Q ss_pred             ChHHHHHHHHHHHHcCCCCcHH---HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHH
Q 011249          326 KSQEALDMFLKMRNEGIEPNQV---TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAH  402 (490)
Q Consensus       326 ~~~~a~~~~~~~~~~~~~p~~~---~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  402 (490)
                      +|-+++...+...+........   .+..+-.++...|++.+|++...++..  -.+.|+.++..-..+|.-...++.|+
T Consensus       284 ~~t~cle~ge~vlk~ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~--~d~~dv~~l~dRAeA~l~dE~YD~AI  361 (504)
T KOG0624|consen  284 HWTECLEAGEKVLKNEPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLD--IDPDDVQVLCDRAEAYLGDEMYDDAI  361 (504)
T ss_pred             hHHHHHHHHHHHHhcCCcccceeeeeeheeeecccccCCHHHHHHHHHHHHh--cCchHHHHHHHHHHHHhhhHHHHHHH
Confidence            8888888888887753221222   345555667888999999999999976  33444888888889999999999999


Q ss_pred             HHHHhcc
Q 011249          403 SLIMDYK  409 (490)
Q Consensus       403 ~~~~~~~  409 (490)
                      .-|+...
T Consensus       362 ~dye~A~  368 (504)
T KOG0624|consen  362 HDYEKAL  368 (504)
T ss_pred             HHHHHHH
Confidence            9998877

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=99.01  E-value=1e-06  Score=83.22  Aligned_cols=188  Identities=15%  Similarity=0.185  Sum_probs=102.5

Q ss_pred             HHHHHhCCChHHHHHHHHHhccCC--chhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHH
Q 011249          155 VAGYANCGNMKAAKEFYDRMTEKN--SVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEM  232 (490)
Q Consensus       155 ~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  232 (490)
                      +.+.....++.+|+.+++.+...+  ..-|..+.+.|...|+++.|.++|.+..     .++--|..|.+.|+|+.|.++
T Consensus       739 ieaai~akew~kai~ildniqdqk~~s~yy~~iadhyan~~dfe~ae~lf~e~~-----~~~dai~my~k~~kw~da~kl  813 (1636)
T KOG3616|consen  739 IEAAIGAKEWKKAISILDNIQDQKTASGYYGEIADHYANKGDFEIAEELFTEAD-----LFKDAIDMYGKAGKWEDAFKL  813 (1636)
T ss_pred             HHHHhhhhhhhhhHhHHHHhhhhccccccchHHHHHhccchhHHHHHHHHHhcc-----hhHHHHHHHhccccHHHHHHH
Confidence            344555666667777776666542  2345666667777777777777775542     344556667777777777666


Q ss_pred             HHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCC-Ch
Q 011249          233 YKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK-DV  311 (490)
Q Consensus       233 ~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-~~  311 (490)
                      -.+..  |.......|..-..-+-..|++.+|+++|-.+.    .|+.     .|.+|-+.|..++.+++.++-... -.
T Consensus       814 a~e~~--~~e~t~~~yiakaedldehgkf~eaeqlyiti~----~p~~-----aiqmydk~~~~ddmirlv~k~h~d~l~  882 (1636)
T KOG3616|consen  814 AEECH--GPEATISLYIAKAEDLDEHGKFAEAEQLYITIG----EPDK-----AIQMYDKHGLDDDMIRLVEKHHGDHLH  882 (1636)
T ss_pred             HHHhc--CchhHHHHHHHhHHhHHhhcchhhhhheeEEcc----CchH-----HHHHHHhhCcchHHHHHHHHhChhhhh
Confidence            54443  223344455555555556666666666553321    2222     355666666666666666544321 12


Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHH
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCK  367 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~  367 (490)
                      .+...+..-|-..|+...|+..|-+..+         |..-+..|...+.|++|.+
T Consensus       883 dt~~~f~~e~e~~g~lkaae~~flea~d---------~kaavnmyk~s~lw~dayr  929 (1636)
T KOG3616|consen  883 DTHKHFAKELEAEGDLKAAEEHFLEAGD---------FKAAVNMYKASELWEDAYR  929 (1636)
T ss_pred             HHHHHHHHHHHhccChhHHHHHHHhhhh---------HHHHHHHhhhhhhHHHHHH
Confidence            3444455555566666666665544332         3333444444555554443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.99  E-value=4.8e-08  Score=85.07  Aligned_cols=182  Identities=11%  Similarity=-0.003  Sum_probs=118.2

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHhcccC--CC-h---hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcH----H
Q 011249          278 RTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KD-V---ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQ----V  347 (490)
Q Consensus       278 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~-~---~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~----~  347 (490)
                      .....+..++..+...|+++.|...|+++.+  |+ +   ..+..+..++...|++++|...++++.+.  .|+.    .
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~  108 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRL--HPNHPDADY  108 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCCchHH
Confidence            3445566677777778888888888877655  22 1   35566777777888888888888887764  3321    1


Q ss_pred             HHHHHHHHhcCC--------CChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHH
Q 011249          348 TFIGVLTACSHG--------GLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGA  419 (490)
Q Consensus       348 ~~~~l~~~~~~~--------g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  419 (490)
                      .+..+..++...        |+.++|.+.++.+.+.  .+.+...+..+...    +......           ......
T Consensus       109 a~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~----~~~~~~~-----------~~~~~~  171 (235)
T TIGR03302       109 AYYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRM----DYLRNRL-----------AGKELY  171 (235)
T ss_pred             HHHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHH----HHHHHHH-----------HHHHHH
Confidence            344444445433        5677777777777663  22222222211111    0000000           001124


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCC---chHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKT---GNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      +...+...|++++|+..++++++..|+++   .++..++.++.+.|++++|..+++.+....
T Consensus       172 ~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~  233 (235)
T TIGR03302       172 VARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGANY  233 (235)
T ss_pred             HHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            55678899999999999999999877654   688999999999999999999999887653

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).

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.99  E-value=2.7e-05  Score=76.57  Aligned_cols=144  Identities=15%  Similarity=0.204  Sum_probs=110.1

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHH
Q 011249          310 DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMV  389 (490)
Q Consensus       310 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  389 (490)
                      .+..|..+..+-.+.|...+|++-|-+      .-|+..|..+++.+.+.|.+++-.+++...+++ .-.|...  ..|+
T Consensus      1103 ~p~vWsqlakAQL~~~~v~dAieSyik------adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk-~~E~~id--~eLi 1173 (1666)
T KOG0985|consen 1103 EPAVWSQLAKAQLQGGLVKDAIESYIK------ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKK-VREPYID--SELI 1173 (1666)
T ss_pred             ChHHHHHHHHHHHhcCchHHHHHHHHh------cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHh-hcCccch--HHHH
Confidence            456788888888888888888776654      236678899999999999999999999988885 6666655  5688


Q ss_pred             HHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHH
Q 011249          390 DLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEI  469 (490)
Q Consensus       390 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~  469 (490)
                      .+|++.++..+-.+++    ..|+......+..-|...|.++.|.-+|..        .+-|..|+..+...|+++.|..
T Consensus      1174 ~AyAkt~rl~elE~fi----~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~--------vSN~a~La~TLV~LgeyQ~AVD 1241 (1666)
T KOG0985|consen 1174 FAYAKTNRLTELEEFI----AGPNVANIQQVGDRCFEEKMYEAAKLLYSN--------VSNFAKLASTLVYLGEYQGAVD 1241 (1666)
T ss_pred             HHHHHhchHHHHHHHh----cCCCchhHHHHhHHHhhhhhhHHHHHHHHH--------hhhHHHHHHHHHHHHHHHHHHH
Confidence            9999999988876654    357777777888888888888888777763        4446677777777777777776


Q ss_pred             HHHHh
Q 011249          470 VKMMI  474 (490)
Q Consensus       470 ~~~~~  474 (490)
                      .-++.
T Consensus      1242 ~aRKA 1246 (1666)
T KOG0985|consen 1242 AARKA 1246 (1666)
T ss_pred             Hhhhc
Confidence            65543

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.97  E-value=3.9e-06  Score=88.66  Aligned_cols=319  Identities=9%  Similarity=-0.056  Sum_probs=211.2

Q ss_pred             HHHHhcCCHHHHHHHHhhcCC----CCHhHHHHHHHHHHhCCChHHHHHHHHHhccC----C---c-----hhHHHHHHH
Q 011249          125 CGYTKIGLMDDAQRLFDSMAE----RNVISWSAMVAGYANCGNMKAAKEFYDRMTEK----N---S-----VTWVAMIAG  188 (490)
Q Consensus       125 ~~~~~~g~~~~A~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~---~-----~~~~~l~~~  188 (490)
                      ......|+++.+..+++.+..    .+..........+...|+++++...+......    +   .     .....+...
T Consensus       382 ~~l~~~g~~~~l~~~l~~lp~~~~~~~~~l~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~  461 (903)
T PRK04841        382 WSLFNQGELSLLEECLNALPWEVLLENPRLVLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQV  461 (903)
T ss_pred             HHHHhcCChHHHHHHHHhCCHHHHhcCcchHHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHH
Confidence            345667888888888887742    23333344555667889999999998876531    1   1     112233455


Q ss_pred             HHhcCChhHHHHHHhhcCC----CCH----HhHHHHHHHHHhcCChHHHHHHHHHHHHc----Cc-ccChhhHHHHHHHH
Q 011249          189 YGKCGEVREAKKVFDEISE----PDA----SCWAAMTVCYVQNGYAKAAIEMYKVMRQE----NV-RISEVAMVGAISAC  255 (490)
Q Consensus       189 ~~~~~~~~~A~~~~~~~~~----~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~-~p~~~~~~~l~~~~  255 (490)
                      +...|++++|...+++...    .+.    ...+.+...+...|++++|...+++....    |. .+...++..+...+
T Consensus       462 ~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~  541 (903)
T PRK04841        462 AINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEIL  541 (903)
T ss_pred             HHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHH
Confidence            6788999999999887543    221    34566777788899999999999888642    11 11123455667778


Q ss_pred             hccCChHHHHHHHHHHHhc----CCCC---chhHHHHHHHHHHhcCChHHHHHHHhcccC------C--ChhHHHHHHHH
Q 011249          256 TQLGDVEMAAILAKHVDEG----CCDR---TNYVSNALIHMHSKCGYLDLAWREFSRIKN------K--DVISYSSMITA  320 (490)
Q Consensus       256 ~~~g~~~~a~~~~~~~~~~----~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~------~--~~~~~~~l~~~  320 (490)
                      ...|+++.|...+++....    +.+.   ....+..+...+...|++++|...+.+...      +  ....+..+...
T Consensus       542 ~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~  621 (903)
T PRK04841        542 FAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKI  621 (903)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHH
Confidence            8999999999998876542    2111   223345566777888999999988887643      1  12344556667


Q ss_pred             HHhcCChHHHHHHHHHHHHcC--CCCcHH--HH--HHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchH----HHHHHH
Q 011249          321 FADHGKSQEALDMFLKMRNEG--IEPNQV--TF--IGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEH----LTCMVD  390 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~--~~p~~~--~~--~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~----~~~l~~  390 (490)
                      +...|++++|...++++....  ......  ..  ...+..+...|+.+.|...+......  .......    ...+..
T Consensus       622 ~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~--~~~~~~~~~~~~~~~a~  699 (903)
T PRK04841        622 SLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKP--EFANNHFLQGQWRNIAR  699 (903)
T ss_pred             HHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCC--CCccchhHHHHHHHHHH
Confidence            888999999999998886521  111110  11  11123345578999999887776431  1111111    345777


Q ss_pred             HHhhcCChHHHHHHHHhcc-------CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCC
Q 011249          391 LLGRSGQLEKAHSLIMDYK-------DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGP  445 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~~~-------~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p  445 (490)
                      ++...|++++|...+++..       ... ...+...+..++...|+.++|...+.++++...
T Consensus       700 ~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la~  762 (903)
T PRK04841        700 AQILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLAN  762 (903)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhC
Confidence            8889999999999998765       111 123556667788899999999999999998663

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=98.97  E-value=3.9e-06  Score=80.46  Aligned_cols=240  Identities=14%  Similarity=0.138  Sum_probs=146.7

Q ss_pred             HHHHHHH--HHhcCCCCHHHHHHHhccCCCCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhc
Q 011249           37 YAQFLIR--LLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACA  114 (490)
Q Consensus        37 ~~~~l~~--~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~  114 (490)
                      +-..+++  .|.--|+ .+.|.+-.+.+.+.   ..|..+.+.|.+.++.+-|.-.+-.|....   .   -..+=.+ .
T Consensus       728 TRkaml~FSfyvtiG~-MD~AfksI~~IkS~---~vW~nmA~McVkT~RLDVAkVClGhm~~aR---g---aRAlR~a-~  796 (1416)
T KOG3617|consen  728 TRKAMLDFSFYVTIGS-MDAAFKSIQFIKSD---SVWDNMASMCVKTRRLDVAKVCLGHMKNAR---G---ARALRRA-Q  796 (1416)
T ss_pred             HHHhhhceeEEEEecc-HHHHHHHHHHHhhh---HHHHHHHHHhhhhccccHHHHhhhhhhhhh---h---HHHHHHH-H
Confidence            4455544  5677788 89888888777653   679999999999999998888887775421   0   1111111 1


Q ss_pred             CCC-ChHHHHHHHHHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccC-CchhHHHHHHHHHhc
Q 011249          115 RVP-SLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEK-NSVTWVAMIAGYGKC  192 (490)
Q Consensus       115 ~~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~l~~~~~~~  192 (490)
                      ..+ +....+.-.-...|.+++|+.++.+-.+     |..|=..|...|.+++|+++-+.-.+- =..||......+-..
T Consensus       797 q~~~e~eakvAvLAieLgMlEeA~~lYr~ckR-----~DLlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear  871 (1416)
T KOG3617|consen  797 QNGEEDEAKVAVLAIELGMLEEALILYRQCKR-----YDLLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEAR  871 (1416)
T ss_pred             hCCcchhhHHHHHHHHHhhHHHHHHHHHHHHH-----HHHHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhh
Confidence            111 1112222234567888999988887654     334556677788999998887654432 234666677777778


Q ss_pred             CChhHHHHHHhhcCCC-----------------------CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHH
Q 011249          193 GEVREAKKVFDEISEP-----------------------DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMV  249 (490)
Q Consensus       193 ~~~~~A~~~~~~~~~~-----------------------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~  249 (490)
                      +|.+.|++.|++...+                       |...|.-...-.-..|+.+.|+.+|...+.         |.
T Consensus       872 ~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D---------~f  942 (1416)
T KOG3617|consen  872 RDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD---------YF  942 (1416)
T ss_pred             ccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh---------hh
Confidence            8888888888876532                       222233333333344555555555544432         34


Q ss_pred             HHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhccc
Q 011249          250 GAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIK  307 (490)
Q Consensus       250 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  307 (490)
                      .+++..+-.|+.++|.++-++      ..|......|.+.|...|++.+|..+|.+..
T Consensus       943 s~VrI~C~qGk~~kAa~iA~e------sgd~AAcYhlaR~YEn~g~v~~Av~FfTrAq  994 (1416)
T KOG3617|consen  943 SMVRIKCIQGKTDKAARIAEE------SGDKAACYHLARMYENDGDVVKAVKFFTRAQ  994 (1416)
T ss_pred             hheeeEeeccCchHHHHHHHh------cccHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence            455555566666666665443      2244444557777777777777777776543

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.96  E-value=3.6e-07  Score=77.00  Aligned_cols=302  Identities=13%  Similarity=0.068  Sum_probs=146.8

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCC--CCHHhHHH-HHHHHHhcC
Q 011249          151 WSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISE--PDASCWAA-MTVCYVQNG  224 (490)
Q Consensus       151 ~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~-l~~~~~~~g  224 (490)
                      +.+.+..+.+..+++.|++++..-.+.   +......+..+|....++..|-..++++..  |...-|.. -...+-+.+
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~P~~~qYrlY~AQSLY~A~   92 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERSPRSRAGLSLLGYCYYRLQEFALAAECYEQLGQLHPELEQYRLYQAQSLYKAC   92 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhChHHHHHHHHHHHHHHHhc
Confidence            344445556666777777776665543   334456666667777777777777776655  43333332 234555666


Q ss_pred             ChHHHHHHHHHHHHcCcccChh--hHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHH
Q 011249          225 YAKAAIEMYKVMRQENVRISEV--AMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWRE  302 (490)
Q Consensus       225 ~~~~A~~~~~~~~~~~~~p~~~--~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  302 (490)
                      .+..|+++...|...   |+..  ....-.......+++..+..+.++....+   +..+.+.......+.|+++.|.+-
T Consensus        93 i~ADALrV~~~~~D~---~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en---~Ad~~in~gCllykegqyEaAvqk  166 (459)
T KOG4340|consen   93 IYADALRVAFLLLDN---PALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSEN---EADGQINLGCLLYKEGQYEAAVQK  166 (459)
T ss_pred             ccHHHHHHHHHhcCC---HHHHHHHHHHHHHHhcccccCcchHHHHHhccCCC---ccchhccchheeeccccHHHHHHH
Confidence            777777776666542   1111  11111112334566666666666554322   233333344445566666666666


Q ss_pred             HhcccC----CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHH-HHHHHHHh--cCCCChHHHHHHHHHHHHH
Q 011249          303 FSRIKN----KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVT-FIGVLTAC--SHGGLVEDGCKQFELMTRV  375 (490)
Q Consensus       303 ~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~-~~~l~~~~--~~~g~~~~a~~~~~~~~~~  375 (490)
                      |+...+    .....|+..+.. .+.|+++.|+++..+++++|++-.+.. ......+-  ...|+.   ..+....   
T Consensus       167 FqaAlqvsGyqpllAYniALaH-y~~~qyasALk~iSEIieRG~r~HPElgIGm~tegiDvrsvgNt---~~lh~Sa---  239 (459)
T KOG4340|consen  167 FQAALQVSGYQPLLAYNLALAH-YSSRQYASALKHISEIIERGIRQHPELGIGMTTEGIDVRSVGNT---LVLHQSA---  239 (459)
T ss_pred             HHHHHhhcCCCchhHHHHHHHH-HhhhhHHHHHHHHHHHHHhhhhcCCccCccceeccCchhcccch---HHHHHHH---
Confidence            666554    233445544433 345666666666666666665432110 00000000  000000   0000000   


Q ss_pred             cCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc----CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchH
Q 011249          376 FGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK----DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       376 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                           -...+|.-.-.+.+.|+++.|.+.+..|+    ...|+.|...+.-. -..+++....+-+.-+++++|-.+.++
T Consensus       240 -----l~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~-n~~~~p~~g~~KLqFLL~~nPfP~ETF  313 (459)
T KOG4340|consen  240 -----LVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALM-NMDARPTEGFEKLQFLLQQNPFPPETF  313 (459)
T ss_pred             -----HHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHh-cccCCccccHHHHHHHHhcCCCChHHH
Confidence                 01112222233445666666666666665    22344454444321 123444455555555555666555566


Q ss_pred             HHHHHHHHhcCCcchHHHHH
Q 011249          452 ALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       452 ~~l~~~~~~~g~~~~A~~~~  471 (490)
                      .++.-.|++..-++-|-.++
T Consensus       314 ANlLllyCKNeyf~lAADvL  333 (459)
T KOG4340|consen  314 ANLLLLYCKNEYFDLAADVL  333 (459)
T ss_pred             HHHHHHHhhhHHHhHHHHHH
Confidence            66666666665555555544

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.95  E-value=2.3e-08  Score=78.88  Aligned_cols=122  Identities=10%  Similarity=-0.017  Sum_probs=83.3

Q ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--
Q 011249          332 DMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--  409 (490)
Q Consensus       332 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--  409 (490)
                      .++++..+  +.|+.  +......+...|++++|...|+.+..  --+.+...+..+..++.+.|++++|...|+...  
T Consensus        14 ~~~~~al~--~~p~~--~~~~g~~~~~~g~~~~A~~~~~~al~--~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l   87 (144)
T PRK15359         14 DILKQLLS--VDPET--VYASGYASWQEGDYSRAVIDFSWLVM--AQPWSWRAHIALAGTWMMLKEYTTAINFYGHALML   87 (144)
T ss_pred             HHHHHHHH--cCHHH--HHHHHHHHHHcCCHHHHHHHHHHHHH--cCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhc
Confidence            44555554  34443  33455566777777777777777765  344566677777777777777777777777665  


Q ss_pred             CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          410 DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       410 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      .+.++..+..+..++...|++++|+..|+++++..|+++..+...+.+..
T Consensus        88 ~p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~p~~~~~~~~~~~~~~  137 (144)
T PRK15359         88 DASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKMSYADASWSEIRQNAQI  137 (144)
T ss_pred             CCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH
Confidence            34456677777777777777777777777777777777777776666544

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.95  E-value=2.5e-06  Score=83.44  Aligned_cols=239  Identities=15%  Similarity=0.116  Sum_probs=145.4

Q ss_pred             CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 011249          209 DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIH  288 (490)
Q Consensus       209 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  288 (490)
                      .+..|..+..+-.+.|...+|++-|-+.      -|+..|..++..+.+.|.+++-.+++..+++....|.+.  ..|+-
T Consensus      1103 ~p~vWsqlakAQL~~~~v~dAieSyika------dDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id--~eLi~ 1174 (1666)
T KOG0985|consen 1103 EPAVWSQLAKAQLQGGLVKDAIESYIKA------DDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYID--SELIF 1174 (1666)
T ss_pred             ChHHHHHHHHHHHhcCchHHHHHHHHhc------CCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccch--HHHHH
Confidence            3457888888888888888888766442      266778888888888888888888887777765555444  46788


Q ss_pred             HHHhcCChHHHHHHHhcccC-----------------------CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc
Q 011249          289 MHSKCGYLDLAWREFSRIKN-----------------------KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN  345 (490)
Q Consensus       289 ~~~~~~~~~~A~~~~~~~~~-----------------------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~  345 (490)
                      +|++.+++.+.++++.--..                       .++.-|..+...+...|++..|...-+++      -+
T Consensus      1175 AyAkt~rl~elE~fi~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vSN~a~La~TLV~LgeyQ~AVD~aRKA------ns 1248 (1666)
T KOG0985|consen 1175 AYAKTNRLTELEEFIAGPNVANIQQVGDRCFEEKMYEAAKLLYSNVSNFAKLASTLVYLGEYQGAVDAARKA------NS 1248 (1666)
T ss_pred             HHHHhchHHHHHHHhcCCCchhHHHHhHHHhhhhhhHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhc------cc
Confidence            88888887776655421100                       13344555555666666666665544432      24


Q ss_pred             HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHH
Q 011249          346 QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGA  423 (490)
Q Consensus       346 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~  423 (490)
                      ..||..+-.+|...+.+..|.     +-- .++.....-...++.-|...|-+++.+.+++...  .+..-..|+-|.-.
T Consensus      1249 ~ktWK~VcfaCvd~~EFrlAQ-----iCG-L~iivhadeLeeli~~Yq~rGyFeElIsl~Ea~LGLERAHMgmfTELaiL 1322 (1666)
T KOG0985|consen 1249 TKTWKEVCFACVDKEEFRLAQ-----ICG-LNIIVHADELEELIEYYQDRGYFEELISLLEAGLGLERAHMGMFTELAIL 1322 (1666)
T ss_pred             hhHHHHHHHHHhchhhhhHHH-----hcC-ceEEEehHhHHHHHHHHHhcCcHHHHHHHHHhhhchhHHHHHHHHHHHHH
Confidence            456777767776655554331     111 1222334445667788888888888888887655  23344466666655


Q ss_pred             HhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHH
Q 011249          424 CKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMM  473 (490)
Q Consensus       424 ~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~  473 (490)
                      |.+. .+++..+.++-....- +    .--+++++.++--|.+..=++.+
T Consensus      1323 Ysky-kp~km~EHl~LFwsRv-N----ipKviRA~eqahlW~ElvfLY~~ 1366 (1666)
T KOG0985|consen 1323 YSKY-KPEKMMEHLKLFWSRV-N----IPKVIRAAEQAHLWSELVFLYDK 1366 (1666)
T ss_pred             HHhc-CHHHHHHHHHHHHHhc-c----hHHHHHHHHHHHHHHHHHHHHHh
Confidence            5544 5666666666555421 0    11244555555556655555443

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.91  E-value=1.7e-07  Score=94.26  Aligned_cols=195  Identities=13%  Similarity=0.085  Sum_probs=85.1

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHhcccCC--------ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHH
Q 011249          280 NYVSNALIHMHSKCGYLDLAWREFSRIKNK--------DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIG  351 (490)
Q Consensus       280 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~  351 (490)
                      ...|-..+......++.++|++++++....        -...|.+++.....-|.-+...++|+++.+.  --....|..
T Consensus      1458 Si~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqy--cd~~~V~~~ 1535 (1710)
T KOG1070|consen 1458 SILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQY--CDAYTVHLK 1535 (1710)
T ss_pred             chHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHh--cchHHHHHH
Confidence            334444444444444444444444444320        1123444444444444444444444444441  111123444


Q ss_pred             HHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC---ChhhHHHHHHHHhhh
Q 011249          352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC---DAGTWGALLGACKVH  427 (490)
Q Consensus       352 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~---~~~~~~~l~~~~~~~  427 (490)
                      |...|.+.+..++|.++++.|.++++  .....|..++..+.+..+-+.|..++.+.. .-|   ......-.+..-.+.
T Consensus      1536 L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk~ 1613 (1710)
T KOG1070|consen 1536 LLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFKY 1613 (1710)
T ss_pred             HHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhc
Confidence            44444444555555555555544333  333444444444444444444444443332 111   122222333333444


Q ss_pred             CChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          428 VNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       428 g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      ||.+++..+|+..+...|.....|+.+++.-.+.|+.+.++.+|+++...+
T Consensus      1614 GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~ 1664 (1710)
T KOG1070|consen 1614 GDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELK 1664 (1710)
T ss_pred             CCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcC
Confidence            555555555555555455444555555555555555555555555444443

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.89  E-value=3.8e-08  Score=77.68  Aligned_cols=108  Identities=10%  Similarity=-0.094  Sum_probs=93.8

Q ss_pred             HHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC
Q 011249          367 KQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELG  444 (490)
Q Consensus       367 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  444 (490)
                      .++++..+   +.|+  .+..+...+...|++++|...|+...  .+.+...|..+..++...|++++|+..|+++.+.+
T Consensus        14 ~~~~~al~---~~p~--~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~   88 (144)
T PRK15359         14 DILKQLLS---VDPE--TVYASGYASWQEGDYSRAVIDFSWLVMAQPWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD   88 (144)
T ss_pred             HHHHHHHH---cCHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            45566554   3344  45567888999999999999998877  45577899999999999999999999999999999


Q ss_pred             CCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          445 PEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       445 p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      |+++.++..++.++.+.|++++|...+++..+..+
T Consensus        89 p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~p  123 (144)
T PRK15359         89 ASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKMSY  123 (144)
T ss_pred             CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            99999999999999999999999999999887654

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=98.89  E-value=1.6e-05  Score=72.87  Aligned_cols=72  Identities=17%  Similarity=0.193  Sum_probs=62.2

Q ss_pred             HHHHHhhhcCCCCchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHh
Q 011249           19 VHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHR   96 (490)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~   96 (490)
                      ..+.+..   +|-|..  .|+.|++-+... . .++++..++++.  .|.....|..-|..-.+..+++....+|.+...
T Consensus         9 ~~~rie~---nP~di~--sw~~lire~qt~-~-~~~~R~~YEq~~~~FP~s~r~W~~yi~~El~skdfe~VEkLF~RCLv   81 (656)
T KOG1914|consen    9 PRERIEE---NPYDID--SWSQLIREAQTQ-P-IDKVRETYEQLVNVFPSSPRAWKLYIERELASKDFESVEKLFSRCLV   81 (656)
T ss_pred             HHHHHhc---CCccHH--HHHHHHHHHccC-C-HHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3566776   778999  999999998877 5 999999999986  566668899999999999999999999999766


Q ss_pred             c
Q 011249           97 L   97 (490)
Q Consensus        97 ~   97 (490)
                      .
T Consensus        82 k   82 (656)
T KOG1914|consen   82 K   82 (656)
T ss_pred             H
Confidence            5

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.89  E-value=2e-07  Score=85.63  Aligned_cols=250  Identities=11%  Similarity=-0.046  Sum_probs=178.3

Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChH
Q 011249          218 VCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLD  297 (490)
Q Consensus       218 ~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  297 (490)
                      .-+.+.|+..+|.-.|+..++..+. +...|..|.......++-..|+..+.+..+.. |.+..+..+|.-.|...|.-.
T Consensus       293 ~~lm~nG~L~~A~LafEAAVkqdP~-haeAW~~LG~~qaENE~E~~ai~AL~rcl~Ld-P~NleaLmaLAVSytNeg~q~  370 (579)
T KOG1125|consen  293 CNLMKNGDLSEAALAFEAAVKQDPQ-HAEAWQKLGITQAENENEQNAISALRRCLELD-PTNLEALMALAVSYTNEGLQN  370 (579)
T ss_pred             HHHHhcCCchHHHHHHHHHHhhChH-HHHHHHHhhhHhhhccchHHHHHHHHHHHhcC-CccHHHHHHHHHHHhhhhhHH
Confidence            3456778888888888887776432 56777777777777788788888888887776 566777777777888888888


Q ss_pred             HHHHHHhcccCCC-hhHHHHHH---------HHHHhcCChHHHHHHHHHHHH-cCCCCcHHHHHHHHHHhcCCCChHHHH
Q 011249          298 LAWREFSRIKNKD-VISYSSMI---------TAFADHGKSQEALDMFLKMRN-EGIEPNQVTFIGVLTACSHGGLVEDGC  366 (490)
Q Consensus       298 ~A~~~~~~~~~~~-~~~~~~l~---------~~~~~~~~~~~a~~~~~~~~~-~~~~p~~~~~~~l~~~~~~~g~~~~a~  366 (490)
                      .|...+++..... ...|....         ..+.....+....++|-++.. .+..+|+.....|.-.|--.|++++|.
T Consensus       371 ~Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdrai  450 (579)
T KOG1125|consen  371 QALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAV  450 (579)
T ss_pred             HHHHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHH
Confidence            8888777654310 00010000         111122234445555555544 444467777777877788899999999


Q ss_pred             HHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCC-hhhHHHHHHHHhhhCChHHHHHHHHHHHhcC
Q 011249          367 KQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD-AGTWGALLGACKVHVNAELGEIAARHLLELG  444 (490)
Q Consensus       367 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  444 (490)
                      ..|+.+..  --|-|..+||.|.-.++...+.++|+..|.+.. .+|+ +.+...|..+|...|.+++|.+.|-.++.+.
T Consensus       451 Dcf~~AL~--v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL~mq  528 (579)
T KOG1125|consen  451 DCFEAALQ--VKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEALSMQ  528 (579)
T ss_pred             HHHHHHHh--cCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHHHhh
Confidence            99999987  445568889999999999999999999998876 5565 4577888889999999999999999988765


Q ss_pred             CC-----C-----CchHHHHHHHHHhcCCcchHHHHH
Q 011249          445 PE-----K-----TGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       445 p~-----~-----~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      +.     .     -.++.+|-.++...++.|-+.+..
T Consensus       529 ~ks~~~~~~~~~se~iw~tLR~als~~~~~D~l~~a~  565 (579)
T KOG1125|consen  529 RKSRNHNKAPMASENIWQTLRLALSAMNRSDLLQEAA  565 (579)
T ss_pred             hcccccccCCcchHHHHHHHHHHHHHcCCchHHHHhc
Confidence            43     1     247777777777777777555543

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.88  E-value=3.5e-06  Score=82.42  Aligned_cols=421  Identities=11%  Similarity=0.024  Sum_probs=252.4

Q ss_pred             CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCC--CCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCH-hhHH
Q 011249           31 HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPK--CKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSG-FTFS  107 (490)
Q Consensus        31 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~-~~~~  107 (490)
                      .=..  .|..|...|+...+ ...|.+.|++.-+  ++...++......|++..+++.|..+.-...+.  .|-. ..++
T Consensus       490 ~~ap--af~~LG~iYrd~~D-m~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~~~qk--a~a~~~k~n  564 (1238)
T KOG1127|consen  490 SLAP--AFAFLGQIYRDSDD-MKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLRAAQK--APAFACKEN  564 (1238)
T ss_pred             chhH--HHHHHHHHHHHHHH-HHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHHHhhh--chHHHHHhh
Confidence            3445  78889999988887 8899999988753  333367888888999999999998884333332  2211 1111


Q ss_pred             HHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC---CCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCch---h
Q 011249          108 SVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE---RNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSV---T  181 (490)
Q Consensus       108 ~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~---~  181 (490)
                      -+-.            .-.|.+.++..+|..-|+...+   .|...|..++.+|.+.|++..|+++|.+...-++.   .
T Consensus       565 W~~r------------G~yyLea~n~h~aV~~fQsALR~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~LrP~s~y~  632 (1238)
T KOG1127|consen  565 WVQR------------GPYYLEAHNLHGAVCEFQSALRTDPKDYNLWLGLGEAYPESGRYSHALKVFTKASLLRPLSKYG  632 (1238)
T ss_pred             hhhc------------cccccCccchhhHHHHHHHHhcCCchhHHHHHHHHHHHHhcCceehHHHhhhhhHhcCcHhHHH
Confidence            1111            1137788899999999998886   36778889999999999999999999887754332   2


Q ss_pred             HHHHHHHHHhcCChhHHHHHHhhcCC----------CCHHhHHHHHHHHHhcCChHHHHHHHHH-------HHHcCcccC
Q 011249          182 WVAMIAGYGKCGEVREAKKVFDEISE----------PDASCWAAMTVCYVQNGYAKAAIEMYKV-------MRQENVRIS  244 (490)
Q Consensus       182 ~~~l~~~~~~~~~~~~A~~~~~~~~~----------~~~~~~~~l~~~~~~~g~~~~A~~~~~~-------~~~~~~~p~  244 (490)
                      --...-+.+..|.+.+|...+..+..          .-..++-.+...+.-.|-..+|...+++       .......-+
T Consensus       633 ~fk~A~~ecd~GkYkeald~l~~ii~~~s~e~~~q~gLaE~~ir~akd~~~~gf~~kavd~~eksie~f~~~l~h~~~~~  712 (1238)
T KOG1127|consen  633 RFKEAVMECDNGKYKEALDALGLIIYAFSLERTGQNGLAESVIRDAKDSAITGFQKKAVDFFEKSIESFIVSLIHSLQSD  712 (1238)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHhhhhh
Confidence            23334445667888888888877653          1112222222222222322233322222       222211111


Q ss_pred             hhhHHHHHHHH-----------------------hccCCh---H---HHHHHHHHHHhcCCCCchhHHHHHHHHHHh---
Q 011249          245 EVAMVGAISAC-----------------------TQLGDV---E---MAAILAKHVDEGCCDRTNYVSNALIHMHSK---  292 (490)
Q Consensus       245 ~~~~~~l~~~~-----------------------~~~g~~---~---~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~---  292 (490)
                      ...|-.+..+|                       ...+..   +   -+.+.+-.-.+  ...+...|..++..|.+   
T Consensus       713 ~~~Wi~asdac~~f~q~e~~~vn~h~l~il~~q~e~~~~l~~~d~l~Lg~~c~~~hls--l~~~~~~WyNLGinylr~f~  790 (1238)
T KOG1127|consen  713 RLQWIVASDACYIFSQEEPSIVNMHYLIILSKQLEKTGALKKNDLLFLGYECGIAHLS--LAIHMYPWYNLGINYLRYFL  790 (1238)
T ss_pred             HHHHHHHhHHHHHHHHhcccchHHHHHHHHHHHHHhcccCcchhHHHHHHHHhhHHHH--HhhccchHHHHhHHHHHHHH
Confidence            11111111111                       111111   1   00000000000  11112233333333322   


Q ss_pred             -cC----ChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHH
Q 011249          293 -CG----YLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVED  364 (490)
Q Consensus       293 -~~----~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~  364 (490)
                       .+    +...|+..+.+..+   .+...|+.|.-. ...|++.-+...|-+-... .+....+|..+.-.+....+++.
T Consensus       791 ~l~et~~~~~~Ai~c~KkaV~L~ann~~~WnaLGVl-sg~gnva~aQHCfIks~~s-ep~~~~~W~NlgvL~l~n~d~E~  868 (1238)
T KOG1127|consen  791 LLGETMKDACTAIRCCKKAVSLCANNEGLWNALGVL-SGIGNVACAQHCFIKSRFS-EPTCHCQWLNLGVLVLENQDFEH  868 (1238)
T ss_pred             HcCCcchhHHHHHHHHHHHHHHhhccHHHHHHHHHh-hccchhhhhhhhhhhhhhc-cccchhheeccceeEEecccHHH
Confidence             11    22356666665544   466677777655 5567777777777666553 13345578888888889999999


Q ss_pred             HHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-------CCCChhhHHHHHHHHhhhCChHHHHHHH
Q 011249          365 GCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-------DFCDAGTWGALLGACKVHVNAELGEIAA  437 (490)
Q Consensus       365 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-------~~~~~~~~~~l~~~~~~~g~~~~a~~~~  437 (490)
                      |...|...+.  -.|.+...|..........|+.-++..+|..-.       ..++...|.+.......+|+.++-+...
T Consensus       869 A~~af~~~qS--LdP~nl~~WlG~Ali~eavG~ii~~~~lfaHs~el~~~~gka~~f~Yw~c~te~h~~Ng~~e~~I~t~  946 (1238)
T KOG1127|consen  869 AEPAFSSVQS--LDPLNLVQWLGEALIPEAVGRIIERLILFAHSDELCSKEGKAKKFQYWLCATEIHLQNGNIEESINTA  946 (1238)
T ss_pred             hhHHHHhhhh--cCchhhHHHHHHHHhHHHHHHHHHHHHHHHhhHHhhccccccchhhHHHHHHHHHHhccchHHHHHHh
Confidence            9999999875  445556666666666667888888888885521       2344445554444556666666555443


Q ss_pred             ----------HHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          438 ----------RHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       438 ----------~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                                ++.....|+...+|...+....+.+.+.+|.+...+.
T Consensus       947 ~ki~sAs~al~~yf~~~p~~~fAy~~~gstlEhL~ey~~a~ela~Rl  993 (1238)
T KOG1127|consen  947 RKISSASLALSYYFLGHPQLCFAYAANGSTLEHLEEYRAALELATRL  993 (1238)
T ss_pred             hhhhhhHHHHHHHHhcCcchhHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence                      4445567999999999999999999999998887764

>PLN02789 farnesyltranstransferase

Probab=98.86  E-value=1.5e-06  Score=78.06  Aligned_cols=176  Identities=13%  Similarity=0.016  Sum_probs=101.3

Q ss_pred             hHHHHHHHhcccC---CChhHHHHHHHHHHhcCC--hHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHH
Q 011249          296 LDLAWREFSRIKN---KDVISYSSMITAFADHGK--SQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQF  369 (490)
Q Consensus       296 ~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~--~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~  369 (490)
                      +++++..++++.+   ++..+|+...-.+.+.|+  .++++.+++++.+.  .| |...|.....++...|+++++++.+
T Consensus        88 l~eeL~~~~~~i~~npknyqaW~~R~~~l~~l~~~~~~~el~~~~kal~~--dpkNy~AW~~R~w~l~~l~~~~eeL~~~  165 (320)
T PLN02789         88 LEEELDFAEDVAEDNPKNYQIWHHRRWLAEKLGPDAANKELEFTRKILSL--DAKNYHAWSHRQWVLRTLGGWEDELEYC  165 (320)
T ss_pred             HHHHHHHHHHHHHHCCcchHHhHHHHHHHHHcCchhhHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHhhhHHHHHHHH
Confidence            4445544444433   223334433333333333  24556666666653  33 3345655555566666677777777


Q ss_pred             HHHHHHcCCCCCchHHHHHHHHHhhc---CCh----HHHHHHHHhcc--CCCChhhHHHHHHHHhhh----CChHHHHHH
Q 011249          370 ELMTRVFGIKPLTEHLTCMVDLLGRS---GQL----EKAHSLIMDYK--DFCDAGTWGALLGACKVH----VNAELGEIA  436 (490)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~l~~~~~~~---g~~----~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~----g~~~~a~~~  436 (490)
                      +++.+.  -+.+...|+....++.+.   |..    ++++++..++.  .+.+...|+.+...+...    +...+|.++
T Consensus       166 ~~~I~~--d~~N~sAW~~R~~vl~~~~~l~~~~~~~e~el~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~  243 (320)
T PLN02789        166 HQLLEE--DVRNNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSV  243 (320)
T ss_pred             HHHHHH--CCCchhHHHHHHHHHHhccccccccccHHHHHHHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHH
Confidence            766662  333445555444444333   222    34555554433  444666777777776652    345668888


Q ss_pred             HHHHHhcCCCCCchHHHHHHHHHhcC------------------CcchHHHHHHHhh
Q 011249          437 ARHLLELGPEKTGNSALLANIYASMG------------------KWKDSEIVKMMIS  475 (490)
Q Consensus       437 ~~~~~~~~p~~~~~~~~l~~~~~~~g------------------~~~~A~~~~~~~~  475 (490)
                      +.++...+|.++.++..|+.+|.+..                  ..++|.++++.+.
T Consensus       244 ~~~~~~~~~~s~~al~~l~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~  300 (320)
T PLN02789        244 CLEVLSKDSNHVFALSDLLDLLCEGLQPTAEFRDTVDTLAEELSDSTLAQAVCSELE  300 (320)
T ss_pred             HHHhhcccCCcHHHHHHHHHHHHhhhccchhhhhhhhccccccccHHHHHHHHHHHH
Confidence            88888888988999999999988642                  2366888888773

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.83  E-value=5.1e-07  Score=75.04  Aligned_cols=155  Identities=12%  Similarity=0.036  Sum_probs=96.8

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh
Q 011249          315 SSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR  394 (490)
Q Consensus       315 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  394 (490)
                      ..+...+...|+-+....+....... ...|.......+....+.|++..|...+.+...  .-++|...|+.+.-+|.+
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~--l~p~d~~~~~~lgaaldq  146 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAAR--LAPTDWEAWNLLGAALDQ  146 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhc--cCCCChhhhhHHHHHHHH
Confidence            44444555566666666655554431 122333444456666666777777777777665  566666777777777777


Q ss_pred             cCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHH
Q 011249          395 SGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKM  472 (490)
Q Consensus       395 ~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  472 (490)
                      .|++++|..-|.+..  ...++...+.+.-.+.-.||.+.|..++..+....+.+..+-..|+.+....|+.++|..+..
T Consensus       147 ~Gr~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~ad~~v~~NLAl~~~~~g~~~~A~~i~~  226 (257)
T COG5010         147 LGRFDEARRAYRQALELAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAADSRVRQNLALVVGLQGDFREAEDIAV  226 (257)
T ss_pred             ccChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhcCChHHHHhhcc
Confidence            777777766665554  334555666666666667777777777777766666667777777777777777777666554

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=98.81  E-value=9.8e-07  Score=86.13  Aligned_cols=156  Identities=15%  Similarity=0.127  Sum_probs=77.4

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCCCC-----HHhHHHHHHHH
Q 011249          149 ISWSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISEPD-----ASCWAAMTVCY  220 (490)
Q Consensus       149 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-----~~~~~~l~~~~  220 (490)
                      ..|..|...|....+...|.+.|++..+-   |..+.....+.|++..+++.|..+.-...+.+     ...|....-.|
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            35666666666655666666666666543   44555566666666666666666532222211     11222233344


Q ss_pred             HhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHH
Q 011249          221 VQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAW  300 (490)
Q Consensus       221 ~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~  300 (490)
                      ...++..+|+..|+...+..+. |...|..+..+|...|++..|.+.|.++.... |.+...---..-+.+..|.+.+|.
T Consensus       573 Lea~n~h~aV~~fQsALR~dPk-D~n~W~gLGeAY~~sGry~~AlKvF~kAs~Lr-P~s~y~~fk~A~~ecd~GkYkeal  650 (1238)
T KOG1127|consen  573 LEAHNLHGAVCEFQSALRTDPK-DYNLWLGLGEAYPESGRYSHALKVFTKASLLR-PLSKYGRFKEAVMECDNGKYKEAL  650 (1238)
T ss_pred             cCccchhhHHHHHHHHhcCCch-hHHHHHHHHHHHHhcCceehHHHhhhhhHhcC-cHhHHHHHHHHHHHHHhhhHHHHH
Confidence            5555555555555555544322 44555555556666666666666655554443 122211111222334445555555


Q ss_pred             HHHhcc
Q 011249          301 REFSRI  306 (490)
Q Consensus       301 ~~~~~~  306 (490)
                      ..+..+
T Consensus       651 d~l~~i  656 (1238)
T KOG1127|consen  651 DALGLI  656 (1238)
T ss_pred             HHHHHH
Confidence            554443

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.79  E-value=6.3e-07  Score=88.59  Aligned_cols=141  Identities=13%  Similarity=0.047  Sum_probs=105.8

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHH
Q 011249          310 DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCM  388 (490)
Q Consensus       310 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l  388 (490)
                      ++..+..|..+..+.|.+++|+.+++...+  +.|+.. ....+...+.+.+++++|+...++...  .-+.+......+
T Consensus        85 ~~~~~~~La~i~~~~g~~~ea~~~l~~~~~--~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~--~~p~~~~~~~~~  160 (694)
T PRK15179         85 TELFQVLVARALEAAHRSDEGLAVWRGIHQ--RFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFS--GGSSSAREILLE  160 (694)
T ss_pred             cHHHHHHHHHHHHHcCCcHHHHHHHHHHHh--hCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhh--cCCCCHHHHHHH
Confidence            577778888888888888888888888887  467654 666677778888888888888888876  455556666777


Q ss_pred             HHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHH
Q 011249          389 VDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALL  454 (490)
Q Consensus       389 ~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l  454 (490)
                      ..++.+.|++++|..+|+++. ..| +..++.++..++...|+.++|...|+++.+...+....|..+
T Consensus       161 a~~l~~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~~  228 (694)
T PRK15179        161 AKSWDEIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDAIGDGARKLTRR  228 (694)
T ss_pred             HHHHHHhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhCcchHHHHHH
Confidence            788888888888888888777 233 356788888888888888888888888887664434444443

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.79  E-value=8e-06  Score=68.08  Aligned_cols=175  Identities=17%  Similarity=0.080  Sum_probs=109.6

Q ss_pred             HHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcH
Q 011249          267 LAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQ  346 (490)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~  346 (490)
                      +.+.+.......+......-...|...|++++|++......  +......=+..+.+..+.+-|.+.+++|.+   --+.
T Consensus        95 l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~--~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~---ided  169 (299)
T KOG3081|consen   95 LYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGE--NLEAAALNVQILLKMHRFDLAEKELKKMQQ---IDED  169 (299)
T ss_pred             HHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccc--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHc---cchH
Confidence            33444443333343333444556777777777777777632  233333333445666777888888888876   2244


Q ss_pred             HHHHHHHHHhc----CCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHH
Q 011249          347 VTFIGVLTACS----HGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGAL  420 (490)
Q Consensus       347 ~~~~~l~~~~~----~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l  420 (490)
                      .|.+.|..++.    ..+...+|.-+|+++.+  ..+|++.+.+..+-++...|++++|..+++...  ...++.+...+
T Consensus       170 ~tLtQLA~awv~la~ggek~qdAfyifeE~s~--k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~dpetL~Nl  247 (299)
T KOG3081|consen  170 ATLTQLAQAWVKLATGGEKIQDAFYIFEELSE--KTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAKDPETLANL  247 (299)
T ss_pred             HHHHHHHHHHHHHhccchhhhhHHHHHHHHhc--ccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHH
Confidence            56666665543    34567788888888876  577777787777778888888888888887766  33456666666


Q ss_pred             HHHHhhhCCh-HHHHHHHHHHHhcCCCCC
Q 011249          421 LGACKVHVNA-ELGEIAARHLLELGPEKT  448 (490)
Q Consensus       421 ~~~~~~~g~~-~~a~~~~~~~~~~~p~~~  448 (490)
                      +..-...|.. +--.+.+.++....|+++
T Consensus       248 iv~a~~~Gkd~~~~~r~l~QLk~~~p~h~  276 (299)
T KOG3081|consen  248 IVLALHLGKDAEVTERNLSQLKLSHPEHP  276 (299)
T ss_pred             HHHHHHhCCChHHHHHHHHHHHhcCCcch
Confidence            6555555543 455566677777777754

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.77  E-value=8.9e-06  Score=73.79  Aligned_cols=232  Identities=11%  Similarity=0.030  Sum_probs=155.6

Q ss_pred             HHHHHHhcC-ChhHHHHHHHHHH---hcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC----
Q 011249           74 LIRNHVLHA-HFRQSILLYAKMH---RLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE----  145 (490)
Q Consensus        74 l~~~~~~~g-~~~~A~~~~~~m~---~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----  145 (490)
                      =+..+.+.| ++....+.|+++.   ..|-.|+..-.+.                  =.-..++.+++..-+.++.    
T Consensus       208 Gi~~L~raGydp~gM~~ff~rl~~~~~~~~~~p~yl~TH------------------Plp~~RIa~lr~ra~q~p~~~~~  269 (484)
T COG4783         208 GITTLVRAGYDPQGMPEFFERLADQLRYGGQPPEYLLTH------------------PLPEERIADLRNRAEQSPPYNKL  269 (484)
T ss_pred             HHHHHHHcCCCchhHHHHHHHHHHHHhcCCCCChHHhcC------------------CCchhHHHHHHHHHHhCCCCCCC
Confidence            344455665 5666677777776   3343444322111                  1122456666666666664    


Q ss_pred             --CCHhHHHHHHHHHHhCCChHHHHHHHHHhccC-CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHH
Q 011249          146 --RNVISWSAMVAGYANCGNMKAAKEFYDRMTEK-NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVC  219 (490)
Q Consensus       146 --~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~  219 (490)
                        |+...+...+.+......-..+-.++-+..++ -....--....+...|++++|+..++.+..   .|+..+......
T Consensus       270 d~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~aa~YG~A~~~~~~~~~d~A~~~l~~L~~~~P~N~~~~~~~~~i  349 (484)
T COG4783         270 DSPDFQLARARIRAKYEALPNQQAADLLAKRSKRGGLAAQYGRALQTYLAGQYDEALKLLQPLIAAQPDNPYYLELAGDI  349 (484)
T ss_pred             CCccHHHHHHHHHHHhccccccchHHHHHHHhCccchHHHHHHHHHHHHhcccchHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence              45566666666655544444444444333332 223333344445677889999998888764   455666677788


Q ss_pred             HHhcCChHHHHHHHHHHHHcCcccC-hhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHH
Q 011249          220 YVQNGYAKAAIEMYKVMRQENVRIS-EVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDL  298 (490)
Q Consensus       220 ~~~~g~~~~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  298 (490)
                      +.+.|+.++|.+.++++...  .|+ ......+..++.+.|++.+|..+++...... +.|+..|..|..+|...|+..+
T Consensus       350 ~~~~nk~~~A~e~~~kal~l--~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~~-p~dp~~w~~LAqay~~~g~~~~  426 (484)
T COG4783         350 LLEANKAKEAIERLKKALAL--DPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFND-PEDPNGWDLLAQAYAELGNRAE  426 (484)
T ss_pred             HHHcCChHHHHHHHHHHHhc--CCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhcC-CCCchHHHHHHHHHHHhCchHH
Confidence            99999999999999998876  444 5566677788889999999999988887775 7788889999999999988777


Q ss_pred             HHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011249          299 AWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNE  340 (490)
Q Consensus       299 A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  340 (490)
                      +....              ...|...|+++.|...+....+.
T Consensus       427 a~~A~--------------AE~~~~~G~~~~A~~~l~~A~~~  454 (484)
T COG4783         427 ALLAR--------------AEGYALAGRLEQAIIFLMRASQQ  454 (484)
T ss_pred             HHHHH--------------HHHHHhCCCHHHHHHHHHHHHHh
Confidence            76543              44677788999998888888775

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.75  E-value=6.5e-07  Score=84.62  Aligned_cols=213  Identities=10%  Similarity=-0.050  Sum_probs=144.5

Q ss_pred             HHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--CChhHHHHHHHHHHhcCCh
Q 011249          250 GAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KDVISYSSMITAFADHGKS  327 (490)
Q Consensus       250 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~  327 (490)
                      .+...+...|-...|..+++++..         +...+.+|...|+..+|..+..+..+  |++..|..+++......-+
T Consensus       403 ~laell~slGitksAl~I~Erlem---------w~~vi~CY~~lg~~~kaeei~~q~lek~~d~~lyc~LGDv~~d~s~y  473 (777)
T KOG1128|consen  403 LLAELLLSLGITKSALVIFERLEM---------WDPVILCYLLLGQHGKAEEINRQELEKDPDPRLYCLLGDVLHDPSLY  473 (777)
T ss_pred             HHHHHHHHcchHHHHHHHHHhHHH---------HHHHHHHHHHhcccchHHHHHHHHhcCCCcchhHHHhhhhccChHHH
Confidence            444555566666666666665432         33456667777777777666655443  5666666666665555556


Q ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHh
Q 011249          328 QEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMD  407 (490)
Q Consensus       328 ~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  407 (490)
                      ++|.++.+.....       .-..+.....+.++++++.+.|+.-.+  -.+....+|..+.-+..+.++++.|.+.|..
T Consensus       474 EkawElsn~~sar-------A~r~~~~~~~~~~~fs~~~~hle~sl~--~nplq~~~wf~~G~~ALqlek~q~av~aF~r  544 (777)
T KOG1128|consen  474 EKAWELSNYISAR-------AQRSLALLILSNKDFSEADKHLERSLE--INPLQLGTWFGLGCAALQLEKEQAAVKAFHR  544 (777)
T ss_pred             HHHHHHhhhhhHH-------HHHhhccccccchhHHHHHHHHHHHhh--cCccchhHHHhccHHHHHHhhhHHHHHHHHH
Confidence            6666665543321       111222223346777888888777766  3344566777777777888888888888866


Q ss_pred             cc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          408 YK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       408 ~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      ..  .+.+...|+++..+|.+.|+-.+|...+.++++.+-.+..++.+..-+....|.+++|.+.+.++.+....
T Consensus       545 cvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~eda~~A~~rll~~~~~  619 (777)
T KOG1128|consen  545 CVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFEDAIKAYHRLLDLRKK  619 (777)
T ss_pred             HhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHHHHHHHHHHHHhhhh
Confidence            55  34456788888888888888888888888888888778888888887888888888888888888766443

>PLN02789 farnesyltranstransferase

Probab=98.72  E-value=2.1e-05  Score=70.75  Aligned_cols=234  Identities=12%  Similarity=0.035  Sum_probs=143.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccC-ChHHHHHHHHHHHhcCCCCchhHHHHHHHHHH
Q 011249          213 WAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLG-DVEMAAILAKHVDEGCCDRTNYVSNALIHMHS  291 (490)
Q Consensus       213 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  291 (490)
                      +..+-.++...++.++|+.++.++++.... +...|.....++...| +++++...++.+.+.. +.+..+|+.-..++.
T Consensus        40 ~~~~ra~l~~~e~serAL~lt~~aI~lnP~-~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n-pknyqaW~~R~~~l~  117 (320)
T PLN02789         40 MDYFRAVYASDERSPRALDLTADVIRLNPG-NYTVWHFRRLCLEALDADLEEELDFAEDVAEDN-PKNYQIWHHRRWLAE  117 (320)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC-CcchHHhHHHHHHHH
Confidence            344444555667778888888877765321 3344444444555556 5677888887777765 455555655444455


Q ss_pred             hcCCh--HHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCC---CC--
Q 011249          292 KCGYL--DLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHG---GL--  361 (490)
Q Consensus       292 ~~~~~--~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~---g~--  361 (490)
                      +.|+.  +++..+++++.+   .+..+|+...-++...|+++++++.++++++.+.. |...|+.....+.+.   |.  
T Consensus       118 ~l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~~~~~l~~~~  196 (320)
T PLN02789        118 KLGPDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVITRSPLLGGLE  196 (320)
T ss_pred             HcCchhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHHhcccccccc
Confidence            55542  566777766665   46677777777777888888888888888875422 344555444444333   22  


Q ss_pred             --hHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh----cCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhC-----
Q 011249          362 --VEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR----SGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHV-----  428 (490)
Q Consensus       362 --~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g-----  428 (490)
                        .++.+.+..++..  ..+-+...|+.+...+..    .++..+|.+.+.+..  ...+......|+..+....     
T Consensus       197 ~~~e~el~y~~~aI~--~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~~  274 (320)
T PLN02789        197 AMRDSELKYTIDAIL--ANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDSNHVFALSDLLDLLCEGLQPTAE  274 (320)
T ss_pred             ccHHHHHHHHHHHHH--hCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccCCcHHHHHHHHHHHHhhhccchh
Confidence              2456666666665  345567777777777766    244566777776654  2335556667777765422     


Q ss_pred             -------------ChHHHHHHHHHHHhcCCCCCchH
Q 011249          429 -------------NAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       429 -------------~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                                   ..++|.++++.+.+.+|-....+
T Consensus       275 ~~~~~~~~~~~~~~~~~a~~~~~~l~~~d~ir~~yw  310 (320)
T PLN02789        275 FRDTVDTLAEELSDSTLAQAVCSELEVADPMRRNYW  310 (320)
T ss_pred             hhhhhhccccccccHHHHHHHHHHHHhhCcHHHHHH
Confidence                         23667777777765666544433

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.72  E-value=8.8e-07  Score=73.69  Aligned_cols=136  Identities=18%  Similarity=0.120  Sum_probs=116.1

Q ss_pred             CCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHH
Q 011249          342 IEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGA  419 (490)
Q Consensus       342 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~  419 (490)
                      ..|+......+-..+...|+-+....+......  ..+.+......++....+.|++.+|...+++..  .++|...|+.
T Consensus        62 ~~p~d~~i~~~a~a~~~~G~a~~~l~~~~~~~~--~~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p~d~~~~~~  139 (257)
T COG5010          62 RNPEDLSIAKLATALYLRGDADSSLAVLQKSAI--AYPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNL  139 (257)
T ss_pred             cCcchHHHHHHHHHHHhcccccchHHHHhhhhc--cCcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccCCCChhhhhH
Confidence            355443335666677788998888888888765  455566677779999999999999999998877  6778899999


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +.-+|.+.|+++.|..-|.+++++.|+++.++++++..|.-.|++++|..++......+.
T Consensus       140 lgaaldq~Gr~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~  199 (257)
T COG5010         140 LGAALDQLGRFDEARRAYRQALELAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPA  199 (257)
T ss_pred             HHHHHHHccChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCC
Confidence            999999999999999999999999999999999999999999999999999988765543

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.72  E-value=2.1e-06  Score=71.69  Aligned_cols=154  Identities=10%  Similarity=0.054  Sum_probs=113.0

Q ss_pred             HHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHH
Q 011249          287 IHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGC  366 (490)
Q Consensus       287 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~  366 (490)
                      +..|...|+++.+....+.+..+.        ..+...++.+++...++...+.. +.+...|..+...|...|++++|.
T Consensus        23 ~~~Y~~~g~~~~v~~~~~~~~~~~--------~~~~~~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~~~~A~   93 (198)
T PRK10370         23 VGSYLLSPKWQAVRAEYQRLADPL--------HQFASQQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRNDYDNAL   93 (198)
T ss_pred             HHHHHHcchHHHHHHHHHHHhCcc--------ccccCchhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHH
Confidence            445777777777655543332221        01223566778888888877742 346668888888999999999999


Q ss_pred             HHHHHHHHHcCCCCCchHHHHHHHHH-hhcCC--hHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHH
Q 011249          367 KQFELMTRVFGIKPLTEHLTCMVDLL-GRSGQ--LEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLL  441 (490)
Q Consensus       367 ~~~~~~~~~~~~~~~~~~~~~l~~~~-~~~g~--~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  441 (490)
                      ..+++..+  -.+.+...+..+..++ ...|+  .++|.+++++..  .+.+...+..+...+...|++++|+..|++++
T Consensus        94 ~a~~~Al~--l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~aL  171 (198)
T PRK10370         94 LAYRQALQ--LRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDANEVTALMLLASDAFMQADYAQAIELWQKVL  171 (198)
T ss_pred             HHHHHHHH--hCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCCChhHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99999887  3455677777888764 67777  589999998877  44567788888889999999999999999999


Q ss_pred             hcCCCCCchH
Q 011249          442 ELGPEKTGNS  451 (490)
Q Consensus       442 ~~~p~~~~~~  451 (490)
                      +..|.+..-+
T Consensus       172 ~l~~~~~~r~  181 (198)
T PRK10370        172 DLNSPRVNRT  181 (198)
T ss_pred             hhCCCCccHH
Confidence            9887765533

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.70  E-value=3e-06  Score=83.88  Aligned_cols=142  Identities=11%  Similarity=0.013  Sum_probs=106.8

Q ss_pred             CCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcH-HHHHH
Q 011249          276 CDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQ-VTFIG  351 (490)
Q Consensus       276 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~~~~  351 (490)
                      .+.++..+..|..+....|.+++|..+++...+  | +...+..++.++.+.+++++|+..+++....  .|+. .....
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~--~p~~~~~~~~  159 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRFPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSG--GSSSAREILL  159 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhc--CCCCHHHHHH
Confidence            356677778888888888888888888888776  4 4556777788888888888888888888874  5544 45666


Q ss_pred             HHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHH
Q 011249          352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALL  421 (490)
Q Consensus       352 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~  421 (490)
                      +..++...|++++|..+|+++..  ..+.+...+..+..++...|+.++|...|++..  ..+....|+.++
T Consensus       160 ~a~~l~~~g~~~~A~~~y~~~~~--~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~~~~~~~~~~~~~  229 (694)
T PRK15179        160 EAKSWDEIGQSEQADACFERLSR--QHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDAIGDGARKLTRRL  229 (694)
T ss_pred             HHHHHHHhcchHHHHHHHHHHHh--cCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhhCcchHHHHHHH
Confidence            67778888888888888888886  344456777788888888888888888888776  334444544443

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.70  E-value=1.5e-06  Score=75.69  Aligned_cols=182  Identities=13%  Similarity=0.034  Sum_probs=129.8

Q ss_pred             cChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCch---hHHHHHHHHHHhcCChHHHHHHHhcccC--CC-hh---H
Q 011249          243 ISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTN---YVSNALIHMHSKCGYLDLAWREFSRIKN--KD-VI---S  313 (490)
Q Consensus       243 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~-~~---~  313 (490)
                      .....+..+...+...|+++.|...++.+.+.. |.++   ..+..+..++...|++++|...++++.+  |+ ..   +
T Consensus        31 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a  109 (235)
T TIGR03302        31 WPAEELYEEAKEALDSGDYTEAIKYFEALESRY-PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYA  109 (235)
T ss_pred             CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHH
Confidence            355678888889999999999999999998765 3332   4567788999999999999999999876  32 22   4


Q ss_pred             HHHHHHHHHhc--------CChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchH
Q 011249          314 YSSMITAFADH--------GKSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEH  384 (490)
Q Consensus       314 ~~~l~~~~~~~--------~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  384 (490)
                      +..+..++...        |++++|.+.++++.+.  .|+.. ....+...              ..+...     ....
T Consensus       110 ~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~--------------~~~~~~-----~~~~  168 (235)
T TIGR03302       110 YYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRM--------------DYLRNR-----LAGK  168 (235)
T ss_pred             HHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHH--------------HHHHHH-----HHHH
Confidence            55566666654        7889999999999874  45442 22222111              111100     0011


Q ss_pred             HHHHHHHHhhcCChHHHHHHHHhcc-CCC----ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          385 LTCMVDLLGRSGQLEKAHSLIMDYK-DFC----DAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       385 ~~~l~~~~~~~g~~~~A~~~~~~~~-~~~----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      ...+...|.+.|++++|...++... ..|    ....+..+..++...|++++|..+++.+....|+
T Consensus       169 ~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l~~~~~~  235 (235)
T TIGR03302       169 ELYVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVLGANYPD  235 (235)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            1246677889999999999998876 222    3467888899999999999999999888876663

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).

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.70  E-value=2.2e-06  Score=81.20  Aligned_cols=188  Identities=13%  Similarity=0.076  Sum_probs=157.3

Q ss_pred             CCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 011249          276 CDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTA  355 (490)
Q Consensus       276 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~  355 (490)
                      .+|-...-..+...+.+.|-...|..+|+++     ..|.-.+.+|...|+..+|..+..+-.+  -+|++..|..+++.
T Consensus       394 lpp~Wq~q~~laell~slGitksAl~I~Erl-----emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv  466 (777)
T KOG1128|consen  394 LPPIWQLQRLLAELLLSLGITKSALVIFERL-----EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDV  466 (777)
T ss_pred             CCCcchHHHHHHHHHHHcchHHHHHHHHHhH-----HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhh
Confidence            3555556677889999999999999999975     4677788899999999999999998887  48899999999998


Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHH
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      .....-+++|.++.+.....        .-..+.....+.++++++.+.|+.-.  .+....+|-.+..+..+.++++.|
T Consensus       467 ~~d~s~yEkawElsn~~sar--------A~r~~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~a  538 (777)
T KOG1128|consen  467 LHDPSLYEKAWELSNYISAR--------AQRSLALLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQAA  538 (777)
T ss_pred             ccChHHHHHHHHHhhhhhHH--------HHHhhccccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHHH
Confidence            88877788898888877552        11223333445799999999997544  345677999999889999999999


Q ss_pred             HHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          434 EIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       434 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      .+.|...+..+|++...|+++..+|.+.|+..+|...+++..+-+
T Consensus       539 v~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn  583 (777)
T KOG1128|consen  539 VKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCN  583 (777)
T ss_pred             HHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcC
Confidence            999999999999999999999999999999999999999988765

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.69  E-value=6.1e-06  Score=83.58  Aligned_cols=219  Identities=16%  Similarity=0.143  Sum_probs=175.4

Q ss_pred             CC-HhHHHHHHHHHHhCCChHHHHHHHHHhccC--------CchhHHHHHHHHHhcCChhHHHHHHhhcCC--CCHHhHH
Q 011249          146 RN-VISWSAMVAGYANCGNMKAAKEFYDRMTEK--------NSVTWVAMIAGYGKCGEVREAKKVFDEISE--PDASCWA  214 (490)
Q Consensus       146 ~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--------~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~  214 (490)
                      || ...|-..|....+.++.++|.++.++++..        -...|.++++.-...|.-+...++|+++.+  .....|.
T Consensus      1455 PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqycd~~~V~~ 1534 (1710)
T KOG1070|consen 1455 PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYCDAYTVHL 1534 (1710)
T ss_pred             CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhcchHHHHH
Confidence            54 456888889999999999999999999853        334788888888888888999999999987  4456788


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCC-CchhHHHHHHHHHHhc
Q 011249          215 AMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCD-RTNYVSNALIHMHSKC  293 (490)
Q Consensus       215 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~  293 (490)
                      .|...|.+.+++++|.++|+.|.+.- .-....|...+..+.+..+-+.|..++.++.+.-.. -......-.+..-.+.
T Consensus      1535 ~L~~iy~k~ek~~~A~ell~~m~KKF-~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLEFk~ 1613 (1710)
T KOG1070|consen 1535 KLLGIYEKSEKNDEADELLRLMLKKF-GQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLEFKY 1613 (1710)
T ss_pred             HHHHHHHHhhcchhHHHHHHHHHHHh-cchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHHhhc
Confidence            99999999999999999999999752 246678888999999999999999999998876422 1344555667777889


Q ss_pred             CChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHH--HHHHHHHHhcCCCChHHH
Q 011249          294 GYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV--TFIGVLTACSHGGLVEDG  365 (490)
Q Consensus       294 ~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~--~~~~l~~~~~~~g~~~~a  365 (490)
                      |+.+.+..+|+....   +....|+..++.-.++|+.+.+..+|++....++.|...  .|...+..--+.|+-+.+
T Consensus      1614 GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde~~v 1690 (1710)
T KOG1070|consen 1614 GDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGDEKNV 1690 (1710)
T ss_pred             CCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCchhhH
Confidence            999999999998876   356789999999999999999999999999988887543  555555544444554433

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.69  E-value=2.3e-07  Score=72.92  Aligned_cols=90  Identities=17%  Similarity=0.137  Sum_probs=42.5

Q ss_pred             HHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCc
Q 011249          387 CMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKW  464 (490)
Q Consensus       387 ~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  464 (490)
                      .++..+...|++++|.+.++.+.  .+.+...+..+...+...|+++.|...++++.+.+|+++..+..++.++...|++
T Consensus        22 ~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~~g~~  101 (135)
T TIGR02552        22 ALAYNLYQQGRYDEALKLFQLLAAYDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAECLLALGEP  101 (135)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHcCCH
Confidence            34444444444444444444433  2223344444444444445555555555555455555455555555555555555


Q ss_pred             chHHHHHHHhhh
Q 011249          465 KDSEIVKMMISE  476 (490)
Q Consensus       465 ~~A~~~~~~~~~  476 (490)
                      ++|...+++..+
T Consensus       102 ~~A~~~~~~al~  113 (135)
T TIGR02552       102 ESALKALDLAIE  113 (135)
T ss_pred             HHHHHHHHHHHH
Confidence            555555544444

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.69  E-value=7.4e-06  Score=82.06  Aligned_cols=238  Identities=11%  Similarity=0.011  Sum_probs=143.2

Q ss_pred             CchhHHHHHHHHHhcCChhHHHHHHhhcCC--C-CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHH
Q 011249          178 NSVTWVAMIAGYGKCGEVREAKKVFDEISE--P-DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISA  254 (490)
Q Consensus       178 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~  254 (490)
                      +...+..|+..+...+++++|.++.+...+  | ....|..+...+.+.++.+.+..+  .               ++..
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~~~~~~lv--~---------------~l~~   92 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRPLNDSNLL--N---------------LIDS   92 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcchhhhhhh--h---------------hhhh
Confidence            445666777777777777777777765544  2 223344444456666664444333  1               2222


Q ss_pred             HhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHH
Q 011249          255 CTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEAL  331 (490)
Q Consensus       255 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~  331 (490)
                      .....++.....++..+.+.  ..+...+..+..+|-+.|+.++|..+++++.+   .|+.+.|.+...|... +.++|.
T Consensus        93 ~~~~~~~~~ve~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~-dL~KA~  169 (906)
T PRK14720         93 FSQNLKWAIVEHICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKADRDNPEIVKKLATSYEEE-DKEKAI  169 (906)
T ss_pred             cccccchhHHHHHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh-hHHHHH
Confidence            22333333333344444442  23334556677777777777777777777765   3566777777777777 777777


Q ss_pred             HHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCC
Q 011249          332 DMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDF  411 (490)
Q Consensus       332 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  411 (490)
                      .++.+.+..               +...+++..+..+|.++..  ..+.+...+..+.+.....-.            ..
T Consensus       170 ~m~~KAV~~---------------~i~~kq~~~~~e~W~k~~~--~~~~d~d~f~~i~~ki~~~~~------------~~  220 (906)
T PRK14720        170 TYLKKAIYR---------------FIKKKQYVGIEEIWSKLVH--YNSDDFDFFLRIERKVLGHRE------------FT  220 (906)
T ss_pred             HHHHHHHHH---------------HHhhhcchHHHHHHHHHHh--cCcccchHHHHHHHHHHhhhc------------cc
Confidence            777776653               4445567777777777765  333344433333322221111            11


Q ss_pred             CChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcch
Q 011249          412 CDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKD  466 (490)
Q Consensus       412 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  466 (490)
                      .-..++..+-..|...++++++..+++.+++.+|.|..+...++.+|.  ++|.+
T Consensus       221 ~~~~~~~~l~~~y~~~~~~~~~i~iLK~iL~~~~~n~~a~~~l~~~y~--~kY~~  273 (906)
T PRK14720        221 RLVGLLEDLYEPYKALEDWDEVIYILKKILEHDNKNNKAREELIRFYK--EKYKD  273 (906)
T ss_pred             hhHHHHHHHHHHHhhhhhhhHHHHHHHHHHhcCCcchhhHHHHHHHHH--HHccC
Confidence            223344445566777889999999999999999999999999988877  44444

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=98.69  E-value=7.2e-07  Score=69.08  Aligned_cols=98  Identities=11%  Similarity=-0.029  Sum_probs=86.7

Q ss_pred             CchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHH
Q 011249          381 LTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY  458 (490)
Q Consensus       381 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  458 (490)
                      +......+..-+...|++++|.++|+.+.  .+.+...|..|.-+|...|++++|+..|.++..++|++|.++..++.++
T Consensus        34 ~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~  113 (157)
T PRK15363         34 PLNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECY  113 (157)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHH
Confidence            34445566777789999999999998876  5567788999999999999999999999999999999999999999999


Q ss_pred             HhcCCcchHHHHHHHhhhcc
Q 011249          459 ASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       459 ~~~g~~~~A~~~~~~~~~~~  478 (490)
                      ...|+.+.|.+.|+......
T Consensus       114 L~lG~~~~A~~aF~~Ai~~~  133 (157)
T PRK15363        114 LACDNVCYAIKALKAVVRIC  133 (157)
T ss_pred             HHcCCHHHHHHHHHHHHHHh
Confidence            99999999999999887654

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.68  E-value=1.4e-05  Score=72.53  Aligned_cols=140  Identities=16%  Similarity=0.141  Sum_probs=95.8

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC-chHHHHHHHHHhh
Q 011249          317 MITAFADHGKSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDLLGR  394 (490)
Q Consensus       317 l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~  394 (490)
                      ....+...|++++|+..++.++..  .|+.. ........+...++..+|.+.++++...   .|+ ......+..+|.+
T Consensus       312 ~A~~~~~~~~~d~A~~~l~~L~~~--~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l---~P~~~~l~~~~a~all~  386 (484)
T COG4783         312 RALQTYLAGQYDEALKLLQPLIAA--QPDNPYYLELAGDILLEANKAKEAIERLKKALAL---DPNSPLLQLNLAQALLK  386 (484)
T ss_pred             HHHHHHHhcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc---CCCccHHHHHHHHHHHh
Confidence            333455677888888888887774  55444 4445556677888888888888888762   333 5555667788888


Q ss_pred             cCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHH
Q 011249          395 SGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKM  472 (490)
Q Consensus       395 ~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~  472 (490)
                      .|++.+|+.+++...  .+.++..|..|..+|...|+..++.....                 ..|.-.|+|++|...+.
T Consensus       387 ~g~~~eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A~A-----------------E~~~~~G~~~~A~~~l~  449 (484)
T COG4783         387 GGKPQEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLARA-----------------EGYALAGRLEQAIIFLM  449 (484)
T ss_pred             cCChHHHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHHHH-----------------HHHHhCCCHHHHHHHHH
Confidence            888888888887665  55577788888888888887777666433                 45555666666666666


Q ss_pred             Hhhhcc
Q 011249          473 MISETE  478 (490)
Q Consensus       473 ~~~~~~  478 (490)
                      ...+..
T Consensus       450 ~A~~~~  455 (484)
T COG4783         450 RASQQV  455 (484)
T ss_pred             HHHHhc
Confidence            655543

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.63  E-value=2.4e-05  Score=65.27  Aligned_cols=243  Identities=14%  Similarity=0.128  Sum_probs=155.8

Q ss_pred             HHhCCChHHHHHHHHHhccC--CchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHH-HHH
Q 011249          158 YANCGNMKAAKEFYDRMTEK--NSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIE-MYK  234 (490)
Q Consensus       158 ~~~~~~~~~a~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~-~~~  234 (490)
                      +.-.|++..++..-......  +...-.-+.++|...|.+.....-...-..+.......+......-++-+.-+. +.+
T Consensus        18 ~fY~Gnyq~~ine~~~~~~~~~~~e~d~y~~raylAlg~~~~~~~eI~~~~~~~lqAvr~~a~~~~~e~~~~~~~~~l~E   97 (299)
T KOG3081|consen   18 YFYLGNYQQCINEAEKFSSSKTDVELDVYMYRAYLALGQYQIVISEIKEGKATPLQAVRLLAEYLELESNKKSILASLYE   97 (299)
T ss_pred             HHHhhHHHHHHHHHHhhccccchhHHHHHHHHHHHHcccccccccccccccCChHHHHHHHHHHhhCcchhHHHHHHHHH
Confidence            34455665555544443322  333344455667777766555444443333555555555555554555444333 444


Q ss_pred             HHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC-CChhH
Q 011249          235 VMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN-KDVIS  313 (490)
Q Consensus       235 ~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~~~~  313 (490)
                      .+......-+......-...|...|++++|.+......      +......=+..+.+..+.+-|.+.+++|.+ .+..+
T Consensus        98 ~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~------~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~ided~t  171 (299)
T KOG3081|consen   98 LVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGE------NLEAAALNVQILLKMHRFDLAEKELKKMQQIDEDAT  171 (299)
T ss_pred             HHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccc------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHccchHHH
Confidence            44444334343444444456888899999988876621      222233335566777888999999999988 45566


Q ss_pred             HHHHHHHHHh----cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHH
Q 011249          314 YSSMITAFAD----HGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMV  389 (490)
Q Consensus       314 ~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  389 (490)
                      .+-|.+++.+    .+....|.-+|++|-+. ..|+..+.+....++...|++++|..+++....  ....++.+...++
T Consensus       172 LtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~--kd~~dpetL~Nli  248 (299)
T KOG3081|consen  172 LTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALD--KDAKDPETLANLI  248 (299)
T ss_pred             HHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHh--ccCCCHHHHHHHH
Confidence            6667776654    35688999999999875 688899999999999999999999999999988  4555677777777


Q ss_pred             HHHhhcCChHHHH-HHHHhcc
Q 011249          390 DLLGRSGQLEKAH-SLIMDYK  409 (490)
Q Consensus       390 ~~~~~~g~~~~A~-~~~~~~~  409 (490)
                      .+-...|...++. +.+.++.
T Consensus       249 v~a~~~Gkd~~~~~r~l~QLk  269 (299)
T KOG3081|consen  249 VLALHLGKDAEVTERNLSQLK  269 (299)
T ss_pred             HHHHHhCCChHHHHHHHHHHH
Confidence            7777777665554 4555555

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.62  E-value=2.9e-06  Score=70.08  Aligned_cols=196  Identities=13%  Similarity=0.080  Sum_probs=130.5

Q ss_pred             ccCChHHHHHHHHHHHh---cC-CCCchh-HHHHHHHHHHhcCChHHHHHHHhcccC--CCh-hHHHHHHHHHHhcCChH
Q 011249          257 QLGDVEMAAILAKHVDE---GC-CDRTNY-VSNALIHMHSKCGYLDLAWREFSRIKN--KDV-ISYSSMITAFADHGKSQ  328 (490)
Q Consensus       257 ~~g~~~~a~~~~~~~~~---~~-~~~~~~-~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~-~~~~~l~~~~~~~~~~~  328 (490)
                      ...+.++..+++.++..   .| ..++.. +|..++-+....|+.+.|...++.+..  |+. .+-..-.-.+-..|+++
T Consensus        24 ~~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~S~RV~~lkam~lEa~~~~~  103 (289)
T KOG3060|consen   24 TVRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRFPGSKRVGKLKAMLLEATGNYK  103 (289)
T ss_pred             cccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhCCCChhHHHHHHHHHHHhhchh
Confidence            45677888888877743   23 344443 344555566677888888888877665  221 11111122344567888


Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhc
Q 011249          329 EALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDY  408 (490)
Q Consensus       329 ~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  408 (490)
                      +|+++++.+.+.. +.|..++..-+...-..|+.-+|++-+....+  .+..|.+.|..+...|...|++++|.-.++++
T Consensus       104 ~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~--~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~  180 (289)
T KOG3060|consen  104 EAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLD--KFMNDQEAWHELAEIYLSEGDFEKAAFCLEEL  180 (289)
T ss_pred             hHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHH--HhcCcHHHHHHHHHHHHhHhHHHHHHHHHHHH
Confidence            8888888888763 33455666555566667777788888888777  57778888888888888888888888888877


Q ss_pred             c-CCC-ChhhHHHHHHHHhhhC---ChHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          409 K-DFC-DAGTWGALLGACKVHV---NAELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       409 ~-~~~-~~~~~~~l~~~~~~~g---~~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      . ..| ++..+..+...+.-.|   +.+.+.++|.+++++.|.+...+..+.
T Consensus       181 ll~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~alkl~~~~~ral~GI~  232 (289)
T KOG3060|consen  181 LLIQPFNPLYFQRLAEVLYTQGGAENLELARKYYERALKLNPKNLRALFGIY  232 (289)
T ss_pred             HHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhChHhHHHHHHHH
Confidence            6 344 5556666666554433   667788888888888886555554443

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=98.55  E-value=0.0001  Score=74.07  Aligned_cols=166  Identities=7%  Similarity=-0.009  Sum_probs=114.3

Q ss_pred             CHhHHHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhc
Q 011249          147 NVISWSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQN  223 (490)
Q Consensus       147 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~  223 (490)
                      +...+..|+..+...+++++|.++.+...+.   ....|-.++..+.+.++.+++.-+             .++......
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~P~~i~~yy~~G~l~~q~~~~~~~~lv-------------~~l~~~~~~   96 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKEHKKSISALYISGILSLSRRPLNDSNLL-------------NLIDSFSQN   96 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCcceehHHHHHHHHHhhcchhhhhhh-------------hhhhhcccc
Confidence            5667888888888899999999998877653   334455555566677765554433             344444455


Q ss_pred             CChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHH
Q 011249          224 GYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREF  303 (490)
Q Consensus       224 g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~  303 (490)
                      .++.-...++..|...+  -+...+..+..+|.+.|+.+++..+|+++.+.. +.++.+.|.+...|... ++++|.+++
T Consensus        97 ~~~~~ve~~~~~i~~~~--~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA~~m~  172 (906)
T PRK14720         97 LKWAIVEHICDKILLYG--ENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKAITYL  172 (906)
T ss_pred             cchhHHHHHHHHHHhhh--hhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHHHHHH
Confidence            55544444555555432  234467778888888888888888888888887 77788888888888888 888888877


Q ss_pred             hcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011249          304 SRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNE  340 (490)
Q Consensus       304 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  340 (490)
                      .+...           .+...+++..+.++|.++...
T Consensus       173 ~KAV~-----------~~i~~kq~~~~~e~W~k~~~~  198 (906)
T PRK14720        173 KKAIY-----------RFIKKKQYVGIEEIWSKLVHY  198 (906)
T ss_pred             HHHHH-----------HHHhhhcchHHHHHHHHHHhc
Confidence            76443           355566777777777777763

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.52  E-value=4e-05  Score=63.55  Aligned_cols=197  Identities=12%  Similarity=0.071  Sum_probs=142.5

Q ss_pred             cCChHHHHHHHHHHHH---cC-cccChh-hHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChH
Q 011249          223 NGYAKAAIEMYKVMRQ---EN-VRISEV-AMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLD  297 (490)
Q Consensus       223 ~g~~~~A~~~~~~~~~---~~-~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  297 (490)
                      ..+.++..+++.++..   .| ..++.. .|..++-+....|+.+.|...++++...- |.+..+-..-.-.+...|+++
T Consensus        25 ~rnseevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f-p~S~RV~~lkam~lEa~~~~~  103 (289)
T KOG3060|consen   25 VRNSEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF-PGSKRVGKLKAMLLEATGNYK  103 (289)
T ss_pred             ccCHHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC-CCChhHHHHHHHHHHHhhchh
Confidence            4568899999988874   34 455554 34455566778899999999999987775 555555444445566789999


Q ss_pred             HHHHHHhcccCC---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Q 011249          298 LAWREFSRIKNK---DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTR  374 (490)
Q Consensus       298 ~A~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  374 (490)
                      +|+++++.+.+.   |..++..-+...-..|+.-+|++-+.+..+. +..|...|.-+...|...|++++|.-.++++.-
T Consensus       104 ~A~e~y~~lL~ddpt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~-F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll  182 (289)
T KOG3060|consen  104 EAIEYYESLLEDDPTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK-FMNDQEAWHELAEIYLSEGDFEKAAFCLEELLL  182 (289)
T ss_pred             hHHHHHHHHhccCcchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH-hcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHH
Confidence            999999998874   4456666666777788888998888888775 667889999999999999999999999999975


Q ss_pred             HcCCCCCchHHHHHHHHHhhcC---ChHHHHHHHHhccCCCChhhHHHHHHHH
Q 011249          375 VFGIKPLTEHLTCMVDLLGRSG---QLEKAHSLIMDYKDFCDAGTWGALLGAC  424 (490)
Q Consensus       375 ~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~~~~~~~~l~~~~  424 (490)
                        ..|.++..+..+.+.+.-.|   +.+-|.++|.+.. +.++.....+...|
T Consensus       183 --~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~al-kl~~~~~ral~GI~  232 (289)
T KOG3060|consen  183 --IQPFNPLYFQRLAEVLYTQGGAENLELARKYYERAL-KLNPKNLRALFGIY  232 (289)
T ss_pred             --cCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH-HhChHhHHHHHHHH
Confidence              44445556667776655444   5677888887766 33333344444333

>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=98.51  E-value=2.4e-06  Score=78.25  Aligned_cols=124  Identities=14%  Similarity=0.065  Sum_probs=102.8

Q ss_pred             HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHH
Q 011249          347 VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGAC  424 (490)
Q Consensus       347 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~  424 (490)
                      .....++..+...++++.|..+++++.+.   .|+  ....+++.+...++-.+|.+++.+..  .+.+...+......|
T Consensus       170 yLv~~Ll~~l~~t~~~~~ai~lle~L~~~---~pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fL  244 (395)
T PF09295_consen  170 YLVDTLLKYLSLTQRYDEAIELLEKLRER---DPE--VAVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFL  244 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHhc---CCc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            34556667777788999999999999874   243  55568888888888899999987766  233556666667778


Q ss_pred             hhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          425 KVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       425 ~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      ...++++.|+.+.+++.+..|++...|..|+.+|.+.|++++|+-.++.+.
T Consensus       245 l~k~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  245 LSKKKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             HhcCCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            899999999999999999999999999999999999999999999999875

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.50  E-value=0.0016  Score=63.94  Aligned_cols=66  Identities=14%  Similarity=0.123  Sum_probs=49.5

Q ss_pred             HHHHHHHHhhhCCh---HHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccccC
Q 011249          417 WGALLGACKVHVNA---ELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKS  482 (490)
Q Consensus       417 ~~~l~~~~~~~g~~---~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~  482 (490)
                      .+.++..|.+.+|.   -+|+-+++......|.|+..-..|+.+|.-.|-...|.++++.+.-+.+..+
T Consensus       439 v~~Lid~~rktnd~~~l~eaI~LLE~glt~s~hnf~~KLlLiriY~~lGa~p~a~~~y~tLdIK~IQ~D  507 (932)
T KOG2053|consen  439 VNHLIDLWRKTNDLTDLFEAITLLENGLTKSPHNFQTKLLLIRIYSYLGAFPDAYELYKTLDIKNIQTD  507 (932)
T ss_pred             HHHHHHHHHhcCcHHHHHHHHHHHHHHhhcCCccHHHHHHHHHHHHHhcCChhHHHHHHhcchHHhhhc
Confidence            35666777777664   4677777777888888888888888888888888888888887765555443

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=98.49  E-value=0.001  Score=61.46  Aligned_cols=154  Identities=14%  Similarity=0.121  Sum_probs=103.1

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHH
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVD  390 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  390 (490)
                      .+|-..+..-.+..-...|..+|.++.+.+..+ +.....+++..++ .++.+-|.++|+.-.+.  +..++......++
T Consensus       367 Lv~~~~mn~irR~eGlkaaR~iF~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkk--f~d~p~yv~~Yld  443 (656)
T KOG1914|consen  367 LVYCQYMNFIRRAEGLKAARKIFKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKK--FGDSPEYVLKYLD  443 (656)
T ss_pred             eehhHHHHHHHHhhhHHHHHHHHHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHh--cCCChHHHHHHHH
Confidence            356666666667777888888888888877666 5556777777665 47778888888887774  3344445566777


Q ss_pred             HHhhcCChHHHHHHHHhccCC---C--ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC----chHHHHHHHHHhc
Q 011249          391 LLGRSGQLEKAHSLIMDYKDF---C--DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT----GNSALLANIYASM  461 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~~~~~---~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~----~~~~~l~~~~~~~  461 (490)
                      -+...++-..|..+|++....   +  ...+|..++.--..-||...+.++-++.....|.+.    ..-..+..-|.-.
T Consensus       444 fL~~lNdd~N~R~LFEr~l~s~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY~~~  523 (656)
T KOG1914|consen  444 FLSHLNDDNNARALFERVLTSVLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRYGIL  523 (656)
T ss_pred             HHHHhCcchhHHHHHHHHHhccCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHHhhc
Confidence            778888888888888877622   2  346888888877888888888888777776555221    1223344455555


Q ss_pred             CCcchHH
Q 011249          462 GKWKDSE  468 (490)
Q Consensus       462 g~~~~A~  468 (490)
                      +.+.--.
T Consensus       524 d~~~c~~  530 (656)
T KOG1914|consen  524 DLYPCSL  530 (656)
T ss_pred             ccccccH
Confidence            5544333

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.48  E-value=4.1e-06  Score=65.74  Aligned_cols=115  Identities=12%  Similarity=-0.007  Sum_probs=91.2

Q ss_pred             HHHHHHHcCCCCcH-HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--
Q 011249          333 MFLKMRNEGIEPNQ-VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--  409 (490)
Q Consensus       333 ~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--  409 (490)
                      .++++..  ..|+. .....+...+...|++++|...++.+..  ..+.+...+..+..++...|++++|..++++..  
T Consensus         5 ~~~~~l~--~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~--~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~   80 (135)
T TIGR02552         5 TLKDLLG--LDSEQLEQIYALAYNLYQQGRYDEALKLFQLLAA--YDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAAL   80 (135)
T ss_pred             hHHHHHc--CChhhHHHHHHHHHHHHHcccHHHHHHHHHHHHH--hCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            4555555  35543 4556667778889999999999999877  345577888889999999999999999998775  


Q ss_pred             CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchH
Q 011249          410 DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       410 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                      .+.+...+..+...+...|++++|...++++++.+|++....
T Consensus        81 ~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~  122 (135)
T TIGR02552        81 DPDDPRPYFHAAECLLALGEPESALKALDLAIEICGENPEYS  122 (135)
T ss_pred             CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHH
Confidence            445667888888889999999999999999999999876643

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>PF12854 PPR_1: PPR repeat

Probab=98.46  E-value=2.2e-07  Score=52.15  Aligned_cols=32  Identities=19%  Similarity=0.386  Sum_probs=15.1

Q ss_pred             CCCCCchHHHHHHHHHhhcCChHHHHHHHHhc
Q 011249          377 GIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDY  408 (490)
Q Consensus       377 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  408 (490)
                      |++||..+|+.|+.+|++.|++++|.++|++|
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            34444444444444444444444444444444

>PF12854 PPR_1: PPR repeat

Probab=98.41  E-value=4.8e-07  Score=50.73  Aligned_cols=34  Identities=26%  Similarity=0.535  Sum_probs=30.5

Q ss_pred             cCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHH
Q 011249          340 EGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMT  373 (490)
Q Consensus       340 ~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  373 (490)
                      .|+.||..||+.+|.+|++.|++++|.++|++|.
T Consensus         1 ~G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    1 RGCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            4789999999999999999999999999999873

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=98.37  E-value=0.0018  Score=58.75  Aligned_cols=444  Identities=9%  Similarity=0.080  Sum_probs=222.3

Q ss_pred             chhhhhhchhhHHHHHHHHhhhcCCC-Cc------hhHhHHHHHHHHHhcCCCCHHHHHHHhccCCCCCCceehHHHHHH
Q 011249            5 YLVPRSKTFNQLKQVHSYLLKTLTKP-HD------QYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRN   77 (490)
Q Consensus         5 ~l~~~~~~~~~~~~~~~~~~~~~~~~-~~------~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~l~~~   77 (490)
                      .+++..++...++.++.++.+   .- .+      .+  .-+.++++|-.++  .+.-...+....+......|-.|..+
T Consensus        14 f~Lqkq~~~~esEkifskI~~---e~~~~~f~lkeEv--l~grilnAffl~n--ld~Me~~l~~l~~~~~~s~~l~LF~~   86 (549)
T PF07079_consen   14 FILQKQKKFQESEKIFSKIYD---EKESSPFLLKEEV--LGGRILNAFFLNN--LDLMEKQLMELRQQFGKSAYLPLFKA   86 (549)
T ss_pred             HHHHHHhhhhHHHHHHHHHHH---HhhcchHHHHHHH--HhhHHHHHHHHhh--HHHHHHHHHHHHHhcCCchHHHHHHH
Confidence            356677788889999888887   43 33      33  4567888887775  45555555544432222667777665


Q ss_pred             H--HhcCChhHHHHHHHHHHhc--CCCCCHh--hHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC------
Q 011249           78 H--VLHAHFRQSILLYAKMHRL--GVLTSGF--TFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE------  145 (490)
Q Consensus        78 ~--~~~g~~~~A~~~~~~m~~~--g~~p~~~--~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~------  145 (490)
                      +  -+.+.+.+|++.+......  +..|.-.  .+..++.-+    -..+..+..+...|++++++.+++++..      
T Consensus        87 L~~Y~~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df----~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE  162 (549)
T PF07079_consen   87 LVAYKQKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDF----FLDEIEAHSLIETGRFSEGRAILNRIIERLLKRE  162 (549)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHH----HHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhh
Confidence            4  4678999999999888765  3333211  111111110    0113445567788888888888887764      


Q ss_pred             --CCHhHHHHHHHHHHhCCChHHHHHHHHHhccC---Cc-hhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHH
Q 011249          146 --RNVISWSAMVAGYANCGNMKAAKEFYDRMTEK---NS-VTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVC  219 (490)
Q Consensus       146 --~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~-~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~  219 (490)
                        -+..+|+.++-.+.+        ..|-++.+.   |. ..|-.++-.|.+.=..-++. -+++. .|.......++..
T Consensus       163 ~~w~~d~yd~~vlmlsr--------SYfLEl~e~~s~dl~pdyYemilfY~kki~~~d~~-~Y~k~-~peeeL~s~imqh  232 (549)
T PF07079_consen  163 CEWNSDMYDRAVLMLSR--------SYFLELKESMSSDLYPDYYEMILFYLKKIHAFDQR-PYEKF-IPEEELFSTIMQH  232 (549)
T ss_pred             hcccHHHHHHHHHHHhH--------HHHHHHHHhcccccChHHHHHHHHHHHHHHHHhhc-hHHhh-CcHHHHHHHHHHH
Confidence              267777776655543        222222211   11 11222222222211000000 00000 0222222222222


Q ss_pred             HHhc--CChHHHHHHHHHHHHcCcccChh-hHHHHHHHHhccCChHHHHHHHHHHHhcCCC----CchhHHHHHHHHHHh
Q 011249          220 YVQN--GYAKAAIEMYKVMRQENVRISEV-AMVGAISACTQLGDVEMAAILAKHVDEGCCD----RTNYVSNALIHMHSK  292 (490)
Q Consensus       220 ~~~~--g~~~~A~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~~~~~l~~~~~~  292 (490)
                      ..-.  .+..--+++++.-.+.-+.|+.. ....+...+.+  +.+++..+-+.+....+.    .-...+..++....+
T Consensus       233 lfi~p~e~l~~~mq~l~~We~~yv~p~~~LVi~~L~~~f~~--~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk  310 (549)
T PF07079_consen  233 LFIVPKERLPPLMQILENWENFYVHPNYDLVIEPLKQQFMS--DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVK  310 (549)
T ss_pred             HHhCCHhhccHHHHHHHHHHhhccCCchhHHHHHHHHHHhc--ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence            2211  11122223333333333344322 12222222222  333443333333222111    112345555666666


Q ss_pred             cCChHHHHHHHhcccC--CChhHH-------HHHHHHHHh----cCChHHHHHHHHHHHHcCCCCcHH-HHHHHHH---H
Q 011249          293 CGYLDLAWREFSRIKN--KDVISY-------SSMITAFAD----HGKSQEALDMFLKMRNEGIEPNQV-TFIGVLT---A  355 (490)
Q Consensus       293 ~~~~~~A~~~~~~~~~--~~~~~~-------~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~---~  355 (490)
                      .++...|.+.+.-+.-  |+...-       ..+-+..+.    .-+...-+.+|+.....  ..|.. ....++.   -
T Consensus       311 ~~~T~~a~q~l~lL~~ldp~~svs~Kllls~~~lq~Iv~~DD~~~Tklr~yL~lwe~~qs~--DiDrqQLvh~L~~~Ak~  388 (549)
T PF07079_consen  311 QVQTEEAKQYLALLKILDPRISVSEKLLLSPKVLQDIVCEDDESYTKLRDYLNLWEEIQSY--DIDRQQLVHYLVFGAKH  388 (549)
T ss_pred             HHhHHHHHHHHHHHHhcCCcchhhhhhhcCHHHHHHHHhcchHHHHHHHHHHHHHHHHHhh--cccHHHHHHHHHHHHHH
Confidence            6666666665554332  222111       111111221    11233345566665553  22332 2222332   2


Q ss_pred             hcCCCC-hHHHHHHHHHHHHHcCCCCCchHHHHHH----HHHhhc---CChHHHHH---HHHhccCCC----ChhhHHHH
Q 011249          356 CSHGGL-VEDGCKQFELMTRVFGIKPLTEHLTCMV----DLLGRS---GQLEKAHS---LIMDYKDFC----DAGTWGAL  420 (490)
Q Consensus       356 ~~~~g~-~~~a~~~~~~~~~~~~~~~~~~~~~~l~----~~~~~~---g~~~~A~~---~~~~~~~~~----~~~~~~~l  420 (490)
                      +-+.|. -++|+++++.+.+  -.+-|..+-+.+.    ..|...   ..+.+-..   .+++...+|    +...-|.|
T Consensus       389 lW~~g~~dekalnLLk~il~--ft~yD~ec~n~v~~fvKq~Y~qaLs~~~~~rLlkLe~fi~e~gl~~i~i~e~eian~L  466 (549)
T PF07079_consen  389 LWEIGQCDEKALNLLKLILQ--FTNYDIECENIVFLFVKQAYKQALSMHAIPRLLKLEDFITEVGLTPITISEEEIANFL  466 (549)
T ss_pred             HHhcCCccHHHHHHHHHHHH--hccccHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCCcccccHHHHHHHH
Confidence            444555 7888899888876  2333333333222    222221   11222221   222222222    34455666


Q ss_pred             HHH--HhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          421 LGA--CKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       421 ~~~--~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      ..+  +...|++.++.-.-..+.+..| ++.+|..+|-++....+|++|+.++.++..
T Consensus       467 aDAEyLysqgey~kc~~ys~WL~~iaP-S~~~~RLlGl~l~e~k~Y~eA~~~l~~LP~  523 (549)
T PF07079_consen  467 ADAEYLYSQGEYHKCYLYSSWLTKIAP-SPQAYRLLGLCLMENKRYQEAWEYLQKLPP  523 (549)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHHhCC-cHHHHHHHHHHHHHHhhHHHHHHHHHhCCC
Confidence            654  4679999999999999999999 799999999999999999999999987654

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=98.34  E-value=0.0039  Score=61.37  Aligned_cols=399  Identities=10%  Similarity=0.069  Sum_probs=212.7

Q ss_pred             HhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHH
Q 011249           45 LQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEA  122 (490)
Q Consensus        45 ~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~  122 (490)
                      ..+.|+ .++|..+++...  .++...+...+-.+|...++.++|..+|++....  .|+......++.+          
T Consensus        53 l~r~gk-~~ea~~~Le~~~~~~~~D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~--~P~eell~~lFma----------  119 (932)
T KOG2053|consen   53 LFRLGK-GDEALKLLEALYGLKGTDDLTLQFLQNVYRDLGKLDEAVHLYERANQK--YPSEELLYHLFMA----------  119 (932)
T ss_pred             HHHhcC-chhHHHHHhhhccCCCCchHHHHHHHHHHHHHhhhhHHHHHHHHHHhh--CCcHHHHHHHHHH----------
Confidence            357788 888988888775  3333377888888899999999999999988775  6666555555554          


Q ss_pred             HHHHHHhcCCH----HHHHHHHhhcCCCCHhHHHHHHHHHHhC-CCh---------HHHHHHHHHhccCC-----chhHH
Q 011249          123 VICGYTKIGLM----DDAQRLFDSMAERNVISWSAMVAGYANC-GNM---------KAAKEFYDRMTEKN-----SVTWV  183 (490)
Q Consensus       123 l~~~~~~~g~~----~~A~~~~~~~~~~~~~~~~~l~~~~~~~-~~~---------~~a~~~~~~~~~~~-----~~~~~  183 (490)
                          |.|.+.+    ..|.++++..++.--..|+ +++...+. ...         .-|.+.++++.+.+     ..-..
T Consensus       120 ----yvR~~~yk~qQkaa~~LyK~~pk~~yyfWs-V~Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~gk~~s~aE~~  194 (932)
T KOG2053|consen  120 ----YVREKSYKKQQKAALQLYKNFPKRAYYFWS-VISLILQSIFSENELLDPILLALAEKMVQKLLEKKGKIESEAEII  194 (932)
T ss_pred             ----HHHHHHHHHHHHHHHHHHHhCCcccchHHH-HHHHHHHhccCCcccccchhHHHHHHHHHHHhccCCccchHHHHH
Confidence                4555444    4466777755443333444 44443332 122         23455555555443     11112


Q ss_pred             HHHHHHHhcCChhHHHHHHhhc-----CCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHH---
Q 011249          184 AMIAGYGKCGEVREAKKVFDEI-----SEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISAC---  255 (490)
Q Consensus       184 ~l~~~~~~~~~~~~A~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~---  255 (490)
                      .-...+...|++++|..++..-     ...+...-+.-+..+...++|.+..++-.++...|.  |.  |...+.+.   
T Consensus       195 Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~Ll~k~~--Dd--y~~~~~sv~kl  270 (932)
T KOG2053|consen  195 LYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRLLEKGN--DD--YKIYTDSVFKL  270 (932)
T ss_pred             HHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHHHHhCC--cc--hHHHHHHHHHH
Confidence            2233445678899999988332     224445556677888889999999999999888753  32  22222211   


Q ss_pred             -------------hccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHH---hcCChHHHHHHH-hcccC-----CCh--
Q 011249          256 -------------TQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHS---KCGYLDLAWREF-SRIKN-----KDV--  311 (490)
Q Consensus       256 -------------~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~---~~~~~~~A~~~~-~~~~~-----~~~--  311 (490)
                                   ...+..+...+...+.....   ....|-+-+.++.   .-|+.+++...| ++.-.     .|.  
T Consensus       271 Le~~~~~~a~~~~s~~~~l~~~~ek~~~~i~~~---~Rgp~LA~lel~kr~~~~gd~ee~~~~y~~kfg~kpcc~~Dl~~  347 (932)
T KOG2053|consen  271 LELLNKEPAEAAHSLSKSLDECIEKAQKNIGSK---SRGPYLARLELDKRYKLIGDSEEMLSYYFKKFGDKPCCAIDLNH  347 (932)
T ss_pred             HHhcccccchhhhhhhhhHHHHHHHHHHhhccc---ccCcHHHHHHHHHHhcccCChHHHHHHHHHHhCCCcHhHhhHHH
Confidence                         11222333333333332221   1222333333333   457888875444 33321     011  


Q ss_pred             -------hHHHHHHHHHH------------------------hcC-----ChHHHHHHHHHHH---HcC------CCCcH
Q 011249          312 -------ISYSSMITAFA------------------------DHG-----KSQEALDMFLKMR---NEG------IEPNQ  346 (490)
Q Consensus       312 -------~~~~~l~~~~~------------------------~~~-----~~~~a~~~~~~~~---~~~------~~p~~  346 (490)
                             .....++..+.                        ..|     ..+....++++..   +.|      .-|+.
T Consensus       348 yl~~l~~~q~~~l~~~l~~~~~~~s~~~k~l~~h~c~l~~~rl~G~~~~l~ad~i~a~~~kl~~~ye~gls~~K~ll~TE  427 (932)
T KOG2053|consen  348 YLGHLNIDQLKSLMSKLVLADDDSSGDEKVLQQHLCVLLLLRLLGLYEKLPADSILAYVRKLKLTYEKGLSLSKDLLPTE  427 (932)
T ss_pred             hhccCCHHHHHHHHHHhhccCCcchhhHHHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHhccccccccccccc
Confidence                   11111222221                        122     1223333333322   223      22332


Q ss_pred             H---------HHHHHHHHhcCCCChH---HHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCC-CC
Q 011249          347 V---------TFIGVLTACSHGGLVE---DGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDF-CD  413 (490)
Q Consensus       347 ~---------~~~~l~~~~~~~g~~~---~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~  413 (490)
                      .         +.+.++..|.+.++..   +|+-+++....  .-+.+..+-..+++.|.-.|-+..|.++|+.+.++ ..
T Consensus       428 ~~~g~~~llLav~~Lid~~rktnd~~~l~eaI~LLE~glt--~s~hnf~~KLlLiriY~~lGa~p~a~~~y~tLdIK~IQ  505 (932)
T KOG2053|consen  428 YSFGDELLLLAVNHLIDLWRKTNDLTDLFEAITLLENGLT--KSPHNFQTKLLLIRIYSYLGAFPDAYELYKTLDIKNIQ  505 (932)
T ss_pred             cccHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhh--cCCccHHHHHHHHHHHHHhcCChhHHHHHHhcchHHhh
Confidence            2         3456667777777765   44455555444  23334444456888999999999999999888722 12


Q ss_pred             hhhHHHHH-HHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHH
Q 011249          414 AGTWGALL-GACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIV  470 (490)
Q Consensus       414 ~~~~~~l~-~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~  470 (490)
                      ..|...++ ..+...|++..+...+....+..-++-.=-..++..-++.|.+.+..++
T Consensus       506 ~DTlgh~~~~~~~t~g~~~~~s~~~~~~lkfy~~~~kE~~eyI~~AYr~g~ySkI~em  563 (932)
T KOG2053|consen  506 TDTLGHLIFRRAETSGRSSFASNTFNEHLKFYDSSLKETPEYIALAYRRGAYSKIPEM  563 (932)
T ss_pred             hccchHHHHHHHHhcccchhHHHHHHHHHHHHhhhhhhhHHHHHHHHHcCchhhhHHH
Confidence            22333333 3345567777777777776664422221112222333445555544443

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=98.34  E-value=8.1e-06  Score=69.92  Aligned_cols=112  Identities=15%  Similarity=0.021  Sum_probs=96.3

Q ss_pred             CCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhh---CChHHHHHHHHHHHhcCCCCCchH
Q 011249          377 GIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVH---VNAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       377 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~---g~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                      ..|-|...|-.|...|...|+.+.|..-|....  .++++..+..+..++...   .+..++..+++++++.+|.++...
T Consensus       151 ~nP~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~~iral  230 (287)
T COG4235         151 QNPGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANIRAL  230 (287)
T ss_pred             hCCCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHH
Confidence            456678999999999999999999999997766  566777888888776443   356899999999999999999999


Q ss_pred             HHHHHHHHhcCCcchHHHHHHHhhhcccccCCCcccc
Q 011249          452 ALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWI  488 (490)
Q Consensus       452 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~  488 (490)
                      ..|+..+.+.|++.+|...++.|.+.....+|+.+-|
T Consensus       231 ~lLA~~afe~g~~~~A~~~Wq~lL~~lp~~~~rr~~i  267 (287)
T COG4235         231 SLLAFAAFEQGDYAEAAAAWQMLLDLLPADDPRRSLI  267 (287)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhcCCCCCchHHHH
Confidence            9999999999999999999999999888777776544

>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=98.33  E-value=4.8e-06  Score=60.65  Aligned_cols=95  Identities=19%  Similarity=0.118  Sum_probs=77.4

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhc
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASM  461 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  461 (490)
                      .+..++..+...|++++|...+++..  .+.+...+..+...+...|++++|.+.++++....|.++..+..++.++...
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYKL   81 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHH
Confidence            34556777888899999999888765  2334466777788888889999999999999999998888899999999999


Q ss_pred             CCcchHHHHHHHhhhcc
Q 011249          462 GKWKDSEIVKMMISETE  478 (490)
Q Consensus       462 g~~~~A~~~~~~~~~~~  478 (490)
                      |++++|...+++..+.+
T Consensus        82 ~~~~~a~~~~~~~~~~~   98 (100)
T cd00189          82 GKYEEALEAYEKALELD   98 (100)
T ss_pred             HhHHHHHHHHHHHHccC
Confidence            99999999998876543

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=98.32  E-value=0.002  Score=57.21  Aligned_cols=241  Identities=20%  Similarity=0.164  Sum_probs=141.0

Q ss_pred             hcCChHHHHHHHHHHHHcCcccCh--hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHH
Q 011249          222 QNGYAKAAIEMYKVMRQENVRISE--VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLA  299 (490)
Q Consensus       222 ~~g~~~~A~~~~~~~~~~~~~p~~--~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  299 (490)
                      -.|+++.|.+-|+.|...   |..  .....|.-...+.|+.+.|.++-+..-..- +.-.....+.+...+..|+++.|
T Consensus       132 ~eG~~~~Ar~kfeAMl~d---PEtRllGLRgLyleAqr~GareaAr~yAe~Aa~~A-p~l~WA~~AtLe~r~~~gdWd~A  207 (531)
T COG3898         132 LEGDYEDARKKFEAMLDD---PETRLLGLRGLYLEAQRLGAREAARHYAERAAEKA-PQLPWAARATLEARCAAGDWDGA  207 (531)
T ss_pred             hcCchHHHHHHHHHHhcC---hHHHHHhHHHHHHHHHhcccHHHHHHHHHHHHhhc-cCCchHHHHHHHHHHhcCChHHH
Confidence            345555565555555531   111  111122222334555666655555554443 33344555556666666666666


Q ss_pred             HHHHhcccC-----CChh--HHHHHHHHHH---hcCChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCCChHHHHHH
Q 011249          300 WREFSRIKN-----KDVI--SYSSMITAFA---DHGKSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGGLVEDGCKQ  368 (490)
Q Consensus       300 ~~~~~~~~~-----~~~~--~~~~l~~~~~---~~~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~  368 (490)
                      +++.+.-..     +++.  .-..|+.+-.   -..+...|...-.+..+  +.||.. .-..-..++.+.|+..++-.+
T Consensus       208 lkLvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~K--L~pdlvPaav~AAralf~d~~~rKg~~i  285 (531)
T COG3898         208 LKLVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANK--LAPDLVPAAVVAARALFRDGNLRKGSKI  285 (531)
T ss_pred             HHHHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhh--cCCccchHHHHHHHHHHhccchhhhhhH
Confidence            666654332     2221  1111222111   12345566665555555  566655 333445678889999999999


Q ss_pred             HHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHH------HhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHh
Q 011249          369 FELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLI------MDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~------~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                      ++.+-+   ..|.+....  +..+.+.|+.  +..-+      +.|. +.+......+..+....|++..|..--+.+..
T Consensus       286 lE~aWK---~ePHP~ia~--lY~~ar~gdt--a~dRlkRa~~L~slk-~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r  357 (531)
T COG3898         286 LETAWK---AEPHPDIAL--LYVRARSGDT--ALDRLKRAKKLESLK-PNNAESSLAVAEAALDAGEFSAARAKAEAAAR  357 (531)
T ss_pred             HHHHHh---cCCChHHHH--HHHHhcCCCc--HHHHHHHHHHHHhcC-ccchHHHHHHHHHHHhccchHHHHHHHHHHhh
Confidence            998865   456666542  2334455543  33322      3333 45666777788888899999999998888888


Q ss_pred             cCCCCCchHHHHHHHHHhc-CCcchHHHHHHHhhhc
Q 011249          443 LGPEKTGNSALLANIYASM-GKWKDSEIVKMMISET  477 (490)
Q Consensus       443 ~~p~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~  477 (490)
                      ..|. .++|..|+.+-... |+-.++...+-+..+.
T Consensus       358 ~~pr-es~~lLlAdIeeAetGDqg~vR~wlAqav~A  392 (531)
T COG3898         358 EAPR-ESAYLLLADIEEAETGDQGKVRQWLAQAVKA  392 (531)
T ss_pred             hCch-hhHHHHHHHHHhhccCchHHHHHHHHHHhcC
Confidence            8888 67788888887655 9999998888776654

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.31  E-value=9.9e-06  Score=61.93  Aligned_cols=91  Identities=10%  Similarity=0.004  Sum_probs=39.8

Q ss_pred             HHHHHHhhcCChHHHHHHHHhcc-CCCC----hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC---CchHHHHHHHH
Q 011249          387 CMVDLLGRSGQLEKAHSLIMDYK-DFCD----AGTWGALLGACKVHVNAELGEIAARHLLELGPEK---TGNSALLANIY  458 (490)
Q Consensus       387 ~l~~~~~~~g~~~~A~~~~~~~~-~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~---~~~~~~l~~~~  458 (490)
                      .++..+.+.|++++|.+.|+.+. ..|+    ...+..+..++...|+++.|...++++....|++   +.++..++.++
T Consensus         7 ~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~   86 (119)
T TIGR02795         7 DAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLGMSL   86 (119)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHHHHH
Confidence            33444444444444444444443 1111    1233334444444455555555555544444442   23344444444


Q ss_pred             HhcCCcchHHHHHHHhhhc
Q 011249          459 ASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       459 ~~~g~~~~A~~~~~~~~~~  477 (490)
                      .+.|++++|...++++.+.
T Consensus        87 ~~~~~~~~A~~~~~~~~~~  105 (119)
T TIGR02795        87 QELGDKEKAKATLQQVIKR  105 (119)
T ss_pred             HHhCChHHHHHHHHHHHHH
Confidence            4555555555555444443

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.

>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=98.31  E-value=1.3e-06  Score=59.19  Aligned_cols=66  Identities=15%  Similarity=0.102  Sum_probs=59.9

Q ss_pred             ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcC-CcchHHHHHHHhhhcc
Q 011249          413 DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMG-KWKDSEIVKMMISETE  478 (490)
Q Consensus       413 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~  478 (490)
                      ++.+|..+...+...|++++|+..|+++++.+|+++.++..++.++.+.| ++++|++.+++..+.+
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~   68 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLD   68 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcC
Confidence            45678888999999999999999999999999999999999999999999 7999999999887653

...

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.30  E-value=1.8e-05  Score=70.21  Aligned_cols=276  Identities=11%  Similarity=-0.008  Sum_probs=140.1

Q ss_pred             HHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCCh
Q 011249          185 MIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDV  261 (490)
Q Consensus       185 l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  261 (490)
                      ....+.+..++.+|+..+....+   .+..-|..-+..+...|++++|.--.++-.+... -.+......-.++...++.
T Consensus        55 ~gn~~yk~k~Y~nal~~yt~Ai~~~pd~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~kd-~~~k~~~r~~~c~~a~~~~  133 (486)
T KOG0550|consen   55 EGNAFYKQKTYGNALKNYTFAIDMCPDNASYYSNRAATLMMLGRFEEALGDARQSVRLKD-GFSKGQLREGQCHLALSDL  133 (486)
T ss_pred             hcchHHHHhhHHHHHHHHHHHHHhCccchhhhchhHHHHHHHHhHhhcccchhhheecCC-CccccccchhhhhhhhHHH
Confidence            34455666677777777766554   3444555566666667777776665555443211 1223445555556666666


Q ss_pred             HHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC-----CChhHHHHHH-HHHHhcCChHHHHHHHH
Q 011249          262 EMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN-----KDVISYSSMI-TAFADHGKSQEALDMFL  335 (490)
Q Consensus       262 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~~~~~~~l~-~~~~~~~~~~~a~~~~~  335 (490)
                      .+|...++.-.         .+           ....++..++.+..     |.-..|..+- .++...|++++|...--
T Consensus       134 i~A~~~~~~~~---------~~-----------~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~ea~  193 (486)
T KOG0550|consen  134 IEAEEKLKSKQ---------AY-----------KAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSEAI  193 (486)
T ss_pred             HHHHHHhhhhh---------hh-----------HHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHHHH
Confidence            66665555211         00           01111122222211     1112222221 24445566666665555


Q ss_pred             HHHHcCCCCcHHHHHHHHH--HhcCCCChHHHHHHHHHHHHHcCCCCCchHHHH-------------HHHHHhhcCChHH
Q 011249          336 KMRNEGIEPNQVTFIGVLT--ACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTC-------------MVDLLGRSGQLEK  400 (490)
Q Consensus       336 ~~~~~~~~p~~~~~~~l~~--~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~-------------l~~~~~~~g~~~~  400 (490)
                      ...+.  .++. .+..+++  ++...++.+.+...|++...   ..|+...-..             =..-..+.|++.+
T Consensus       194 ~ilkl--d~~n-~~al~vrg~~~yy~~~~~ka~~hf~qal~---ldpdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~  267 (486)
T KOG0550|consen  194 DILKL--DATN-AEALYVRGLCLYYNDNADKAINHFQQALR---LDPDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRK  267 (486)
T ss_pred             HHHhc--ccch-hHHHHhcccccccccchHHHHHHHhhhhc---cChhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhH
Confidence            54442  2211 1222222  23344555666666655543   2333221111             1122345666777


Q ss_pred             HHHHHHhcc------CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          401 AHSLIMDYK------DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       401 A~~~~~~~~------~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      |.+.|.+..      ..|+...|.....+..+.|+.++|+.-.+.+++++|.-..+|..-++++...++|++|.+-+++.
T Consensus       268 A~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  268 AYECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEALKIDSSYIKALLRRANCHLALEKWEEAVEDYEKA  347 (486)
T ss_pred             HHHHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777765554      22344445555555666777777777777777777776667777777777777777777777766


Q ss_pred             hhcccccCCCccc
Q 011249          475 SETEKKKSPGCSW  487 (490)
Q Consensus       475 ~~~~~~~~~~~~~  487 (490)
                      .+..-...++.+|
T Consensus       348 ~q~~~s~e~r~~l  360 (486)
T KOG0550|consen  348 MQLEKDCEIRRTL  360 (486)
T ss_pred             HhhccccchHHHH
Confidence            5554444444433

>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=98.28  E-value=3e-05  Score=71.10  Aligned_cols=124  Identities=11%  Similarity=0.022  Sum_probs=96.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCC
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGG  360 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g  360 (490)
                      ....|+..+...++++.|+.+|+++.+.++.....++..+...++-.+|.+++++..+.  .| +...+..-...+.+.+
T Consensus       171 Lv~~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  171 LVDTLLKYLSLTQRYDEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRLLNEALKE--NPQDSELLNLQAEFLLSKK  248 (395)
T ss_pred             HHHHHHHHHhhcccHHHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHhcC
Confidence            44456666777788888888888888877777777888888888888888888888864  33 4455555566678888


Q ss_pred             ChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          361 LVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       361 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                      +.+.|+.+.+++..  -.|.+..+|..|+.+|...|++++|+-.++.++
T Consensus       249 ~~~lAL~iAk~av~--lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  249 KYELALEIAKKAVE--LSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             CHHHHHHHHHHHHH--hCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            88889888888886  455556788888899999999999988888877

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.28  E-value=2.4e-05  Score=62.02  Aligned_cols=84  Identities=12%  Similarity=0.061  Sum_probs=37.2

Q ss_pred             HHHHhhcCChHHHHHHHHhcc-CCCCh----hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCC
Q 011249          389 VDLLGRSGQLEKAHSLIMDYK-DFCDA----GTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGK  463 (490)
Q Consensus       389 ~~~~~~~g~~~~A~~~~~~~~-~~~~~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  463 (490)
                      ...+...|++++|...|+.+. ..|++    .....+...+...|++++|+..++.. ...+-.+..+..++.+|.+.|+
T Consensus        55 A~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~-~~~~~~~~~~~~~Gdi~~~~g~  133 (145)
T PF09976_consen   55 AKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLARILLQQGQYDEALATLQQI-PDEAFKALAAELLGDIYLAQGD  133 (145)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhc-cCcchHHHHHHHHHHHHHHCCC
Confidence            344444455555555544444 11121    12223344444555555555555432 1122233444455555555555


Q ss_pred             cchHHHHHHH
Q 011249          464 WKDSEIVKMM  473 (490)
Q Consensus       464 ~~~A~~~~~~  473 (490)
                      +++|...|++
T Consensus       134 ~~~A~~~y~~  143 (145)
T PF09976_consen  134 YDEARAAYQK  143 (145)
T ss_pred             HHHHHHHHHH
Confidence            5555555543

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=98.26  E-value=3.7e-06  Score=77.37  Aligned_cols=108  Identities=10%  Similarity=-0.071  Sum_probs=91.3

Q ss_pred             HHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCC
Q 011249          352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVN  429 (490)
Q Consensus       352 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~  429 (490)
                      -...+...|++++|+..|+++.+  ..+.+...|..+..+|...|++++|+..++++.  .+.+...|..+..+|...|+
T Consensus         8 ~a~~a~~~~~~~~Ai~~~~~Al~--~~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~   85 (356)
T PLN03088          8 KAKEAFVDDDFALAVDLYTQAID--LDPNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEE   85 (356)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCC
Confidence            34556788999999999999987  445567788888999999999999999998886  44567788889999999999


Q ss_pred             hHHHHHHHHHHHhcCCCCCchHHHHHHHHHhc
Q 011249          430 AELGEIAARHLLELGPEKTGNSALLANIYASM  461 (490)
Q Consensus       430 ~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  461 (490)
                      +++|+..|+++++++|+++.+...+..+..+.
T Consensus        86 ~~eA~~~~~~al~l~P~~~~~~~~l~~~~~kl  117 (356)
T PLN03088         86 YQTAKAALEKGASLAPGDSRFTKLIKECDEKI  117 (356)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHH
Confidence            99999999999999999998888877665444

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.25  E-value=1.9e-06  Score=49.23  Aligned_cols=35  Identities=14%  Similarity=0.262  Sum_probs=32.9

Q ss_pred             eehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCH
Q 011249           69 FLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSG  103 (490)
Q Consensus        69 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~  103 (490)
                      .+||++|.+|++.|++++|.++|++|.+.|+.||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            37999999999999999999999999999999973

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.

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=98.25  E-value=8.1e-07  Score=62.90  Aligned_cols=78  Identities=17%  Similarity=0.067  Sum_probs=51.0

Q ss_pred             cCChHHHHHHHHhcc-CCC---ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHH
Q 011249          395 SGQLEKAHSLIMDYK-DFC---DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIV  470 (490)
Q Consensus       395 ~g~~~~A~~~~~~~~-~~~---~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~  470 (490)
                      .|++++|+.+++++. ..|   +...+..+..++.+.|++++|.+++++ .+.+|.++.....++.++.+.|++++|+++
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~   80 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDPSNPDIHYLLARCLLKLGKYEEAIKA   80 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHHCHHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCCCCHHHHHHHHHHHHHhCCHHHHHHH
Confidence            466677777776665 122   334455567777777777777777777 666666666666677777777777777777


Q ss_pred             HHH
Q 011249          471 KMM  473 (490)
Q Consensus       471 ~~~  473 (490)
                      +++
T Consensus        81 l~~   83 (84)
T PF12895_consen   81 LEK   83 (84)
T ss_dssp             HHH
T ss_pred             Hhc
Confidence            764

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=98.24  E-value=8.5e-05  Score=58.89  Aligned_cols=126  Identities=13%  Similarity=0.089  Sum_probs=85.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc---HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC--chHHHH
Q 011249          313 SYSSMITAFADHGKSQEALDMFLKMRNEGIEPN---QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL--TEHLTC  387 (490)
Q Consensus       313 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~---~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~~  387 (490)
                      .|..++..+ ..++...+...++.+.+.. +.+   ......+...+...|++++|...|+.+... ...|.  ......
T Consensus        14 ~y~~~~~~~-~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~-~~d~~l~~~a~l~   90 (145)
T PF09976_consen   14 LYEQALQAL-QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALAN-APDPELKPLARLR   90 (145)
T ss_pred             HHHHHHHHH-HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh-CCCHHHHHHHHHH
Confidence            344455544 4778888888888888752 222   123344556678888999999999888874 32222  223345


Q ss_pred             HHHHHhhcCChHHHHHHHHhccCC-CChhhHHHHHHHHhhhCChHHHHHHHHHHH
Q 011249          388 MVDLLGRSGQLEKAHSLIMDYKDF-CDAGTWGALLGACKVHVNAELGEIAARHLL  441 (490)
Q Consensus       388 l~~~~~~~g~~~~A~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  441 (490)
                      +...+...|++++|+..++..... ..+..+......+...|++++|...|++++
T Consensus        91 LA~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~Al  145 (145)
T PF09976_consen   91 LARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQKAL  145 (145)
T ss_pred             HHHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHHhC
Confidence            677888889999999888776522 344566667778888899999998888763

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=98.23  E-value=2.4e-06  Score=57.07  Aligned_cols=60  Identities=17%  Similarity=0.120  Sum_probs=50.2

Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +...+...|++++|+..|+++++..|+++.++..++.++...|++++|...++++.+..+
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P   62 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALELDP   62 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence            456678888999999999999999999899999999999999999999999988876544

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=98.22  E-value=0.00046  Score=61.63  Aligned_cols=214  Identities=16%  Similarity=0.164  Sum_probs=116.6

Q ss_pred             ehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCH--hhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCC
Q 011249           70 LWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSG--FTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERN  147 (490)
Q Consensus        70 ~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~--~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  147 (490)
                      .|......|-..|++++|.+.|.+..+.....+.  ..-..+..           ... +.+.+++++|...+++     
T Consensus        37 ~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~-----------Aa~-~~k~~~~~~Ai~~~~~-----   99 (282)
T PF14938_consen   37 LYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEE-----------AAN-CYKKGDPDEAIECYEK-----   99 (282)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHH-----------HHH-HHHHTTHHHHHHHHHH-----
T ss_pred             HHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHH-----------HHH-HHHhhCHHHHHHHHHH-----
Confidence            3444556666777777777777765432111000  00011111           011 1222355555554443     


Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhc-CChhHHHHHHhhcCC-----C----CHHhHHHHH
Q 011249          148 VISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKC-GEVREAKKVFDEISE-----P----DASCWAAMT  217 (490)
Q Consensus       148 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~-~~~~~A~~~~~~~~~-----~----~~~~~~~l~  217 (490)
                            .+..|...|++..|-+++.+           +...|... |++++|++.|++..+     .    -...+..++
T Consensus       100 ------A~~~y~~~G~~~~aA~~~~~-----------lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A  162 (282)
T PF14938_consen  100 ------AIEIYREAGRFSQAAKCLKE-----------LAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAA  162 (282)
T ss_dssp             ------HHHHHHHCT-HHHHHHHHHH-----------HHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             ------HHHHHHhcCcHHHHHHHHHH-----------HHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHH
Confidence                  45667777777777666654           45666666 777777777766543     1    123566778


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCcc-----cChh-hHHHHHHHHhccCChHHHHHHHHHHHhcC--CCCc--hhHHHHHH
Q 011249          218 VCYVQNGYAKAAIEMYKVMRQENVR-----ISEV-AMVGAISACTQLGDVEMAAILAKHVDEGC--CDRT--NYVSNALI  287 (490)
Q Consensus       218 ~~~~~~g~~~~A~~~~~~~~~~~~~-----p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~--~~~~--~~~~~~l~  287 (490)
                      ..+.+.|++++|+++|++.......     .+.. .+...+-++...||...|...++......  +..+  ..+...|+
T Consensus       163 ~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~  242 (282)
T PF14938_consen  163 DLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLL  242 (282)
T ss_dssp             HHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHH
T ss_pred             HHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHH
Confidence            8889999999999999988764322     2222 23334446667788999999888887553  2222  33455566


Q ss_pred             HHHHh--cCChHHHHHHHhcccCCChhHHHHH
Q 011249          288 HMHSK--CGYLDLAWREFSRIKNKDVISYSSM  317 (490)
Q Consensus       288 ~~~~~--~~~~~~A~~~~~~~~~~~~~~~~~l  317 (490)
                      .++-.  ...++.+..-|+.+.+-|..--..|
T Consensus       243 ~A~~~~D~e~f~~av~~~d~~~~ld~w~~~~l  274 (282)
T PF14938_consen  243 EAYEEGDVEAFTEAVAEYDSISRLDNWKTKML  274 (282)
T ss_dssp             HHHHTT-CCCHHHHCHHHTTSS---HHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHcccCccHHHHHHHH
Confidence            66654  2456777777777776555433333

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=98.19  E-value=3.3e-05  Score=58.96  Aligned_cols=106  Identities=8%  Similarity=0.063  Sum_probs=72.7

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCC-CchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCC----hhhHHHHH
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKP-LTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD----AGTWGALL  421 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~----~~~~~~l~  421 (490)
                      ++..++..+...|++++|.+.+..+...+.-.+ ....+..+..++.+.|++++|...|+.+. ..|+    +..+..+.
T Consensus         4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~   83 (119)
T TIGR02795         4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG   83 (119)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence            445556666777888888888887776421111 13455567778888888888888887765 2232    34566777


Q ss_pred             HHHhhhCChHHHHHHHHHHHhcCCCCCchHHH
Q 011249          422 GACKVHVNAELGEIAARHLLELGPEKTGNSAL  453 (490)
Q Consensus       422 ~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~  453 (490)
                      .++...|+.++|...++++.+..|+++.....
T Consensus        84 ~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~  115 (119)
T TIGR02795        84 MSLQELGDKEKAKATLQQVIKRYPGSSAAKLA  115 (119)
T ss_pred             HHHHHhCChHHHHHHHHHHHHHCcCChhHHHH
Confidence            77888888889999998888888887665443

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.

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.18  E-value=1.5e-05  Score=67.81  Aligned_cols=107  Identities=12%  Similarity=-0.053  Sum_probs=62.0

Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHHHhhhCChHHH
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      ..+.+++++|+..|.++++  -.+-|...|..-..+|.+.|.++.|++-.+... ..| ...+|..|..+|...|++++|
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~--l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A  168 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIE--LDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEA  168 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHh--cCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHH
Confidence            3445666666666666654  233344445555566666666666666655544 222 344666666666666666666


Q ss_pred             HHHHHHHHhcCCCCCchHHHHHHHHHhcCCc
Q 011249          434 EIAARHLLELGPEKTGNSALLANIYASMGKW  464 (490)
Q Consensus       434 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  464 (490)
                      ++.|+++++++|++......|-.+-.+.+..
T Consensus       169 ~~aykKaLeldP~Ne~~K~nL~~Ae~~l~e~  199 (304)
T KOG0553|consen  169 IEAYKKALELDPDNESYKSNLKIAEQKLNEP  199 (304)
T ss_pred             HHHHHhhhccCCCcHHHHHHHHHHHHHhcCC
Confidence            6666666666666665555555554444433

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.16  E-value=3.3e-06  Score=47.79  Aligned_cols=33  Identities=18%  Similarity=0.325  Sum_probs=31.8

Q ss_pred             eehHHHHHHHHhcCChhHHHHHHHHHHhcCCCC
Q 011249           69 FLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLT  101 (490)
Q Consensus        69 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p  101 (490)
                      .+|+.++.+|++.|+++.|.++|++|.+.|+.|
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            689999999999999999999999999999988

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=98.16  E-value=3.6e-05  Score=70.93  Aligned_cols=101  Identities=9%  Similarity=-0.019  Sum_probs=79.6

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhc
Q 011249          317 MITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRS  395 (490)
Q Consensus       317 l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  395 (490)
                      ....+...|++++|+..|+++++.  .| +...+..+..+|...|++++|+..++++..  -.+.+...|..+..+|...
T Consensus         8 ~a~~a~~~~~~~~Ai~~~~~Al~~--~P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~--l~P~~~~a~~~lg~~~~~l   83 (356)
T PLN03088          8 KAKEAFVDDDFALAVDLYTQAIDL--DPNNAELYADRAQANIKLGNFTEAVADANKAIE--LDPSLAKAYLRKGTACMKL   83 (356)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hCcCCHHHHHHHHHHHHHh
Confidence            345667789999999999999985  44 456778888889999999999999999987  3445677888889999999


Q ss_pred             CChHHHHHHHHhcc-CCCChhhHHHHH
Q 011249          396 GQLEKAHSLIMDYK-DFCDAGTWGALL  421 (490)
Q Consensus       396 g~~~~A~~~~~~~~-~~~~~~~~~~l~  421 (490)
                      |++++|...|++.. ..|+.......+
T Consensus        84 g~~~eA~~~~~~al~l~P~~~~~~~~l  110 (356)
T PLN03088         84 EEYQTAKAALEKGASLAPGDSRFTKLI  110 (356)
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            99999999998876 445544444443

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.08  E-value=0.011  Score=57.17  Aligned_cols=353  Identities=10%  Similarity=0.055  Sum_probs=201.4

Q ss_pred             HHhcCChhHHHHHHHHH--------HhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCC--
Q 011249           78 HVLHAHFRQSILLYAKM--------HRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERN--  147 (490)
Q Consensus        78 ~~~~g~~~~A~~~~~~m--------~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--  147 (490)
                      +.+.-++++-..+.+..        ..-|++.+..-|..+=.         ..++.-+...+.+..|+++-+.+..|.  
T Consensus       399 ~l~~~~~d~~~~v~~~lrVln~~r~~~~gIplT~~qy~~l~~---------~~vi~Rl~~r~~Y~vaIQva~~l~~p~~~  469 (829)
T KOG2280|consen  399 SLRTPNPDEYMRVCRELRVLNALRDVRIGIPLTHEQYRHLSE---------EVVIDRLVDRHLYSVAIQVAKLLNLPESQ  469 (829)
T ss_pred             ccccCChHHHHHHHHHHHHHhhhcccccCccccHHHHhhhch---------hhhhHHHHhcchhHHHHHHHHHhCCcccc
Confidence            33444556555555443        33466666666655533         336667888899999999999988775  


Q ss_pred             -HhHHHHHHHHHHhCCC---hHHHHHHHHHhcc--CCchhHHHHHHHHHhcCChhHHHHHHhhcCC--------CCHHhH
Q 011249          148 -VISWSAMVAGYANCGN---MKAAKEFYDRMTE--KNSVTWVAMIAGYGKCGEVREAKKVFDEISE--------PDASCW  213 (490)
Q Consensus       148 -~~~~~~l~~~~~~~~~---~~~a~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--------~~~~~~  213 (490)
                       ...|.....-+.+..+   .+-+..+-+++..  -...+|..++......|+.+-|..+++.=..        -+..-+
T Consensus       470 ~~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~~~~~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~  549 (829)
T KOG2280|consen  470 GDRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAKLTPGISYAAIARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDS  549 (829)
T ss_pred             ccHHHHHHHHHHHhccCccchHHHHHHHHHhcccCCCceeHHHHHHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchH
Confidence             5667777777776632   2333334444444  3667888899888899999999999876443        122233


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc
Q 011249          214 AAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC  293 (490)
Q Consensus       214 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  293 (490)
                      ..-+.-..+.|+.+....++-.+.+.-   +...|...+      .+...|..+|.+..+..-..      .+-+.|-. 
T Consensus       550 ~~AL~kaies~d~~Li~~Vllhlk~~~---~~s~l~~~l------~~~p~a~~lY~~~~r~~~~~------~l~d~y~q-  613 (829)
T KOG2280|consen  550 SLALKKAIESGDTDLIIQVLLHLKNKL---NRSSLFMTL------RNQPLALSLYRQFMRHQDRA------TLYDFYNQ-  613 (829)
T ss_pred             HHHHHHHHhcCCchhHHHHHHHHHHHH---HHHHHHHHH------HhchhhhHHHHHHHHhhchh------hhhhhhhc-
Confidence            444555666777777766666665421   111222211      23445556665554421111      01111111 


Q ss_pred             CChHHHHHHHh--cc-----cCCChhHHHHHHHHHHhcCC----------hHHHHHHHHHHHH-cCCCCcHHHHHHHHHH
Q 011249          294 GYLDLAWREFS--RI-----KNKDVISYSSMITAFADHGK----------SQEALDMFLKMRN-EGIEPNQVTFIGVLTA  355 (490)
Q Consensus       294 ~~~~~A~~~~~--~~-----~~~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~-~~~~p~~~~~~~l~~~  355 (490)
                      ++-.++...|.  ..     .++-.........++.+...          ..+-+++.+.+.. .|......+.+--+.-
T Consensus       614 ~dn~~~~a~~~~q~~~~~~~~~~r~~~lk~~a~~~a~sk~~s~e~ka~ed~~kLl~lQ~~Le~q~~~~f~dlSl~dTv~~  693 (829)
T KOG2280|consen  614 DDNHQALASFHLQASYAAETIEGRIPALKTAANAFAKSKEKSFEAKALEDQMKLLKLQRTLEDQFGGSFVDLSLHDTVTT  693 (829)
T ss_pred             ccchhhhhhhhhhhhhhhhhhcccchhHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHhccccccCcHHHHHHH
Confidence            11111111111  10     01111122223333333322          1122223333322 2323333344555555


Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHH
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEI  435 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~  435 (490)
                      +...|+..+|.++-.+.+     -||-..|..-+.+++..+++++-+++-+...   .+..|.-...+|.+.|+.++|.+
T Consensus       694 li~~g~~k~a~ql~~~Fk-----ipdKr~~wLk~~aLa~~~kweeLekfAkskk---sPIGy~PFVe~c~~~~n~~EA~K  765 (829)
T KOG2280|consen  694 LILIGQNKRAEQLKSDFK-----IPDKRLWWLKLTALADIKKWEELEKFAKSKK---SPIGYLPFVEACLKQGNKDEAKK  765 (829)
T ss_pred             HHHccchHHHHHHHHhcC-----CcchhhHHHHHHHHHhhhhHHHHHHHHhccC---CCCCchhHHHHHHhcccHHHHhh
Confidence            666788888877766653     3677788778888899999988888777665   36677778888999999998888


Q ss_pred             HHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHH
Q 011249          436 AARHLLELGPEKTGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       436 ~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      ++-+...        +...+.+|.+.|++.+|.+.-
T Consensus       766 Yiprv~~--------l~ekv~ay~~~~~~~eAad~A  793 (829)
T KOG2280|consen  766 YIPRVGG--------LQEKVKAYLRVGDVKEAADLA  793 (829)
T ss_pred             hhhccCC--------hHHHHHHHHHhccHHHHHHHH
Confidence            7765432        225667777778877777654

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.08  E-value=1.1e-05  Score=68.66  Aligned_cols=91  Identities=14%  Similarity=0.083  Sum_probs=80.9

Q ss_pred             HHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchH
Q 011249          390 DLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDS  467 (490)
Q Consensus       390 ~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  467 (490)
                      .-+.+.+++++|+..|.+..  .+.|+..|..-..+|.+.|.++.|++-.+.++.++|....+|..|+.+|...|++++|
T Consensus        89 N~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~iDp~yskay~RLG~A~~~~gk~~~A  168 (304)
T KOG0553|consen   89 NKLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALSIDPHYSKAYGRLGLAYLALGKYEEA  168 (304)
T ss_pred             HHHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHhcChHHHHHHHHHHHHHHccCcHHHH
Confidence            34567899999999998877  4557778888889999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhcccc
Q 011249          468 EIVKMMISETEKK  480 (490)
Q Consensus       468 ~~~~~~~~~~~~~  480 (490)
                      ++.|++..+..+.
T Consensus       169 ~~aykKaLeldP~  181 (304)
T KOG0553|consen  169 IEAYKKALELDPD  181 (304)
T ss_pred             HHHHHhhhccCCC
Confidence            9999988766543

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.06  E-value=8.4e-06  Score=46.45  Aligned_cols=34  Identities=15%  Similarity=0.302  Sum_probs=30.3

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCcccCh
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISE  245 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~  245 (490)
                      +|+.++.+|++.|++++|.++|++|.+.|+.||.
T Consensus         2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         2 TYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            6899999999999999999999999999988873

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.

>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=98.05  E-value=6.7e-06  Score=55.48  Aligned_cols=55  Identities=15%  Similarity=0.197  Sum_probs=43.5

Q ss_pred             hhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          425 KVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       425 ~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ...|++++|++.|+++.+.+|+++.++..++.+|.+.|++++|.++++++.....
T Consensus         2 l~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~   56 (68)
T PF14559_consen    2 LKQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDP   56 (68)
T ss_dssp             HHTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGT
T ss_pred             hhccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence            3567888888888888888888888888888888888888888888887776544

...

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=98.04  E-value=0.014  Score=56.07  Aligned_cols=69  Identities=13%  Similarity=0.189  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccC-----CchhHHHHHHHHHhcCChhHHHHHHhh
Q 011249          131 GLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEK-----NSVTWVAMIAGYGKCGEVREAKKVFDE  204 (490)
Q Consensus       131 g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-----~~~~~~~l~~~~~~~~~~~~A~~~~~~  204 (490)
                      |++++|++++-++.++|.     .+....+.|++-.+.++++.--..     -...|+.+...+.....|++|.+.|..
T Consensus       748 g~feeaek~yld~drrDL-----Aielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~fa~~~~We~A~~yY~~  821 (1189)
T KOG2041|consen  748 GEFEEAEKLYLDADRRDL-----AIELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGETFAEMMEWEEAAKYYSY  821 (1189)
T ss_pred             cchhHhhhhhhccchhhh-----hHHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            566666666655555443     234444555555555555442211     123455555555555555555555544

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.04  E-value=9.8e-06  Score=45.80  Aligned_cols=33  Identities=18%  Similarity=0.415  Sum_probs=27.3

Q ss_pred             HhHHHHHHHHHhcCChHHHHHHHHHHHHcCccc
Q 011249          211 SCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRI  243 (490)
Q Consensus       211 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p  243 (490)
                      .+|+.++.+|.+.|+++.|.++|++|.+.|++|
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            478888888888888888888888888888776

>PRK15331 chaperone protein SicA; Provisional

Probab=98.03  E-value=4.3e-05  Score=59.67  Aligned_cols=89  Identities=12%  Similarity=0.046  Sum_probs=71.2

Q ss_pred             HHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcc
Q 011249          388 MVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWK  465 (490)
Q Consensus       388 l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  465 (490)
                      ...-+...|++++|..+|+-+.  .+-++..|..|..++-..+++++|+..|..+..++++||..+...+.+|...|+.+
T Consensus        43 ~Ay~~y~~Gk~~eA~~~F~~L~~~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~agqC~l~l~~~~  122 (165)
T PRK15331         43 HAYEFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKAA  122 (165)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCHH
Confidence            3444567788888888887665  45567777788888888888888888888888888888888888888888888888


Q ss_pred             hHHHHHHHhhh
Q 011249          466 DSEIVKMMISE  476 (490)
Q Consensus       466 ~A~~~~~~~~~  476 (490)
                      .|...|+...+
T Consensus       123 ~A~~~f~~a~~  133 (165)
T PRK15331        123 KARQCFELVNE  133 (165)
T ss_pred             HHHHHHHHHHh
Confidence            88888887665

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=98.01  E-value=0.00019  Score=58.78  Aligned_cols=131  Identities=11%  Similarity=0.106  Sum_probs=86.7

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc--HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHH
Q 011249          310 DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN--QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTC  387 (490)
Q Consensus       310 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~  387 (490)
                      ....+..+...+...|++++|...|++..+....+.  ...+..+...+.+.|++++|...+++....  .+.+...+..
T Consensus        34 ~a~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~  111 (172)
T PRK02603         34 EAFVYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALEL--NPKQPSALNN  111 (172)
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHH
Confidence            344566677777778888888888888776432222  346677777788888888888888888762  3334555666


Q ss_pred             HHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCC
Q 011249          388 MVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGK  463 (490)
Q Consensus       388 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  463 (490)
                      +..++...|+...+..-++...                  ..+++|.++++++.+.+|++   |..++..+...|+
T Consensus       112 lg~~~~~~g~~~~a~~~~~~A~------------------~~~~~A~~~~~~a~~~~p~~---~~~~~~~~~~~~~  166 (172)
T PRK02603        112 IAVIYHKRGEKAEEAGDQDEAE------------------ALFDKAAEYWKQAIRLAPNN---YIEAQNWLKTTGR  166 (172)
T ss_pred             HHHHHHHcCChHhHhhCHHHHH------------------HHHHHHHHHHHHHHhhCchh---HHHHHHHHHhcCc
Confidence            6777777777666554333221                  23678888999988888886   4444445544443

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=98.01  E-value=5.4e-05  Score=62.06  Aligned_cols=95  Identities=12%  Similarity=-0.070  Sum_probs=64.6

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc-CCCC----hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHH
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD----AGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY  458 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  458 (490)
                      .+..+...+...|++++|...|++.. ..|+    ...+..+...+...|++++|...++++++..|.++..+..++.++
T Consensus        37 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~  116 (172)
T PRK02603         37 VYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQPSALNNIAVIY  116 (172)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            44555666666677777777766554 1111    346667777777888888888888888888888777777788787


Q ss_pred             HhcCC--------------cchHHHHHHHhhhcc
Q 011249          459 ASMGK--------------WKDSEIVKMMISETE  478 (490)
Q Consensus       459 ~~~g~--------------~~~A~~~~~~~~~~~  478 (490)
                      ...|+              +++|.+.+++....+
T Consensus       117 ~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~~~  150 (172)
T PRK02603        117 HKRGEKAEEAGDQDEAEALFDKAAEYWKQAIRLA  150 (172)
T ss_pred             HHcCChHhHhhCHHHHHHHHHHHHHHHHHHHhhC
Confidence            77766              456666666665543

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=98.01  E-value=1.9e-05  Score=52.68  Aligned_cols=61  Identities=16%  Similarity=0.128  Sum_probs=50.7

Q ss_pred             HHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC
Q 011249          388 MVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       388 l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      +...+...|++++|.+.|+++.  .+.+...+..+..++...|++++|...|+++++..|++|
T Consensus         3 ~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~~p   65 (65)
T PF13432_consen    3 LARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALELDPDNP   65 (65)
T ss_dssp             HHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-H
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCC
Confidence            4667889999999999998887  333667888889999999999999999999999999875

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=98.00  E-value=0.00031  Score=62.68  Aligned_cols=149  Identities=13%  Similarity=0.062  Sum_probs=86.8

Q ss_pred             ChHHHHHHHHHHHHc---CCCCcH--HHHHHHHHHhcCC-CChHHHHHHHHHHHHHcCCCCC----chHHHHHHHHHhhc
Q 011249          326 KSQEALDMFLKMRNE---GIEPNQ--VTFIGVLTACSHG-GLVEDGCKQFELMTRVFGIKPL----TEHLTCMVDLLGRS  395 (490)
Q Consensus       326 ~~~~a~~~~~~~~~~---~~~p~~--~~~~~l~~~~~~~-g~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~  395 (490)
                      ++++|...+++..+.   .-.|+.  ..+..+...|... |++++|.+.|++..+-+.....    ..++..++..+.+.
T Consensus        89 ~~~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l  168 (282)
T PF14938_consen   89 DPDEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARL  168 (282)
T ss_dssp             THHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHh
Confidence            555555555554431   112222  2455566677777 8999999999888774322222    34456778888999


Q ss_pred             CChHHHHHHHHhccC----CC----Chh-hHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc-----hHHHHHHHHHhc
Q 011249          396 GQLEKAHSLIMDYKD----FC----DAG-TWGALLGACKVHVNAELGEIAARHLLELGPEKTG-----NSALLANIYASM  461 (490)
Q Consensus       396 g~~~~A~~~~~~~~~----~~----~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~-----~~~~l~~~~~~~  461 (490)
                      |++++|.++|+++..    .+    +.. .+...+-.+...||...|.+.+++....+|....     +...|+.++...
T Consensus       169 ~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~  248 (282)
T PF14938_consen  169 GRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEG  248 (282)
T ss_dssp             T-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhC
Confidence            999999999987651    11    111 2233334566788999999999999988875433     444555555432


Q ss_pred             --CCcchHHHHHHHh
Q 011249          462 --GKWKDSEIVKMMI  474 (490)
Q Consensus       462 --g~~~~A~~~~~~~  474 (490)
                        ..++++..-|+.+
T Consensus       249 D~e~f~~av~~~d~~  263 (282)
T PF14938_consen  249 DVEAFTEAVAEYDSI  263 (282)
T ss_dssp             -CCCHHHHCHHHTTS
T ss_pred             CHHHHHHHHHHHccc
Confidence              2344444444444

>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=97.99  E-value=7e-05  Score=54.27  Aligned_cols=90  Identities=17%  Similarity=-0.018  Sum_probs=44.6

Q ss_pred             HHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChH
Q 011249          354 TACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAE  431 (490)
Q Consensus       354 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~  431 (490)
                      ..+...|++++|...++.+.+  ..+.+...+..+..++...|++++|.+.++...  .+.+..++..+...+...|+++
T Consensus         8 ~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (100)
T cd00189           8 NLYYKLGDYDEALEYYEKALE--LDPDNADAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAYYKLGKYE   85 (100)
T ss_pred             HHHHHHhcHHHHHHHHHHHHh--cCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHHHhHH
Confidence            334444555555555555443  122222344444555555555555555554433  1222334555555556666666


Q ss_pred             HHHHHHHHHHhcCC
Q 011249          432 LGEIAARHLLELGP  445 (490)
Q Consensus       432 ~a~~~~~~~~~~~p  445 (490)
                      .|...++++.+..|
T Consensus        86 ~a~~~~~~~~~~~~   99 (100)
T cd00189          86 EALEAYEKALELDP   99 (100)
T ss_pred             HHHHHHHHHHccCC
Confidence            66666666655544

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.96  E-value=2.3e-05  Score=53.76  Aligned_cols=58  Identities=14%  Similarity=0.025  Sum_probs=48.9

Q ss_pred             HHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          422 GACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       422 ~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ..+.+.+++++|.++++++++.+|+++..+...+.++.+.|++++|.+.+++..+.++
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p   60 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELSP   60 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCC
Confidence            4567788888888888888888888888888888888888888888888888877655

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.94  E-value=0.0018  Score=51.28  Aligned_cols=130  Identities=12%  Similarity=0.038  Sum_probs=77.4

Q ss_pred             ccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC-----CChhHHHH
Q 011249          242 RISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN-----KDVISYSS  316 (490)
Q Consensus       242 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~~~~~~~  316 (490)
                      .|+......|..+....|+..+|...|++....-+..|......+.++....++...|...++++.+     .++.+...
T Consensus        86 ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~Ll  165 (251)
T COG4700          86 APTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGHLL  165 (251)
T ss_pred             chhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCchHH
Confidence            5566666666677777777777777777766655566666666666666666666666666666554     23344455


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHH
Q 011249          317 MITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMT  373 (490)
Q Consensus       317 l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  373 (490)
                      +...+...|.+..|+..|+.....  -|+...-......+.++|+.+++..-+..+.
T Consensus       166 ~aR~laa~g~~a~Aesafe~a~~~--ypg~~ar~~Y~e~La~qgr~~ea~aq~~~v~  220 (251)
T COG4700         166 FARTLAAQGKYADAESAFEVAISY--YPGPQARIYYAEMLAKQGRLREANAQYVAVV  220 (251)
T ss_pred             HHHHHHhcCCchhHHHHHHHHHHh--CCCHHHHHHHHHHHHHhcchhHHHHHHHHHH
Confidence            556666666666666666666663  4444333333333455565555544444433

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=97.92  E-value=0.0013  Score=52.14  Aligned_cols=130  Identities=10%  Similarity=0.010  Sum_probs=78.4

Q ss_pred             CCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC---ChhhH
Q 011249          342 IEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC---DAGTW  417 (490)
Q Consensus       342 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~---~~~~~  417 (490)
                      ..|+...-..|..+....|+..+|...|++.... -+..|......+.++....+++..|...++++- ..|   ++.+.
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG-~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd~~  163 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALSG-IFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPDGH  163 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhcc-ccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCCch
Confidence            3555555555666666667777777777666652 344555666666666666677777766665554 111   23344


Q ss_pred             HHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHH
Q 011249          418 GALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMM  473 (490)
Q Consensus       418 ~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~  473 (490)
                      ..+...+...|.++.|+..|+.+....|+ +......+..+.++|+.+++..-+..
T Consensus       164 Ll~aR~laa~g~~a~Aesafe~a~~~ypg-~~ar~~Y~e~La~qgr~~ea~aq~~~  218 (251)
T COG4700         164 LLFARTLAAQGKYADAESAFEVAISYYPG-PQARIYYAEMLAKQGRLREANAQYVA  218 (251)
T ss_pred             HHHHHHHHhcCCchhHHHHHHHHHHhCCC-HHHHHHHHHHHHHhcchhHHHHHHHH
Confidence            45556666677777777777777776665 55555556666666766655544433

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=97.92  E-value=0.017  Score=52.66  Aligned_cols=135  Identities=14%  Similarity=0.086  Sum_probs=104.9

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHH
Q 011249          310 DVISYSSMITAFADHGKSQEALDMFLKMRNEG-IEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCM  388 (490)
Q Consensus       310 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l  388 (490)
                      -..+|...+..-.+....+.|..+|-+..+.| +.++...+++++..++ .|+..-|..+|+.-..  .++.++...+..
T Consensus       396 ~t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~--~f~d~~~y~~ky  472 (660)
T COG5107         396 LTFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLL--KFPDSTLYKEKY  472 (660)
T ss_pred             hhhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHH--hCCCchHHHHHH
Confidence            34567777887778888899999999999988 6677788888888665 5788889999988776  344444444567


Q ss_pred             HHHHhhcCChHHHHHHHHhcc----CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC
Q 011249          389 VDLLGRSGQLEKAHSLIMDYK----DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK  447 (490)
Q Consensus       389 ~~~~~~~g~~~~A~~~~~~~~----~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~  447 (490)
                      +..+.+.++-+.|..+|+...    ...-..+|..++.--...|+...+..+-+++.+..|..
T Consensus       473 l~fLi~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~~pQe  535 (660)
T COG5107         473 LLFLIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRELVPQE  535 (660)
T ss_pred             HHHHHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHHcCcH
Confidence            777889999999999998554    22235688888888888899988888888888877763

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.91  E-value=7.3e-05  Score=61.08  Aligned_cols=92  Identities=10%  Similarity=-0.209  Sum_probs=70.6

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc-CCC----ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC----DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLAN  456 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~  456 (490)
                      ...+..++..+...|++++|...|++.. ..|    ...++..+...+...|++++|+..++++++..|.....+..++.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~  114 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAV  114 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHH
Confidence            4555667777778888888888887764 222    23477888888999999999999999999999988888888888


Q ss_pred             HHH-------hcCCcchHHHHHHH
Q 011249          457 IYA-------SMGKWKDSEIVKMM  473 (490)
Q Consensus       457 ~~~-------~~g~~~~A~~~~~~  473 (490)
                      ++.       +.|++++|+..+++
T Consensus       115 i~~~~~~~~~~~g~~~~A~~~~~~  138 (168)
T CHL00033        115 ICHYRGEQAIEQGDSEIAEAWFDQ  138 (168)
T ss_pred             HHHHhhHHHHHcccHHHHHHHHHH
Confidence            888       77887755555543

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.90  E-value=0.00023  Score=68.55  Aligned_cols=139  Identities=12%  Similarity=0.013  Sum_probs=76.5

Q ss_pred             CChhHHHHHHHHHHh--cC---ChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCC--------ChHHHHHHHHHHHH
Q 011249          309 KDVISYSSMITAFAD--HG---KSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGG--------LVEDGCKQFELMTR  374 (490)
Q Consensus       309 ~~~~~~~~l~~~~~~--~~---~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g--------~~~~a~~~~~~~~~  374 (490)
                      .+...|...+.+...  .+   +...|..+|+++++  ..|+.. .+..+..++....        +...+.+...+...
T Consensus       335 ~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~--ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a~a  412 (517)
T PRK10153        335 HQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILK--SEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNIVA  412 (517)
T ss_pred             CCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH--hCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhhh
Confidence            466677776665433  22   25677777777777  356543 4444433332111        12222333333222


Q ss_pred             HcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          375 VFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       375 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                      ....+.++..|..+.......|++++|...+++.. ..|+...|..+...+...|+.++|.+.++++..++|.++.
T Consensus       413 l~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~pt  488 (517)
T PRK10153        413 LPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMSWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGENT  488 (517)
T ss_pred             cccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCch
Confidence            10123334555555555556677777777776655 4456666666666777777777777777777777777665

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.89  E-value=0.00056  Score=65.98  Aligned_cols=141  Identities=11%  Similarity=-0.015  Sum_probs=94.5

Q ss_pred             CCCcHHHHHHHHHHh--cCC---CChHHHHHHHHHHHHHcCCCCC-chHHHHHHHHHhhc--------CChHHHHHHHHh
Q 011249          342 IEPNQVTFIGVLTAC--SHG---GLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDLLGRS--------GQLEKAHSLIMD  407 (490)
Q Consensus       342 ~~p~~~~~~~l~~~~--~~~---g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~--------g~~~~A~~~~~~  407 (490)
                      .+.+...|...+++.  ...   +..+.|..+|+++.+.   .|+ ...+..+..++...        ++...+.+..++
T Consensus       333 ~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~l---dP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~  409 (517)
T PRK10153        333 LPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKS---EPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDN  409 (517)
T ss_pred             CCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHH
Confidence            455667777777763  333   2366888888888763   454 34444444433221        234455555554


Q ss_pred             cc----CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccccCC
Q 011249          408 YK----DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKKSP  483 (490)
Q Consensus       408 ~~----~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  483 (490)
                      ..    .+.++..+..+.......|++++|...++++++++|. ...|..++.++...|+.++|.+.+++....++ ..|
T Consensus       410 a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L~ps-~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P-~~p  487 (517)
T PRK10153        410 IVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDLEMS-WLNYVLLGKVYELKGDNRLAADAYSTAFNLRP-GEN  487 (517)
T ss_pred             hhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCC-HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCC-CCc
Confidence            32    3345567777766667788999999999999999984 77888899999999999999999988877665 333


Q ss_pred             Cccc
Q 011249          484 GCSW  487 (490)
Q Consensus       484 ~~~~  487 (490)
                      .+.|
T Consensus       488 t~~~  491 (517)
T PRK10153        488 TLYW  491 (517)
T ss_pred             hHHH
Confidence            3444

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.89  E-value=4.5e-05  Score=53.93  Aligned_cols=80  Identities=18%  Similarity=0.056  Sum_probs=30.7

Q ss_pred             CChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCC-ChhhHHHHHHHHhhhCChHHHHHHHH
Q 011249          360 GLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFC-DAGTWGALLGACKVHVNAELGEIAAR  438 (490)
Q Consensus       360 g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~  438 (490)
                      |+++.|+.+++++.+.....++...+..+..+|.+.|++++|..++++....+ +......+..++...|++++|+++++
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            44444444444444421111122223334444444444444444444421111 12222233444444555555554444


Q ss_pred             H
Q 011249          439 H  439 (490)
Q Consensus       439 ~  439 (490)
                      +
T Consensus        83 ~   83 (84)
T PF12895_consen   83 K   83 (84)
T ss_dssp             H
T ss_pred             c
Confidence            3

>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=97.88  E-value=2.4e-05  Score=52.70  Aligned_cols=62  Identities=18%  Similarity=0.149  Sum_probs=37.3

Q ss_pred             hcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          394 RSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       394 ~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      ..|++++|+++|+++.  .+.+...+..++.+|.+.|++++|.++++++...+|+++..+..++
T Consensus         3 ~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~l~a   66 (68)
T PF14559_consen    3 KQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQLLA   66 (68)
T ss_dssp             HTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHHHHh
Confidence            4566666666666654  3335556666666666666666666666666666666555444443

...

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.85  E-value=2.3e-05  Score=43.09  Aligned_cols=31  Identities=19%  Similarity=0.439  Sum_probs=27.7

Q ss_pred             eehHHHHHHHHhcCChhHHHHHHHHHHhcCC
Q 011249           69 FLWTSLIRNHVLHAHFRQSILLYAKMHRLGV   99 (490)
Q Consensus        69 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~   99 (490)
                      .+||.++++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            3799999999999999999999999998764

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.

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.83  E-value=0.00075  Score=59.99  Aligned_cols=134  Identities=12%  Similarity=0.094  Sum_probs=94.0

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH-hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHH
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTA-CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVD  390 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~-~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  390 (490)
                      .+|-.++....+.+..+.|..+|.++.+.+ ..+...|...... +...++.+.|.++|+...+.  ++.+...+...++
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~--f~~~~~~~~~Y~~   78 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK--FPSDPDFWLEYLD   78 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH--HTT-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHH
Confidence            457777777777778888888888887542 2223333333333 33356777799999998884  5666777888888


Q ss_pred             HHhhcCChHHHHHHHHhcc-CCC----ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC
Q 011249          391 LLGRSGQLEKAHSLIMDYK-DFC----DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~~~-~~~----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      .+.+.|+.+.|..+|++.. .-+    ....|...+.--.+.|+.+....+.+++.+..|++.
T Consensus        79 ~l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~~~~~~  141 (280)
T PF05843_consen   79 FLIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEELFPEDN  141 (280)
T ss_dssp             HHHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHTTTS-
T ss_pred             HHHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhhh
Confidence            8888999999999998776 222    234888888888888999999999999888877744

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.

>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=97.82  E-value=6.1e-05  Score=50.89  Aligned_cols=65  Identities=18%  Similarity=0.032  Sum_probs=54.7

Q ss_pred             CchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhC-ChHHHHHHHHHHHhcCC
Q 011249          381 LTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHV-NAELGEIAARHLLELGP  445 (490)
Q Consensus       381 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g-~~~~a~~~~~~~~~~~p  445 (490)
                      ++..|..+...+...|++++|+..|++..  .+.++..|..+..++...| ++++|++.++++++++|
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P   69 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP   69 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence            35677788888899999999999998776  5556778888888999998 79999999999999887

...

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.79  E-value=0.026  Score=50.91  Aligned_cols=20  Identities=15%  Similarity=0.039  Sum_probs=13.7

Q ss_pred             HHHhcCCHHHHHHHHhhcCC
Q 011249          126 GYTKIGLMDDAQRLFDSMAE  145 (490)
Q Consensus       126 ~~~~~g~~~~A~~~~~~~~~  145 (490)
                      .-...|+.+-|..+++.=+.
T Consensus         9 ~A~~~GR~~LA~~LL~~Ep~   28 (319)
T PF04840_consen    9 KAYEEGRPKLATKLLELEPR   28 (319)
T ss_pred             HHHHcChHHHHHHHHHcCCC
Confidence            35677888888887765443

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

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.74  E-value=0.0012  Score=49.52  Aligned_cols=107  Identities=16%  Similarity=0.094  Sum_probs=65.8

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCcccC--hhhHHHHHHHHhccCChHHHHHHHHHHHhcCCC--CchhHHHHHHHHH
Q 011249          215 AMTVCYVQNGYAKAAIEMYKVMRQENVRIS--EVAMVGAISACTQLGDVEMAAILAKHVDEGCCD--RTNYVSNALIHMH  290 (490)
Q Consensus       215 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~~~  290 (490)
                      .+..++-..|+.++|+.+|++....|...+  ...+..+..++...|++++|..+++........  .+......+.-++
T Consensus         6 ~~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L   85 (120)
T PF12688_consen    6 ELAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALAL   85 (120)
T ss_pred             HHHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHH
Confidence            455667778888888888888887775543  245566677777888888888888877665311  0222222334455


Q ss_pred             HhcCChHHHHHHHhcccCCChhHHHHHHHHH
Q 011249          291 SKCGYLDLAWREFSRIKNKDVISYSSMITAF  321 (490)
Q Consensus       291 ~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~  321 (490)
                      ...|+.++|++.+-....++...|..-|..|
T Consensus        86 ~~~gr~~eAl~~~l~~la~~~~~y~ra~~~y  116 (120)
T PF12688_consen   86 YNLGRPKEALEWLLEALAETLPRYRRAIRFY  116 (120)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            6667777777666554444444444444433

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.73  E-value=0.00087  Score=52.27  Aligned_cols=88  Identities=8%  Similarity=-0.046  Sum_probs=36.5

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcC
Q 011249          215 AMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCG  294 (490)
Q Consensus       215 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  294 (490)
                      .+...+...|++++|.++|+.+....+ -+..-|..|..++...|++++|+..|....... +.++..+-.+..++...|
T Consensus        40 ~~A~~ly~~G~l~~A~~~f~~L~~~Dp-~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~-~ddp~~~~~ag~c~L~lG  117 (157)
T PRK15363         40 RYAMQLMEVKEFAGAARLFQLLTIYDA-WSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIK-IDAPQAPWAAAECYLACD  117 (157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhCc-ccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHHcC
Confidence            333344444444444444444443321 123333344444444444444444444444433 233333333444444444


Q ss_pred             ChHHHHHHHh
Q 011249          295 YLDLAWREFS  304 (490)
Q Consensus       295 ~~~~A~~~~~  304 (490)
                      +.+.|.+.|+
T Consensus       118 ~~~~A~~aF~  127 (157)
T PRK15363        118 NVCYAIKALK  127 (157)
T ss_pred             CHHHHHHHHH
Confidence            4444444443

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.72  E-value=0.0081  Score=52.05  Aligned_cols=173  Identities=12%  Similarity=0.050  Sum_probs=99.3

Q ss_pred             HHHHHHhcCChHHHHHHHhcccC--CCh-hH---HHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcC-
Q 011249          286 LIHMHSKCGYLDLAWREFSRIKN--KDV-IS---YSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSH-  358 (490)
Q Consensus       286 l~~~~~~~~~~~~A~~~~~~~~~--~~~-~~---~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~-  358 (490)
                      ....+...|++++|.+.|+++..  |+. ..   .-.++.++.+.+++++|...+++.++....-....+...+.+.+. 
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~~~  117 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLTNM  117 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHhhh
Confidence            34444556777777777776655  222 11   234556677777888888888877764211111223223322210 


Q ss_pred             -C---------------CC---hHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHH
Q 011249          359 -G---------------GL---VEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGA  419 (490)
Q Consensus       359 -~---------------g~---~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~  419 (490)
                       .               .+   ...|+..|+.+.+.  . |+..             -..+|...+..+........ ..
T Consensus       118 ~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~--y-P~S~-------------ya~~A~~rl~~l~~~la~~e-~~  180 (243)
T PRK10866        118 ALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRG--Y-PNSQ-------------YTTDATKRLVFLKDRLAKYE-LS  180 (243)
T ss_pred             hcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHH--C-cCCh-------------hHHHHHHHHHHHHHHHHHHH-HH
Confidence             1               11   23455666666653  2 2221             12333333332221111111 13


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCC---chHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKT---GNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      +..-|.+.|.+.-|..-++.+++..|+.+   .++..++.+|...|..++|..+...+.
T Consensus       181 ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        181 VAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            45668889999999999999999887755   567778899999999999999877553

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.72  E-value=0.0045  Score=52.02  Aligned_cols=135  Identities=16%  Similarity=0.177  Sum_probs=90.4

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCch-----hHHHHH
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTN-----YVSNAL  286 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-----~~~~~l  286 (490)
                      ..+.++.++...|.+.-.+..+++.++...+.++.....+.+...+.||.+.|..++++..+..-..+.     .+....
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            445666777777888888888888887765667777777888888888888888888877654323332     233333


Q ss_pred             HHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHH
Q 011249          287 IHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVT  348 (490)
Q Consensus       287 ~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~  348 (490)
                      ...|.-.+++..|...|.++..   .++..-|.-.-+..-.|+...|++.++.|.+.  .|...+
T Consensus       259 a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~--~P~~~l  321 (366)
T KOG2796|consen  259 AFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQ--DPRHYL  321 (366)
T ss_pred             hhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhcc--CCccch
Confidence            4456666777778777777765   34455555555555567888888888888774  444443

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=97.70  E-value=0.016  Score=50.25  Aligned_cols=67  Identities=16%  Similarity=-0.004  Sum_probs=43.7

Q ss_pred             CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccCh--hhHHHHHHHHhccCChHHHHHHHHHHHhcC
Q 011249          209 DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISE--VAMVGAISACTQLGDVEMAAILAKHVDEGC  275 (490)
Q Consensus       209 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~--~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  275 (490)
                      ++..+-.....+...|++++|++.|+++......+..  .....++.++.+.++++.|...+++..+..
T Consensus        31 ~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~   99 (243)
T PRK10866         31 PPSEIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLN   99 (243)
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC
Confidence            4444445566667778888888888888765322211  122455667778888888888888877764

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.69  E-value=0.00035  Score=62.20  Aligned_cols=252  Identities=15%  Similarity=0.051  Sum_probs=155.7

Q ss_pred             HHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcC------C---CC
Q 011249           77 NHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMA------E---RN  147 (490)
Q Consensus        77 ~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~------~---~~  147 (490)
                      -+++.|+....+.+|+...+.|.. |..|.+.   .|+.       +..+|.-.+++++|++....=.      .   -.
T Consensus        26 RLck~gdcraGv~ff~aA~qvGTe-Dl~tLSA---IYsQ-------LGNAyfyL~DY~kAl~yH~hDltlar~lgdklGE   94 (639)
T KOG1130|consen   26 RLCKMGDCRAGVDFFKAALQVGTE-DLSTLSA---IYSQ-------LGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGE   94 (639)
T ss_pred             HHHhccchhhhHHHHHHHHHhcch-HHHHHHH---HHHH-------hcchhhhHhhHHHHHhhhhhhHHHHHHhcchhcc
Confidence            467889999999999998887643 4334333   3322       3345777788888887643221      1   12


Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHHHhcc-------C--CchhHHHHHHHHHhcCC--------------------hhHH
Q 011249          148 VISWSAMVAGYANCGNMKAAKEFYDRMTE-------K--NSVTWVAMIAGYGKCGE--------------------VREA  198 (490)
Q Consensus       148 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-------~--~~~~~~~l~~~~~~~~~--------------------~~~A  198 (490)
                      ..+...|.+.+--.|.+++|+-.-.+-+.       +  ....+..+...|...|+                    ++.|
T Consensus        95 AKssgNLGNtlKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~~al~~A  174 (639)
T KOG1130|consen   95 AKSSGNLGNTLKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVTSALENA  174 (639)
T ss_pred             ccccccccchhhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHHHHHHHH
Confidence            33445566666677788877655443321       1  44566667777765543                    2233


Q ss_pred             HHHHhhcCC---------CCHHhHHHHHHHHHhcCChHHHHHHHHHHH----HcCcc-cChhhHHHHHHHHhccCChHHH
Q 011249          199 KKVFDEISE---------PDASCWAAMTVCYVQNGYAKAAIEMYKVMR----QENVR-ISEVAMVGAISACTQLGDVEMA  264 (490)
Q Consensus       199 ~~~~~~~~~---------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~~-p~~~~~~~l~~~~~~~g~~~~a  264 (490)
                      .++|.+-.+         .-...|..|...|--.|+++.|+..-+.=.    +-|-+ .....+..+.+++.-.|+++.|
T Consensus       175 v~fy~eNL~l~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A  254 (639)
T KOG1130|consen  175 VKFYMENLELSEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELA  254 (639)
T ss_pred             HHHHHHHHHHHHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhH
Confidence            334433211         112345556666666788888876544322    22211 1235677788888888999999


Q ss_pred             HHHHHHHH----hcCC-CCchhHHHHHHHHHHhcCChHHHHHHHhcccC---------CChhHHHHHHHHHHhcCChHHH
Q 011249          265 AILAKHVD----EGCC-DRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---------KDVISYSSMITAFADHGKSQEA  330 (490)
Q Consensus       265 ~~~~~~~~----~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---------~~~~~~~~l~~~~~~~~~~~~a  330 (490)
                      .+.|+...    +.|- ........+|.+.|.-..++++|+.++.+-..         ....++-+|..+|...|..++|
T Consensus       255 ~ehYK~tl~LAielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kA  334 (639)
T KOG1130|consen  255 IEHYKLTLNLAIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKA  334 (639)
T ss_pred             HHHHHHHHHHHHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHH
Confidence            88887643    3331 23345566788888888888888888765442         2345777888888888888888


Q ss_pred             HHHHHHHHH
Q 011249          331 LDMFLKMRN  339 (490)
Q Consensus       331 ~~~~~~~~~  339 (490)
                      +.+.+.-.+
T Consensus       335 l~fae~hl~  343 (639)
T KOG1130|consen  335 LYFAELHLR  343 (639)
T ss_pred             HHHHHHHHH
Confidence            877776554

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.68  E-value=0.00035  Score=60.89  Aligned_cols=91  Identities=8%  Similarity=0.018  Sum_probs=40.0

Q ss_pred             cCCCChHHHHHHHHHHHHHcCCCC-CchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC----ChhhHHHHHHHHhhhCCh
Q 011249          357 SHGGLVEDGCKQFELMTRVFGIKP-LTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC----DAGTWGALLGACKVHVNA  430 (490)
Q Consensus       357 ~~~g~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~----~~~~~~~l~~~~~~~g~~  430 (490)
                      .+.|++++|...|+.+.+.+.-.+ .+..+..+..+|...|++++|...|+.+. ..|    .+..+..++..+...|+.
T Consensus       154 ~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~~~~g~~  233 (263)
T PRK10803        154 QDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIMQDKGDT  233 (263)
T ss_pred             HhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHHHHcCCH
Confidence            344555555555555554311110 01233444455555555555555554443 111    122333333344445555


Q ss_pred             HHHHHHHHHHHhcCCCC
Q 011249          431 ELGEIAARHLLELGPEK  447 (490)
Q Consensus       431 ~~a~~~~~~~~~~~p~~  447 (490)
                      ++|..+|+++++..|++
T Consensus       234 ~~A~~~~~~vi~~yP~s  250 (263)
T PRK10803        234 AKAKAVYQQVIKKYPGT  250 (263)
T ss_pred             HHHHHHHHHHHHHCcCC
Confidence            55555555555555543

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.68  E-value=0.00037  Score=62.10  Aligned_cols=129  Identities=10%  Similarity=0.007  Sum_probs=72.6

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHH---HHcCCCC-CchHHHHHHHHHhhcCChHHHHHHHHhcc--------CCCChh
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMT---RVFGIKP-LTEHLTCMVDLLGRSGQLEKAHSLIMDYK--------DFCDAG  415 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~---~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--------~~~~~~  415 (490)
                      .|..|...|.-.|+++.|+...+.-.   +++|-.. ....+..+..++.-.|+++.|.+.|+.-.        ......
T Consensus       197 a~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r~vEAQ  276 (639)
T KOG1130|consen  197 AYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNRTVEAQ  276 (639)
T ss_pred             hhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcchhHHHH
Confidence            45555555555667776665544322   1223221 13345556666666777777777665432        112333


Q ss_pred             hHHHHHHHHhhhCChHHHHHHHHHHHhcC------CCCCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          416 TWGALLGACKVHVNAELGEIAARHLLELG------PEKTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       416 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~------p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      ...+|.++|.-..++++|+.++.+-+.+.      -....++..|+.++...|..++|+.+.++-++
T Consensus       277 scYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~hl~  343 (639)
T KOG1130|consen  277 SCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELHLR  343 (639)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence            45566666666667777777766654422      12345667777777777777777766655443

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.67  E-value=0.00047  Score=51.78  Aligned_cols=56  Identities=14%  Similarity=0.007  Sum_probs=27.5

Q ss_pred             hHHHHHHHHhhhCChHHHHHHHHHHHhcCCC---CCchHHHHHHHHHhcCCcchHHHHH
Q 011249          416 TWGALLGACKVHVNAELGEIAARHLLELGPE---KTGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       416 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~---~~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      .+..+..++...|++++|..++++.....|+   +......++.++...|++++|++.+
T Consensus        40 a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~~~gr~~eAl~~~   98 (120)
T PF12688_consen   40 ALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALYNLGRPKEALEWL   98 (120)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            3334444455555555555555555554444   3334444444555555555555544

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.66  E-value=0.0014  Score=53.42  Aligned_cols=81  Identities=11%  Similarity=-0.061  Sum_probs=49.8

Q ss_pred             HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCccc--ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHH
Q 011249          210 ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRI--SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALI  287 (490)
Q Consensus       210 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  287 (490)
                      ...|..++..+...|++++|+..|++.......|  ...++..+..++...|++++|...++...+.. +.....+..+.
T Consensus        35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la  113 (168)
T CHL00033         35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMA  113 (168)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHH
Confidence            3455666677777777777777777776543222  12466667777777777777777777776553 33334444444


Q ss_pred             HHHH
Q 011249          288 HMHS  291 (490)
Q Consensus       288 ~~~~  291 (490)
                      .++.
T Consensus       114 ~i~~  117 (168)
T CHL00033        114 VICH  117 (168)
T ss_pred             HHHH
Confidence            4444

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.65  E-value=0.0018  Score=57.93  Aligned_cols=273  Identities=12%  Similarity=-0.005  Sum_probs=147.6

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcC
Q 011249          151 WSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNG  224 (490)
Q Consensus       151 ~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g  224 (490)
                      .......+.+..++..|+..+....+  | +..-|..-+..+...|++++|.--.+.-.+   .......-.-+++...+
T Consensus        52 ~k~~gn~~yk~k~Y~nal~~yt~Ai~~~pd~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~kd~~~k~~~r~~~c~~a~~  131 (486)
T KOG0550|consen   52 AKEEGNAFYKQKTYGNALKNYTFAIDMCPDNASYYSNRAATLMMLGRFEEALGDARQSVRLKDGFSKGQLREGQCHLALS  131 (486)
T ss_pred             HHhhcchHHHHhhHHHHHHHHHHHHHhCccchhhhchhHHHHHHHHhHhhcccchhhheecCCCccccccchhhhhhhhH
Confidence            33455778888899999999998886  3 555666667777777888887766554443   23334555566666667


Q ss_pred             ChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcC-CCCchhHHHHH-HHHHHhcCChHHHHHH
Q 011249          225 YAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGC-CDRTNYVSNAL-IHMHSKCGYLDLAWRE  302 (490)
Q Consensus       225 ~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~~~l-~~~~~~~~~~~~A~~~  302 (490)
                      +..+|.+.++.-.         .+           ....+...++.+.... -+|....+..+ ..++...|++++|.+.
T Consensus       132 ~~i~A~~~~~~~~---------~~-----------~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~e  191 (486)
T KOG0550|consen  132 DLIEAEEKLKSKQ---------AY-----------KAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSE  191 (486)
T ss_pred             HHHHHHHHhhhhh---------hh-----------HHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHH
Confidence            7667766665211         01           0111111222221111 12222333222 2344455666666665


Q ss_pred             HhcccCCCh-hHHHHHHH--HHHhcCChHHHHHHHHHHHHcCCCCcHHHHHH---H----------HHHhcCCCChHHHH
Q 011249          303 FSRIKNKDV-ISYSSMIT--AFADHGKSQEALDMFLKMRNEGIEPNQVTFIG---V----------LTACSHGGLVEDGC  366 (490)
Q Consensus       303 ~~~~~~~~~-~~~~~l~~--~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~---l----------~~~~~~~g~~~~a~  366 (490)
                      --.+.+-|. ..+...+.  ++...++.+.+...|++.+.  ..|+...-..   .          ..-..+.|++..|.
T Consensus       192 a~~ilkld~~n~~al~vrg~~~yy~~~~~ka~~hf~qal~--ldpdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~  269 (486)
T KOG0550|consen  192 AIDILKLDATNAEALYVRGLCLYYNDNADKAINHFQQALR--LDPDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAY  269 (486)
T ss_pred             HHHHHhcccchhHHHHhcccccccccchHHHHHHHhhhhc--cChhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHH
Confidence            555544222 12222222  33445666677777766665  3444332111   1          11234667777777


Q ss_pred             HHHHHHHHH--cCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhh---HHHHHHHHhhhCChHHHHHHHHHHH
Q 011249          367 KQFELMTRV--FGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGT---WGALLGACKVHVNAELGEIAARHLL  441 (490)
Q Consensus       367 ~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~---~~~l~~~~~~~g~~~~a~~~~~~~~  441 (490)
                      +.+.+.+..  .+..|+...|.....+..+.|+..+|+.-.+... ..|+..   +..-..++...+++++|++-++++.
T Consensus       270 E~Yteal~idP~n~~~naklY~nra~v~~rLgrl~eaisdc~~Al-~iD~syikall~ra~c~l~le~~e~AV~d~~~a~  348 (486)
T KOG0550|consen  270 ECYTEALNIDPSNKKTNAKLYGNRALVNIRLGRLREAISDCNEAL-KIDSSYIKALLRRANCHLALEKWEEAVEDYEKAM  348 (486)
T ss_pred             HHHHHhhcCCccccchhHHHHHHhHhhhcccCCchhhhhhhhhhh-hcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            777777531  0122334455555666677777777777776655 333332   2222345566677777777777777


Q ss_pred             hcCCC
Q 011249          442 ELGPE  446 (490)
Q Consensus       442 ~~~p~  446 (490)
                      +...+
T Consensus       349 q~~~s  353 (486)
T KOG0550|consen  349 QLEKD  353 (486)
T ss_pred             hhccc
Confidence            75544

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=97.65  E-value=6.9e-05  Score=41.14  Aligned_cols=30  Identities=40%  Similarity=0.804  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcCC
Q 011249          313 SYSSMITAFADHGKSQEALDMFLKMRNEGI  342 (490)
Q Consensus       313 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~  342 (490)
                      +|+.++++|++.|++++|.++|++|.+.|+
T Consensus         2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    2 TYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            677777777777777777777777777653

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.

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.64  E-value=0.0024  Score=53.61  Aligned_cols=136  Identities=12%  Similarity=-0.031  Sum_probs=97.5

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHH-----H
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHL-----T  386 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~-----~  386 (490)
                      .+.+.++..+.-.|.+.-.+..+.+.++...+-++.....+++.-.+.|+.+.|..+|++..+. .-..+....     .
T Consensus       178 ~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~-~~kL~~~q~~~~V~~  256 (366)
T KOG2796|consen  178 RVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKV-TQKLDGLQGKIMVLM  256 (366)
T ss_pred             HHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHH-HhhhhccchhHHHHh
Confidence            4556677777777888888888988888655557778888888888899999999999987764 333333332     3


Q ss_pred             HHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC
Q 011249          387 CMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       387 ~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      .....|.-.+++.+|...+.+++  ++.++...|.-.-...-.|+...|++.++.+.+..|...
T Consensus       257 n~a~i~lg~nn~a~a~r~~~~i~~~D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~P~~~  320 (366)
T KOG2796|consen  257 NSAFLHLGQNNFAEAHRFFTEILRMDPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQDPRHY  320 (366)
T ss_pred             hhhhheecccchHHHHHHHhhccccCCCchhhhchHHHHHHHHHHHHHHHHHHHHHhccCCccc
Confidence            33445667778888888888877  333444555555455667888889999998888888733

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=97.63  E-value=2.9e-05  Score=43.44  Aligned_cols=34  Identities=24%  Similarity=0.462  Sum_probs=31.2

Q ss_pred             HHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHH
Q 011249          436 AARHLLELGPEKTGNSALLANIYASMGKWKDSEI  469 (490)
Q Consensus       436 ~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~  469 (490)
                      +|+++++.+|+++.+|..|+.+|...|++++|++
T Consensus         1 ~y~kAie~~P~n~~a~~nla~~~~~~g~~~~A~~   34 (34)
T PF13431_consen    1 CYKKAIELNPNNAEAYNNLANLYLNQGDYEEAIA   34 (34)
T ss_pred             ChHHHHHHCCCCHHHHHHHHHHHHHCcCHHhhcC
Confidence            3788999999999999999999999999999863

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.58  E-value=0.018  Score=52.38  Aligned_cols=122  Identities=16%  Similarity=0.081  Sum_probs=66.7

Q ss_pred             cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhc----C-----CCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh
Q 011249          324 HGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACS----H-----GGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR  394 (490)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~----~-----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  394 (490)
                      .|+.++|+.++..+....-.+++.++..+.+.|-    .     ....++|+..|.+.-   .+.|+...--.++..+..
T Consensus       195 ~gdre~Al~il~~~l~~~~~~~~d~~gL~GRIyKD~~~~s~~~d~~~ldkAi~~Y~kgF---e~~~~~Y~GIN~AtLL~~  271 (374)
T PF13281_consen  195 PGDREKALQILLPVLESDENPDPDTLGLLGRIYKDLFLESNFTDRESLDKAIEWYRKGF---EIEPDYYSGINAATLLML  271 (374)
T ss_pred             CCCHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHHcCccchHHHHHHHHHHHHHH---cCCccccchHHHHHHHHH
Confidence            5566666666666444444555555555555431    1     123556666666553   334543333333333333


Q ss_pred             cCChHHH----HHHH---Hhcc-------CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC
Q 011249          395 SGQLEKA----HSLI---MDYK-------DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       395 ~g~~~~A----~~~~---~~~~-------~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      .|...+.    .++-   ..+.       ...+-..+.+++.++.-.||.++|.+.++++.+..|+.-
T Consensus       272 ~g~~~~~~~el~~i~~~l~~llg~kg~~~~~~dYWd~ATl~Ea~vL~~d~~ka~~a~e~~~~l~~~~W  339 (374)
T PF13281_consen  272 AGHDFETSEELRKIGVKLSSLLGRKGSLEKMQDYWDVATLLEASVLAGDYEKAIQAAEKAFKLKPPAW  339 (374)
T ss_pred             cCCcccchHHHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHHHcCCHHHHHHHHHHHhhcCCcch
Confidence            4432211    1211   1100       223444566788889999999999999999999887643

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.58  E-value=0.0017  Score=57.70  Aligned_cols=142  Identities=11%  Similarity=0.011  Sum_probs=102.0

Q ss_pred             HhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHH-HhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 011249          211 SCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISA-CTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHM  289 (490)
Q Consensus       211 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~-~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  289 (490)
                      .+|-.+++...+.+..+.|..+|.+..+.+ ..+...|...... +...++.+.|.++|+...+. ++.+...+...++.
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~-f~~~~~~~~~Y~~~   79 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKK-FPSDPDFWLEYLDF   79 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHH-HTT-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-CCCCHHHHHHHHHH
Confidence            467788888888888999999999998543 2234445444444 33457777799999998876 47788888888999


Q ss_pred             HHhcCChHHHHHHHhcccC--C----ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHh
Q 011249          290 HSKCGYLDLAWREFSRIKN--K----DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTAC  356 (490)
Q Consensus       290 ~~~~~~~~~A~~~~~~~~~--~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  356 (490)
                      +.+.++.+.|..+|++...  +    ....|...+..-.+.|+.+.+.++.+++.+.  .|+...+..++.-|
T Consensus        80 l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~~--~~~~~~~~~f~~ry  150 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEEL--FPEDNSLELFSDRY  150 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH--TTTS-HHHHHHCCT
T ss_pred             HHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhhhHHHHHHHHh
Confidence            9999999999999998876  2    2358888888888899999999999988874  55544444444433

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.

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.56  E-value=0.0019  Score=59.94  Aligned_cols=115  Identities=15%  Similarity=0.132  Sum_probs=61.2

Q ss_pred             ccChhhHHHHHHHHhccCChHHHHHHHHHHHhc--CCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC----CChhHHH
Q 011249          242 RISEVAMVGAISACTQLGDVEMAAILAKHVDEG--CCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN----KDVISYS  315 (490)
Q Consensus       242 ~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~~~~~  315 (490)
                      +.+......+++.+....+.+.+..++-.....  .....+.+..++++.|.+.|..+.+..++..=..    ||..++|
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            334455555555555555555555555555443  2222233344566666666666666666555443    5566666


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHh
Q 011249          316 SMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTAC  356 (490)
Q Consensus       316 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  356 (490)
                      .+++.+.+.|++..|.++...|...+...+..|+..-+.+|
T Consensus       143 ~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~  183 (429)
T PF10037_consen  143 LLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSC  183 (429)
T ss_pred             HHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHH
Confidence            66666666666666666666555544444444444444333

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 [].

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=97.55  E-value=0.00015  Score=43.64  Aligned_cols=42  Identities=26%  Similarity=0.293  Sum_probs=38.0

Q ss_pred             hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHH
Q 011249          415 GTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLAN  456 (490)
Q Consensus       415 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~  456 (490)
                      .++..+..++...|++++|+++|+++++..|+++.++..|+.
T Consensus         2 ~~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~La~   43 (44)
T PF13428_consen    2 AAWLALARAYRRLGQPDEAERLLRRALALDPDDPEAWRALAQ   43 (44)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHHhhh
Confidence            467788999999999999999999999999999998888764

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=97.54  E-value=0.085  Score=50.19  Aligned_cols=179  Identities=13%  Similarity=0.055  Sum_probs=123.2

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHhcccCC---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC--CcHHHHHHHH
Q 011249          279 TNYVSNALIHMHSKCGYLDLAWREFSRIKNK---DVISYSSMITAFADHGKSQEALDMFLKMRNEGIE--PNQVTFIGVL  353 (490)
Q Consensus       279 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~--p~~~~~~~l~  353 (490)
                      +...|...+..-...|+.+.+.-.|+...-|   -...|-..+.-....|+.+.|..++....+--.+  |....+.+.+
T Consensus       296 ql~nw~~yLdf~i~~g~~~~~~~l~ercli~cA~Y~efWiky~~~m~~~~~~~~~~~~~~~~~~i~~k~~~~i~L~~a~f  375 (577)
T KOG1258|consen  296 QLKNWRYYLDFEITLGDFSRVFILFERCLIPCALYDEFWIKYARWMESSGDVSLANNVLARACKIHVKKTPIIHLLEARF  375 (577)
T ss_pred             HHHHHHHHhhhhhhcccHHHHHHHHHHHHhHHhhhHHHHHHHHHHHHHcCchhHHHHHHHhhhhhcCCCCcHHHHHHHHH
Confidence            4567777888888899999999999887764   2344555555555569999998888877664322  3333333333


Q ss_pred             HHhcCCCChHHHHHHHHHHHHHcCCCCC-chHHHHHHHHHhhcCChHHHH---HHHHhcc-CCCChhhHHHHHH-----H
Q 011249          354 TACSHGGLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDLLGRSGQLEKAH---SLIMDYK-DFCDAGTWGALLG-----A  423 (490)
Q Consensus       354 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~---~~~~~~~-~~~~~~~~~~l~~-----~  423 (490)
                        +...|++..|..+++.+...  . |+ ...-..-+....+.|..+.+.   +++.... ...+..+...+..     .
T Consensus       376 --~e~~~n~~~A~~~lq~i~~e--~-pg~v~~~l~~~~~e~r~~~~~~~~~~~~l~s~~~~~~~~~~i~~~l~~~~~r~~  450 (577)
T KOG1258|consen  376 --EESNGNFDDAKVILQRIESE--Y-PGLVEVVLRKINWERRKGNLEDANYKNELYSSIYEGKENNGILEKLYVKFARLR  450 (577)
T ss_pred             --HHhhccHHHHHHHHHHHHhh--C-CchhhhHHHHHhHHHHhcchhhhhHHHHHHHHhcccccCcchhHHHHHHHHHHH
Confidence              45678999999999999985  3 44 333334456667888888888   4444433 2333333333332     2


Q ss_pred             HhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcC
Q 011249          424 CKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMG  462 (490)
Q Consensus       424 ~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  462 (490)
                      +...++.+.|..++.++.+..|.+...|..+.......+
T Consensus       451 ~~i~~d~~~a~~~l~~~~~~~~~~k~~~~~~~~~~~~~~  489 (577)
T KOG1258|consen  451 YKIREDADLARIILLEANDILPDCKVLYLELIRFELIQP  489 (577)
T ss_pred             HHHhcCHHHHHHHHHHhhhcCCccHHHHHHHHHHHHhCC
Confidence            345789999999999999999999999999988877665

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=97.54  E-value=0.00037  Score=47.63  Aligned_cols=66  Identities=18%  Similarity=0.086  Sum_probs=52.8

Q ss_pred             HHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHH
Q 011249          389 VDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALL  454 (490)
Q Consensus       389 ~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l  454 (490)
                      ...|.+.+++++|.++++.+.  .+.++..+......+...|++++|.+.++++++..|+++......
T Consensus         2 ~~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~~~~~~~~~   69 (73)
T PF13371_consen    2 KQIYLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALELSPDDPDARALR   69 (73)
T ss_pred             HHHHHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCCcHHHHHHH
Confidence            356788889999999988877  445666777788888999999999999999999999877655443

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=97.52  E-value=0.00033  Score=64.17  Aligned_cols=62  Identities=10%  Similarity=-0.083  Sum_probs=33.7

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc-CCCChh----hHHHHHHHHhhhCChHHHHHHHHHHHhc
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAG----TWGALLGACKVHVNAELGEIAARHLLEL  443 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~----~~~~l~~~~~~~g~~~~a~~~~~~~~~~  443 (490)
                      ...++.+..+|.+.|++++|+..|++.. ..|+..    .|..+..+|...|+.++|++.++++++.
T Consensus        75 a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         75 AEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4445555555556666666666655533 333322    3555555555566666666666666554

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=97.50  E-value=0.066  Score=48.02  Aligned_cols=299  Identities=15%  Similarity=0.100  Sum_probs=174.3

Q ss_pred             HHHHHHHhccCCCCCCceehHHHHHHHHh--cCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHh
Q 011249           52 LSYARQVFDQIPKCKTQFLWTSLIRNHVL--HAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTK  129 (490)
Q Consensus        52 ~~~A~~~~~~~~~~~~~~~~~~l~~~~~~--~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~  129 (490)
                      +..+.+.|..-.+.   ..|.+|-.++..  .||-..|.++-.+.... +.-|..-...++.+-            .-.-
T Consensus        69 P~t~~Ryfr~rKRd---rgyqALStGliAagAGda~lARkmt~~~~~l-lssDqepLIhlLeAQ------------aal~  132 (531)
T COG3898          69 PYTARRYFRERKRD---RGYQALSTGLIAAGAGDASLARKMTARASKL-LSSDQEPLIHLLEAQ------------AALL  132 (531)
T ss_pred             cHHHHHHHHHHHhh---hHHHHHhhhhhhhccCchHHHHHHHHHHHhh-hhccchHHHHHHHHH------------HHHh
Confidence            44455555544332   456677666654  46777777766654422 334555555555542            3455


Q ss_pred             cCCHHHHHHHHhhcCC-CCHh--HHHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHh
Q 011249          130 IGLMDDAQRLFDSMAE-RNVI--SWSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFD  203 (490)
Q Consensus       130 ~g~~~~A~~~~~~~~~-~~~~--~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~  203 (490)
                      .|+.+.|.+-|+.|.. |...  -...|.-...+.|+.+.|.++-++.-+.   -...+...+...+..|+|+.|+++++
T Consensus       133 eG~~~~Ar~kfeAMl~dPEtRllGLRgLyleAqr~GareaAr~yAe~Aa~~Ap~l~WA~~AtLe~r~~~gdWd~AlkLvd  212 (531)
T COG3898         133 EGDYEDARKKFEAMLDDPETRLLGLRGLYLEAQRLGAREAARHYAERAAEKAPQLPWAARATLEARCAAGDWDGALKLVD  212 (531)
T ss_pred             cCchHHHHHHHHHHhcChHHHHHhHHHHHHHHHhcccHHHHHHHHHHHHhhccCCchHHHHHHHHHHhcCChHHHHHHHH
Confidence            6899999999999876 4332  2334444456678888888887777643   34566777888888888888888887


Q ss_pred             hcCC-----CCHHh--HHHHHHHHH---hcCChHHHHHHHHHHHHcCcccChh-hHHHHHHHHhccCChHHHHHHHHHHH
Q 011249          204 EISE-----PDASC--WAAMTVCYV---QNGYAKAAIEMYKVMRQENVRISEV-AMVGAISACTQLGDVEMAAILAKHVD  272 (490)
Q Consensus       204 ~~~~-----~~~~~--~~~l~~~~~---~~g~~~~A~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~  272 (490)
                      .-..     ++..-  -..|+.+-.   -..+...|...-.+..+  +.||.. .-..-..++.+.|+..++-.+++.+-
T Consensus       213 ~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~K--L~pdlvPaav~AAralf~d~~~rKg~~ilE~aW  290 (531)
T COG3898         213 AQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANK--LAPDLVPAAVVAARALFRDGNLRKGSKILETAW  290 (531)
T ss_pred             HHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhh--cCCccchHHHHHHHHHHhccchhhhhhHHHHHH
Confidence            6543     33211  111221111   12234445444433333  344432 22233456777788888888888777


Q ss_pred             hcCCCCchhHHHHHHHHHHhcCChHHH----HHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHH
Q 011249          273 EGCCDRTNYVSNALIHMHSKCGYLDLA----WREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVT  348 (490)
Q Consensus       273 ~~~~~~~~~~~~~l~~~~~~~~~~~~A----~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~  348 (490)
                      +....|++.    .+..+.+.|+....    .+-++.|...+..+...+..+-...|++..|..--+....  ..|....
T Consensus       291 K~ePHP~ia----~lY~~ar~gdta~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r--~~pres~  364 (531)
T COG3898         291 KAEPHPDIA----LLYVRARSGDTALDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAAR--EAPRESA  364 (531)
T ss_pred             hcCCChHHH----HHHHHhcCCCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhh--hCchhhH
Confidence            765445432    23334455543322    1233445555666666666666677777777666555554  4666777


Q ss_pred             HHHHHHHh-cCCCChHHHHHHHHHHHH
Q 011249          349 FIGVLTAC-SHGGLVEDGCKQFELMTR  374 (490)
Q Consensus       349 ~~~l~~~~-~~~g~~~~a~~~~~~~~~  374 (490)
                      |..+.+.- ...|+-.++...+.+..+
T Consensus       365 ~lLlAdIeeAetGDqg~vR~wlAqav~  391 (531)
T COG3898         365 YLLLADIEEAETGDQGKVRQWLAQAVK  391 (531)
T ss_pred             HHHHHHHHhhccCchHHHHHHHHHHhc
Confidence            76666653 345777777777777665

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=97.45  E-value=0.0017  Score=58.28  Aligned_cols=96  Identities=9%  Similarity=-0.014  Sum_probs=80.4

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ..++..+.-+|.+.+++.+|++...+..  .++|....-.-..++...|+++.|+..|+++++.+|+|..+-..|+.+-.
T Consensus       257 ~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~Nka~~~el~~l~~  336 (397)
T KOG0543|consen  257 LACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKALYRRGQALLALGEYDLARDDFQKALKLEPSNKAARAELIKLKQ  336 (397)
T ss_pred             HHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            3466778899999999999999998776  56788888888899999999999999999999999999999998987777


Q ss_pred             hcCCcchH-HHHHHHhhhc
Q 011249          460 SMGKWKDS-EIVKMMISET  477 (490)
Q Consensus       460 ~~g~~~~A-~~~~~~~~~~  477 (490)
                      +..++.+. .++|..|-..
T Consensus       337 k~~~~~~kekk~y~~mF~k  355 (397)
T KOG0543|consen  337 KIREYEEKEKKMYANMFAK  355 (397)
T ss_pred             HHHHHHHHHHHHHHHHhhc
Confidence            76655444 7788887654

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=97.43  E-value=0.0034  Score=54.81  Aligned_cols=94  Identities=9%  Similarity=0.015  Sum_probs=61.4

Q ss_pred             HHHHHHHHhhcCChHHHHHHHHhcc-CCCCh----hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC---CchHHHHHH
Q 011249          385 LTCMVDLLGRSGQLEKAHSLIMDYK-DFCDA----GTWGALLGACKVHVNAELGEIAARHLLELGPEK---TGNSALLAN  456 (490)
Q Consensus       385 ~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~---~~~~~~l~~  456 (490)
                      |......+.+.|++++|...|+.+. ..|+.    ..+..+..++...|++++|...|+++.+..|++   +.++..++.
T Consensus       146 Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~  225 (263)
T PRK10803        146 YNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGV  225 (263)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHH
Confidence            3333333455677777777777666 23332    356666677777777777777777777766664   345555577


Q ss_pred             HHHhcCCcchHHHHHHHhhhcc
Q 011249          457 IYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       457 ~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      ++...|++++|.++++++.+..
T Consensus       226 ~~~~~g~~~~A~~~~~~vi~~y  247 (263)
T PRK10803        226 IMQDKGDTAKAKAVYQQVIKKY  247 (263)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHC
Confidence            7777777777777777776543

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.42  E-value=0.0024  Score=59.25  Aligned_cols=120  Identities=10%  Similarity=0.014  Sum_probs=97.3

Q ss_pred             CCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC-C-----ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHH
Q 011249          275 CCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN-K-----DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVT  348 (490)
Q Consensus       275 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~-----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~  348 (490)
                      +.+.+......+++.+....+++.+..++.+... |     .+.+..+++..|...|..++++.++..=...|+-||..+
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            3456666777788888888888899888877664 2     245667999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhc
Q 011249          349 FIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRS  395 (490)
Q Consensus       349 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  395 (490)
                      ++.|+..+.+.|++..|.++...|..+ ....++.++..-+.+|.+.
T Consensus       141 ~n~Lmd~fl~~~~~~~A~~V~~~~~lQ-e~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  141 FNLLMDHFLKKGNYKSAAKVATEMMLQ-EEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHHHhhcccHHHHHHHHHHHHHh-hccCCchHHHHHHHHHHHh
Confidence            999999999999999999999988875 5556666655444444443

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 [].

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.41  E-value=0.0031  Score=45.64  Aligned_cols=80  Identities=13%  Similarity=0.159  Sum_probs=64.8

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCC-CCcHHHHHHHHHHhcCCC--------ChHHHHHHHHHHHHHcCCCCCchH
Q 011249          314 YSSMITAFADHGKSQEALDMFLKMRNEGI-EPNQVTFIGVLTACSHGG--------LVEDGCKQFELMTRVFGIKPLTEH  384 (490)
Q Consensus       314 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~p~~~~~~~l~~~~~~~g--------~~~~a~~~~~~~~~~~~~~~~~~~  384 (490)
                      ....|..+...+++.....+|+.+++.|+ .|+..+|+.++.+..+..        ++-..+.+++.+... +++|+..+
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~-~lKP~~et  106 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSN-KLKPNDET  106 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHh-ccCCcHHH
Confidence            34455556667999999999999999999 899999999999866432        345678889999885 89999999


Q ss_pred             HHHHHHHHhh
Q 011249          385 LTCMVDLLGR  394 (490)
Q Consensus       385 ~~~l~~~~~~  394 (490)
                      |+.++..+.+
T Consensus       107 Ynivl~~Llk  116 (120)
T PF08579_consen  107 YNIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHHH
Confidence            9998887764

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 [, , ].

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.41  E-value=0.0028  Score=45.85  Aligned_cols=80  Identities=6%  Similarity=-0.016  Sum_probs=65.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCc-ccChhhHHHHHHHHhccC--------ChHHHHHHHHHHHhcCCCCchhHH
Q 011249          213 WAAMTVCYVQNGYAKAAIEMYKVMRQENV-RISEVAMVGAISACTQLG--------DVEMAAILAKHVDEGCCDRTNYVS  283 (490)
Q Consensus       213 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~p~~~~~~~l~~~~~~~g--------~~~~a~~~~~~~~~~~~~~~~~~~  283 (490)
                      -...|.-+...+++.....+|+.+++.|+ .|+..+|+.++.+..+..        +......+|+++...+++|+..+|
T Consensus        28 ~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etY  107 (120)
T PF08579_consen   28 QIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETY  107 (120)
T ss_pred             HHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHH
Confidence            34456667777999999999999999999 899999999999876543        234567888899888899999999


Q ss_pred             HHHHHHHHh
Q 011249          284 NALIHMHSK  292 (490)
Q Consensus       284 ~~l~~~~~~  292 (490)
                      +.++..+.+
T Consensus       108 nivl~~Llk  116 (120)
T PF08579_consen  108 NIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHH
Confidence            988887764

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 [, , ].

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.41  E-value=0.017  Score=54.98  Aligned_cols=239  Identities=12%  Similarity=0.043  Sum_probs=138.0

Q ss_pred             HHHHHHHHHhcCChhHHHHHHhhcC-----------CCCHHhHHHHHHHHHhcCC--hHHHHHHHHHHHHcCcccChhhH
Q 011249          182 WVAMIAGYGKCGEVREAKKVFDEIS-----------EPDASCWAAMTVCYVQNGY--AKAAIEMYKVMRQENVRISEVAM  248 (490)
Q Consensus       182 ~~~l~~~~~~~~~~~~A~~~~~~~~-----------~~~~~~~~~l~~~~~~~g~--~~~A~~~~~~~~~~~~~p~~~~~  248 (490)
                      +.+-+..|...|.+++|.++----.           ..+...++.--.+|.+..+  +-+.+.-++++++.|-.|+... 
T Consensus       559 ~~~~m~q~Ieag~f~ea~~iaclgVv~~DW~~LA~~ALeAL~f~~ARkAY~rVRdl~~L~li~EL~~~k~rge~P~~iL-  637 (1081)
T KOG1538|consen  559 QSAPMYQYIERGLFKEAYQIACLGVTDTDWRELAMEALEALDFETARKAYIRVRDLRYLELISELEERKKRGETPNDLL-  637 (1081)
T ss_pred             ccccchhhhhccchhhhhcccccceecchHHHHHHHHHhhhhhHHHHHHHHHHhccHHHHHHHHHHHHHhcCCCchHHH-
Confidence            3444555677777777754321110           0223334445556666554  3345556677788887787653 


Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--------------CChhHH
Q 011249          249 VGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--------------KDVISY  314 (490)
Q Consensus       249 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--------------~~~~~~  314 (490)
                        +...|+-.|++.+|.++|.+-   |..      +..+.+|.....++.|.+++.....              .++.--
T Consensus       638 --lA~~~Ay~gKF~EAAklFk~~---G~e------nRAlEmyTDlRMFD~aQE~~~~g~~~eKKmL~RKRA~WAr~~keP  706 (1081)
T KOG1538|consen  638 --LADVFAYQGKFHEAAKLFKRS---GHE------NRALEMYTDLRMFDYAQEFLGSGDPKEKKMLIRKRADWARNIKEP  706 (1081)
T ss_pred             --HHHHHHhhhhHHHHHHHHHHc---Cch------hhHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHhhhcCCc
Confidence              455677788999998888653   211      2245566666666666666544321              111111


Q ss_pred             HHHHHHHHhcCChHHHHHHHHH------HHHcC--C-CCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHH
Q 011249          315 SSMITAFADHGKSQEALDMFLK------MRNEG--I-EPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHL  385 (490)
Q Consensus       315 ~~l~~~~~~~~~~~~a~~~~~~------~~~~~--~-~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~  385 (490)
                      .+....+...|+.++|..+.-+      +.+-+  + ..+..+...+...+.+...+..|-++|.++-..          
T Consensus       707 kaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD~----------  776 (1081)
T KOG1538|consen  707 KAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKMGDL----------  776 (1081)
T ss_pred             HHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhhhHHHHHHHHHhhccccchHHHHHHHhccH----------
Confidence            2344555667777777654321      12211  1 123345555555566777788888888887442          


Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc-CCCChh-----------hHHHHHHHHhhhCChHHHHHHHHHHHh
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK-DFCDAG-----------TWGALLGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~-----------~~~~l~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                      ..+++.....++|++|..+-++.+ ..|+..           -|...-.+|.+.|+..+|.++++++..
T Consensus       777 ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQLtn  845 (1081)
T KOG1538|consen  777 KSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQLTN  845 (1081)
T ss_pred             HHHhhheeecccchHhHhhhhhCccccccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHHhhh
Confidence            457788889999999999998887 223321           112222456667777777777776654

>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=97.23  E-value=0.00036  Score=48.43  Aligned_cols=62  Identities=10%  Similarity=0.116  Sum_probs=43.2

Q ss_pred             hhHHHHHHHHhhhCChHHHHHHHHHHHhc----CCC---CCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          415 GTWGALLGACKVHVNAELGEIAARHLLEL----GPE---KTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       415 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~p~---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      .+++.+...+...|++++|+..+++++++    +++   -..++..++.++...|++++|++++++..+
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~   74 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALD   74 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            45667777777778888888877777753    222   245677788888888888888888877654

...

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=97.18  E-value=0.0015  Score=58.54  Aligned_cols=67  Identities=10%  Similarity=-0.011  Sum_probs=60.9

Q ss_pred             hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          414 AGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       414 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      ...+..+.-++.+.+++..|++...++++.+|+|..++..-+.+|...|+++.|+..|+++.+..+.
T Consensus       257 ~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~~~N~KALyRrG~A~l~~~e~~~A~~df~ka~k~~P~  323 (397)
T KOG0543|consen  257 LACHLNLAACYLKLKEYKEAIESCNKVLELDPNNVKALYRRGQALLALGEYDLARDDFQKALKLEPS  323 (397)
T ss_pred             HHHhhHHHHHHHhhhhHHHHHHHHHHHHhcCCCchhHHHHHHHHHHhhccHHHHHHHHHHHHHhCCC
Confidence            3466778888999999999999999999999999999999999999999999999999999876543

>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=97.16  E-value=0.0076  Score=49.54  Aligned_cols=97  Identities=21%  Similarity=0.329  Sum_probs=75.0

Q ss_pred             HHHHhcc--cCCChhHHHHHHHHHHh-----cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCC------------
Q 011249          300 WREFSRI--KNKDVISYSSMITAFAD-----HGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGG------------  360 (490)
Q Consensus       300 ~~~~~~~--~~~~~~~~~~l~~~~~~-----~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g------------  360 (490)
                      ...|+..  ..++-.+|..+++.|.+     .|..+-....+..|.+.|+.-|..+|+.|++.+=+..            
T Consensus        34 ~~~f~~~~~~~k~K~~F~~~V~~f~~~~~~RRGHVeFI~aAL~~M~efgv~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~  113 (228)
T PF06239_consen   34 EELFERAPGQAKDKATFLEAVDIFKQRDVRRRGHVEFIYAALKKMDEFGVEKDLEVYKALLDVFPKGKFVPRNFFQAEFM  113 (228)
T ss_pred             HHHHHHHhhccccHHHHHHHHHHHHhcCCCCcChHHHHHHHHHHHHHcCCcccHHHHHHHHHhCCCCCcccccHHHHHhc
Confidence            3444444  33566777777777764     4677888888999999999999999999999876522            


Q ss_pred             ----ChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCC
Q 011249          361 ----LVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ  397 (490)
Q Consensus       361 ----~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  397 (490)
                          +-+-|++++++|.. +|+-||.+++..++..+++.+.
T Consensus       114 hyp~Qq~c~i~lL~qME~-~gV~Pd~Et~~~ll~iFG~~s~  153 (228)
T PF06239_consen  114 HYPRQQECAIDLLEQMEN-NGVMPDKETEQMLLNIFGRKSH  153 (228)
T ss_pred             cCcHHHHHHHHHHHHHHH-cCCCCcHHHHHHHHHHhccccH
Confidence                34678899999988 5999999999999998877664

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.16  E-value=0.12  Score=43.60  Aligned_cols=64  Identities=16%  Similarity=0.068  Sum_probs=40.6

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCcc--cChhhHHHHHHHHhccCChHHHHHHHHHHHhcC
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQENVR--ISEVAMVGAISACTQLGDVEMAAILAKHVDEGC  275 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  275 (490)
                      ..-.....+...|++++|++.|+.+......  -.......++.++.+.|+++.|...++.+.+.-
T Consensus         7 ~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~y   72 (203)
T PF13525_consen    7 ALYQKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLY   72 (203)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence            3444556677788888888888888764221  122455566777778888888888888776654

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.12  E-value=0.19  Score=45.37  Aligned_cols=104  Identities=15%  Similarity=0.092  Sum_probs=50.0

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc
Q 011249          214 AAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC  293 (490)
Q Consensus       214 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  293 (490)
                      +..+.-+...|+...|.++-++..    .|+...|...+.+++..++|++-.++...      .-++.-|..++.+|.+.
T Consensus       181 ~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s------kKsPIGyepFv~~~~~~  250 (319)
T PF04840_consen  181 NDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS------KKSPIGYEPFVEACLKY  250 (319)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC------CCCCCChHHHHHHHHHC
Confidence            333444455555555554443332    34555555555555555555554443221      11223344455555555


Q ss_pred             CChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHH
Q 011249          294 GYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDM  333 (490)
Q Consensus       294 ~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~  333 (490)
                      |+..+|..++..+.      +..-+..|.+.|++.+|.+.
T Consensus       251 ~~~~eA~~yI~k~~------~~~rv~~y~~~~~~~~A~~~  284 (319)
T PF04840_consen  251 GNKKEASKYIPKIP------DEERVEMYLKCGDYKEAAQE  284 (319)
T ss_pred             CCHHHHHHHHHhCC------hHHHHHHHHHCCCHHHHHHH
Confidence            55555555555422      13334445555555555443

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

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=97.10  E-value=0.042  Score=46.34  Aligned_cols=56  Identities=20%  Similarity=0.293  Sum_probs=36.9

Q ss_pred             HHHHHHHhcCChhHHHHHHhhcCC--C----CHHhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011249          184 AMIAGYGKCGEVREAKKVFDEISE--P----DASCWAAMTVCYVQNGYAKAAIEMYKVMRQE  239 (490)
Q Consensus       184 ~l~~~~~~~~~~~~A~~~~~~~~~--~----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  239 (490)
                      ..+..+...|++++|.+.|+.+..  |    .....-.++.++.+.|+++.|...++++.+.
T Consensus        10 ~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~   71 (203)
T PF13525_consen   10 QKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKL   71 (203)
T ss_dssp             HHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            344555667777777777777654  2    2334556777888888888888888887765

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=97.05  E-value=0.023  Score=49.24  Aligned_cols=103  Identities=17%  Similarity=0.021  Sum_probs=72.4

Q ss_pred             cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhc---CChHHHHHHHHhcc--CCCChhhHHH
Q 011249          345 NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRS---GQLEKAHSLIMDYK--DFCDAGTWGA  419 (490)
Q Consensus       345 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---g~~~~A~~~~~~~~--~~~~~~~~~~  419 (490)
                      |...|..|...|...|+.+.|...|....+  -.++++..+..+..++...   ....++..+|+++.  ++.++....-
T Consensus       155 d~egW~~Lg~~ym~~~~~~~A~~AY~~A~r--L~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~~iral~l  232 (287)
T COG4235         155 DAEGWDLLGRAYMALGRASDALLAYRNALR--LAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANIRALSL  232 (287)
T ss_pred             CchhHHHHHHHHHHhcchhHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHHHH
Confidence            556788888888888888888888888876  3445566666666655432   24567777787766  4445666666


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                      |...+...|++.+|...|+.+++..|.+..
T Consensus       233 LA~~afe~g~~~~A~~~Wq~lL~~lp~~~~  262 (287)
T COG4235         233 LAFAAFEQGDYAEAAAAWQMLLDLLPADDP  262 (287)
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhcCCCCCc
Confidence            777788888888888888888887765443

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=97.03  E-value=0.013  Score=45.07  Aligned_cols=90  Identities=11%  Similarity=-0.047  Sum_probs=61.4

Q ss_pred             HHHHHhhcCChHHHHHHHHhcc-----CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc---hHHHHHHHHH
Q 011249          388 MVDLLGRSGQLEKAHSLIMDYK-----DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG---NSALLANIYA  459 (490)
Q Consensus       388 l~~~~~~~g~~~~A~~~~~~~~-----~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~---~~~~l~~~~~  459 (490)
                      -.....+.|++++|.+.|+.+.     .+-....-..++.++...+++++|...+++.+++.|.++.   ++...+-++.
T Consensus        16 ~a~~~l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~vdYa~Y~~gL~~~   95 (142)
T PF13512_consen   16 EAQEALQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNVDYAYYMRGLSYY   95 (142)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCccHHHHHHHHHHH
Confidence            3445567788888888887776     1123445667778888889999999999999998887764   4444454555


Q ss_pred             hcCC---------------cchHHHHHHHhhhc
Q 011249          460 SMGK---------------WKDSEIVKMMISET  477 (490)
Q Consensus       460 ~~g~---------------~~~A~~~~~~~~~~  477 (490)
                      +...               ..+|...|+++++.
T Consensus        96 ~~~~~~~~~~~~~drD~~~~~~A~~~f~~lv~~  128 (142)
T PF13512_consen   96 EQDEGSLQSFFRSDRDPTPARQAFRDFEQLVRR  128 (142)
T ss_pred             HHhhhHHhhhcccccCcHHHHHHHHHHHHHHHH
Confidence            5544               55677777766643

>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=97.01  E-value=0.0013  Score=45.64  Aligned_cols=61  Identities=13%  Similarity=-0.022  Sum_probs=38.3

Q ss_pred             hHHHHHHHHHhhcCChHHHHHHHHhcc-----CC---CC-hhhHHHHHHHHhhhCChHHHHHHHHHHHhc
Q 011249          383 EHLTCMVDLLGRSGQLEKAHSLIMDYK-----DF---CD-AGTWGALLGACKVHVNAELGEIAARHLLEL  443 (490)
Q Consensus       383 ~~~~~l~~~~~~~g~~~~A~~~~~~~~-----~~---~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  443 (490)
                      .+++.+..+|...|++++|++.|++..     ..   |+ ..++..+...+...|++++|++.++++.++
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i   75 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALDI   75 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            345566666666666666666665544     11   22 346667777777788888888888777653

...

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.00  E-value=0.26  Score=47.43  Aligned_cols=98  Identities=10%  Similarity=0.066  Sum_probs=63.7

Q ss_pred             HHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCC
Q 011249          300 WREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIK  379 (490)
Q Consensus       300 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~  379 (490)
                      .++-.++...+..+...+..-+.+...+.-|-++|.+|-+         ...+++.....++|++|..+-++..+   +.
T Consensus       736 idI~rkld~~ere~l~~~a~ylk~l~~~gLAaeIF~k~gD---------~ksiVqlHve~~~W~eAFalAe~hPe---~~  803 (1081)
T KOG1538|consen  736 IDIARKLDKAEREPLLLCATYLKKLDSPGLAAEIFLKMGD---------LKSLVQLHVETQRWDEAFALAEKHPE---FK  803 (1081)
T ss_pred             HHHHhhcchhhhhHHHHHHHHHhhccccchHHHHHHHhcc---------HHHHhhheeecccchHhHhhhhhCcc---cc
Confidence            3333444445556666666667777788888888887754         33567778889999999988877654   34


Q ss_pred             CCchH-----------HHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          380 PLTEH-----------LTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       380 ~~~~~-----------~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                      |++..           +...-.+|.+.|+-.||.++++++.
T Consensus       804 ~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQLt  844 (1081)
T KOG1538|consen  804 DDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQLT  844 (1081)
T ss_pred             ccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHHhh
Confidence            44321           2222346667777777777777665

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=97.00  E-value=0.11  Score=47.39  Aligned_cols=78  Identities=5%  Similarity=0.014  Sum_probs=48.0

Q ss_pred             CchhHHHHHHHHHhcCChhHHHHHHhhcCCC-------CHHhHHHHHHHHHh---cCChHHHHHHHHHHHHcCcccChhh
Q 011249          178 NSVTWVAMIAGYGKCGEVREAKKVFDEISEP-------DASCWAAMTVCYVQ---NGYAKAAIEMYKVMRQENVRISEVA  247 (490)
Q Consensus       178 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-------~~~~~~~l~~~~~~---~g~~~~A~~~~~~~~~~~~~p~~~~  247 (490)
                      ++.+...++-+|....+++..+++.+.+...       ....-...+-++-+   .|+.++|++++..+....-.+++.+
T Consensus       140 s~div~~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~  219 (374)
T PF13281_consen  140 SPDIVINLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDT  219 (374)
T ss_pred             ChhHHHHHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHH
Confidence            3344445555677777777777777777652       22222234445555   6777888888777555445667777


Q ss_pred             HHHHHHHH
Q 011249          248 MVGAISAC  255 (490)
Q Consensus       248 ~~~l~~~~  255 (490)
                      +..+.+.|
T Consensus       220 ~gL~GRIy  227 (374)
T PF13281_consen  220 LGLLGRIY  227 (374)
T ss_pred             HHHHHHHH
Confidence            77766655

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=96.93  E-value=0.05  Score=52.30  Aligned_cols=163  Identities=14%  Similarity=0.050  Sum_probs=107.8

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCcH-----HHHHHHHHHhc----CCCChHHHHHHHHHHHHHcCCCCCch
Q 011249          314 YSSMITAFADHGKSQEALDMFLKMRNEG-IEPNQ-----VTFIGVLTACS----HGGLVEDGCKQFELMTRVFGIKPLTE  383 (490)
Q Consensus       314 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~-----~~~~~l~~~~~----~~g~~~~a~~~~~~~~~~~~~~~~~~  383 (490)
                      ...+++...=.|+-+.+++.+.+..+.+ +.-..     -.|..++..+.    .....+.|.++++.+.+.   -|+..
T Consensus       191 ~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~~~a~~lL~~~~~~---yP~s~  267 (468)
T PF10300_consen  191 VLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPLEEAEELLEEMLKR---YPNSA  267 (468)
T ss_pred             HHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCHHHHHHHHHHHHHh---CCCcH
Confidence            3444555555677777777777766532 22111     12333333333    245678899999999873   34544


Q ss_pred             HHH-HHHHHHhhcCChHHHHHHHHhccC------CCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHH-H
Q 011249          384 HLT-CMVDLLGRSGQLEKAHSLIMDYKD------FCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALL-A  455 (490)
Q Consensus       384 ~~~-~l~~~~~~~g~~~~A~~~~~~~~~------~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l-~  455 (490)
                      .|. .-.+.+...|++++|++.|+....      +.....+--++..+....++++|.+.|.++.+.+.-+..+|..+ +
T Consensus       268 lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~~L~~~s~WSka~Y~Y~~a  347 (468)
T PF10300_consen  268 LFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFLRLLKESKWSKAFYAYLAA  347 (468)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHHHHHhccccHHHHHHHHHH
Confidence            443 445677788999999999986551      12333455566778889999999999999999776656555554 5


Q ss_pred             HHHHhcCCc-------chHHHHHHHhhhccc
Q 011249          456 NIYASMGKW-------KDSEIVKMMISETEK  479 (490)
Q Consensus       456 ~~~~~~g~~-------~~A~~~~~~~~~~~~  479 (490)
                      -++...|+.       ++|.++++++.....
T Consensus       348 ~c~~~l~~~~~~~~~~~~a~~l~~~vp~l~~  378 (468)
T PF10300_consen  348 ACLLMLGREEEAKEHKKEAEELFRKVPKLKQ  378 (468)
T ss_pred             HHHHhhccchhhhhhHHHHHHHHHHHHHHHh
Confidence            567778888       888889888766543

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.

>PRK15331 chaperone protein SicA; Provisional

Probab=96.92  E-value=0.044  Score=43.19  Aligned_cols=89  Identities=11%  Similarity=-0.113  Sum_probs=67.1

Q ss_pred             HhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHH
Q 011249          355 ACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAEL  432 (490)
Q Consensus       355 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~  432 (490)
                      -+...|++++|..+|.-+..  --+-+...+..|..++-..+++++|+..|....  ...|+..+-.....+...|+.+.
T Consensus        46 ~~y~~Gk~~eA~~~F~~L~~--~d~~n~~Y~~GLaa~~Q~~k~y~~Ai~~Y~~A~~l~~~dp~p~f~agqC~l~l~~~~~  123 (165)
T PRK15331         46 EFYNQGRLDEAETFFRFLCI--YDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKAAK  123 (165)
T ss_pred             HHHHCCCHHHHHHHHHHHHH--hCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCHHH
Confidence            35678999999999988876  233455667788888888899999999886544  34555556667778888899999


Q ss_pred             HHHHHHHHHhcCCC
Q 011249          433 GEIAARHLLELGPE  446 (490)
Q Consensus       433 a~~~~~~~~~~~p~  446 (490)
                      |...|+.+.+ .|.
T Consensus       124 A~~~f~~a~~-~~~  136 (165)
T PRK15331        124 ARQCFELVNE-RTE  136 (165)
T ss_pred             HHHHHHHHHh-Ccc
Confidence            9999988888 344

>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=96.90  E-value=0.0027  Score=50.44  Aligned_cols=60  Identities=18%  Similarity=0.056  Sum_probs=47.8

Q ss_pred             hHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          416 TWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       416 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      ....++..+...|++++|.+.+++++..+|-+..++..++.+|...|+..+|.+.|+++.
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~  123 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALDPYDEEAYRLLMRALAAQGRRAEALRVYERYR  123 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence            445566677788899999999999999999988899999999999999999999888764

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>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=96.89  E-value=0.014  Score=47.99  Aligned_cols=87  Identities=11%  Similarity=0.084  Sum_probs=51.5

Q ss_pred             CCHHhHHHHHHHHHhc-----CChHHHHHHHHHHHHcCcccChhhHHHHHHHHhcc----------------CChHHHHH
Q 011249          208 PDASCWAAMTVCYVQN-----GYAKAAIEMYKVMRQENVRISEVAMVGAISACTQL----------------GDVEMAAI  266 (490)
Q Consensus       208 ~~~~~~~~l~~~~~~~-----g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~----------------g~~~~a~~  266 (490)
                      .+-.+|..++..|.+.     |..+=....++.|.+-|+.-|..+|+.|++++-+.                .+.+-|.+
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            4455555555555432     44555555566666666666666666666665431                12355666


Q ss_pred             HHHHHHhcCCCCchhHHHHHHHHHHhcC
Q 011249          267 LAKHVDEGCCDRTNYVSNALIHMHSKCG  294 (490)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~  294 (490)
                      ++++|...|+-||..++..+++.+.+.+
T Consensus       125 lL~qME~~gV~Pd~Et~~~ll~iFG~~s  152 (228)
T PF06239_consen  125 LLEQMENNGVMPDKETEQMLLNIFGRKS  152 (228)
T ss_pred             HHHHHHHcCCCCcHHHHHHHHHHhcccc
Confidence            7777777777777777776666665544

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.88  E-value=0.1  Score=43.67  Aligned_cols=53  Identities=15%  Similarity=0.098  Sum_probs=26.2

Q ss_pred             HHHHHHHHhhhCChHHHHHHHHHHHhc----CCCCCchHHHHHHHHHhcCCcchHHHH
Q 011249          417 WGALLGACKVHVNAELGEIAARHLLEL----GPEKTGNSALLANIYASMGKWKDSEIV  470 (490)
Q Consensus       417 ~~~l~~~~~~~g~~~~a~~~~~~~~~~----~p~~~~~~~~l~~~~~~~g~~~~A~~~  470 (490)
                      +...+-.+....|+..|.+.++...+.    +|++......|+.+| ..|+.+++..+
T Consensus       193 ~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ay-d~gD~E~~~kv  249 (308)
T KOG1585|consen  193 YVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAY-DEGDIEEIKKV  249 (308)
T ss_pred             HHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHh-ccCCHHHHHHH
Confidence            334444444555666666666654442    244555555555443 33444544443

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.82  E-value=0.58  Score=45.97  Aligned_cols=303  Identities=14%  Similarity=0.060  Sum_probs=176.7

Q ss_pred             HHHHHHHHhCCChHHHHHHHHHhccCC---chhHHHHHHHHHhcCCh---hHHHHHHhhcCC--CCHHhHHHHHHHHHhc
Q 011249          152 SAMVAGYANCGNMKAAKEFYDRMTEKN---SVTWVAMIAGYGKCGEV---REAKKVFDEISE--PDASCWAAMTVCYVQN  223 (490)
Q Consensus       152 ~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~~~~~l~~~~~~~~~~---~~A~~~~~~~~~--~~~~~~~~l~~~~~~~  223 (490)
                      ..++.-+...+.+..|+++-..+..|.   ...|......+++..+.   +-+..+=+++..  ....+|..+++.....
T Consensus       441 ~~vi~Rl~~r~~Y~vaIQva~~l~~p~~~~~~Vl~~Wa~~kI~~~d~~d~~vld~I~~kls~~~~~~iSy~~iA~~Ay~~  520 (829)
T KOG2280|consen  441 EVVIDRLVDRHLYSVAIQVAKLLNLPESQGDRVLLEWARRKIKQSDKMDEEVLDKIDEKLSAKLTPGISYAAIARRAYQE  520 (829)
T ss_pred             hhhhHHHHhcchhHHHHHHHHHhCCccccccHHHHHHHHHHHhccCccchHHHHHHHHHhcccCCCceeHHHHHHHHHhc
Confidence            346777888999999999999998875   67788888888876432   223333344444  4556788888888899


Q ss_pred             CChHHHHHHHHHHHHcCcc----cChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHH
Q 011249          224 GYAKAAIEMYKVMRQENVR----ISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLA  299 (490)
Q Consensus       224 g~~~~A~~~~~~~~~~~~~----p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  299 (490)
                      |+++.|..+++.=...+-+    .+..-+...+.-+...|+.+-...++-++...-   +.      ........+...|
T Consensus       521 GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~~---~~------s~l~~~l~~~p~a  591 (829)
T KOG2280|consen  521 GRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNKL---NR------SSLFMTLRNQPLA  591 (829)
T ss_pred             CcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHHH---HH------HHHHHHHHhchhh
Confidence            9999999887652221111    011122233333444455554444444443321   00      0111112334445


Q ss_pred             HHHHhcccCC-ChhHHHHHHHHHHhcCChHHHHH-HHHHHH----HcCCCCcHHHHHHHHHHhcCCCC----------hH
Q 011249          300 WREFSRIKNK-DVISYSSMITAFADHGKSQEALD-MFLKMR----NEGIEPNQVTFIGVLTACSHGGL----------VE  363 (490)
Q Consensus       300 ~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~-~~~~~~----~~~~~p~~~~~~~l~~~~~~~g~----------~~  363 (490)
                      ..+|.+..+. |..+   +-+.|....+...+-. .++...    ..|..|+..   .....|.+...          ..
T Consensus       592 ~~lY~~~~r~~~~~~---l~d~y~q~dn~~~~a~~~~q~~~~~~~~~~r~~~lk---~~a~~~a~sk~~s~e~ka~ed~~  665 (829)
T KOG2280|consen  592 LSLYRQFMRHQDRAT---LYDFYNQDDNHQALASFHLQASYAAETIEGRIPALK---TAANAFAKSKEKSFEAKALEDQM  665 (829)
T ss_pred             hHHHHHHHHhhchhh---hhhhhhcccchhhhhhhhhhhhhhhhhhcccchhHH---HHHHHHhhhhhhhhHHHHHHHHH
Confidence            5555554431 1111   1112222222222111 111111    122333333   23333333322          22


Q ss_pred             HHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhc
Q 011249          364 DGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLEL  443 (490)
Q Consensus       364 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  443 (490)
                      +-.++.+.+..+++..-..-+.+--+.-+...|+..+|.++-.+.. -|+...|.--+.++...+++++-+++-+.   .
T Consensus       666 kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk-ipdKr~~wLk~~aLa~~~kweeLekfAks---k  741 (829)
T KOG2280|consen  666 KLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK-IPDKRLWWLKLTALADIKKWEELEKFAKS---K  741 (829)
T ss_pred             HHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC-CcchhhHHHHHHHHHhhhhHHHHHHHHhc---c
Confidence            3334455555555655555556666777888999999999999998 67888888888899999998876665443   2


Q ss_pred             CCCCCchHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          444 GPEKTGNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       444 ~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      .  +|.-|.-...+|.+.|+.++|.+++.+..
T Consensus       742 k--sPIGy~PFVe~c~~~~n~~EA~KYiprv~  771 (829)
T KOG2280|consen  742 K--SPIGYLPFVEACLKQGNKDEAKKYIPRVG  771 (829)
T ss_pred             C--CCCCchhHHHHHHhcccHHHHhhhhhccC
Confidence            2  37778888999999999999999987653

>PRK11906 transcriptional regulator; Provisional

Probab=96.72  E-value=0.024  Score=52.47  Aligned_cols=145  Identities=14%  Similarity=0.082  Sum_probs=93.0

Q ss_pred             ChHHHHHHHHHHHH-cCCCCcH-HHHHHHHHHhcC---------CCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh
Q 011249          326 KSQEALDMFLKMRN-EGIEPNQ-VTFIGVLTACSH---------GGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR  394 (490)
Q Consensus       326 ~~~~a~~~~~~~~~-~~~~p~~-~~~~~l~~~~~~---------~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  394 (490)
                      ..+.|+.+|.+... ..+.|+. ..|..+..++..         .....+|.+.-++..+  --+.|+.....+..++.-
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAve--ld~~Da~a~~~~g~~~~~  350 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSD--ITTVDGKILAIMGLITGL  350 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHh--cCCCCHHHHHHHHHHHHh
Confidence            35678888888882 2256654 356555554321         1233455666666655  344556666667777777


Q ss_pred             cCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchH--HHHHHHHHhcCCcchHHHH
Q 011249          395 SGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNS--ALLANIYASMGKWKDSEIV  470 (490)
Q Consensus       395 ~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~--~~l~~~~~~~g~~~~A~~~  470 (490)
                      .|+++.|...|++..  .+....+|......+.-.|+.++|.+.++++++++|....+-  ...+..|+.. ..++|+++
T Consensus       351 ~~~~~~a~~~f~rA~~L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLsP~~~~~~~~~~~~~~~~~~-~~~~~~~~  429 (458)
T PRK11906        351 SGQAKVSHILFEQAKIHSTDIASLYYYRALVHFHNEKIEEARICIDKSLQLEPRRRKAVVIKECVDMYVPN-PLKNNIKL  429 (458)
T ss_pred             hcchhhHHHHHHHHhhcCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCchhhHHHHHHHHHHHHcCC-chhhhHHH
Confidence            778888888888776  334455777777777788888888888888888888754433  3333345544 45777777


Q ss_pred             HHH
Q 011249          471 KMM  473 (490)
Q Consensus       471 ~~~  473 (490)
                      +-+
T Consensus       430 ~~~  432 (458)
T PRK11906        430 YYK  432 (458)
T ss_pred             Hhh
Confidence            643

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.69  E-value=0.12  Score=44.78  Aligned_cols=119  Identities=8%  Similarity=0.025  Sum_probs=58.2

Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHH---HHHHHhhhCChHH
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGA---LLGACKVHVNAEL  432 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~---l~~~~~~~g~~~~  432 (490)
                      ....|+..+|...|+....  -.+-+...-..++.+|...|+.+.|..++..++..-...-+..   -+..+.+..+..+
T Consensus       144 ~~~~e~~~~a~~~~~~al~--~~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~~  221 (304)
T COG3118         144 LIEAEDFGEAAPLLKQALQ--AAPENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATPE  221 (304)
T ss_pred             hhhccchhhHHHHHHHHHH--hCcccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCCC
Confidence            3445666666666666655  2233344445556666666666666666666652222222221   1222222222222


Q ss_pred             HHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          433 GEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       433 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      ... ++.-...+|+|...-..++..+...|+.++|.+.+=.+.++
T Consensus       222 ~~~-l~~~~aadPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~  265 (304)
T COG3118         222 IQD-LQRRLAADPDDVEAALALADQLHLVGRNEAALEHLLALLRR  265 (304)
T ss_pred             HHH-HHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            222 22223345666666666666666666666666655444433

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.62  E-value=0.77  Score=44.78  Aligned_cols=40  Identities=10%  Similarity=0.095  Sum_probs=26.8

Q ss_pred             hcCCCCHHHHHHHhccCCCCCCceehHHHHHHHHhcCChhHHHHHHH
Q 011249           46 QLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYA   92 (490)
Q Consensus        46 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~   92 (490)
                      +--|. +++|.+++=.+.++|.      -|....+-|+|-...++++
T Consensus       745 ~~~g~-feeaek~yld~drrDL------Aielr~klgDwfrV~qL~r  784 (1189)
T KOG2041|consen  745 AFYGE-FEEAEKLYLDADRRDL------AIELRKKLGDWFRVYQLIR  784 (1189)
T ss_pred             hhhcc-hhHhhhhhhccchhhh------hHHHHHhhhhHHHHHHHHH
Confidence            34567 8888888887777665      4455556667666666654

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.54  E-value=0.027  Score=48.20  Aligned_cols=89  Identities=10%  Similarity=0.020  Sum_probs=44.6

Q ss_pred             CCChHHHHHHHHHHHHHcCCCCC---chHHHHHHHHHhhcCChHHHHHHHHhcc----CC-CChhhHHHHHHHHhhhCCh
Q 011249          359 GGLVEDGCKQFELMTRVFGIKPL---TEHLTCMVDLLGRSGQLEKAHSLIMDYK----DF-CDAGTWGALLGACKVHVNA  430 (490)
Q Consensus       359 ~g~~~~a~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~-~~~~~~~~l~~~~~~~g~~  430 (490)
                      .|++..|...|....+.  .|-+   +..+..|..++...|++++|..+|..+.    .. .-+..+--|.....+.|+.
T Consensus       154 sgdy~~A~~~F~~fi~~--YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg~~~~~l~~~  231 (262)
T COG1729         154 SGDYAEAEQAFQAFIKK--YPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLGVSLGRLGNT  231 (262)
T ss_pred             cCCHHHHHHHHHHHHHc--CCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhcCH
Confidence            44555555555555552  2221   2223345555555555555555554443    11 1223444444555556666


Q ss_pred             HHHHHHHHHHHhcCCCCCc
Q 011249          431 ELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       431 ~~a~~~~~~~~~~~p~~~~  449 (490)
                      ++|...|+++.+..|+.+.
T Consensus       232 d~A~atl~qv~k~YP~t~a  250 (262)
T COG1729         232 DEACATLQQVIKRYPGTDA  250 (262)
T ss_pred             HHHHHHHHHHHHHCCCCHH
Confidence            6666666666666665443

>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=96.53  E-value=0.038  Score=42.06  Aligned_cols=53  Identities=13%  Similarity=0.198  Sum_probs=42.4

Q ss_pred             CCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHh
Q 011249          341 GIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLG  393 (490)
Q Consensus       341 ~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  393 (490)
                      ...|+..+..+++.+|+..|++..|+++++.+.+.++++.+..+|..|+.-..
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 PLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEWAY   99 (126)
T ss_pred             CCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            35678888888888888888888888888888888888777778877776443

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=96.51  E-value=0.028  Score=41.90  Aligned_cols=51  Identities=12%  Similarity=0.004  Sum_probs=24.3

Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhc
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDY  408 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  408 (490)
                      ....|+.+.|++.|.+...  -.|.....||.-..++.-.|+.++|++-+++.
T Consensus        53 laE~g~Ld~AlE~F~qal~--l~P~raSayNNRAQa~RLq~~~e~ALdDLn~A  103 (175)
T KOG4555|consen   53 LAEAGDLDGALELFGQALC--LAPERASAYNNRAQALRLQGDDEEALDDLNKA  103 (175)
T ss_pred             HHhccchHHHHHHHHHHHH--hcccchHhhccHHHHHHHcCChHHHHHHHHHH
Confidence            3444555555555555443  23334444555455555555555555444433

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=96.50  E-value=0.46  Score=40.77  Aligned_cols=219  Identities=18%  Similarity=0.051  Sum_probs=120.2

Q ss_pred             CChHHHHHHHHHHHHcCccc-ChhhHHHHHHHHhccCChHHHHHHHHHHHhc-CCCCchhHHHHHHHHHHhcCChHHHHH
Q 011249          224 GYAKAAIEMYKVMRQENVRI-SEVAMVGAISACTQLGDVEMAAILAKHVDEG-CCDRTNYVSNALIHMHSKCGYLDLAWR  301 (490)
Q Consensus       224 g~~~~A~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~A~~  301 (490)
                      +....+...+.......... ....+......+...+++..+...+...... ........+......+...+++..+..
T Consensus        37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  116 (291)
T COG0457          37 GELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALE  116 (291)
T ss_pred             hhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHH
Confidence            44555555555555432221 2455556666666777777777766666542 223444555555666666666777777


Q ss_pred             HHhcccC--CCh-hHHHHHHH-HHHhcCChHHHHHHHHHHHHcCCCC----cHHHHHHHHHHhcCCCChHHHHHHHHHHH
Q 011249          302 EFSRIKN--KDV-ISYSSMIT-AFADHGKSQEALDMFLKMRNEGIEP----NQVTFIGVLTACSHGGLVEDGCKQFELMT  373 (490)
Q Consensus       302 ~~~~~~~--~~~-~~~~~l~~-~~~~~~~~~~a~~~~~~~~~~~~~p----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  373 (490)
                      .+.....  ++. ........ .+...|+++.+...+.+...  ..|    ....+......+...++.+.+...+....
T Consensus       117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~  194 (291)
T COG0457         117 LLEKALALDPDPDLAEALLALGALYELGDYEEALELYEKALE--LDPELNELAEALLALGALLEALGRYEEALELLEKAL  194 (291)
T ss_pred             HHHHHHcCCCCcchHHHHHHHHHHHHcCCHHHHHHHHHHHHh--cCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHH
Confidence            7766654  221 22222223 56667777777777777644  222    22233333333555666777777776666


Q ss_pred             HHcCCCC-CchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCC-hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          374 RVFGIKP-LTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD-AGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       374 ~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      .  ..+. ....+..+...+...+++++|...+.... ..|+ ...+..+...+...+..+.+...+.+..+..|.
T Consensus       195 ~--~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  268 (291)
T COG0457         195 K--LNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKALELDPD  268 (291)
T ss_pred             h--hCcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHhCcc
Confidence            5  2333 34555566666666666666666665554 2222 233333444444555566666666666666665

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.48  E-value=0.022  Score=48.69  Aligned_cols=94  Identities=11%  Similarity=0.065  Sum_probs=75.6

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc-CCC----ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC---CchHHHHH
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK-DFC----DAGTWGALLGACKVHVNAELGEIAARHLLELGPEK---TGNSALLA  455 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~---~~~~~~l~  455 (490)
                      .|+.-+. +...|++.+|...|.... .-|    .+..+--|..++...|+++.|..+|..+.+..|++   |+.+.-|+
T Consensus       144 ~Y~~A~~-~~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y~qg~y~~Aa~~f~~~~k~~P~s~KApdallKlg  222 (262)
T COG1729         144 LYNAALD-LYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHH-HHHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            4665444 456788999999998776 222    33455568899999999999999999999977665   56788999


Q ss_pred             HHHHhcCCcchHHHHHHHhhhcc
Q 011249          456 NIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       456 ~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      .+..+.|+.++|..+++++.+.=
T Consensus       223 ~~~~~l~~~d~A~atl~qv~k~Y  245 (262)
T COG1729         223 VSLGRLGNTDEACATLQQVIKRY  245 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHC
Confidence            99999999999999999988653

>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=96.47  E-value=0.05  Score=43.08  Aligned_cols=71  Identities=11%  Similarity=0.027  Sum_probs=44.2

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHH-----hcCCCCchhHH
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVD-----EGCCDRTNYVS  283 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~-----~~~~~~~~~~~  283 (490)
                      ....++..+...|++++|+.+++.+.... +.+...+..++.++...|+...|.+.|+.+.     +.|++|++.+-
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            44456666777788888888887777654 3366777778888888888888877777653     34667766543

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>KOG1258 consensus mRNA processing protein [RNA processing and modification]

Probab=96.44  E-value=0.92  Score=43.53  Aligned_cols=108  Identities=12%  Similarity=0.225  Sum_probs=67.8

Q ss_pred             CHHHHHHHHhhcCC--CCHh-HHHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHH-hcCChhHHHHHHhh
Q 011249          132 LMDDAQRLFDSMAE--RNVI-SWSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYG-KCGEVREAKKVFDE  204 (490)
Q Consensus       132 ~~~~A~~~~~~~~~--~~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~-~~~~~~~A~~~~~~  204 (490)
                      +++.+..++..+..  |... -|......-.+.|..+.+.++|++.+..   +...|.....-+. ..|+.+...+.|+.
T Consensus        60 ~~~~~r~~y~~fL~kyPl~~gyW~kfA~~E~klg~~~~s~~Vfergv~aip~SvdlW~~Y~~f~~n~~~d~~~lr~~fe~  139 (577)
T KOG1258|consen   60 DVDALREVYDIFLSKYPLCYGYWKKFADYEYKLGNAENSVKVFERGVQAIPLSVDLWLSYLAFLKNNNGDPETLRDLFER  139 (577)
T ss_pred             HHHHHHHHHHHHHhhCccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhccCCCHHHHHHHHHH
Confidence            34555666666654  4443 3455555666777888888888877753   4444444443332 35666667777766


Q ss_pred             cCC------CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011249          205 ISE------PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQE  239 (490)
Q Consensus       205 ~~~------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  239 (490)
                      ...      .+...|...|..-...+++.....+|++..+.
T Consensus       140 A~~~vG~dF~S~~lWdkyie~en~qks~k~v~~iyeRilei  180 (577)
T KOG1258|consen  140 AKSYVGLDFLSDPLWDKYIEFENGQKSWKRVANIYERILEI  180 (577)
T ss_pred             HHHhcccchhccHHHHHHHHHHhccccHHHHHHHHHHHHhh
Confidence            654      44556777777777777788888888777754

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.40  E-value=0.12  Score=45.53  Aligned_cols=113  Identities=12%  Similarity=-0.042  Sum_probs=47.5

Q ss_pred             cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHH----HHHHHHhhcCChH
Q 011249          324 HGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLT----CMVDLLGRSGQLE  399 (490)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~----~l~~~~~~~g~~~  399 (490)
                      .|++.+|...|+++.+. .+.|...+...-.+|...|+.+.-...++++..  ...++...|.    .+..++..+|-++
T Consensus       116 ~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip--~wn~dlp~~sYv~GmyaFgL~E~g~y~  192 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIP--KWNADLPCYSYVHGMYAFGLEECGIYD  192 (491)
T ss_pred             cccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhcc--ccCCCCcHHHHHHHHHHhhHHHhccch
Confidence            34444444445444443 233333444444444445555444444444443  2233332222    2222333455555


Q ss_pred             HHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHH
Q 011249          400 KAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARH  439 (490)
Q Consensus       400 ~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  439 (490)
                      +|++.-++..  .+.|...-.++...+...|+..++.++..+
T Consensus       193 dAEk~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~  234 (491)
T KOG2610|consen  193 DAEKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYK  234 (491)
T ss_pred             hHHHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHh
Confidence            5555544443  122233333344444444555555444443

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=96.38  E-value=0.4  Score=42.79  Aligned_cols=122  Identities=15%  Similarity=0.020  Sum_probs=53.8

Q ss_pred             HHHHHhccCChHHHHHHHHHHHhcC-----CCCchhHHHHHHHHHHhcCChHHHHHHHhcccC-------CChh------
Q 011249          251 AISACTQLGDVEMAAILAKHVDEGC-----CDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN-------KDVI------  312 (490)
Q Consensus       251 l~~~~~~~g~~~~a~~~~~~~~~~~-----~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-------~~~~------  312 (490)
                      +..++...+.++++.+.|+...+.-     ......++..|...|....++++|.-+..+..+       .|..      
T Consensus       128 ~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~  207 (518)
T KOG1941|consen  128 MGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYEKALFFPCKAAELVNSYGLKDWSLKYRAM  207 (518)
T ss_pred             HHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhhHHhhhhHhHHHHHHhcCcCchhHHHHHH
Confidence            4444444455555555554443221     011234455555555555555555443333221       1111      


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHH----cCCCCcH-HHHHHHHHHhcCCCChHHHHHHHHHH
Q 011249          313 SYSSMITAFADHGKSQEALDMFLKMRN----EGIEPNQ-VTFIGVLTACSHGGLVEDGCKQFELM  372 (490)
Q Consensus       313 ~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~  372 (490)
                      ....|.-++...|+.-.|.+.-++..+    .|-+|.. .....+.+.|...|+.+.|..-|+..
T Consensus       208 ~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDIyR~~gd~e~af~rYe~A  272 (518)
T KOG1941|consen  208 SLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADIYRSRGDLERAFRRYEQA  272 (518)
T ss_pred             HHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHhcccHhHHHHHHHHH
Confidence            111223344455555555554444332    2322221 23444555566666666665555544

>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=96.38  E-value=0.67  Score=41.32  Aligned_cols=99  Identities=8%  Similarity=-0.054  Sum_probs=44.6

Q ss_pred             hHHHHHHHHhccCChHH---HHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCC---ChhHHHHHHHH
Q 011249          247 AMVGAISACTQLGDVEM---AAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK---DVISYSSMITA  320 (490)
Q Consensus       247 ~~~~l~~~~~~~g~~~~---a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~---~~~~~~~l~~~  320 (490)
                      ++..++.++...+..+.   |..+++.+.... +..+.++..-+..+.+.++.+.+.+.+.+|...   ....+..++..
T Consensus        86 iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~-~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~~~e~~~~~~l~~  164 (278)
T PF08631_consen   86 ILRLLANAYLEWDTYESVEKALNALRLLESEY-GNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSVDHSESNFDSILHH  164 (278)
T ss_pred             HHHHHHHHHHcCCChHHHHHHHHHHHHHHHhC-CCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhcccccchHHHHHHH
Confidence            44455555555554433   333444443322 222334434455555566666666666665541   22333333333


Q ss_pred             HH--hcCChHHHHHHHHHHHHcCCCCcH
Q 011249          321 FA--DHGKSQEALDMFLKMRNEGIEPNQ  346 (490)
Q Consensus       321 ~~--~~~~~~~a~~~~~~~~~~~~~p~~  346 (490)
                      +.  .......+...+..+....+.|..
T Consensus       165 i~~l~~~~~~~a~~~ld~~l~~r~~~~~  192 (278)
T PF08631_consen  165 IKQLAEKSPELAAFCLDYLLLNRFKSSE  192 (278)
T ss_pred             HHHHHhhCcHHHHHHHHHHHHHHhCCCh
Confidence            31  112334455555555543344433

It is also involved in sporulation [].

>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=96.38  E-value=0.2  Score=37.63  Aligned_cols=141  Identities=11%  Similarity=0.091  Sum_probs=83.6

Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHH
Q 011249          321 FADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEK  400 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  400 (490)
                      +.-.|..++..++..+....   .+..-++.++.-....-+-+-..+.++.+-+-|.+.+- .....++.+|...|.   
T Consensus        12 ~ildG~V~qGveii~k~v~S---sni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis~C-~NlKrVi~C~~~~n~---   84 (161)
T PF09205_consen   12 RILDGDVKQGVEIIEKTVNS---SNIKEYNWVICNIIDAADCDYVVETLDSIGKIFDISKC-GNLKRVIECYAKRNK---   84 (161)
T ss_dssp             HHHTT-HHHHHHHHHHHHHH---S-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GGG--S-THHHHHHHHHTT----
T ss_pred             HHHhchHHHHHHHHHHHcCc---CCccccceeeeecchhhchhHHHHHHHHHhhhcCchhh-cchHHHHHHHHHhcc---
Confidence            34567888888888887763   34455666665444444445555555555442221111 112234444444432   


Q ss_pred             HHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          401 AHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       401 A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                                  +....+..+......|.-+.-.+++..+.+.+..+|.++..++.+|.+.|+..++.+++++.-+.|++
T Consensus        85 ------------~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   85 ------------LSEYVDLALDILVKQGKKDQLDKIYNELKKNEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             --------------HHHHHHHHHHHHTT-HHHHHHHHHHH-----S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             ------------hHHHHHHHHHHHHHhccHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence                        34445556677788899999999999988766667999999999999999999999999999888863

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=96.37  E-value=0.56  Score=40.25  Aligned_cols=215  Identities=19%  Similarity=0.077  Sum_probs=107.1

Q ss_pred             ChHHHHHHHHHHHhcCCC-CchhHHHHHHHHHHhcCChHHHHHHHhcccC-----CChhHHHHHHHHHHhcCChHHHHHH
Q 011249          260 DVEMAAILAKHVDEGCCD-RTNYVSNALIHMHSKCGYLDLAWREFSRIKN-----KDVISYSSMITAFADHGKSQEALDM  333 (490)
Q Consensus       260 ~~~~a~~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~~~~~~~l~~~~~~~~~~~~a~~~  333 (490)
                      ....+...+......... ............+...+.+..+...+.....     .....+......+...+++..+...
T Consensus        38 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  117 (291)
T COG0457          38 ELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEALEL  117 (291)
T ss_pred             hHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHHHH
Confidence            334444444444433211 1234444555555666666666555555431     2334445555555555666666666


Q ss_pred             HHHHHHcCCCCcHHHHHHHHH-HhcCCCChHHHHHHHHHHHHHcCC--CCCchHHHHHHHHHhhcCChHHHHHHHHhcc-
Q 011249          334 FLKMRNEGIEPNQVTFIGVLT-ACSHGGLVEDGCKQFELMTRVFGI--KPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-  409 (490)
Q Consensus       334 ~~~~~~~~~~p~~~~~~~l~~-~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-  409 (490)
                      +.........+. ........ .+...|+++.+...+.+.... ..  ......+......+...++.+++...+.... 
T Consensus       118 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  195 (291)
T COG0457         118 LEKALALDPDPD-LAEALLALGALYELGDYEEALELYEKALEL-DPELNELAEALLALGALLEALGRYEEALELLEKALK  195 (291)
T ss_pred             HHHHHcCCCCcc-hHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-CCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHh
Confidence            666655322221 11111122 455666666666666666331 11  0122223333333455666666666665554 


Q ss_pred             -CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          410 -DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       410 -~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                       .+. ....+..+...+...++++.+...+..+....|.....+..++..+...|.++++...+++...
T Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (291)
T COG0457         196 LNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKALE  264 (291)
T ss_pred             hCcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHH
Confidence             122 2345555555566666666666666666666665444455555555555556666665555443

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=96.35  E-value=0.85  Score=42.13  Aligned_cols=127  Identities=12%  Similarity=0.020  Sum_probs=86.0

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHcC-CCCCchHHHHHHHHHhhcCChHHHHHHHHhc-cCCCChhhH-HHHHHHH
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVFG-IKPLTEHLTCMVDLLGRSGQLEKAHSLIMDY-KDFCDAGTW-GALLGAC  424 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~-~~~~~~~~~-~~l~~~~  424 (490)
                      .|...+..-.+..-++.|..+|-++.+. + ..+++..+++++..++ .|+..-|.++|+.- ...||...| .-.+.-+
T Consensus       399 v~C~~~N~v~r~~Gl~aaR~~F~k~rk~-~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~f~d~~~y~~kyl~fL  476 (660)
T COG5107         399 VFCVHLNYVLRKRGLEAARKLFIKLRKE-GIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLKFPDSTLYKEKYLLFL  476 (660)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHhcc-CCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHhCCCchHHHHHHHHHH
Confidence            3444555555666678888888888885 5 5677778888777554 57788888888643 344555544 4455556


Q ss_pred             hhhCChHHHHHHHHHHHhcCCC--CCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          425 KVHVNAELGEIAARHLLELGPE--KTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       425 ~~~g~~~~a~~~~~~~~~~~p~--~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      ...++-+.|..+|+..++.-..  -..+|..++..-..-|+...+..+-++|.+
T Consensus       477 i~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e  530 (660)
T COG5107         477 IRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFRE  530 (660)
T ss_pred             HHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHH
Confidence            7778888888888877653222  255677777777777887777666666544

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=96.29  E-value=0.065  Score=47.57  Aligned_cols=223  Identities=11%  Similarity=0.000  Sum_probs=99.1

Q ss_pred             HHhcCChHHHHHHHHHHHHcC--cccChhhHHHHHHHHhccCChHHHHHHHHHHHhc--CCCCchh---HHHHHHHHHHh
Q 011249          220 YVQNGYAKAAIEMYKVMRQEN--VRISEVAMVGAISACTQLGDVEMAAILAKHVDEG--CCDRTNY---VSNALIHMHSK  292 (490)
Q Consensus       220 ~~~~g~~~~A~~~~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~---~~~~l~~~~~~  292 (490)
                      +....+.++|+..+.+-...-  ..--..++..+..+.++.|.++++...--.....  ....+..   .|..+..++.+
T Consensus        16 Ly~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~mL~~a~sqi~~a~~~~ds~~~~ea~lnlar~~e~   95 (518)
T KOG1941|consen   16 LYQSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEMLKFAVSQIDTARELEDSDFLLEAYLNLARSNEK   95 (518)
T ss_pred             HhcCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345667777777776655321  1112245556666666777666665443221111  0011111   22223333333


Q ss_pred             cCChHHHHHHHhcccC-C-------ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC---CCC--cHHHHHHHHHHhcCC
Q 011249          293 CGYLDLAWREFSRIKN-K-------DVISYSSMITAFADHGKSQEALDMFLKMRNEG---IEP--NQVTFIGVLTACSHG  359 (490)
Q Consensus       293 ~~~~~~A~~~~~~~~~-~-------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~p--~~~~~~~l~~~~~~~  359 (490)
                      .-++.+++.+-+.-.. |       ......++..++...+.++++++.|+...+--   -.|  ....+..|...|...
T Consensus        96 l~~f~kt~~y~k~~l~lpgt~~~~~~gq~~l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l  175 (518)
T KOG1941|consen   96 LCEFHKTISYCKTCLGLPGTRAGQLGGQVSLSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQL  175 (518)
T ss_pred             HHHhhhHHHHHHHHhcCCCCCcccccchhhhhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHH
Confidence            3333333333222111 1       11223344455555566666666666655411   111  123555566666666


Q ss_pred             CChHHHHHHHHHHHHH---cCCCCCchHHH-----HHHHHHhhcCChHHHHHHHHhcc----CCCChh----hHHHHHHH
Q 011249          360 GLVEDGCKQFELMTRV---FGIKPLTEHLT-----CMVDLLGRSGQLEKAHSLIMDYK----DFCDAG----TWGALLGA  423 (490)
Q Consensus       360 g~~~~a~~~~~~~~~~---~~~~~~~~~~~-----~l~~~~~~~g~~~~A~~~~~~~~----~~~~~~----~~~~l~~~  423 (490)
                      .++++|.-+..+..+-   +++..-...|.     .|.-++...|+.-.|.+..++..    ...|..    ....+...
T Consensus       176 ~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDI  255 (518)
T KOG1941|consen  176 KDYEKALFFPCKAAELVNSYGLKDWSLKYRAMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADI  255 (518)
T ss_pred             HhhhHHhhhhHhHHHHHHhcCcCchhHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence            6666666555544331   12222222222     22334445555555555544332    122222    23344455


Q ss_pred             HhhhCChHHHHHHHHHHHh
Q 011249          424 CKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       424 ~~~~g~~~~a~~~~~~~~~  442 (490)
                      |...|+.|.|..-|+.+..
T Consensus       256 yR~~gd~e~af~rYe~Am~  274 (518)
T KOG1941|consen  256 YRSRGDLERAFRRYEQAMG  274 (518)
T ss_pred             HHhcccHhHHHHHHHHHHH
Confidence            5666666666666665555

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.17  E-value=0.053  Score=47.54  Aligned_cols=116  Identities=11%  Similarity=-0.028  Sum_probs=93.8

Q ss_pred             cCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCC--CChh----hHHHHHHHHhhhCCh
Q 011249          357 SHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDF--CDAG----TWGALLGACKVHVNA  430 (490)
Q Consensus       357 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~----~~~~l~~~~~~~g~~  430 (490)
                      ...|+..+|-..|+++.+  ..|.|.-.+...-+++.-.|+.+.-...++++..+  ++.+    +-..+..++...|-+
T Consensus       114 ~~~g~~h~a~~~wdklL~--d~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y  191 (491)
T KOG2610|consen  114 WGRGKHHEAAIEWDKLLD--DYPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIY  191 (491)
T ss_pred             hccccccHHHHHHHHHHH--hCchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccc
Confidence            346888888899999998  57777777777778888899998888888887722  3433    334455566789999


Q ss_pred             HHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          431 ELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       431 ~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      ++|++..+++.+++|.|.-+...++-++...|+..++.+++.+-
T Consensus       192 ~dAEk~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~t  235 (491)
T KOG2610|consen  192 DDAEKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKT  235 (491)
T ss_pred             hhHHHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhc
Confidence            99999999999999999998889999999999999998887653

>PRK11906 transcriptional regulator; Provisional

Probab=96.15  E-value=0.3  Score=45.57  Aligned_cols=143  Identities=10%  Similarity=-0.062  Sum_probs=92.7

Q ss_pred             ChHHHHHHHhccc---CCC---hhHHHHHHHHHHhc---------CChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCC
Q 011249          295 YLDLAWREFSRIK---NKD---VISYSSMITAFADH---------GKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHG  359 (490)
Q Consensus       295 ~~~~A~~~~~~~~---~~~---~~~~~~l~~~~~~~---------~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  359 (490)
                      ..+.|..+|.+..   +-|   ...|..+..++...         ....+|.++.++.++.+ +-|......+..+....
T Consensus       273 ~~~~Al~lf~ra~~~~~ldp~~a~a~~~lA~~h~~~~~~g~~~~~~~~~~a~~~A~rAveld-~~Da~a~~~~g~~~~~~  351 (458)
T PRK11906        273 SIYRAMTIFDRLQNKSDIQTLKTECYCLLAECHMSLALHGKSELELAAQKALELLDYVSDIT-TVDGKILAIMGLITGLS  351 (458)
T ss_pred             HHHHHHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHhh
Confidence            3567888898887   433   45565555544322         23456777777777753 34667777777777777


Q ss_pred             CChHHHHHHHHHHHHHcCCCCC-chHHHHHHHHHhhcCChHHHHHHHHh-ccCCCChh---hHHHHHHHHhhhCChHHHH
Q 011249          360 GLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDLLGRSGQLEKAHSLIMD-YKDFCDAG---TWGALLGACKVHVNAELGE  434 (490)
Q Consensus       360 g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~-~~~~~~~~---~~~~l~~~~~~~g~~~~a~  434 (490)
                      ++.+.|...|++...   +.|+ ...|........-.|+.++|.+.+++ +...|...   +....+..|. ....+.|+
T Consensus       352 ~~~~~a~~~f~rA~~---L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i~~alrLsP~~~~~~~~~~~~~~~~-~~~~~~~~  427 (458)
T PRK11906        352 GQAKVSHILFEQAKI---HSTDIASLYYYRALVHFHNEKIEEARICIDKSLQLEPRRRKAVVIKECVDMYV-PNPLKNNI  427 (458)
T ss_pred             cchhhHHHHHHHHhh---cCCccHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCchhhHHHHHHHHHHHHc-CCchhhhH
Confidence            889999999999975   4454 55566666667778999999999988 44444332   2222222343 34567777


Q ss_pred             HHHHHHHh
Q 011249          435 IAARHLLE  442 (490)
Q Consensus       435 ~~~~~~~~  442 (490)
                      .+|-+-.+
T Consensus       428 ~~~~~~~~  435 (458)
T PRK11906        428 KLYYKETE  435 (458)
T ss_pred             HHHhhccc
Confidence            77765444

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=96.15  E-value=0.015  Score=32.39  Aligned_cols=32  Identities=28%  Similarity=0.149  Sum_probs=23.2

Q ss_pred             hHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC
Q 011249          416 TWGALLGACKVHVNAELGEIAARHLLELGPEK  447 (490)
Q Consensus       416 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~  447 (490)
                      .|..+...+...|++++|++.++++++++|++
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~~   34 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALELDPNN   34 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTS
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHHHCcCC
Confidence            45666777777888888888888888877764

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 ....

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=96.15  E-value=0.036  Score=51.31  Aligned_cols=62  Identities=15%  Similarity=0.038  Sum_probs=43.3

Q ss_pred             cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCc----hHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          345 NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLT----EHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       345 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                      +...+..+..+|...|++++|+..|++..+   +.|+.    ..|..+..+|...|+.++|++.+++..
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALe---L~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrAL  139 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALE---LNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTAL  139 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHh---hCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            345677777777777777777777777765   24443    236777777777777777777777665

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=96.14  E-value=0.01  Score=33.05  Aligned_cols=32  Identities=22%  Similarity=0.063  Sum_probs=24.5

Q ss_pred             hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          415 GTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       415 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      .+|..+...+...|++++|+..|+++++++|+
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~   33 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALELDPD   33 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHCcC
Confidence            45677777888888888888888888888876

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 ....

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=96.08  E-value=0.79  Score=39.18  Aligned_cols=55  Identities=13%  Similarity=0.074  Sum_probs=39.9

Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCc---hHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTG---NSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~---~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      +..-|.+.|.+..|..-++.+++..|+.+.   .+..+..+|...|-.++|.+.-+-+
T Consensus       173 IaryY~kr~~~~AA~nR~~~v~e~y~~t~~~~eaL~~l~eaY~~lgl~~~a~~~~~vl  230 (254)
T COG4105         173 IARYYLKRGAYVAAINRFEEVLENYPDTSAVREALARLEEAYYALGLTDEAKKTAKVL  230 (254)
T ss_pred             HHHHHHHhcChHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhCChHHHHHHHHHH
Confidence            345677888888888888888887666443   5556677788888888888766544

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=96.07  E-value=0.77  Score=40.04  Aligned_cols=149  Identities=13%  Similarity=0.048  Sum_probs=93.1

Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChH
Q 011249          320 AFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLE  399 (490)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  399 (490)
                      .....|++.+|..+|....... .-+......+..+|...|+.+.|..++..+..+ --.........-+..+.+.....
T Consensus       143 ~~~~~e~~~~a~~~~~~al~~~-~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~-~~~~~~~~l~a~i~ll~qaa~~~  220 (304)
T COG3118         143 ELIEAEDFGEAAPLLKQALQAA-PENSEAKLLLAECLLAAGDVEAAQAILAALPLQ-AQDKAAHGLQAQIELLEQAAATP  220 (304)
T ss_pred             hhhhccchhhHHHHHHHHHHhC-cccchHHHHHHHHHHHcCChHHHHHHHHhCccc-chhhHHHHHHHHHHHHHHHhcCC
Confidence            4556778888888888877642 223445666777788888888888888776542 11111111122344455555555


Q ss_pred             HHHHHHHhccCCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC--CCCCchHHHHHHHHHhcCCcchHHHH
Q 011249          400 KAHSLIMDYKDFC-DAGTWGALLGACKVHVNAELGEIAARHLLELG--PEKTGNSALLANIYASMGKWKDSEIV  470 (490)
Q Consensus       400 ~A~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~--p~~~~~~~~l~~~~~~~g~~~~A~~~  470 (490)
                      +...+-.++...| |...-..+...+...|+.+.|.+.+-.+++.+  -++...-..+..++.-.|.-+.+-..
T Consensus       221 ~~~~l~~~~aadPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~d~~~Rk~lle~f~~~g~~Dp~~~~  294 (304)
T COG3118         221 EIQDLQRRLAADPDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFEDGEARKTLLELFEAFGPADPLVLA  294 (304)
T ss_pred             CHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcccccCcHHHHHHHHHHHhcCCCCHHHHH
Confidence            5555555544333 56666677777888888888888877777654  45667777787777777755544333

>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=96.04  E-value=0.39  Score=45.65  Aligned_cols=155  Identities=16%  Similarity=0.137  Sum_probs=104.2

Q ss_pred             HHhcCCHHHHHHHHh--hcCC-CCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHh
Q 011249          127 YTKIGLMDDAQRLFD--SMAE-RNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFD  203 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~--~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~  203 (490)
                      ..-.|+++++.++.+  ++.. -.....+.++.-+.+.|..+.|+++-..     +   ..-.+...+.|+++.|.++.+
T Consensus       271 av~~~d~~~v~~~i~~~~ll~~i~~~~~~~i~~fL~~~G~~e~AL~~~~D-----~---~~rFeLAl~lg~L~~A~~~a~  342 (443)
T PF04053_consen  271 AVLRGDFEEVLRMIAASNLLPNIPKDQGQSIARFLEKKGYPELALQFVTD-----P---DHRFELALQLGNLDIALEIAK  342 (443)
T ss_dssp             HHHTT-HHH-----HHHHTGGG--HHHHHHHHHHHHHTT-HHHHHHHSS------H---HHHHHHHHHCT-HHHHHHHCC
T ss_pred             HHHcCChhhhhhhhhhhhhcccCChhHHHHHHHHHHHCCCHHHHHhhcCC-----h---HHHhHHHHhcCCHHHHHHHHH
Confidence            445688988766665  2221 1345688889999999999999887643     2   234566788999999999887


Q ss_pred             hcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHH
Q 011249          204 EISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVS  283 (490)
Q Consensus       204 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~  283 (490)
                      +..  +...|..|.....+.|+++-|.+.|.+...         +..|+-.|.-.|+.+...++.+.....| .     +
T Consensus       343 ~~~--~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~~~~-~-----~  405 (443)
T PF04053_consen  343 ELD--DPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAEERG-D-----I  405 (443)
T ss_dssp             CCS--THHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHHTT-------H
T ss_pred             hcC--cHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHHHcc-C-----H
Confidence            765  677999999999999999999999987542         4455666777888888888888777766 2     3


Q ss_pred             HHHHHHHHhcCChHHHHHHHhcc
Q 011249          284 NALIHMHSKCGYLDLAWREFSRI  306 (490)
Q Consensus       284 ~~l~~~~~~~~~~~~A~~~~~~~  306 (490)
                      +....++.-.|+.++..+++.+.
T Consensus       406 n~af~~~~~lgd~~~cv~lL~~~  428 (443)
T PF04053_consen  406 NIAFQAALLLGDVEECVDLLIET  428 (443)
T ss_dssp             HHHHHHHHHHT-HHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHc
Confidence            33444555567777777766543

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.

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.03  E-value=0.02  Score=46.22  Aligned_cols=104  Identities=11%  Similarity=-0.036  Sum_probs=67.2

Q ss_pred             HHhcCCCChHHHHHHHHHHHHHcCCCCCc-----hHHHHHHHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHHHhh
Q 011249          354 TACSHGGLVEDGCKQFELMTRVFGIKPLT-----EHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGACKV  426 (490)
Q Consensus       354 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~  426 (490)
                      .-+...|++++|..-|..+..  ..++..     ..|..-.-++.+.+.++.|++-..+.. ..| .......-..+|.+
T Consensus       103 N~~F~ngdyeeA~skY~~Ale--~cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaiel~pty~kAl~RRAeayek  180 (271)
T KOG4234|consen  103 NELFKNGDYEEANSKYQEALE--SCPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIELNPTYEKALERRAEAYEK  180 (271)
T ss_pred             HHhhhcccHHHHHHHHHHHHH--hCccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHhcCchhHHHHHHHHHHHHh
Confidence            347788899999988888887  344432     233344456677788888887776555 222 22333333456777


Q ss_pred             hCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          427 HVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       427 ~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ...++.|++-|+++++.+|....+....+++--
T Consensus       181 ~ek~eealeDyKki~E~dPs~~ear~~i~rl~~  213 (271)
T KOG4234|consen  181 MEKYEEALEDYKKILESDPSRREAREAIARLPP  213 (271)
T ss_pred             hhhHHHHHHHHHHHHHhCcchHHHHHHHHhcCH
Confidence            778888888888888888876655555554433

>PRK11619 lytic murein transglycosylase; Provisional

Probab=96.01  E-value=2  Score=43.26  Aligned_cols=315  Identities=10%  Similarity=-0.015  Sum_probs=167.4

Q ss_pred             HHhcCCHHHHHHHHhhcCCCCHh---HHHHHHHHHHhCCChHHHHHHHHHhcc-C-CchhHHHHHHHHHhcCChhHHHHH
Q 011249          127 YTKIGLMDDAQRLFDSMAERNVI---SWSAMVAGYANCGNMKAAKEFYDRMTE-K-NSVTWVAMIAGYGKCGEVREAKKV  201 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~~~~~~~~~---~~~~l~~~~~~~~~~~~a~~~~~~~~~-~-~~~~~~~l~~~~~~~~~~~~A~~~  201 (490)
                      ..+.|++..+.++...+...-..   .|..+..... ...+++...++++-.. | ....-......+.+.+++....++
T Consensus        43 a~~~g~~~~~~~~~~~l~d~pL~~yl~y~~L~~~l~-~~~~~ev~~Fl~~~~~~P~~~~Lr~~~l~~La~~~~w~~~~~~  121 (644)
T PRK11619         43 AWDNRQMDVVEQLMPTLKDYPLYPYLEYRQLTQDLM-NQPAVQVTNFIRANPTLPPARSLQSRFVNELARREDWRGLLAF  121 (644)
T ss_pred             HHHCCCHHHHHHHHHhccCCCcHhHHHHHHHHhccc-cCCHHHHHHHHHHCCCCchHHHHHHHHHHHHHHccCHHHHHHh
Confidence            46778899988888887643222   3333332221 3356666666666543 3 222223445556678888888884


Q ss_pred             HhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHH--HHHHHHHhcCC---
Q 011249          202 FDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAA--ILAKHVDEGCC---  276 (490)
Q Consensus       202 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~--~~~~~~~~~~~---  276 (490)
                      +..- ..+...-.....+....|+.++|......+-..| ...+..+..++..+.+.|.+....  +-+..+...+-   
T Consensus       122 ~~~~-p~~~~~~c~~~~A~~~~G~~~~A~~~a~~lW~~g-~~~p~~cd~l~~~~~~~g~lt~~d~w~R~~~al~~~~~~l  199 (644)
T PRK11619        122 SPEK-PKPVEARCNYYYAKWATGQQQEAWQGAKELWLTG-KSLPNACDKLFSVWQQSGKQDPLAYLERIRLAMKAGNTGL  199 (644)
T ss_pred             cCCC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccC-CCCChHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHH
Confidence            4332 3455556667778888899888877777765554 334556677777776655544322  11222222221   


Q ss_pred             --------CCc-hhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHH--HhcCChHHHHHHHHHHHHc-CCCC
Q 011249          277 --------DRT-NYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAF--ADHGKSQEALDMFLKMRNE-GIEP  344 (490)
Q Consensus       277 --------~~~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~--~~~~~~~~a~~~~~~~~~~-~~~p  344 (490)
                              +++ ......++..+.   +...+...+.... ++...-..++.++  ....+.+.|..++...... ++.+
T Consensus       200 A~~l~~~l~~~~~~~a~a~~al~~---~p~~~~~~~~~~~-~~~~~~~~~~~~l~Rlar~d~~~A~~~~~~~~~~~~~~~  275 (644)
T PRK11619        200 VTYLAKQLPADYQTIASALIKLQN---DPNTVETFARTTG-PTDFTRQMAAVAFASVARQDAENARLMIPSLVRAQKLNE  275 (644)
T ss_pred             HHHHHHhcChhHHHHHHHHHHHHH---CHHHHHHHhhccC-CChhhHHHHHHHHHHHHHhCHHHHHHHHHHHHHhcCCCH
Confidence                    111 111112222221   2222332222221 1211111111122  2345668888888877543 2333


Q ss_pred             cHH--HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHH
Q 011249          345 NQV--TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGAL  420 (490)
Q Consensus       345 ~~~--~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l  420 (490)
                      ...  ....+.......+...++...++....   ...+......-+..-.+.++++.+...+..|.  ......-.--+
T Consensus       276 ~~~~~~~~~lA~~~a~~~~~~~a~~w~~~~~~---~~~~~~~~e~r~r~Al~~~dw~~~~~~i~~L~~~~~~~~rw~YW~  352 (644)
T PRK11619        276 DQRQELRDIVAWRLMGNDVTDEQAKWRDDVIM---RSQSTSLLERRVRMALGTGDRRGLNTWLARLPMEAKEKDEWRYWQ  352 (644)
T ss_pred             HHHHHHHHHHHHHHHhccCCHHHHHHHHhccc---ccCCcHHHHHHHHHHHHccCHHHHHHHHHhcCHhhccCHhhHHHH
Confidence            322  334444333443325566666665543   12344455555666668889998888888887  12223333445


Q ss_pred             HHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          421 LGACKVHVNAELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       421 ~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      ..++...|+.++|...|+++..  +  .++|-.|+
T Consensus       353 aRa~~~~g~~~~A~~~~~~~a~--~--~~fYG~LA  383 (644)
T PRK11619        353 ADLLLEQGRKAEAEEILRQLMQ--Q--RGFYPMVA  383 (644)
T ss_pred             HHHHHHcCCHHHHHHHHHHHhc--C--CCcHHHHH
Confidence            6666678999999999998744  2  34555553

>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=95.98  E-value=0.16  Score=38.15  Aligned_cols=135  Identities=14%  Similarity=0.162  Sum_probs=77.5

Q ss_pred             HHhcCCHHHHHHHHhhcCC-CCHhHHHHHHHHHHhCCChHHHHHHHHHhccC-Cchh---HHHHHHHHHhcCChhHHHHH
Q 011249          127 YTKIGLMDDAQRLFDSMAE-RNVISWSAMVAGYANCGNMKAAKEFYDRMTEK-NSVT---WVAMIAGYGKCGEVREAKKV  201 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~---~~~l~~~~~~~~~~~~A~~~  201 (490)
                      ..-.|.+++..++..+... .+..-+|-++--....-+-+-..++++.+-+- |...   ...++.+|+..|.       
T Consensus        12 ~ildG~V~qGveii~k~v~Ssni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis~C~NlKrVi~C~~~~n~-------   84 (161)
T PF09205_consen   12 RILDGDVKQGVEIIEKTVNSSNIKEYNWVICNIIDAADCDYVVETLDSIGKIFDISKCGNLKRVIECYAKRNK-------   84 (161)
T ss_dssp             HHHTT-HHHHHHHHHHHHHHS-HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GGG-S-THHHHHHHHHTT--------
T ss_pred             HHHhchHHHHHHHHHHHcCcCCccccceeeeecchhhchhHHHHHHHHHhhhcCchhhcchHHHHHHHHHhcc-------
Confidence            3456777777777777665 34555665555555555666666666665442 2221   1233444443332       


Q ss_pred             HhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCC
Q 011249          202 FDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCC  276 (490)
Q Consensus       202 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  276 (490)
                             +......-+......|+-++-.+++..+.+.+ .+++.....+..+|.+.|+..++..++.++-+.|+
T Consensus        85 -------~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~-~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~  151 (161)
T PF09205_consen   85 -------LSEYVDLALDILVKQGKKDQLDKIYNELKKNE-EINPEFLVKIANAYKKLGNTREANELLKEACEKGL  151 (161)
T ss_dssp             ---------HHHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-
T ss_pred             -------hHHHHHHHHHHHHHhccHHHHHHHHHHHhhcc-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhch
Confidence                   22344555667778888888888888877533 66777788888888888888888888888877774

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=95.94  E-value=0.66  Score=43.53  Aligned_cols=103  Identities=13%  Similarity=0.091  Sum_probs=70.4

Q ss_pred             HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccC--CCCh--hhHHHHH
Q 011249          346 QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKD--FCDA--GTWGALL  421 (490)
Q Consensus       346 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~~~~--~~~~~l~  421 (490)
                      ...-..+..++.+.|+.++|.+.++++.+.+.......+...|+.++...+.+.++..++.+..+  -|..  ..|+..+
T Consensus       259 ~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaAL  338 (539)
T PF04184_consen  259 VYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAAL  338 (539)
T ss_pred             hhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHH
Confidence            33445567777899999999999999987533223455667899999999999999999988762  2332  3555544


Q ss_pred             HHHhhhCC---------------hHHHHHHHHHHHhcCCCCC
Q 011249          422 GACKVHVN---------------AELGEIAARHLLELGPEKT  448 (490)
Q Consensus       422 ~~~~~~g~---------------~~~a~~~~~~~~~~~p~~~  448 (490)
                      -.+...+|               -..|.+.+.++.+.+|.-|
T Consensus       339 LkaRav~d~fs~e~a~rRGls~ae~~aveAi~RAvefNPHVp  380 (539)
T PF04184_consen  339 LKARAVGDKFSPEAASRRGLSPAEMNAVEAIHRAVEFNPHVP  380 (539)
T ss_pred             HHHHhhccccCchhhhhcCCChhHHHHHHHHHHHHHhCCCCc
Confidence            33332332               2346788899988887654

The molecular function of this protein is uncertain.

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=95.82  E-value=1.6  Score=40.55  Aligned_cols=149  Identities=11%  Similarity=-0.036  Sum_probs=76.9

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC---cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC--chH
Q 011249          310 DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP---NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL--TEH  384 (490)
Q Consensus       310 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p---~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~--~~~  384 (490)
                      ...+|..++..+.+.|.++.|...+.++...+..+   .+.....-+...-..|+..+|+..++..... .....  ...
T Consensus       145 ~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~~-~~~~~~~~~~  223 (352)
T PF02259_consen  145 LAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLKC-RLSKNIDSIS  223 (352)
T ss_pred             HHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHHH-Hhhhcccccc
Confidence            44567777777888888888888887777643111   2223333344455667778888877777662 11111  111


Q ss_pred             HHHHHHHHhhcCChHHHHHH-HHhccCCCChhhHHHHHHHHhh------hCChHHHHHHHHHHHhcCCCCCchHHHHHHH
Q 011249          385 LTCMVDLLGRSGQLEKAHSL-IMDYKDFCDAGTWGALLGACKV------HVNAELGEIAARHLLELGPEKTGNSALLANI  457 (490)
Q Consensus       385 ~~~l~~~~~~~g~~~~A~~~-~~~~~~~~~~~~~~~l~~~~~~------~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  457 (490)
                      ...+...+..  ..+..... ........-...+..+..-+..      .++.+.+...|.++.+..|.....+..++..
T Consensus       224 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~a~~~l~~a~w~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~k~~~~~a~~  301 (352)
T PF02259_consen  224 NAELKSGLLE--SLEVISSTNLDKESKELKAKAFLLLAKWLDELYSKLSSESSDEILKYYKEATKLDPSWEKAWHSWALF  301 (352)
T ss_pred             HHHHhhcccc--ccccccccchhhhhHHHHHHHHHHHHHHHHhhccccccccHHHHHHHHHHHHHhChhHHHHHHHHHHH
Confidence            1111111000  00000000 0000000011122222222223      3788889999999999999888888888777


Q ss_pred             HHhc
Q 011249          458 YASM  461 (490)
Q Consensus       458 ~~~~  461 (490)
                      +.+.
T Consensus       302 ~~~~  305 (352)
T PF02259_consen  302 NDKL  305 (352)
T ss_pred             HHHH
Confidence            6654

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=95.81  E-value=0.34  Score=37.41  Aligned_cols=119  Identities=12%  Similarity=0.071  Sum_probs=66.2

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHcCCCC---cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHH
Q 011249          315 SSMITAFADHGKSQEALDMFLKMRNEGIEP---NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDL  391 (490)
Q Consensus       315 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p---~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  391 (490)
                      -.-.....+.|++++|.+.|+.+... .+.   ....-..++.+|.+.+++++|...+++..+.+...|++ -|...+.+
T Consensus        14 y~~a~~~l~~~~Y~~A~~~le~L~~r-yP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirLhP~hp~v-dYa~Y~~g   91 (142)
T PF13512_consen   14 YQEAQEALQKGNYEEAIKQLEALDTR-YPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRLHPTHPNV-DYAYYMRG   91 (142)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHhc-CCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCCCc-cHHHHHHH
Confidence            33344455677777777777777764 111   23355666777777777777777777777753334432 23333333


Q ss_pred             HhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCch
Q 011249          392 LGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGN  450 (490)
Q Consensus       392 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~  450 (490)
                      +..-...+..   +..+.            ..=...+....|..-|++++...|++..+
T Consensus        92 L~~~~~~~~~---~~~~~------------~~drD~~~~~~A~~~f~~lv~~yP~S~ya  135 (142)
T PF13512_consen   92 LSYYEQDEGS---LQSFF------------RSDRDPTPARQAFRDFEQLVRRYPNSEYA  135 (142)
T ss_pred             HHHHHHhhhH---Hhhhc------------ccccCcHHHHHHHHHHHHHHHHCcCChhH
Confidence            3322222111   11111            00011233568888999999999987643

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=95.79  E-value=0.9  Score=37.61  Aligned_cols=162  Identities=12%  Similarity=0.084  Sum_probs=87.1

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcH-HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHH
Q 011249          310 DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQ-VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCM  388 (490)
Q Consensus       310 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l  388 (490)
                      -+.+||-+.--+...|+++.|.+.|+...+.  .|.. .+...-.-++.-.|++..|.+-+...-+.-...|-...|..+
T Consensus        98 m~~vfNyLG~Yl~~a~~fdaa~eaFds~~EL--Dp~y~Ya~lNRgi~~YY~gR~~LAq~d~~~fYQ~D~~DPfR~LWLYl  175 (297)
T COG4785          98 MPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL--DPTYNYAHLNRGIALYYGGRYKLAQDDLLAFYQDDPNDPFRSLWLYL  175 (297)
T ss_pred             cHHHHHHHHHHHHhcccchHHHHHhhhHhcc--CCcchHHHhccceeeeecCchHhhHHHHHHHHhcCCCChHHHHHHHH
Confidence            3457777777777888888888888887773  3422 222222223445678887777666654421111212222211


Q ss_pred             HHHHhhcCChHHHHHHH-HhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC-------CchHHHHHHHHHh
Q 011249          389 VDLLGRSGQLEKAHSLI-MDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK-------TGNSALLANIYAS  460 (490)
Q Consensus       389 ~~~~~~~g~~~~A~~~~-~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~-------~~~~~~l~~~~~~  460 (490)
                         -.+.-++.+|..-+ ++.. ..+..-|...+..+.- |... ...+++++.+-..++       ..+|..|+..+..
T Consensus       176 ---~E~k~dP~~A~tnL~qR~~-~~d~e~WG~~iV~~yL-gkiS-~e~l~~~~~a~a~~n~~~Ae~LTEtyFYL~K~~l~  249 (297)
T COG4785         176 ---NEQKLDPKQAKTNLKQRAE-KSDKEQWGWNIVEFYL-GKIS-EETLMERLKADATDNTSLAEHLTETYFYLGKYYLS  249 (297)
T ss_pred             ---HHhhCCHHHHHHHHHHHHH-hccHhhhhHHHHHHHH-hhcc-HHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHhc
Confidence               12334666666544 3333 4454555544443322 2111 122333333322222       3567788888888


Q ss_pred             cCCcchHHHHHHHhhhccc
Q 011249          461 MGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       461 ~g~~~~A~~~~~~~~~~~~  479 (490)
                      .|+.++|..+|+.....++
T Consensus       250 ~G~~~~A~~LfKLaiannV  268 (297)
T COG4785         250 LGDLDEATALFKLAVANNV  268 (297)
T ss_pred             cccHHHHHHHHHHHHHHhH
Confidence            8888888888887665543

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.64  E-value=0.8  Score=35.84  Aligned_cols=126  Identities=10%  Similarity=0.005  Sum_probs=71.7

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHh
Q 011249          314 YSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLG  393 (490)
Q Consensus       314 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  393 (490)
                      ...++..+...+.+.....+++.+...+ ..+....+.++..|++.+ ..+....++.       .++.......++.|.
T Consensus        10 ~~~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~~-~~~ll~~l~~-------~~~~yd~~~~~~~c~   80 (140)
T smart00299       10 VSEVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKYD-PQKEIERLDN-------KSNHYDIEKVGKLCE   80 (140)
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHHC-HHHHHHHHHh-------ccccCCHHHHHHHHH
Confidence            3445666666677777777777777665 345556677777776543 2333333331       122233344666777


Q ss_pred             hcCChHHHHHHHHhccCCCChhhHHHHHHHHhhh-CChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          394 RSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVH-VNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       394 ~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~-g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      +.+.++++.-++.++..      +...+..+... ++++.|.+++.+     +.++..|..++..+.
T Consensus        81 ~~~l~~~~~~l~~k~~~------~~~Al~~~l~~~~d~~~a~~~~~~-----~~~~~lw~~~~~~~l  136 (140)
T smart00299       81 KAKLYEEAVELYKKDGN------FKDAIVTLIEHLGNYEKAIEYFVK-----QNNPELWAEVLKALL  136 (140)
T ss_pred             HcCcHHHHHHHHHhhcC------HHHHHHHHHHcccCHHHHHHHHHh-----CCCHHHHHHHHHHHH
Confidence            77777777777777651      22222223333 677777777765     335556666665544

>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=95.64  E-value=0.9  Score=43.24  Aligned_cols=161  Identities=16%  Similarity=0.143  Sum_probs=83.9

Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChH
Q 011249          218 VCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLD  297 (490)
Q Consensus       218 ~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  297 (490)
                      ....-.++++.+.+..+.-.-.. ..+......++..+.+.|..+.|.++..         |+.+   -.....+.|+++
T Consensus       269 k~av~~~d~~~v~~~i~~~~ll~-~i~~~~~~~i~~fL~~~G~~e~AL~~~~---------D~~~---rFeLAl~lg~L~  335 (443)
T PF04053_consen  269 KTAVLRGDFEEVLRMIAASNLLP-NIPKDQGQSIARFLEKKGYPELALQFVT---------DPDH---RFELALQLGNLD  335 (443)
T ss_dssp             HHHHHTT-HHH-----HHHHTGG-G--HHHHHHHHHHHHHTT-HHHHHHHSS----------HHH---HHHHHHHCT-HH
T ss_pred             HHHHHcCChhhhhhhhhhhhhcc-cCChhHHHHHHHHHHHCCCHHHHHhhcC---------ChHH---HhHHHHhcCCHH
Confidence            34445666766655553111000 1123446666666777777777766632         2221   234455677777


Q ss_pred             HHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcC
Q 011249          298 LAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFG  377 (490)
Q Consensus       298 ~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  377 (490)
                      .|.++.++..  +...|..|.....+.|+++-|++.|++..+         +..|+-.|...|+.+.-.++.+..... |
T Consensus       336 ~A~~~a~~~~--~~~~W~~Lg~~AL~~g~~~lAe~c~~k~~d---------~~~L~lLy~~~g~~~~L~kl~~~a~~~-~  403 (443)
T PF04053_consen  336 IALEIAKELD--DPEKWKQLGDEALRQGNIELAEECYQKAKD---------FSGLLLLYSSTGDREKLSKLAKIAEER-G  403 (443)
T ss_dssp             HHHHHCCCCS--THHHHHHHHHHHHHTTBHHHHHHHHHHCT----------HHHHHHHHHHCT-HHHHHHHHHHHHHT-T
T ss_pred             HHHHHHHhcC--cHHHHHHHHHHHHHcCCHHHHHHHHHhhcC---------ccccHHHHHHhCCHHHHHHHHHHHHHc-c
Confidence            7777766655  455777777777777777777777776443         344444555667766666665555442 1


Q ss_pred             CCCCchHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          378 IKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       378 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                            -++....++.-.|+.++..+++.+-.
T Consensus       404 ------~~n~af~~~~~lgd~~~cv~lL~~~~  429 (443)
T PF04053_consen  404 ------DINIAFQAALLLGDVEECVDLLIETG  429 (443)
T ss_dssp             -------HHHHHHHHHHHT-HHHHHHHHHHTT
T ss_pred             ------CHHHHHHHHHHcCCHHHHHHHHHHcC
Confidence                  13333444555567666666665543

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.

>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=95.61  E-value=0.19  Score=38.25  Aligned_cols=78  Identities=9%  Similarity=0.037  Sum_probs=39.8

Q ss_pred             HhHHHHHHHHHhcCChHHHHHHHHHHH---------------HcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhc-
Q 011249          211 SCWAAMTVCYVQNGYAKAAIEMYKVMR---------------QENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEG-  274 (490)
Q Consensus       211 ~~~~~l~~~~~~~g~~~~A~~~~~~~~---------------~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-  274 (490)
                      .++..++.++++.|+.+....+++..-               .....|+..+..+++.+++..|++..|.++.+.+.+. 
T Consensus         3 ~~~~~ii~al~r~g~~~~i~~~i~~~WgI~~~~~~~~~~~~~~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y   82 (126)
T PF12921_consen    3 ELLCNIIYALGRSGQLDSIKSYIKSVWGIDVNGKKKEGDYPPSSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKY   82 (126)
T ss_pred             HHHHHHHHHHhhcCCHHHHHHHHHHhcCCCCCCccccCccCCCCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHc
Confidence            344555555555555555554444331               1223455555666666666666666666666555332 


Q ss_pred             CCCCchhHHHHHHH
Q 011249          275 CCDRTNYVSNALIH  288 (490)
Q Consensus       275 ~~~~~~~~~~~l~~  288 (490)
                      +++.+..+|..|++
T Consensus        83 ~I~i~~~~W~~Ll~   96 (126)
T PF12921_consen   83 PIPIPKEFWRRLLE   96 (126)
T ss_pred             CCCCCHHHHHHHHH
Confidence            34444555555444

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=95.42  E-value=0.4  Score=44.93  Aligned_cols=67  Identities=12%  Similarity=0.054  Sum_probs=38.7

Q ss_pred             HHHHHHhhcCChHHHHHHHHhcc-CCC---ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC-CCCCchHHH
Q 011249          387 CMVDLLGRSGQLEKAHSLIMDYK-DFC---DAGTWGALLGACKVHVNAELGEIAARHLLELG-PEKTGNSAL  453 (490)
Q Consensus       387 ~l~~~~~~~g~~~~A~~~~~~~~-~~~---~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-p~~~~~~~~  453 (490)
                      .+..++-+.|+.+||++.++++. ..|   +..+...|+.++...+.+.++..++.+.-... |.++....+
T Consensus       264 RLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YT  335 (539)
T PF04184_consen  264 RLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYT  335 (539)
T ss_pred             HHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHH
Confidence            45555666677777777766664 122   22355566666677777777777766654432 554444433

The molecular function of this protein is uncertain.

>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=95.30  E-value=4.9  Score=45.48  Aligned_cols=307  Identities=10%  Similarity=0.030  Sum_probs=164.4

Q ss_pred             HHHHHHHhCCChHHHHHHHHHh----ccC--CchhHHHHHHHHHhcCChhHHHHHHhh-cCCCCHHhHHHHHHHHHhcCC
Q 011249          153 AMVAGYANCGNMKAAKEFYDRM----TEK--NSVTWVAMIAGYGKCGEVREAKKVFDE-ISEPDASCWAAMTVCYVQNGY  225 (490)
Q Consensus       153 ~l~~~~~~~~~~~~a~~~~~~~----~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~-~~~~~~~~~~~l~~~~~~~g~  225 (490)
                      .+..+=.+.+.+..|+-.+++-    .+.  ...-|..+...|...+++|...-+... ...|+.   ..-|......|+
T Consensus      1388 tLa~aSfrc~~y~RalmylEs~~~~ek~~~~~e~l~fllq~lY~~i~dpDgV~Gv~~~r~a~~sl---~~qil~~e~~g~ 1464 (2382)
T KOG0890|consen 1388 TLARASFRCKAYARALMYLESHRSTEKEKETEEALYFLLQNLYGSIHDPDGVEGVSARRFADPSL---YQQILEHEASGN 1464 (2382)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHhcCCcchhhhHHHHhhcCccH---HHHHHHHHhhcc
Confidence            3444556677788888888772    221  222344444578888888877766663 322332   234445666788


Q ss_pred             hHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHH-HHHHHHhcCChHHHHHHHh
Q 011249          226 AKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNA-LIHMHSKCGYLDLAWREFS  304 (490)
Q Consensus       226 ~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~-l~~~~~~~~~~~~A~~~~~  304 (490)
                      +..|...|+++.+.+ ++...++..++......|.++...-..+-..... .+....++. =+.+--+.++++.......
T Consensus      1465 ~~da~~Cye~~~q~~-p~~~~~~~g~l~sml~~~~l~t~i~~~dg~~~~~-se~~~~~~s~~~eaaW~l~qwD~~e~~l~ 1542 (2382)
T KOG0890|consen 1465 WADAAACYERLIQKD-PDKEKHHSGVLKSMLAIQHLSTEILHLDGLIINR-SEEVDELNSLGVEAAWRLSQWDLLESYLS 1542 (2382)
T ss_pred             HHHHHHHHHHhhcCC-CccccchhhHHHhhhcccchhHHHhhhcchhhcc-CHHHHHHHHHHHHHHhhhcchhhhhhhhh
Confidence            888888888888664 2235677777777777777777666554443332 233333322 2334456667766666555


Q ss_pred             cccCCChhHHHHH--HHHHHhcC--ChHHHHHHHHHHHHcCCCCc-------H--HHHHHHHHHhcCCCChHHHHHHHHH
Q 011249          305 RIKNKDVISYSSM--ITAFADHG--KSQEALDMFLKMRNEGIEPN-------Q--VTFIGVLTACSHGGLVEDGCKQFEL  371 (490)
Q Consensus       305 ~~~~~~~~~~~~l--~~~~~~~~--~~~~a~~~~~~~~~~~~~p~-------~--~~~~~l~~~~~~~g~~~~a~~~~~~  371 (490)
                         ..+..+|...  +....+..  +.-.-.+..+.+.+.-+.|-       .  ..|..++....-       .++-..
T Consensus      1543 ---~~n~e~w~~~~~g~~ll~~~~kD~~~~~~~i~~~r~~~i~~lsa~s~~~Sy~~~Y~~~~kLH~l-------~el~~~ 1612 (2382)
T KOG0890|consen 1543 ---DRNIEYWSVESIGKLLLRNKKKDEIATLDLIENSRELVIENLSACSIEGSYVRSYEILMKLHLL-------LELENS 1612 (2382)
T ss_pred             ---cccccchhHHHHHHHHHhhcccchhhHHHHHHHHHHHhhhhHHHhhccchHHHHHHHHHHHHHH-------HHHHHH
Confidence               3344444433  22222222  11111123333332211110       0  122222222110       011111


Q ss_pred             HHHHcCCCCCch------HHHHHHHHHhhcCChHHHHHH---HHhc------c---CCCChhhHHHHHHHHhhhCChHHH
Q 011249          372 MTRVFGIKPLTE------HLTCMVDLLGRSGQLEKAHSL---IMDY------K---DFCDAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       372 ~~~~~~~~~~~~------~~~~l~~~~~~~g~~~~A~~~---~~~~------~---~~~~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      .....+..++..      .|..-+.   +.+..-.+.+-   +++.      .   ...-..+|-..++.+...|.++.|
T Consensus      1613 ~~~l~~~s~~~~s~~~sd~W~~Rl~---~tq~s~~~~epILa~RRs~l~~~~~~~~~~~~ge~wLqsAriaR~aG~~q~A 1689 (2382)
T KOG0890|consen 1613 IEELKKVSYDEDSANNSDNWKNRLE---RTQPSFRIKEPILAFRRSMLDLRMRSNLKSRLGECWLQSARIARLAGHLQRA 1689 (2382)
T ss_pred             HHHhhccCccccccccchhHHHHHH---HhchhHHHHhHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHhcccHHHH
Confidence            111112233221      1211111   11111112221   1111      1   122356888888999999999999


Q ss_pred             HHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          434 EIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       434 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ...+-++.+..  -+.++...+..+...|+...|+.++++..+...
T Consensus      1690 ~nall~A~e~r--~~~i~~E~AK~lW~~gd~~~Al~~Lq~~l~~~~ 1733 (2382)
T KOG0890|consen 1690 QNALLNAKESR--LPEIVLERAKLLWQTGDELNALSVLQEILSKNF 1733 (2382)
T ss_pred             HHHHHhhhhcc--cchHHHHHHHHHHhhccHHHHHHHHHHHHHhhc
Confidence            99998888876  467888999999999999999999998876543

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=95.28  E-value=0.67  Score=44.75  Aligned_cols=109  Identities=20%  Similarity=0.206  Sum_probs=53.5

Q ss_pred             ChHHHHHHHHHhcc--CCchhHHH-HHHHHHhcCChhHHHHHHhhcCC-------CCHHhHHHHHHHHHhcCChHHHHHH
Q 011249          163 NMKAAKEFYDRMTE--KNSVTWVA-MIAGYGKCGEVREAKKVFDEISE-------PDASCWAAMTVCYVQNGYAKAAIEM  232 (490)
Q Consensus       163 ~~~~a~~~~~~~~~--~~~~~~~~-l~~~~~~~~~~~~A~~~~~~~~~-------~~~~~~~~l~~~~~~~g~~~~A~~~  232 (490)
                      +.+.|.++++.+.+  |+...|.. -.+.+...|++++|++.|++...       .....+--++.++.-..+|++|.+.
T Consensus       248 ~~~~a~~lL~~~~~~yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~  327 (468)
T PF10300_consen  248 PLEEAEELLEEMLKRYPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEY  327 (468)
T ss_pred             CHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHH
Confidence            34445555555444  33333322 23344445555555555554322       1222344455566666777777777


Q ss_pred             HHHHHHcCcccChhhHHHHHHH-HhccCCh-------HHHHHHHHHHH
Q 011249          233 YKVMRQENVRISEVAMVGAISA-CTQLGDV-------EMAAILAKHVD  272 (490)
Q Consensus       233 ~~~~~~~~~~p~~~~~~~l~~~-~~~~g~~-------~~a~~~~~~~~  272 (490)
                      |..+.+.. .-+..+|.-+..+ +...|+.       ++|..++.++.
T Consensus       328 f~~L~~~s-~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~~vp  374 (468)
T PF10300_consen  328 FLRLLKES-KWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFRKVP  374 (468)
T ss_pred             HHHHHhcc-ccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHHH
Confidence            77776542 2233333333333 3345555       66666666653

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.

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=95.14  E-value=1.7  Score=36.73  Aligned_cols=196  Identities=12%  Similarity=0.063  Sum_probs=86.9

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHhccC--CchhHHHHHHHHHhcCChhHHHHHHhhcCCC--CHHhHHHHHHHHHhcCCh
Q 011249          151 WSAMVAGYANCGNMKAAKEFYDRMTEK--NSVTWVAMIAGYGKCGEVREAKKVFDEISEP--DASCWAAMTVCYVQNGYA  226 (490)
Q Consensus       151 ~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~l~~~~~~~g~~  226 (490)
                      |.....+|....++++|...+.+..+-  +..++-.-.      ..++.|.-+.+++.+-  -+..|+--...|...|.+
T Consensus        34 yekAAvafRnAk~feKakdcLlkA~~~yEnnrslfhAA------KayEqaamLake~~klsEvvdl~eKAs~lY~E~Gsp  107 (308)
T KOG1585|consen   34 YEKAAVAFRNAKKFEKAKDCLLKASKGYENNRSLFHAA------KAYEQAAMLAKELSKLSEVVDLYEKASELYVECGSP  107 (308)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHHHHHHhcccHHHHH------HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhCCc
Confidence            444456666667777777666665421  111111111      1223333333333331  122344445556666666


Q ss_pred             HHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhc---C--CCCchhHHHHHHHHHHhcCChHHHHH
Q 011249          227 KAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEG---C--CDRTNYVSNALIHMHSKCGYLDLAWR  301 (490)
Q Consensus       227 ~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~---~--~~~~~~~~~~l~~~~~~~~~~~~A~~  301 (490)
                      +.|-..+++.-+.                ....+++.|.++|++....   +  ...-...+....+.+.+...+++|-.
T Consensus       108 dtAAmaleKAak~----------------lenv~Pd~AlqlYqralavve~~dr~~ma~el~gk~sr~lVrl~kf~Eaa~  171 (308)
T KOG1585|consen  108 DTAAMALEKAAKA----------------LENVKPDDALQLYQRALAVVEEDDRDQMAFELYGKCSRVLVRLEKFTEAAT  171 (308)
T ss_pred             chHHHHHHHHHHH----------------hhcCCHHHHHHHHHHHHHHHhccchHHHHHHHHHHhhhHhhhhHHhhHHHH
Confidence            6655555544321                1122334444444433211   1  00011122333444555555555544


Q ss_pred             HHhcccC--------CCh-hHHHHHHHHHHhcCChHHHHHHHHHHHHcC---CCCcHHHHHHHHHHhcCCCChHHHHHHH
Q 011249          302 EFSRIKN--------KDV-ISYSSMITAFADHGKSQEALDMFLKMRNEG---IEPNQVTFIGVLTACSHGGLVEDGCKQF  369 (490)
Q Consensus       302 ~~~~~~~--------~~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~p~~~~~~~l~~~~~~~g~~~~a~~~~  369 (490)
                      .|.+-..        ++. ..|-..|-.+....++..|.+.++.--+.+   -+-+..+...|+.+|- .|+.+++.+++
T Consensus       172 a~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ayd-~gD~E~~~kvl  250 (308)
T KOG1585|consen  172 AFLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAYD-EGDIEEIKKVL  250 (308)
T ss_pred             HHHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHhc-cCCHHHHHHHH
Confidence            4433221        111 234444555555667777777777644322   1123346666666663 45665554443

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=95.11  E-value=2.7  Score=44.01  Aligned_cols=159  Identities=14%  Similarity=0.089  Sum_probs=83.9

Q ss_pred             CCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCH
Q 011249          131 GLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDA  210 (490)
Q Consensus       131 g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~  210 (490)
                      ++++.|+.-+.++.   ...|.-.++.--+.|-+.+|+.++.--.+.-...|....+.+.....+++|--.|+...+.  
T Consensus       894 ~ry~~AL~hLs~~~---~~~~~e~~n~I~kh~Ly~~aL~ly~~~~e~~k~i~~~ya~hL~~~~~~~~Aal~Ye~~Gkl--  968 (1265)
T KOG1920|consen  894 KRYEDALSHLSECG---ETYFPECKNYIKKHGLYDEALALYKPDSEKQKVIYEAYADHLREELMSDEAALMYERCGKL--  968 (1265)
T ss_pred             HHHHHHHHHHHHcC---ccccHHHHHHHHhcccchhhhheeccCHHHHHHHHHHHHHHHHHhccccHHHHHHHHhccH--
Confidence            34444444443332   2233333444444555555555553222222233444445555566677776666655431  


Q ss_pred             HhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccCh--hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 011249          211 SCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISE--VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIH  288 (490)
Q Consensus       211 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~--~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  288 (490)
                         .--+.+|...|+|.+|+.+-.++....   +.  .+-..|+.-+...+++-+|-++.......   |     .-.+.
T Consensus       969 ---ekAl~a~~~~~dWr~~l~~a~ql~~~~---de~~~~a~~L~s~L~e~~kh~eAa~il~e~~sd---~-----~~av~ 1034 (1265)
T KOG1920|consen  969 ---EKALKAYKECGDWREALSLAAQLSEGK---DELVILAEELVSRLVEQRKHYEAAKILLEYLSD---P-----EEAVA 1034 (1265)
T ss_pred             ---HHHHHHHHHhccHHHHHHHHHhhcCCH---HHHHHHHHHHHHHHHHcccchhHHHHHHHHhcC---H-----HHHHH
Confidence               223456677778888777776664211   11  11245566667777777777766655432   1     22345


Q ss_pred             HHHhcCChHHHHHHHhcccC
Q 011249          289 MHSKCGYLDLAWREFSRIKN  308 (490)
Q Consensus       289 ~~~~~~~~~~A~~~~~~~~~  308 (490)
                      .|++...+++|.++......
T Consensus      1035 ll~ka~~~~eAlrva~~~~~ 1054 (1265)
T KOG1920|consen 1035 LLCKAKEWEEALRVASKAKR 1054 (1265)
T ss_pred             HHhhHhHHHHHHHHHHhccc
Confidence            56666778888777665554

>PRK09687 putative lyase; Provisional

Probab=95.05  E-value=2.4  Score=37.77  Aligned_cols=19  Identities=11%  Similarity=0.109  Sum_probs=8.4

Q ss_pred             CCCHhHHHHHHHHHHhCCC
Q 011249          145 ERNVISWSAMVAGYANCGN  163 (490)
Q Consensus       145 ~~~~~~~~~l~~~~~~~~~  163 (490)
                      .+|.......+.++...|.
T Consensus        34 d~d~~vR~~A~~aL~~~~~   52 (280)
T PRK09687         34 DHNSLKRISSIRVLQLRGG   52 (280)
T ss_pred             CCCHHHHHHHHHHHHhcCc
Confidence            3444444444444444443

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=95.04  E-value=1.2  Score=36.94  Aligned_cols=34  Identities=9%  Similarity=0.045  Sum_probs=20.0

Q ss_pred             CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhc
Q 011249           64 KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRL   97 (490)
Q Consensus        64 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~   97 (490)
                      .|+.+..||.|.--+...|+++.|.+.|+...+.
T Consensus        95 ~P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~EL  128 (297)
T COG4785          95 RPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLEL  128 (297)
T ss_pred             CCCcHHHHHHHHHHHHhcccchHHHHHhhhHhcc
Confidence            4554455666666666666666666666655554

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=95.04  E-value=1.8  Score=37.14  Aligned_cols=148  Identities=16%  Similarity=0.208  Sum_probs=89.5

Q ss_pred             hcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC-------C--CHhH
Q 011249           80 LHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE-------R--NVIS  150 (490)
Q Consensus        80 ~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-------~--~~~~  150 (490)
                      +..++++|+.-|++..+..-.-....|.++-.           ++..+.+.|++++....+.++..       +  +..+
T Consensus        39 ~e~~p~~Al~sF~kVlelEgEKgeWGFKALKQ-----------miKI~f~l~~~~eMm~~Y~qlLTYIkSAVTrNySEKs  107 (440)
T KOG1464|consen   39 KEDEPKEALSSFQKVLELEGEKGEWGFKALKQ-----------MIKINFRLGNYKEMMERYKQLLTYIKSAVTRNYSEKS  107 (440)
T ss_pred             cccCHHHHHHHHHHHHhcccccchhHHHHHHH-----------HHHHHhccccHHHHHHHHHHHHHHHHHHHhccccHHH
Confidence            44588999999988887643334444443322           45567788888888887777753       1  3345


Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHhcc-----CCch----hHHHHHHHHHhcCChhHHHHHHhhcCC--------------
Q 011249          151 WSAMVAGYANCGNMKAAKEFYDRMTE-----KNSV----TWVAMIAGYGKCGEVREAKKVFDEISE--------------  207 (490)
Q Consensus       151 ~~~l~~~~~~~~~~~~a~~~~~~~~~-----~~~~----~~~~l~~~~~~~~~~~~A~~~~~~~~~--------------  207 (490)
                      .|.++..-....+.+-...+|+.-.+     .|..    |-..+...|...+.+....+++.++.+              
T Consensus       108 IN~IlDyiStS~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKG  187 (440)
T KOG1464|consen  108 INSILDYISTSKNMDLLQEFYETTLDALKDAKNERLWFKTNTKLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKG  187 (440)
T ss_pred             HHHHHHHHhhhhhhHHHHHHHHHHHHHHHhhhcceeeeeccchHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhcc
Confidence            66677666666666555555554332     1222    234566677777777666666666532              


Q ss_pred             -CCHHhHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011249          208 -PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQ  238 (490)
Q Consensus       208 -~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  238 (490)
                       .-...|..-|..|....+-..-..+|++...
T Consensus       188 tQLLEiYAlEIQmYT~qKnNKkLK~lYeqalh  219 (440)
T KOG1464|consen  188 TQLLEIYALEIQMYTEQKNNKKLKALYEQALH  219 (440)
T ss_pred             chhhhhHhhHhhhhhhhcccHHHHHHHHHHHH
Confidence             1123556666666666666666666766553

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=95.04  E-value=0.19  Score=37.67  Aligned_cols=55  Identities=16%  Similarity=0.153  Sum_probs=36.5

Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHH
Q 011249          320 AFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRV  375 (490)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  375 (490)
                      +....|+.+.|++.|.+.+.. .+-....|+.-..++.-+|+.++|+.-+.+..+-
T Consensus        52 alaE~g~Ld~AlE~F~qal~l-~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleL  106 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCL-APERASAYNNRAQALRLQGDDEEALDDLNKALEL  106 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHh-cccchHhhccHHHHHHHcCChHHHHHHHHHHHHh
Confidence            456667777777777776663 2234566777777777777777777777766663

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.99  E-value=4.3  Score=40.48  Aligned_cols=150  Identities=10%  Similarity=0.111  Sum_probs=82.4

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCCHhHHHH
Q 011249           74 LIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSA  153 (490)
Q Consensus        74 l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~  153 (490)
                      -+..+.+.+.+++|+..-+.-...  .|...+-.           .....+..+.-.|++++|-...-.|...+..-|..
T Consensus       362 hi~Wll~~k~yeeAl~~~k~~~~~--~~~~~i~k-----------v~~~yI~HLl~~~~y~~Aas~~p~m~gn~~~eWe~  428 (846)
T KOG2066|consen  362 HIDWLLEKKKYEEALDAAKASIGN--EERFVIKK-----------VGKTYIDHLLFEGKYDEAASLCPKMLGNNAAEWEL  428 (846)
T ss_pred             hHHHHHHhhHHHHHHHHHHhccCC--ccccchHH-----------HHHHHHHHHHhcchHHHHHhhhHHHhcchHHHHHH
Confidence            345566788888888877654332  33211100           00224445677788888888888888888777777


Q ss_pred             HHHHHHhCCChHHHHHHHHHhcc-CCchhHHHHHHHHHhcCChhHHHHHHh--------------hcCC------CCHHh
Q 011249          154 MVAGYANCGNMKAAKEFYDRMTE-KNSVTWVAMIAGYGKCGEVREAKKVFD--------------EISE------PDASC  212 (490)
Q Consensus       154 l~~~~~~~~~~~~a~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~--------------~~~~------~~~~~  212 (490)
                      .+..+...++......++=.-.. -++..|..++..+.. .+...-.+...              ....      .+...
T Consensus       429 ~V~~f~e~~~l~~Ia~~lPt~~~rL~p~vYemvLve~L~-~~~~~F~e~i~~Wp~~Lys~l~iisa~~~q~~q~Se~~~L  507 (846)
T KOG2066|consen  429 WVFKFAELDQLTDIAPYLPTGPPRLKPLVYEMVLVEFLA-SDVKGFLELIKEWPGHLYSVLTIISATEPQIKQNSESTAL  507 (846)
T ss_pred             HHHHhccccccchhhccCCCCCcccCchHHHHHHHHHHH-HHHHHHHHHHHhCChhhhhhhHHHhhcchHHHhhccchhH
Confidence            77777777766554443321111 144556555555544 11111111111              1100      12233


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHH
Q 011249          213 WAAMTVCYVQNGYAKAAIEMYKVMR  237 (490)
Q Consensus       213 ~~~l~~~~~~~g~~~~A~~~~~~~~  237 (490)
                      -..|+..|...+++..|+..+-.++
T Consensus       508 ~e~La~LYl~d~~Y~~Al~~ylklk  532 (846)
T KOG2066|consen  508 LEVLAHLYLYDNKYEKALPIYLKLQ  532 (846)
T ss_pred             HHHHHHHHHHccChHHHHHHHHhcc
Confidence            3447777777777777777776654

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=94.82  E-value=0.18  Score=38.97  Aligned_cols=72  Identities=17%  Similarity=-0.005  Sum_probs=42.5

Q ss_pred             hcCChHHHHHHHHhcc-CCCChhhHHH-HHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcc
Q 011249          394 RSGQLEKAHSLIMDYK-DFCDAGTWGA-LLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWK  465 (490)
Q Consensus       394 ~~g~~~~A~~~~~~~~-~~~~~~~~~~-l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  465 (490)
                      ..++++++..+++.+. ..|+...... -...+...|++++|.++++.+.+..|..+..-..++.++.-.|+.+
T Consensus        22 ~~~d~~D~e~lLdALrvLrP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~~~~p~~kAL~A~CL~al~Dp~   95 (153)
T TIGR02561        22 RSADPYDAQAMLDALRVLRPNLKELDMFDGWLLIARGNYDEAARILRELLSSAGAPPYGKALLALCLNAKGDAE   95 (153)
T ss_pred             hcCCHHHHHHHHHHHHHhCCCccccchhHHHHHHHcCCHHHHHHHHHhhhccCCCchHHHHHHHHHHHhcCChH
Confidence            4667777777776665 3333322211 2234566777777777777777766665555555565666666533

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>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=94.74  E-value=0.059  Score=29.86  Aligned_cols=31  Identities=19%  Similarity=0.062  Sum_probs=22.2

Q ss_pred             hHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          416 TWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       416 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      +|..+...+...|++++|.+.|+++++++|+
T Consensus         3 ~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~~   33 (34)
T PF13181_consen    3 AYYNLGKIYEQLGDYEEALEYFEKALELNPD   33 (34)
T ss_dssp             HHHHHHHHHHHTTSHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            4556666777777777777777777777764

...

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=94.69  E-value=1.7  Score=40.33  Aligned_cols=65  Identities=17%  Similarity=0.079  Sum_probs=50.8

Q ss_pred             CChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCC----CCCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          412 CDAGTWGALLGACKVHVNAELGEIAARHLLELGP----EKTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       412 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p----~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      ....+|..++..+.+.|.++.|...+.++...++    ..+.+...-+..+...|+..+|...++...+
T Consensus       144 ~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~~e~akllw~~g~~~~Ai~~L~~~~~  212 (352)
T PF02259_consen  144 ELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVFLEYAKLLWAQGEQEEAIQKLRELLK  212 (352)
T ss_pred             HHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3456778888888888999888888888887552    2466777778888888888888888887776

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=94.58  E-value=0.54  Score=40.50  Aligned_cols=98  Identities=19%  Similarity=0.286  Sum_probs=70.8

Q ss_pred             HHHHhccc--CCChhHHHHHHHHHHhc-----CChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCC------------
Q 011249          300 WREFSRIK--NKDVISYSSMITAFADH-----GKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGG------------  360 (490)
Q Consensus       300 ~~~~~~~~--~~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g------------  360 (490)
                      +..|..+.  ++|-.+|...+..+...     +..+-....++.|.+.|+.-|..+|+.|+..+-+..            
T Consensus        54 e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~  133 (406)
T KOG3941|consen   54 EKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFL  133 (406)
T ss_pred             hhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHh
Confidence            44555554  35666777777766543     456667777888888888888888888888765432            


Q ss_pred             ----ChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCCh
Q 011249          361 ----LVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQL  398 (490)
Q Consensus       361 ----~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  398 (490)
                          +-+-+++++++|.. +|+.||.++-..++.++.+.+-.
T Consensus       134 HYP~QQ~C~I~vLeqME~-hGVmPdkE~e~~lvn~FGr~~~p  174 (406)
T KOG3941|consen  134 HYPQQQNCAIKVLEQMEW-HGVMPDKEIEDILVNAFGRWNFP  174 (406)
T ss_pred             hCchhhhHHHHHHHHHHH-cCCCCchHHHHHHHHHhcccccc
Confidence                22447788888888 69999988888888888877753

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=94.51  E-value=6.3  Score=40.13  Aligned_cols=193  Identities=14%  Similarity=0.071  Sum_probs=91.1

Q ss_pred             HhcCChHHHHHHHhcccC----CCh-------hHHHHHHH-HHHhcCChHHHHHHHHHHHHc----CCCCcHHHHHHHHH
Q 011249          291 SKCGYLDLAWREFSRIKN----KDV-------ISYSSMIT-AFADHGKSQEALDMFLKMRNE----GIEPNQVTFIGVLT  354 (490)
Q Consensus       291 ~~~~~~~~A~~~~~~~~~----~~~-------~~~~~l~~-~~~~~~~~~~a~~~~~~~~~~----~~~p~~~~~~~l~~  354 (490)
                      ....++++|..++.++..    |+.       ..|+.+-. .....|++++++++.+.....    -..+....+..+..
T Consensus       426 ~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv~~~  505 (894)
T COG2909         426 ASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVLGE  505 (894)
T ss_pred             HHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhhhhH
Confidence            345666676666655432    211       13333322 233456777777777766542    11223344555555


Q ss_pred             HhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHH-----HHHHhhcCCh--HHHHHHHHhcc-----CCC----ChhhHH
Q 011249          355 ACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCM-----VDLLGRSGQL--EKAHSLIMDYK-----DFC----DAGTWG  418 (490)
Q Consensus       355 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l-----~~~~~~~g~~--~~A~~~~~~~~-----~~~----~~~~~~  418 (490)
                      +..-.|++++|..+.+...+. .-.-+...+...     ...+...|+.  .+....|....     .+|    -..+..
T Consensus       506 a~~~~G~~~~Al~~~~~a~~~-a~~~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f~~~~r~  584 (894)
T COG2909         506 AAHIRGELTQALALMQQAEQM-ARQHDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRIRA  584 (894)
T ss_pred             HHHHhchHHHHHHHHHHHHHH-HHHcccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchhHHHHHH
Confidence            666677777777777666553 222333332221     1234455522  22222232222     111    122333


Q ss_pred             HHHHHHhhhCChHHHHHHHHHHHh----cCCCCCc---hHHHHHHHHHhcCCcchHHHHHHHhhhcccccCCCccc
Q 011249          419 ALLGACKVHVNAELGEIAARHLLE----LGPEKTG---NSALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSW  487 (490)
Q Consensus       419 ~l~~~~~~~g~~~~a~~~~~~~~~----~~p~~~~---~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~  487 (490)
                      .+..++.+   .+.+..-.....+    ..|....   .+..|+.++...|+.++|...++.+........+...|
T Consensus       585 ~ll~~~~r---~~~~~~ear~~~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~~~~~~~~~~  657 (894)
T COG2909         585 QLLRAWLR---LDLAEAEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNGQYHVDY  657 (894)
T ss_pred             HHHHHHHH---HhhhhHHhhhcchhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCCCchH
Confidence            34444433   3333333333333    2222211   22356777777777777777777776554444344333

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=94.41  E-value=0.071  Score=30.14  Aligned_cols=24  Identities=8%  Similarity=-0.158  Sum_probs=11.8

Q ss_pred             HHHHHHHHhhhCChHHHHHHHHHH
Q 011249          417 WGALLGACKVHVNAELGEIAARHL  440 (490)
Q Consensus       417 ~~~l~~~~~~~g~~~~a~~~~~~~  440 (490)
                      |..|...|...|++++|+++|+++
T Consensus         2 l~~Lg~~~~~~g~~~~Ai~~y~~a   25 (36)
T PF13176_consen    2 LNNLGRIYRQQGDYEKAIEYYEQA   25 (36)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Confidence            344455555555555555555553

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=94.38  E-value=0.55  Score=40.47  Aligned_cols=88  Identities=9%  Similarity=0.102  Sum_probs=54.6

Q ss_pred             CCHHhHHHHHHHHHh-----cCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccC----------------ChHHHHH
Q 011249          208 PDASCWAAMTVCYVQ-----NGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLG----------------DVEMAAI  266 (490)
Q Consensus       208 ~~~~~~~~l~~~~~~-----~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g----------------~~~~a~~  266 (490)
                      .|-.+|...+..+..     .+..+-....++.|.+-|+.-|..+|..|++.+-+..                +-.-+++
T Consensus        65 RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I~  144 (406)
T KOG3941|consen   65 RDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAIK  144 (406)
T ss_pred             ccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHHH
Confidence            444555555544433     2344555555666666676667777777666654422                2345677


Q ss_pred             HHHHHHhcCCCCchhHHHHHHHHHHhcCC
Q 011249          267 LAKHVDEGCCDRTNYVSNALIHMHSKCGY  295 (490)
Q Consensus       267 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~  295 (490)
                      ++++|...|+.||-.+-..|++++.+.+-
T Consensus       145 vLeqME~hGVmPdkE~e~~lvn~FGr~~~  173 (406)
T KOG3941|consen  145 VLEQMEWHGVMPDKEIEDILVNAFGRWNF  173 (406)
T ss_pred             HHHHHHHcCCCCchHHHHHHHHHhccccc
Confidence            77788888888887777777777776654

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.31  E-value=0.7  Score=36.71  Aligned_cols=117  Identities=14%  Similarity=0.085  Sum_probs=51.9

Q ss_pred             hcCChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHH-----HHHHhhcC
Q 011249          323 DHGKSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCM-----VDLLGRSG  396 (490)
Q Consensus       323 ~~~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l-----~~~~~~~g  396 (490)
                      +.+..++|+.-|..+.+.|...=+. .-..........|+...|...|+++-.. .  |.+.....+     ...+...|
T Consensus        70 ~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~d-t--~~P~~~rd~ARlraa~lLvD~g  146 (221)
T COG4649          70 QENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAAD-T--SIPQIGRDLARLRAAYLLVDNG  146 (221)
T ss_pred             HcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhcc-C--CCcchhhHHHHHHHHHHHhccc
Confidence            3445555555555555543221111 1111122234555555566666555443 1  111111111     12334555


Q ss_pred             ChHHHHHHHHhccCCCC---hhhHHHHHHHHhhhCChHHHHHHHHHHHh
Q 011249          397 QLEKAHSLIMDYKDFCD---AGTWGALLGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       397 ~~~~A~~~~~~~~~~~~---~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                      .++......+.+....+   ...-..|.-+-.+.|++.+|...|+++..
T Consensus       147 sy~dV~srvepLa~d~n~mR~sArEALglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         147 SYDDVSSRVEPLAGDGNPMRHSAREALGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             cHHHHHHHhhhccCCCChhHHHHHHHHhHHHHhccchHHHHHHHHHHHc
Confidence            66665555555542111   12223444445566666666666666554

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.31  E-value=2.5  Score=34.58  Aligned_cols=84  Identities=12%  Similarity=0.053  Sum_probs=42.3

Q ss_pred             HHHHhCCChHHHHHHHHHhcc-CCchh-----HHHHHHHHHhcCChhHHHHHHhhcCCCCHHh--HHHHHHHHHhcCChH
Q 011249          156 AGYANCGNMKAAKEFYDRMTE-KNSVT-----WVAMIAGYGKCGEVREAKKVFDEISEPDASC--WAAMTVCYVQNGYAK  227 (490)
Q Consensus       156 ~~~~~~~~~~~a~~~~~~~~~-~~~~~-----~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~--~~~l~~~~~~~g~~~  227 (490)
                      ..+...|++++|..-++.... +....     -..|.+.....|.+|+|++.++....++-..  ...-.+.+...|+-+
T Consensus        97 k~~ve~~~~d~A~aqL~~~l~~t~De~lk~l~~lRLArvq~q~~k~D~AL~~L~t~~~~~w~~~~~elrGDill~kg~k~  176 (207)
T COG2976          97 KAEVEANNLDKAEAQLKQALAQTKDENLKALAALRLARVQLQQKKADAALKTLDTIKEESWAAIVAELRGDILLAKGDKQ  176 (207)
T ss_pred             HHHHhhccHHHHHHHHHHHHccchhHHHHHHHHHHHHHHHHHhhhHHHHHHHHhccccccHHHHHHHHhhhHHHHcCchH
Confidence            345556666666666665552 21111     2233444555566666666665555543222  233344555556666


Q ss_pred             HHHHHHHHHHHc
Q 011249          228 AAIEMYKVMRQE  239 (490)
Q Consensus       228 ~A~~~~~~~~~~  239 (490)
                      +|..-|++....
T Consensus       177 ~Ar~ay~kAl~~  188 (207)
T COG2976         177 EARAAYEKALES  188 (207)
T ss_pred             HHHHHHHHHHHc
Confidence            666655555544

>KOG4234 consensus TPR repeat-containing protein [General function prediction only]

Probab=94.27  E-value=0.58  Score=38.12  Aligned_cols=88  Identities=10%  Similarity=0.053  Sum_probs=54.5

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCCCCcH-----HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC-chHHHHHHHH
Q 011249          318 ITAFADHGKSQEALDMFLKMRNEGIEPNQ-----VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDL  391 (490)
Q Consensus       318 ~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~  391 (490)
                      ..-+...|++++|..-|..+++. +++..     ..|..-..++.+.+.++.|+.-..+..+   +.|+ ......-..+
T Consensus       102 GN~~F~ngdyeeA~skY~~Ale~-cp~~~~e~rsIly~Nraaa~iKl~k~e~aI~dcsKaie---l~pty~kAl~RRAea  177 (271)
T KOG4234|consen  102 GNELFKNGDYEEANSKYQEALES-CPSTSTEERSILYSNRAAALIKLRKWESAIEDCSKAIE---LNPTYEKALERRAEA  177 (271)
T ss_pred             HHHhhhcccHHHHHHHHHHHHHh-CccccHHHHHHHHhhhHHHHHHhhhHHHHHHHHHhhHh---cCchhHHHHHHHHHH
Confidence            33466778888888888888774 23222     2344444456677777777777766665   2222 2222233457


Q ss_pred             HhhcCChHHHHHHHHhcc
Q 011249          392 LGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       392 ~~~~g~~~~A~~~~~~~~  409 (490)
                      |.+...+++|++-|+++.
T Consensus       178 yek~ek~eealeDyKki~  195 (271)
T KOG4234|consen  178 YEKMEKYEEALEDYKKIL  195 (271)
T ss_pred             HHhhhhHHHHHHHHHHHH
Confidence            777788888888887776

>COG2976 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.20  E-value=1.4  Score=36.00  Aligned_cols=129  Identities=12%  Similarity=0.007  Sum_probs=73.1

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHH--HHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHH----
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFI--GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHL----  385 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~--~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~----  385 (490)
                      ..|..++.... .+.+ +.....+++........--.+.  .+...+...+++++|...++.....    |..+.+    
T Consensus        55 ~~Y~~~i~~~~-ak~~-~~~~~~ekf~~~n~~t~Ya~laaL~lAk~~ve~~~~d~A~aqL~~~l~~----t~De~lk~l~  128 (207)
T COG2976          55 AQYQNAIKAVQ-AKKP-KSIAAAEKFVQANGKTIYAVLAALELAKAEVEANNLDKAEAQLKQALAQ----TKDENLKALA  128 (207)
T ss_pred             HHHHHHHHHHh-cCCc-hhHHHHHHHHhhccccHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHcc----chhHHHHHHH
Confidence            34555555543 3333 5555556665532111111222  2334467778888888888777642    222222    


Q ss_pred             -HHHHHHHhhcCChHHHHHHHHhccCCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          386 -TCMVDLLGRSGQLEKAHSLIMDYKDFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       386 -~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                       ..|.+.....|.+|+|+..++....+. .......-...+...|+-++|...|+++++.+++
T Consensus       129 ~lRLArvq~q~~k~D~AL~~L~t~~~~~w~~~~~elrGDill~kg~k~~Ar~ay~kAl~~~~s  191 (207)
T COG2976         129 ALRLARVQLQQKKADAALKTLDTIKEESWAAIVAELRGDILLAKGDKQEARAAYEKALESDAS  191 (207)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHhccccccHHHHHHHHhhhHHHHcCchHHHHHHHHHHHHccCC
Confidence             235566777788888888877766221 2223333446677778888888888888877643

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=94.15  E-value=7.2  Score=39.38  Aligned_cols=82  Identities=10%  Similarity=-0.015  Sum_probs=37.2

Q ss_pred             HHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHH
Q 011249          219 CYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDL  298 (490)
Q Consensus       219 ~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  298 (490)
                      -+.+.|++++|...|-+-+.. +.|+     .++.-+.......+-..+++.+.+.|+ .+...-..|+.+|.+.++.++
T Consensus       377 ~Ly~Kgdf~~A~~qYI~tI~~-le~s-----~Vi~kfLdaq~IknLt~YLe~L~~~gl-a~~dhttlLLncYiKlkd~~k  449 (933)
T KOG2114|consen  377 YLYGKGDFDEATDQYIETIGF-LEPS-----EVIKKFLDAQRIKNLTSYLEALHKKGL-ANSDHTTLLLNCYIKLKDVEK  449 (933)
T ss_pred             HHHhcCCHHHHHHHHHHHccc-CChH-----HHHHHhcCHHHHHHHHHHHHHHHHccc-ccchhHHHHHHHHHHhcchHH
Confidence            344455555555555444321 1111     122333344444444455555555553 223333445555555555555


Q ss_pred             HHHHHhccc
Q 011249          299 AWREFSRIK  307 (490)
Q Consensus       299 A~~~~~~~~  307 (490)
                      -.++.+...
T Consensus       450 L~efI~~~~  458 (933)
T KOG2114|consen  450 LTEFISKCD  458 (933)
T ss_pred             HHHHHhcCC
Confidence            555554444

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.14  E-value=0.9  Score=36.13  Aligned_cols=23  Identities=22%  Similarity=0.229  Sum_probs=10.3

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHH
Q 011249          317 MITAFADHGKSQEALDMFLKMRN  339 (490)
Q Consensus       317 l~~~~~~~~~~~~a~~~~~~~~~  339 (490)
                      |.-+-.+.|++.+|.+.|..+..
T Consensus       173 LglAa~kagd~a~A~~~F~qia~  195 (221)
T COG4649         173 LGLAAYKAGDFAKAKSWFVQIAN  195 (221)
T ss_pred             HhHHHHhccchHHHHHHHHHHHc
Confidence            33333444444444444444443

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=94.11  E-value=0.069  Score=30.19  Aligned_cols=27  Identities=15%  Similarity=0.113  Sum_probs=23.0

Q ss_pred             hHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          450 NSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       450 ~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      ++..|+.+|.+.|+|++|++++++...
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL~   27 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQALA   27 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            478899999999999999999998553

>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=94.08  E-value=0.29  Score=38.53  Aligned_cols=83  Identities=19%  Similarity=0.050  Sum_probs=58.7

Q ss_pred             hHHHHHHHHH---hhcCChHHHHHHHHhcc-CCCChhhHHH-HHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHH
Q 011249          383 EHLTCMVDLL---GRSGQLEKAHSLIMDYK-DFCDAGTWGA-LLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANI  457 (490)
Q Consensus       383 ~~~~~l~~~~---~~~g~~~~A~~~~~~~~-~~~~~~~~~~-l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  457 (490)
                      .+.+.|+...   .+.++.+++..++..+. ..|....... -...+...|++.+|+++++.+.+..|..+..-..++.+
T Consensus         8 ~iv~gLie~~~~al~~~~~~D~e~lL~ALrvLRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~~~~p~~kALlA~C   87 (160)
T PF09613_consen    8 EIVGGLIEVLSVALRLGDPDDAEALLDALRVLRPEFPELDLFDGWLHIVRGDWDDALRLLRELEERAPGFPYAKALLALC   87 (160)
T ss_pred             HHHHHHHHHHHHHHccCChHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCChHHHHHHHHH
Confidence            3445555443   46788999999988877 4454443322 23457788999999999999888888888777777777


Q ss_pred             HHhcCCcc
Q 011249          458 YASMGKWK  465 (490)
Q Consensus       458 ~~~~g~~~  465 (490)
                      +...|+.+
T Consensus        88 L~~~~D~~   95 (160)
T PF09613_consen   88 LYALGDPS   95 (160)
T ss_pred             HHHcCChH
Confidence            77777644

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=93.96  E-value=0.21  Score=44.05  Aligned_cols=96  Identities=9%  Similarity=-0.057  Sum_probs=60.8

Q ss_pred             HhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHH
Q 011249          355 ACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAEL  432 (490)
Q Consensus       355 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~  432 (490)
                      -|.++|.+++|+..|.....  -.+.++.++..-..+|.+..++..|..-.....  ...-...|..-+.+-...|+..+
T Consensus       106 ~yFKQgKy~EAIDCYs~~ia--~~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd~~Y~KAYSRR~~AR~~Lg~~~E  183 (536)
T KOG4648|consen  106 TYFKQGKYEEAIDCYSTAIA--VYPHNPVYHINRALAYLKQKSFAQAEEDCEAAIALDKLYVKAYSRRMQARESLGNNME  183 (536)
T ss_pred             hhhhccchhHHHHHhhhhhc--cCCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHHHHHHHHHhhHHH
Confidence            36677777777777776654  233366666666677777777776666555444  12223344444455556677888


Q ss_pred             HHHHHHHHHhcCCCCCchHH
Q 011249          433 GEIAARHLLELGPEKTGNSA  452 (490)
Q Consensus       433 a~~~~~~~~~~~p~~~~~~~  452 (490)
                      |.+-++.++++.|++...-.
T Consensus       184 AKkD~E~vL~LEP~~~ELkK  203 (536)
T KOG4648|consen  184 AKKDCETVLALEPKNIELKK  203 (536)
T ss_pred             HHHhHHHHHhhCcccHHHHH
Confidence            88888888888888655333

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=93.90  E-value=0.21  Score=29.71  Aligned_cols=28  Identities=18%  Similarity=0.305  Sum_probs=16.1

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQE  239 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~  239 (490)
                      ++..+...|...|++++|+++|++..+.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4455555566666666666666665554

>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=93.89  E-value=3.5  Score=34.79  Aligned_cols=17  Identities=0%  Similarity=-0.292  Sum_probs=8.8

Q ss_pred             hhCChHHHHHHHHHHHh
Q 011249          426 VHVNAELGEIAARHLLE  442 (490)
Q Consensus       426 ~~g~~~~a~~~~~~~~~  442 (490)
                      ..+++.+|+.+|+++..
T Consensus       166 ~leqY~~Ai~iyeqva~  182 (288)
T KOG1586|consen  166 QLEQYSKAIDIYEQVAR  182 (288)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            34455555555555544

>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=93.87  E-value=1.5  Score=35.96  Aligned_cols=97  Identities=14%  Similarity=0.090  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHH--HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHH--HH
Q 011249          313 SYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV--TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLT--CM  388 (490)
Q Consensus       313 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~--~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~--~l  388 (490)
                      .+..+...|.+.|+.+.|.+.|.++.+....|...  .+..+++.....+++..+...+.++........+...-+  ..
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            55667777777888888888888877754444433  556667777777788777777777765311111111111  11


Q ss_pred             --HHHHhhcCChHHHHHHHHhcc
Q 011249          389 --VDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       389 --~~~~~~~g~~~~A~~~~~~~~  409 (490)
                        .-.+...+++.+|-+.|-...
T Consensus       118 ~~gL~~l~~r~f~~AA~~fl~~~  140 (177)
T PF10602_consen  118 YEGLANLAQRDFKEAAELFLDSL  140 (177)
T ss_pred             HHHHHHHHhchHHHHHHHHHccC
Confidence              122345677888777775554

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.

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=93.75  E-value=5.9  Score=36.99  Aligned_cols=128  Identities=9%  Similarity=0.102  Sum_probs=81.9

Q ss_pred             HHhcCCHHHHHHHHhhcCCC---C------HhHHHHHHHHHHhCCChHHHHHHHHHhccC-CchhHHHHHHH--HHhcCC
Q 011249          127 YTKIGLMDDAQRLFDSMAER---N------VISWSAMVAGYANCGNMKAAKEFYDRMTEK-NSVTWVAMIAG--YGKCGE  194 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~~~~~~---~------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~l~~~--~~~~~~  194 (490)
                      +-+.+++.+|..+|.++.+.   +      ...-+.++++|.. ++.+.....+....+. ....|..+..+  +-+.++
T Consensus        16 Lqkq~~~~esEkifskI~~e~~~~~f~lkeEvl~grilnAffl-~nld~Me~~l~~l~~~~~~s~~l~LF~~L~~Y~~k~   94 (549)
T PF07079_consen   16 LQKQKKFQESEKIFSKIYDEKESSPFLLKEEVLGGRILNAFFL-NNLDLMEKQLMELRQQFGKSAYLPLFKALVAYKQKE   94 (549)
T ss_pred             HHHHhhhhHHHHHHHHHHHHhhcchHHHHHHHHhhHHHHHHHH-hhHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhhh
Confidence            56789999999999988752   2      2234556677764 4555555555555432 23344444443  346788


Q ss_pred             hhHHHHHHhhcCC------------------CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCc----ccChhhHHHHH
Q 011249          195 VREAKKVFDEISE------------------PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENV----RISEVAMVGAI  252 (490)
Q Consensus       195 ~~~A~~~~~~~~~------------------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~----~p~~~~~~~l~  252 (490)
                      +++|.+.+..-..                  +|-..=+..+.++...|++.++..+++++...=.    .-+..+|+.++
T Consensus        95 ~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~v  174 (549)
T PF07079_consen   95 YRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRAV  174 (549)
T ss_pred             HHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHHH
Confidence            8888887754321                  2223345677889999999999999999876433    35677777754


Q ss_pred             HHH
Q 011249          253 SAC  255 (490)
Q Consensus       253 ~~~  255 (490)
                      -.+
T Consensus       175 lml  177 (549)
T PF07079_consen  175 LML  177 (549)
T ss_pred             HHH
Confidence            443

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=93.75  E-value=0.91  Score=42.24  Aligned_cols=121  Identities=18%  Similarity=0.188  Sum_probs=75.5

Q ss_pred             HhcCChHHHHHHHHH-HHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHH
Q 011249          322 ADHGKSQEALDMFLK-MRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEK  400 (490)
Q Consensus       322 ~~~~~~~~a~~~~~~-~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  400 (490)
                      ...|+...|-+-+.. +....-.|+.......|  +...|+++.+.+.+.....  -+.....+...+++...+.|++++
T Consensus       300 ~~~gd~~aas~~~~~~lr~~~~~p~~i~l~~~i--~~~lg~ye~~~~~~s~~~~--~~~s~~~~~~~~~r~~~~l~r~~~  375 (831)
T PRK15180        300 LADGDIIAASQQLFAALRNQQQDPVLIQLRSVI--FSHLGYYEQAYQDISDVEK--IIGTTDSTLRCRLRSLHGLARWRE  375 (831)
T ss_pred             hhccCHHHHHHHHHHHHHhCCCCchhhHHHHHH--HHHhhhHHHHHHHhhchhh--hhcCCchHHHHHHHhhhchhhHHH
Confidence            345666666544443 33333345544443333  4567888888888777765  344555666777888888888888


Q ss_pred             HHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          401 AHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       401 A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      |...-..|.  .-.++.+...........|-++++...|+++..++|+
T Consensus       376 a~s~a~~~l~~eie~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~~~  423 (831)
T PRK15180        376 ALSTAEMMLSNEIEDEEVLTVAAGSADALQLFDKSYHYWKRVLLLNPE  423 (831)
T ss_pred             HHHHHHHHhccccCChhheeeecccHHHHhHHHHHHHHHHHHhccCCh
Confidence            888777666  1123334433344455667788888888888887754

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=93.72  E-value=5  Score=36.02  Aligned_cols=125  Identities=11%  Similarity=0.180  Sum_probs=67.9

Q ss_pred             HHHHHHHHhcCCCCchhHHHHHHHHHHh--cC----ChHHHHHHHhcccC-------CChhHHHHHHHHHHhcCC----h
Q 011249          265 AILAKHVDEGCCDRTNYVSNALIHMHSK--CG----YLDLAWREFSRIKN-------KDVISYSSMITAFADHGK----S  327 (490)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~----~~~~A~~~~~~~~~-------~~~~~~~~l~~~~~~~~~----~  327 (490)
                      ..+++.+.+.|+..+..+|-+.......  ..    ....|..+|+.|.+       ++..++..++..  ..++    .
T Consensus        82 ~~~y~~L~~~gFk~~~y~~laA~~i~~~~~~~~~~~~~~ra~~iy~~mKk~H~fLTs~~D~~~a~lLA~--~~~~~e~l~  159 (297)
T PF13170_consen   82 LDIYEKLKEAGFKRSEYLYLAALIILEEEEKEDYDEIIQRAKEIYKEMKKKHPFLTSPEDYPFAALLAM--TSEDVEELA  159 (297)
T ss_pred             HHHHHHHHHhccCccChHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHhCccccCccchhHHHHHhc--ccccHHHHH
Confidence            4455555555555555444332222221  11    23455666666665       233444444332  2222    3


Q ss_pred             HHHHHHHHHHHHcCCCCcHH--HHHHHHHHhcCCCC--hHHHHHHHHHHHHHcCCCCCchHHHHHHHHH
Q 011249          328 QEALDMFLKMRNEGIEPNQV--TFIGVLTACSHGGL--VEDGCKQFELMTRVFGIKPLTEHLTCMVDLL  392 (490)
Q Consensus       328 ~~a~~~~~~~~~~~~~p~~~--~~~~l~~~~~~~g~--~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  392 (490)
                      +.++.+|+.+.+.|+..+..  ....++..+.....  ...+.++++.+.+. ++++....|..++-..
T Consensus       160 ~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~-~~kik~~~yp~lGlLa  227 (297)
T PF13170_consen  160 ERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKN-GVKIKYMHYPTLGLLA  227 (297)
T ss_pred             HHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHc-CCccccccccHHHHHH
Confidence            56777888888878776543  44444444333222  34778888888885 8888877776654433

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=93.68  E-value=0.31  Score=42.59  Aligned_cols=59  Identities=20%  Similarity=0.138  Sum_probs=34.6

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHh
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                      ++..++..+...|+.+.+.+.++++.  .+-+...|..++.+|...|+...|+..|+++.+
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~  215 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKK  215 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHH
Confidence            44555566666666666666665554  333555666666666666666666666665554

>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=93.51  E-value=3.1  Score=32.97  Aligned_cols=19  Identities=21%  Similarity=0.260  Sum_probs=10.0

Q ss_pred             HHhhcCChHHHHHHHHhcc
Q 011249          391 LLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~~~  409 (490)
                      .+.+.|++.+|..+|+.+.
T Consensus        53 l~i~r~~w~dA~rlLr~l~   71 (160)
T PF09613_consen   53 LHIVRGDWDDALRLLRELE   71 (160)
T ss_pred             HHHHhCCHHHHHHHHHHHh
Confidence            3445555555555555544

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=93.44  E-value=0.088  Score=29.10  Aligned_cols=31  Identities=13%  Similarity=0.122  Sum_probs=26.3

Q ss_pred             chHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          449 GNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       449 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .++..++.++...|++++|++.+++..+..+
T Consensus         2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p   32 (34)
T PF07719_consen    2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDP   32 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCc
Confidence            4688999999999999999999999887543

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 ....

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=93.31  E-value=10  Score=38.30  Aligned_cols=213  Identities=15%  Similarity=0.053  Sum_probs=89.5

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--C--CH
Q 011249           73 SLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--R--NV  148 (490)
Q Consensus        73 ~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~--~~  148 (490)
                      .+|--|.|.|++++|.++....... .......+...+..+...++..       .....-++...-|+...+  +  |+
T Consensus       116 a~Iyy~LR~G~~~~A~~~~~~~~~~-~~~~~~~f~~~l~~~~~s~~~~-------l~~~~~~~l~~ey~~~~r~~~~~Dp  187 (613)
T PF04097_consen  116 ALIYYCLRCGDYDEALEVANENRNQ-FQKIERSFPTYLKAYASSPDRR-------LPPELRDKLKLEYNQRIRNSTDGDP  187 (613)
T ss_dssp             HHHHHHHTTT-HHHHHHHHHHTGGG-S-TTTTHHHHHHHHCTTTTSS----------TCCCHHHHHHHHHHTTT-TTS-H
T ss_pred             HHHHHHHhcCCHHHHHHHHHHhhhh-hcchhHHHHHHHHHHHhCCCCC-------CCHHHHHHHHHHHHHHhcCCCCCCh
Confidence            5677889999999999999665543 4556677788888876643322       122233444455555443  2  44


Q ss_pred             h---HHHHHHHHHHhCCChHHH---HHHHHHhc-----cC--------CchhHHHHHHHHHhcCChhHHHHHHhhcCCCC
Q 011249          149 I---SWSAMVAGYANCGNMKAA---KEFYDRMT-----EK--------NSVTWVAMIAGYGKCGEVREAKKVFDEISEPD  209 (490)
Q Consensus       149 ~---~~~~l~~~~~~~~~~~~a---~~~~~~~~-----~~--------~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  209 (490)
                      .   .|..+..+=.........   .+-|-++.     +.        +..++..+-....+-|.     +.|..  ..+
T Consensus       188 yK~AvY~ilg~cD~~~~~~~~V~~tiED~LW~~L~~vr~~~~~~~~~~e~~~L~~LQ~~i~~~Ge-----~~F~~--~~~  260 (613)
T PF04097_consen  188 YKRAVYKILGRCDLSRRHLPEVARTIEDWLWLQLSLVREDERSSSSAYERYTLEDLQKLILKYGE-----SHFNA--GSN  260 (613)
T ss_dssp             HHHHHHHHHHT--CCC-S-TTC--SHHHHHHHHHHH---TTSSSSSSS----HHHHHHHHHHH-G-----GGCTT-----
T ss_pred             HHHHHHHHHhcCCccccchHHHhCcHHHHHHHHHHhhccCCCccccccccccHHHHHHHHHHhch-----hhccc--chh
Confidence            3   344442211111111111   11111111     00        01122222211111111     11111  112


Q ss_pred             HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCC-CCchhHHHHHHH
Q 011249          210 ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCC-DRTNYVSNALIH  288 (490)
Q Consensus       210 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~-~~~~~~~~~l~~  288 (490)
                      +.   .....+.-.|+++.|++++-+  ..+...+.+++...+..+.-.+-.+...   ..+..... .+.+.-+..||.
T Consensus       261 p~---~Yf~~LlLtgqFE~AI~~L~~--~~~~~~dAVH~AIaL~~~gLL~~~~~~~---~~lls~~~~~~~~ln~arLI~  332 (613)
T PF04097_consen  261 PL---LYFQVLLLTGQFEAAIEFLYR--NEFNRVDAVHFAIALAYYGLLRVSDSSS---APLLSVDPGDPPPLNFARLIG  332 (613)
T ss_dssp             ------HHHHHHHTT-HHHHHHHHHT----T-HHHHHHHHHHHHHTT---------------------------HHHHHH
T ss_pred             HH---HHHHHHHHHhhHHHHHHHHHh--hccCcccHHHHHHHHHHcCCCCCCCccc---cceeeecCCCCCCcCHHHHHH
Confidence            22   334566778999999998877  2334556666666665554332222211   22211110 111134556777


Q ss_pred             HHHh---cCChHHHHHHHhcccC
Q 011249          289 MHSK---CGYLDLAWREFSRIKN  308 (490)
Q Consensus       289 ~~~~---~~~~~~A~~~~~~~~~  308 (490)
                      .|.+   ..+..+|.+.|--+..
T Consensus       333 ~Y~~~F~~td~~~Al~Y~~li~~  355 (613)
T PF04097_consen  333 QYTRSFEITDPREALQYLYLICL  355 (613)
T ss_dssp             HHHHTTTTT-HHHHHHHHHGGGG
T ss_pred             HHHHHHhccCHHHHHHHHHHHHH
Confidence            7765   3567778887766654

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>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=93.23  E-value=5.9  Score=35.35  Aligned_cols=120  Identities=8%  Similarity=-0.004  Sum_probs=52.8

Q ss_pred             HhcCChHHHHHHHHHHHHcC--cccChh-----hHHHHHHHHhccC-ChHHHHHHHHHHHhc----C----CCCc-----
Q 011249          221 VQNGYAKAAIEMYKVMRQEN--VRISEV-----AMVGAISACTQLG-DVEMAAILAKHVDEG----C----CDRT-----  279 (490)
Q Consensus       221 ~~~g~~~~A~~~~~~~~~~~--~~p~~~-----~~~~l~~~~~~~g-~~~~a~~~~~~~~~~----~----~~~~-----  279 (490)
                      .+.|+.+.|...+.+.....  ..|+..     .+..+.......+ +++.|..++++..+.    +    ..++     
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            35666666766666665422  122211     1111222223344 666666666554332    1    1111     


Q ss_pred             hhHHHHHHHHHHhcCChHH---HHHHHhcccC--CC-hhHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011249          280 NYVSNALIHMHSKCGYLDL---AWREFSRIKN--KD-VISYSSMITAFADHGKSQEALDMFLKMRNE  340 (490)
Q Consensus       280 ~~~~~~l~~~~~~~~~~~~---A~~~~~~~~~--~~-~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  340 (490)
                      ..+...++.+|...+..+.   |..+++.+..  ++ +.++..-+..+.+.++.+.+.+.+.+|+..
T Consensus        84 ~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e~~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~  150 (278)
T PF08631_consen   84 LSILRLLANAYLEWDTYESVEKALNALRLLESEYGNKPEVFLLKLEILLKSFDEEEYEEILMRMIRS  150 (278)
T ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHhccCChhHHHHHHHHHHHh
Confidence            1234445555555544332   3333333322  22 333334444444455555555555555553

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=93.16  E-value=0.1  Score=28.87  Aligned_cols=31  Identities=16%  Similarity=0.154  Sum_probs=26.5

Q ss_pred             chHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          449 GNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       449 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .+|..++.+|...|++++|++.+++..+..+
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p   32 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALELDP   32 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHCc
Confidence            4688999999999999999999999887654

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 ....

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=93.08  E-value=8.5  Score=40.58  Aligned_cols=25  Identities=24%  Similarity=0.392  Sum_probs=14.1

Q ss_pred             HHHHHHHHHhcC--ChhHHHHHHhhcC
Q 011249          182 WVAMIAGYGKCG--EVREAKKVFDEIS  206 (490)
Q Consensus       182 ~~~l~~~~~~~~--~~~~A~~~~~~~~  206 (490)
                      ...++..|.+.+  .+++|+....+..
T Consensus       793 ~~~ilTs~vk~~~~~ie~aL~kI~~l~  819 (1265)
T KOG1920|consen  793 NLFILTSYVKSNPPEIEEALQKIKELQ  819 (1265)
T ss_pred             hHHHHHHHHhcCcHHHHHHHHHHHHHH
Confidence            345666666665  5555555554444

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=93.06  E-value=0.2  Score=27.32  Aligned_cols=27  Identities=11%  Similarity=-0.028  Sum_probs=15.1

Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      +..++...|++++|.+.|+++++..|+
T Consensus         6 ~a~~~~~~g~~~~A~~~~~~~~~~~P~   32 (33)
T PF13174_consen    6 LARCYYKLGDYDEAIEYFQRLIKRYPD   32 (33)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence            344455555666666666665555554

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=92.98  E-value=5.4  Score=34.29  Aligned_cols=64  Identities=16%  Similarity=0.116  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCc--ccChhhHHHHHHHHhccCChHHHHHHHHHHHhcC
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQENV--RISEVAMVGAISACTQLGDVEMAAILAKHVDEGC  275 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  275 (490)
                      .+-.-+..-.+.|++++|.+.|+.+....+  +-...+...++-++.+.++++.|....++..+.-
T Consensus        36 ~LY~~g~~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~ly  101 (254)
T COG4105          36 ELYNEGLTELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLY  101 (254)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhC
Confidence            333444455667777777777777765321  1123455556666667777777777777766554

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=92.92  E-value=8.7  Score=36.53  Aligned_cols=89  Identities=6%  Similarity=0.068  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccC--CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcC
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKN--KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSH  358 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~  358 (490)
                      ...+++..+.....+.-.+.+..++..  .+-..|..++++|... ..++-..+|+++.+.  ..|.. .-..|...|.+
T Consensus        68 ~l~~~~~~f~~n~k~~~veh~c~~~l~~~e~kmal~el~q~y~en-~n~~l~~lWer~ve~--dfnDvv~~ReLa~~yEk  144 (711)
T COG1747          68 CLVTLLTIFGDNHKNQIVEHLCTRVLEYGESKMALLELLQCYKEN-GNEQLYSLWERLVEY--DFNDVVIGRELADKYEK  144 (711)
T ss_pred             HHHHHHHHhccchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhc-CchhhHHHHHHHHHh--cchhHHHHHHHHHHHHH
Confidence            333444444444444444444444443  2334455555555544 334455555555542  22222 22222332322


Q ss_pred             CCChHHHHHHHHHHHH
Q 011249          359 GGLVEDGCKQFELMTR  374 (490)
Q Consensus       359 ~g~~~~a~~~~~~~~~  374 (490)
                       ++.+.+..+|.++..
T Consensus       145 -ik~sk~a~~f~Ka~y  159 (711)
T COG1747         145 -IKKSKAAEFFGKALY  159 (711)
T ss_pred             -hchhhHHHHHHHHHH
Confidence             445555555555544

>KOG1550 consensus Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=92.75  E-value=11  Score=37.41  Aligned_cols=273  Identities=16%  Similarity=0.098  Sum_probs=156.3

Q ss_pred             hhHHHHHHhhcCC-CCHHhHHHHHHH-----HHhcCChHHHHHHHHHHHH-------cCcccChhhHHHHHHHHhccC--
Q 011249          195 VREAKKVFDEISE-PDASCWAAMTVC-----YVQNGYAKAAIEMYKVMRQ-------ENVRISEVAMVGAISACTQLG--  259 (490)
Q Consensus       195 ~~~A~~~~~~~~~-~~~~~~~~l~~~-----~~~~g~~~~A~~~~~~~~~-------~~~~p~~~~~~~l~~~~~~~g--  259 (490)
                      ...|.++++...+ .+...-..+..+     +....+.+.|+.+|+.+.+       .|   .......+..+|.+..  
T Consensus       228 ~~~a~~~~~~~a~~g~~~a~~~~g~~y~~G~~g~~~d~e~a~~~l~~aa~~~~~~a~~~---~~~a~~~lg~~Y~~g~~~  304 (552)
T KOG1550|consen  228 LSEAFKYYREAAKLGHSEAQYALGICYLAGTYGVTQDLESAIEYLKLAAESFKKAATKG---LPPAQYGLGRLYLQGLGV  304 (552)
T ss_pred             hhHHHHHHHHHHhhcchHHHHHHHHHHhhccccccccHHHHHHHHHHHHHHHHHHHhhc---CCccccHHHHHHhcCCCC
Confidence            4567777777655 333333333333     3345678889988888866       44   3334555666665533  


Q ss_pred             ---ChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHh-cCChHHHHHHHhcccC-CChhHHHHHHHHHH----hcCChHHH
Q 011249          260 ---DVEMAAILAKHVDEGCCDRTNYVSNALIHMHSK-CGYLDLAWREFSRIKN-KDVISYSSMITAFA----DHGKSQEA  330 (490)
Q Consensus       260 ---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~A~~~~~~~~~-~~~~~~~~l~~~~~----~~~~~~~a  330 (490)
                         +.+.|..++....+.| .|+.......+..... ..+...|.++|....+ -.+..+-.+..+|.    -..+...|
T Consensus       305 ~~~d~~~A~~~~~~aA~~g-~~~a~~~lg~~~~~g~~~~d~~~A~~yy~~Aa~~G~~~A~~~la~~y~~G~gv~r~~~~A  383 (552)
T KOG1550|consen  305 EKIDYEKALKLYTKAAELG-NPDAQYLLGVLYETGTKERDYRRAFEYYSLAAKAGHILAIYRLALCYELGLGVERNLELA  383 (552)
T ss_pred             ccccHHHHHHHHHHHHhcC-CchHHHHHHHHHHcCCccccHHHHHHHHHHHHHcCChHHHHHHHHHHHhCCCcCCCHHHH
Confidence               5677888888888887 5555544333333222 2457788888888775 33444433433332    23478888


Q ss_pred             HHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHH---hh----cCChHHHHH
Q 011249          331 LDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLL---GR----SGQLEKAHS  403 (490)
Q Consensus       331 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~---~~----~g~~~~A~~  403 (490)
                      ..++.+..+.| .|...--...+..+.. ++++.+.-.+..+... +.+.....-..++...   ..    ..+.+.+..
T Consensus       384 ~~~~k~aA~~g-~~~A~~~~~~~~~~g~-~~~~~~~~~~~~~a~~-g~~~~q~~a~~l~~~~~~~~~~~~~~~~~~~~~~  460 (552)
T KOG1550|consen  384 FAYYKKAAEKG-NPSAAYLLGAFYEYGV-GRYDTALALYLYLAEL-GYEVAQSNAAYLLDQSEEDLFSRGVISTLERAFS  460 (552)
T ss_pred             HHHHHHHHHcc-ChhhHHHHHHHHHHcc-ccccHHHHHHHHHHHh-hhhHHhhHHHHHHHhccccccccccccchhHHHH
Confidence            88999888877 4432222233333434 6666666666655552 4332221111111111   11    224555666


Q ss_pred             HHHhccCCCChhhHHHHHHHHhh----hCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhc-C--CcchHHHHHHHhhh
Q 011249          404 LIMDYKDFCDAGTWGALLGACKV----HVNAELGEIAARHLLELGPEKTGNSALLANIYASM-G--KWKDSEIVKMMISE  476 (490)
Q Consensus       404 ~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~-g--~~~~A~~~~~~~~~  476 (490)
                      .+.+...+-+......+...|..    ..+++.|...+..+....   +.....++.++..- |  ++..|.+++++..+
T Consensus       461 ~~~~a~~~g~~~a~~~lgd~y~~g~g~~~d~~~a~~~y~~a~~~~---~~~~~nlg~~~e~g~g~~~~~~a~~~~~~~~~  537 (552)
T KOG1550|consen  461 LYSRAAAQGNADAILKLGDYYYYGLGTGRDPEKAAAQYARASEQG---AQALFNLGYMHEHGEGIKVLHLAKRYYDQASE  537 (552)
T ss_pred             HHHHHHhccCHHHHhhhcceeeecCCCCCChHHHHHHHHHHHHhh---hHHHhhhhhHHhcCcCcchhHHHHHHHHHHHh
Confidence            66665545555555555554433    236888888888888766   66677777766542 1  25677777777665


Q ss_pred             c
Q 011249          477 T  477 (490)
Q Consensus       477 ~  477 (490)
                      .
T Consensus       538 ~  538 (552)
T KOG1550|consen  538 E  538 (552)
T ss_pred             c
Confidence            4

>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=92.58  E-value=1.1  Score=36.68  Aligned_cols=55  Identities=13%  Similarity=0.116  Sum_probs=25.2

Q ss_pred             HHHHHHHHhcCChhHHHHHHhhcCC------CCHHhHHHHHHHHHhcCChHHHHHHHHHHH
Q 011249          183 VAMIAGYGKCGEVREAKKVFDEISE------PDASCWAAMTVCYVQNGYAKAAIEMYKVMR  237 (490)
Q Consensus       183 ~~l~~~~~~~~~~~~A~~~~~~~~~------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  237 (490)
                      ..++..|.+.|+.+.|.+.|.++.+      .-...+-.+|+.....+++..+...+.+..
T Consensus        40 ~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~  100 (177)
T PF10602_consen   40 EDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAE  100 (177)
T ss_pred             HHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            3444444444444444444444433      112233444555555555555555544443

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.

>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=92.57  E-value=0.012  Score=46.38  Aligned_cols=83  Identities=14%  Similarity=0.119  Sum_probs=42.6

Q ss_pred             HHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHH
Q 011249          251 AISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEA  330 (490)
Q Consensus       251 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  330 (490)
                      ++..+.+.+.+.....+++.+...+...+....+.++..|++.++.+...++++....   .-...++..+.+.|.++++
T Consensus        13 vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~~~~~---yd~~~~~~~c~~~~l~~~a   89 (143)
T PF00637_consen   13 VISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLKTSNN---YDLDKALRLCEKHGLYEEA   89 (143)
T ss_dssp             CHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTTSSSS---S-CTHHHHHHHTTTSHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcccccc---cCHHHHHHHHHhcchHHHH
Confidence            3444555566666666666666555445566666666666666555666655552222   2223344444444555555


Q ss_pred             HHHHHH
Q 011249          331 LDMFLK  336 (490)
Q Consensus       331 ~~~~~~  336 (490)
                      .-++.+
T Consensus        90 ~~Ly~~   95 (143)
T PF00637_consen   90 VYLYSK   95 (143)
T ss_dssp             HHHHHC
T ss_pred             HHHHHH
Confidence            444443

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.

>PRK09687 putative lyase; Provisional

Probab=92.49  E-value=7.5  Score=34.66  Aligned_cols=236  Identities=11%  Similarity=0.016  Sum_probs=103.7

Q ss_pred             cCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCCh----HHHHHHHHHHHHcCcccChhhHHHH
Q 011249          176 EKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYA----KAAIEMYKVMRQENVRISEVAMVGA  251 (490)
Q Consensus       176 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~----~~A~~~~~~~~~~~~~p~~~~~~~l  251 (490)
                      .+|.......+..+...|..+-...+..-+..+|+..-...+.++.+.|+.    +++...+..+...  .|+...-...
T Consensus        34 d~d~~vR~~A~~aL~~~~~~~~~~~l~~ll~~~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~--D~d~~VR~~A  111 (280)
T PRK09687         34 DHNSLKRISSIRVLQLRGGQDVFRLAIELCSSKNPIERDIGADILSQLGMAKRCQDNVFNILNNLALE--DKSACVRASA  111 (280)
T ss_pred             CCCHHHHHHHHHHHHhcCcchHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhc--CCCHHHHHHH
Confidence            445555555555555555433222222222334555555555555555542    3455555544322  2344444444


Q ss_pred             HHHHhccCChHH--HHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcC-ChH
Q 011249          252 ISACTQLGDVEM--AAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHG-KSQ  328 (490)
Q Consensus       252 ~~~~~~~g~~~~--a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~  328 (490)
                      +.++...+....  .......+...-..++..+-...+.++.+.++.+....+..-+..++..+-...+.++.+.+ +..
T Consensus       112 ~~aLG~~~~~~~~~~~~a~~~l~~~~~D~~~~VR~~a~~aLg~~~~~~ai~~L~~~L~d~~~~VR~~A~~aLg~~~~~~~  191 (280)
T PRK09687        112 INATGHRCKKNPLYSPKIVEQSQITAFDKSTNVRFAVAFALSVINDEAAIPLLINLLKDPNGDVRNWAAFALNSNKYDNP  191 (280)
T ss_pred             HHHHhcccccccccchHHHHHHHHHhhCCCHHHHHHHHHHHhccCCHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCCCCH
Confidence            444443322110  01112222111112344444455555555555333333333333344444444444444432 133


Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhc
Q 011249          329 EALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDY  408 (490)
Q Consensus       329 ~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  408 (490)
                      .+...+..+..   .++...-...+.++.+.|+. .+...+-...+.    ++  .....+.++...|.. +|...+..+
T Consensus       192 ~~~~~L~~~L~---D~~~~VR~~A~~aLg~~~~~-~av~~Li~~L~~----~~--~~~~a~~ALg~ig~~-~a~p~L~~l  260 (280)
T PRK09687        192 DIREAFVAMLQ---DKNEEIRIEAIIGLALRKDK-RVLSVLIKELKK----GT--VGDLIIEAAGELGDK-TLLPVLDTL  260 (280)
T ss_pred             HHHHHHHHHhc---CCChHHHHHHHHHHHccCCh-hHHHHHHHHHcC----Cc--hHHHHHHHHHhcCCH-hHHHHHHHH
Confidence            45555555543   34444445555555555553 344444444331    11  223455666666664 566666555


Q ss_pred             c-CCCChhhHHHHHHHH
Q 011249          409 K-DFCDAGTWGALLGAC  424 (490)
Q Consensus       409 ~-~~~~~~~~~~l~~~~  424 (490)
                      . ..+|..+-...+.+|
T Consensus       261 ~~~~~d~~v~~~a~~a~  277 (280)
T PRK09687        261 LYKFDDNEIITKAIDKL  277 (280)
T ss_pred             HhhCCChhHHHHHHHHH
Confidence            5 245555555544444

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=92.46  E-value=0.27  Score=28.61  Aligned_cols=27  Identities=19%  Similarity=0.058  Sum_probs=14.9

Q ss_pred             hHHHHHHHHhhhCChHHHHHHHHHHHh
Q 011249          416 TWGALLGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       416 ~~~~l~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                      +++.+...|...|++++|..+++++++
T Consensus         4 ~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    4 ALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            445555555556666666666655554

>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]

Probab=92.38  E-value=0.28  Score=43.40  Aligned_cols=90  Identities=10%  Similarity=-0.086  Sum_probs=75.7

Q ss_pred             HHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcch
Q 011249          389 VDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKD  466 (490)
Q Consensus       389 ~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  466 (490)
                      ..-|.++|.+++|+..|.... ..| ++.++..-..+|.+...+..|+.-...++.++.....+|+.-+.+-...|+..+
T Consensus       104 GN~yFKQgKy~EAIDCYs~~ia~~P~NpV~~~NRA~AYlk~K~FA~AE~DC~~AiaLd~~Y~KAYSRR~~AR~~Lg~~~E  183 (536)
T KOG4648|consen  104 GNTYFKQGKYEEAIDCYSTAIAVYPHNPVYHINRALAYLKQKSFAQAEEDCEAAIALDKLYVKAYSRRMQARESLGNNME  183 (536)
T ss_pred             hhhhhhccchhHHHHHhhhhhccCCCCccchhhHHHHHHHHHHHHHHHHhHHHHHHhhHHHHHHHHHHHHHHHHHhhHHH
Confidence            456889999999999997655 445 888888888999999999999999999999887778888888888888888888


Q ss_pred             HHHHHHHhhhcc
Q 011249          467 SEIVKMMISETE  478 (490)
Q Consensus       467 A~~~~~~~~~~~  478 (490)
                      |.+-++...+..
T Consensus       184 AKkD~E~vL~LE  195 (536)
T KOG4648|consen  184 AKKDCETVLALE  195 (536)
T ss_pred             HHHhHHHHHhhC
Confidence            888777766543

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=92.30  E-value=4.4  Score=31.59  Aligned_cols=42  Identities=7%  Similarity=0.021  Sum_probs=21.0

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhc
Q 011249          215 AMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQ  257 (490)
Q Consensus       215 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~  257 (490)
                      .++..+...+.+.....+++.+...+. .+...++.++..+++
T Consensus        12 ~vv~~~~~~~~~~~l~~yLe~~~~~~~-~~~~~~~~li~ly~~   53 (140)
T smart00299       12 EVVELFEKRNLLEELIPYLESALKLNS-ENPALQTKLIELYAK   53 (140)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHccCc-cchhHHHHHHHHHHH
Confidence            344444445555555555555554442 344455555555544

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.27  E-value=14  Score=37.42  Aligned_cols=54  Identities=15%  Similarity=0.026  Sum_probs=37.7

Q ss_pred             HHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHh
Q 011249          388 MVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       388 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                      ++..+....+++.+..+.+... +.++..|..++..+.+.+..+.-.+...+.++
T Consensus       711 l~~~~~q~~d~E~~it~~~~~g-~~~p~l~~~~L~yF~~~~~i~~~~~~v~~vl~  764 (933)
T KOG2114|consen  711 LMLYFQQISDPETVITLCERLG-KEDPSLWLHALKYFVSEESIEDCYEIVYKVLE  764 (933)
T ss_pred             HHHHHHHhhChHHHHHHHHHhC-ccChHHHHHHHHHHhhhcchhhHHHHHHHHHH
Confidence            5556666777777777777776 44777888888888887766666665555544

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=92.21  E-value=1.5  Score=35.28  Aligned_cols=59  Identities=12%  Similarity=0.008  Sum_probs=33.9

Q ss_pred             ChhhHHHHHHHHhhhC-----------ChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          413 DAGTWGALLGACKVHV-----------NAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       413 ~~~~~~~l~~~~~~~g-----------~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      ...++..+..++...+           .+++|.+.|+++...+|++......|- +.      .+|-++..++.+.+
T Consensus        68 ~hdAlw~lGnA~ts~A~l~~d~~~A~~~F~kA~~~FqkAv~~~P~ne~Y~ksLe-~~------~kap~lh~e~~~~~  137 (186)
T PF06552_consen   68 KHDALWCLGNAYTSLAFLTPDTAEAEEYFEKATEYFQKAVDEDPNNELYRKSLE-MA------AKAPELHMEIHKQG  137 (186)
T ss_dssp             -HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHH-HH------HTHHHHHHHHHHSS
T ss_pred             hHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHH-HH------HhhHHHHHHHHHHH
Confidence            3456666666665433           266777788888888898665444443 32      34566666655554

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=92.16  E-value=1.1  Score=39.25  Aligned_cols=75  Identities=15%  Similarity=0.229  Sum_probs=53.3

Q ss_pred             hhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHH-----cCcccChhhHHHH
Q 011249          180 VTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQ-----ENVRISEVAMVGA  251 (490)
Q Consensus       180 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~p~~~~~~~l  251 (490)
                      .++..++..+...|+++.+...++++..   -+...|..++.+|.+.|+...|+..|+++.+     .|+.|...+....
T Consensus       154 ~~l~~lae~~~~~~~~~~~~~~l~~Li~~dp~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         154 KALTKLAEALIACGRADAVIEHLERLIELDPYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            3456677777778888888888877765   4667788888888888888888888887765     4666666554444


Q ss_pred             HHH
Q 011249          252 ISA  254 (490)
Q Consensus       252 ~~~  254 (490)
                      ..+
T Consensus       234 ~~~  236 (280)
T COG3629         234 EEI  236 (280)
T ss_pred             HHH
Confidence            433

>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]

Probab=92.15  E-value=7.1  Score=34.19  Aligned_cols=60  Identities=15%  Similarity=0.028  Sum_probs=52.5

Q ss_pred             HHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          417 WGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       417 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      ++.....|...|.+.+|.++.++++..+|-+...+..|...+...|+--.|.+-++++.+
T Consensus       282 lgkva~~yle~g~~neAi~l~qr~ltldpL~e~~nk~lm~~la~~gD~is~~khyerya~  341 (361)
T COG3947         282 LGKVARAYLEAGKPNEAIQLHQRALTLDPLSEQDNKGLMASLATLGDEISAIKHYERYAE  341 (361)
T ss_pred             HHHHHHHHHHcCChHHHHHHHHHHhhcChhhhHHHHHHHHHHHHhccchhhhhHHHHHHH
Confidence            344557789999999999999999999999999999999999999998888888777654

>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=92.14  E-value=0.074  Score=41.94  Aligned_cols=129  Identities=10%  Similarity=0.101  Sum_probs=65.3

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCCHhHHH
Q 011249           73 SLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWS  152 (490)
Q Consensus        73 ~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~  152 (490)
                      .+++.+.+.+.+......++.+...+...+....+.++.              .|++.++.++..++++...   ..-..
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~--------------ly~~~~~~~~l~~~L~~~~---~yd~~   74 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLE--------------LYIKYDPYEKLLEFLKTSN---NYDLD   74 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHH--------------HHHCTTTCCHHHHTTTSSS---SS-CT
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHH--------------HHHhcCCchHHHHHccccc---ccCHH
Confidence            356666667777777777777776554444444544444              3666666666666665222   23334


Q ss_pred             HHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCC
Q 011249          153 AMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGY  225 (490)
Q Consensus       153 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~  225 (490)
                      .++..|.+.|-++++.-++.++...+..     +..+...++++.|.+++.+.  +++..|..++..+...+.
T Consensus        75 ~~~~~c~~~~l~~~a~~Ly~~~~~~~~a-----l~i~~~~~~~~~a~e~~~~~--~~~~l~~~l~~~~l~~~~  140 (143)
T PF00637_consen   75 KALRLCEKHGLYEEAVYLYSKLGNHDEA-----LEILHKLKDYEEAIEYAKKV--DDPELWEQLLKYCLDSKP  140 (143)
T ss_dssp             HHHHHHHTTTSHHHHHHHHHCCTTHTTC-----SSTSSSTHCSCCCTTTGGGC--SSSHHHHHHHHHHCTSTC
T ss_pred             HHHHHHHhcchHHHHHHHHHHcccHHHH-----HHHHHHHccHHHHHHHHHhc--CcHHHHHHHHHHHHhcCc
Confidence            4566666666666666655443221000     00012223333333222222  445667777766665544

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.

>PF10345 Cohesin_load: Cohesin loading factor; InterPro: IPR019440 Cohesin loading factor is a conserved protein that has been characterised in fungi

Probab=92.08  E-value=15  Score=37.19  Aligned_cols=183  Identities=10%  Similarity=0.059  Sum_probs=91.8

Q ss_pred             CCHhHHHHHHHHHHhCCChHHHHHHHHHhcc-C------CchhHHHHHHHHH-hcCChhHHHHHHhhcCC----CCH---
Q 011249          146 RNVISWSAMVAGYANCGNMKAAKEFYDRMTE-K------NSVTWVAMIAGYG-KCGEVREAKKVFDEISE----PDA---  210 (490)
Q Consensus       146 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-~------~~~~~~~l~~~~~-~~~~~~~A~~~~~~~~~----~~~---  210 (490)
                      .+...|..||..         |++.++-+.+ .      +..++..++..+. ...+++.|+..+++...    ++.   
T Consensus        28 ~~l~~Y~kLI~~---------ai~CL~~~~~~~~l~p~~ea~~~l~la~iL~~eT~n~~~Ae~~L~k~~~l~~~~~~~d~   98 (608)
T PF10345_consen   28 EQLKQYYKLIAT---------AIKCLEAVLKQFKLSPRQEARVRLRLASILLEETENLDLAETYLEKAILLCERHRLTDL   98 (608)
T ss_pred             hhHHHHHHHHHH---------HHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHHH
Confidence            355677777765         3455555542 1      4556667777666 56778888888876532    111   


Q ss_pred             --HhHHHHHHHHHhcCChHHHHHHHHHHHHcC----cccChhhHHHH-HHHHhccCChHHHHHHHHHHHhcC---CCCch
Q 011249          211 --SCWAAMTVCYVQNGYAKAAIEMYKVMRQEN----VRISEVAMVGA-ISACTQLGDVEMAAILAKHVDEGC---CDRTN  280 (490)
Q Consensus       211 --~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~----~~p~~~~~~~l-~~~~~~~g~~~~a~~~~~~~~~~~---~~~~~  280 (490)
                        ..-..++..+.+.+... |...+++.++.-    ..+-...|..+ +..+...++...|.+.++.+....   ..+..
T Consensus        99 k~~~~~ll~~i~~~~~~~~-a~~~l~~~I~~~~~~~~~~w~~~frll~~~l~~~~~d~~~Al~~L~~~~~~a~~~~d~~~  177 (608)
T PF10345_consen   99 KFRCQFLLARIYFKTNPKA-ALKNLDKAIEDSETYGHSAWYYAFRLLKIQLALQHKDYNAALENLQSIAQLANQRGDPAV  177 (608)
T ss_pred             HHHHHHHHHHHHHhcCHHH-HHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhhhcCCHHH
Confidence              12234556666666555 877777766431    11122233333 222223367777777777664432   13333


Q ss_pred             hHHHHHHHHHH--hcCChHHHHHHHhcccC-------------CChhHHHHHHHH--HHhcCChHHHHHHHHHHH
Q 011249          281 YVSNALIHMHS--KCGYLDLAWREFSRIKN-------------KDVISYSSMITA--FADHGKSQEALDMFLKMR  338 (490)
Q Consensus       281 ~~~~~l~~~~~--~~~~~~~A~~~~~~~~~-------------~~~~~~~~l~~~--~~~~~~~~~a~~~~~~~~  338 (490)
                      .++..++.+..  ..+..+++.+..+.+..             |...+|..+++.  +...|+++.+...++++.
T Consensus       178 ~v~~~l~~~~l~l~~~~~~d~~~~l~~~~~~~~~~q~~~~~~~~qL~~~~lll~l~~~l~~~~~~~~~~~L~~lq  252 (608)
T PF10345_consen  178 FVLASLSEALLHLRRGSPDDVLELLQRAIAQARSLQLDPSVHIPQLKALFLLLDLCCSLQQGDVKNSKQKLKQLQ  252 (608)
T ss_pred             HHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHhhcccCCCCCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            33333333322  33444445444443311             123344444443  334555555555544443

It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes, but is dispensable in G2 when cohesion has been established. It is often referred to as Ssl3 in Schizosaccharomyces pombe (Fission yeast), and Scc4 in Saccharomyces cerevisiae (Baker's yeast). It complexes with Mis4 [].

>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins

Probab=92.05  E-value=0.49  Score=38.00  Aligned_cols=49  Identities=16%  Similarity=0.122  Sum_probs=35.1

Q ss_pred             ChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCC-----------cchHHHHHHHhhhc
Q 011249          429 NAELGEIAARHLLELGPEKTGNSALLANIYASMGK-----------WKDSEIVKMMISET  477 (490)
Q Consensus       429 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~-----------~~~A~~~~~~~~~~  477 (490)
                      .+++|+.-|++++.++|+...++.+++.+|...+.           +++|.+.|++..+.
T Consensus        50 miedAisK~eeAL~I~P~~hdAlw~lGnA~ts~A~l~~d~~~A~~~F~kA~~~FqkAv~~  109 (186)
T PF06552_consen   50 MIEDAISKFEEALKINPNKHDALWCLGNAYTSLAFLTPDTAEAEEYFEKATEYFQKAVDE  109 (186)
T ss_dssp             HHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHHHHHHhc
Confidence            45678888888899999999999999999887654           44555555555443

Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.

>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=91.52  E-value=31  Score=39.72  Aligned_cols=306  Identities=8%  Similarity=0.022  Sum_probs=158.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHhhc----CCCC--HhHHHHHHHHHHhCCChHHHHHHHHH-hccCCchhHHHHHHHHHhcCC
Q 011249          122 AVICGYTKIGLMDDAQRLFDSM----AERN--VISWSAMVAGYANCGNMKAAKEFYDR-MTEKNSVTWVAMIAGYGKCGE  194 (490)
Q Consensus       122 ~l~~~~~~~g~~~~A~~~~~~~----~~~~--~~~~~~l~~~~~~~~~~~~a~~~~~~-~~~~~~~~~~~l~~~~~~~~~  194 (490)
                      .+..+-.+++.+.+|...++.-    .+.+  ..-|-.+...|...+++|.+.-+... ...++   ...-+......|+
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---LYQQILEHEASGN 1464 (2382)
T ss_pred             HHHHHHHhhHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHhcCCcchhhhHHHHhhcCcc---HHHHHHHHHhhcc
Confidence            3444567889999999999983    2222  23455566699999999998888874 32332   2334455677899


Q ss_pred             hhHHHHHHhhcCC--CC-HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHH-HHHHHHhccCChHHHHHHHHH
Q 011249          195 VREAKKVFDEISE--PD-ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMV-GAISACTQLGDVEMAAILAKH  270 (490)
Q Consensus       195 ~~~A~~~~~~~~~--~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~-~l~~~~~~~g~~~~a~~~~~~  270 (490)
                      +..|...|+.+.+  |+ ..+++-++......|.++..+-..+-..... .+....++ .=+.+-=+.++++..+.... 
T Consensus      1465 ~~da~~Cye~~~q~~p~~~~~~~g~l~sml~~~~l~t~i~~~dg~~~~~-se~~~~~~s~~~eaaW~l~qwD~~e~~l~- 1542 (2382)
T KOG0890|consen 1465 WADAAACYERLIQKDPDKEKHHSGVLKSMLAIQHLSTEILHLDGLIINR-SEEVDELNSLGVEAAWRLSQWDLLESYLS- 1542 (2382)
T ss_pred             HHHHHHHHHHhhcCCCccccchhhHHHhhhcccchhHHHhhhcchhhcc-CHHHHHHHHHHHHHHhhhcchhhhhhhhh-
Confidence            9999999999987  33 5678888888888888887776555544321 22222222 22233345667776666544 


Q ss_pred             HHhcCCCCchhHHHH--HHHHHHhcCChHH--HHHHHhcccC----C-------C--hhHHHHHHHHHHhcCChHHHHHH
Q 011249          271 VDEGCCDRTNYVSNA--LIHMHSKCGYLDL--AWREFSRIKN----K-------D--VISYSSMITAFADHGKSQEALDM  333 (490)
Q Consensus       271 ~~~~~~~~~~~~~~~--l~~~~~~~~~~~~--A~~~~~~~~~----~-------~--~~~~~~l~~~~~~~~~~~~a~~~  333 (490)
                        ..+    ..+|..  ++....+..+-+.  -.+..+.+.+    +       .  ...|..++....-..-    ...
T Consensus      1543 --~~n----~e~w~~~~~g~~ll~~~~kD~~~~~~~i~~~r~~~i~~lsa~s~~~Sy~~~Y~~~~kLH~l~el----~~~ 1612 (2382)
T KOG0890|consen 1543 --DRN----IEYWSVESIGKLLLRNKKKDEIATLDLIENSRELVIENLSACSIEGSYVRSYEILMKLHLLLEL----ENS 1612 (2382)
T ss_pred             --ccc----ccchhHHHHHHHHHhhcccchhhHHHHHHHHHHHhhhhHHHhhccchHHHHHHHHHHHHHHHHH----HHH
Confidence              111    111111  2222221111110  0011111110    0       0  1233333332221110    000


Q ss_pred             HHHHHHcCCCCcHH------HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCC-----CchHHHHHHHHHhhcCChHHHH
Q 011249          334 FLKMRNEGIEPNQV------TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKP-----LTEHLTCMVDLLGRSGQLEKAH  402 (490)
Q Consensus       334 ~~~~~~~~~~p~~~------~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~-----~~~~~~~l~~~~~~~g~~~~A~  402 (490)
                      .+..  .+..++..      -|..-+..-....+..+-+--+++..-.....|     ...+|...++.....|+++.|.
T Consensus      1613 ~~~l--~~~s~~~~s~~~sd~W~~Rl~~tq~s~~~~epILa~RRs~l~~~~~~~~~~~~ge~wLqsAriaR~aG~~q~A~ 1690 (2382)
T KOG0890|consen 1613 IEEL--KKVSYDEDSANNSDNWKNRLERTQPSFRIKEPILAFRRSMLDLRMRSNLKSRLGECWLQSARIARLAGHLQRAQ 1690 (2382)
T ss_pred             HHHh--hccCccccccccchhHHHHHHHhchhHHHHhHHHHHHHHHHHHhccccccchhHHHHHHHHHHHHhcccHHHHH
Confidence            1100  11222221      111122111111112222222222211111122     2556777777777899999998


Q ss_pred             HHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC
Q 011249          403 SLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELG  444 (490)
Q Consensus       403 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  444 (490)
                      ..+-......-+..+...+.-....|+...|+.++++.++..
T Consensus      1691 nall~A~e~r~~~i~~E~AK~lW~~gd~~~Al~~Lq~~l~~~ 1732 (2382)
T KOG0890|consen 1691 NALLNAKESRLPEIVLERAKLLWQTGDELNALSVLQEILSKN 1732 (2382)
T ss_pred             HHHHhhhhcccchHHHHHHHHHHhhccHHHHHHHHHHHHHhh
Confidence            876554423345566666777788999999999999988643

>KOG0545 consensus Aryl-hydrocarbon receptor-interacting protein [Posttranslational modification, protein turnover, chaperones]

Probab=91.44  E-value=1.1  Score=37.82  Aligned_cols=56  Identities=9%  Similarity=-0.139  Sum_probs=31.0

Q ss_pred             HHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          422 GACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       422 ~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      ..+...|++-++++....++...|.+..+|..-+.+....=+.++|..-|.+..+.
T Consensus       238 QC~L~~~e~yevleh~seiL~~~~~nvKA~frRakAhaa~Wn~~eA~~D~~~vL~l  293 (329)
T KOG0545|consen  238 QCLLKKEEYYEVLEHCSEILRHHPGNVKAYFRRAKAHAAVWNEAEAKADLQKVLEL  293 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHhhcCHHHHHHHHHHHHhc
Confidence            33445555555666555666666666665555555555555555555555555443

>KOG1586 consensus Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.37  E-value=8.1  Score=32.71  Aligned_cols=57  Identities=19%  Similarity=0.114  Sum_probs=29.2

Q ss_pred             hhcCChHHHHHHHHhcc---CCC-----ChhhHHHHHHHH-hhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          393 GRSGQLEKAHSLIMDYK---DFC-----DAGTWGALLGAC-KVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       393 ~~~g~~~~A~~~~~~~~---~~~-----~~~~~~~l~~~~-~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                      ...|++.+|+++|+++.   ...     ...-|---...| ....|.-.+...+++..+.+|....
T Consensus       165 a~leqY~~Ai~iyeqva~~s~~n~LLKys~KdyflkAgLChl~~~D~v~a~~ALeky~~~dP~F~d  230 (288)
T KOG1586|consen  165 AQLEQYSKAIDIYEQVARSSLDNNLLKYSAKDYFLKAGLCHLCKADEVNAQRALEKYQELDPAFTD  230 (288)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccchHHHhHHHHHHHHHHHHhHhcccHHHHHHHHHHHHhcCCcccc
Confidence            45667777777776654   011     111111111122 2235666677777777777776443

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=91.35  E-value=14  Score=35.31  Aligned_cols=159  Identities=10%  Similarity=0.058  Sum_probs=74.7

Q ss_pred             ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHH
Q 011249          244 SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITA  320 (490)
Q Consensus       244 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~  320 (490)
                      |.....+++..+.+...+.-.+.+..++...|  .+-..+..++..|... ..++-..+++++.+   .|++.-..|+.-
T Consensus        65 ~d~~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~dfnDvv~~ReLa~~  141 (711)
T COG1747          65 DDSCLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEYDFNDVVIGRELADK  141 (711)
T ss_pred             cchHHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcchhHHHHHHHHHH
Confidence            33444455555555555555555555555543  2334444555555554 33444444544443   222222333333


Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCCcH------HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh
Q 011249          321 FADHGKSQEALDMFLKMRNEGIEPNQ------VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR  394 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~~~p~~------~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  394 (490)
                      |-+ ++.+.+..+|.++... +.|..      ..|..+...  -..+.+....+..++....|...-...+..+-.-|..
T Consensus       142 yEk-ik~sk~a~~f~Ka~yr-fI~~~q~~~i~evWeKL~~~--i~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv~~~Ys~  217 (711)
T COG1747         142 YEK-IKKSKAAEFFGKALYR-FIPRRQNAAIKEVWEKLPEL--IGDDKDFFLRLQKKIQTKLGEGRGSVLMQDVYKKYSE  217 (711)
T ss_pred             HHH-hchhhHHHHHHHHHHH-hcchhhhhhHHHHHHHHHHh--ccccHHHHHHHHHHHHHhhccchHHHHHHHHHHHhcc
Confidence            332 5555555555555443 22210      123333221  1344555555555555554444444445555556666


Q ss_pred             cCChHHHHHHHHhcc
Q 011249          395 SGQLEKAHSLIMDYK  409 (490)
Q Consensus       395 ~g~~~~A~~~~~~~~  409 (490)
                      ..++.+|++++..+.
T Consensus       218 ~eN~~eai~Ilk~il  232 (711)
T COG1747         218 NENWTEAIRILKHIL  232 (711)
T ss_pred             ccCHHHHHHHHHHHh
Confidence            666666666666554

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=91.34  E-value=2.2  Score=33.15  Aligned_cols=99  Identities=12%  Similarity=0.023  Sum_probs=58.9

Q ss_pred             CcHHHHHHHHHH---hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCC-ChhhHHH
Q 011249          344 PNQVTFIGVLTA---CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFC-DAGTWGA  419 (490)
Q Consensus       344 p~~~~~~~l~~~---~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~  419 (490)
                      -+....+.|+..   -...++.+++..+++.+.--..-.+...++  -...+...|++++|.++|+.+.... ....-..
T Consensus         5 Cs~~iv~gLi~~~~~aL~~~d~~D~e~lLdALrvLrP~~~e~d~~--dg~l~i~rg~w~eA~rvlr~l~~~~~~~p~~kA   82 (153)
T TIGR02561         5 CSNRLLGGLIEVLMYALRSADPYDAQAMLDALRVLRPNLKELDMF--DGWLLIARGNYDEAARILRELLSSAGAPPYGKA   82 (153)
T ss_pred             CcHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCCccccchh--HHHHHHHcCCHHHHHHHHHhhhccCCCchHHHH
Confidence            344455555554   346889999999999997532222334444  3455788999999999999998443 4344445


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcC
Q 011249          420 LLGACKVHVNAELGEIAARHLLELG  444 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~  444 (490)
                      |+..|.....-..=...-.++++.+
T Consensus        83 L~A~CL~al~Dp~Wr~~A~~~le~~  107 (153)
T TIGR02561        83 LLALCLNAKGDAEWHVHADEVLARD  107 (153)
T ss_pred             HHHHHHHhcCChHHHHHHHHHHHhC
Confidence            5555544332222333334444443

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=91.27  E-value=9.1  Score=33.10  Aligned_cols=218  Identities=13%  Similarity=0.127  Sum_probs=102.6

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHH---cCc--ccChhhHHHHHHHHhccCChHHHHHHHHHHHhc-CCCCch----hHHH
Q 011249          215 AMTVCYVQNGYAKAAIEMYKVMRQ---ENV--RISEVAMVGAISACTQLGDVEMAAILAKHVDEG-CCDRTN----YVSN  284 (490)
Q Consensus       215 ~l~~~~~~~g~~~~A~~~~~~~~~---~~~--~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-~~~~~~----~~~~  284 (490)
                      .++....+.|++++.++.|.++..   ..+  .-+....+.++.......+.+-...+|+.-.+. .-..+.    .+-.
T Consensus        70 QmiKI~f~l~~~~eMm~~Y~qlLTYIkSAVTrNySEKsIN~IlDyiStS~~m~LLQ~FYeTTL~ALkdAKNeRLWFKTNt  149 (440)
T KOG1464|consen   70 QMIKINFRLGNYKEMMERYKQLLTYIKSAVTRNYSEKSINSILDYISTSKNMDLLQEFYETTLDALKDAKNERLWFKTNT  149 (440)
T ss_pred             HHHHHHhccccHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHhhhcceeeeeccc
Confidence            445555666666666666555542   111  112334445555444444444333333322110 000010    1123


Q ss_pred             HHHHHHHhcCChHHHHHHHhcccC------------C---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHc-CCCCcHHH
Q 011249          285 ALIHMHSKCGYLDLAWREFSRIKN------------K---DVISYSSMITAFADHGKSQEALDMFLKMRNE-GIEPNQVT  348 (490)
Q Consensus       285 ~l~~~~~~~~~~~~A~~~~~~~~~------------~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~p~~~~  348 (490)
                      -|...|...+++.+..++++++..            +   -...|..-|+.|...++-.+-..+|++...- ...|.+..
T Consensus       150 KLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAlEIQmYT~qKnNKkLK~lYeqalhiKSAIPHPlI  229 (440)
T KOG1464|consen  150 KLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYALEIQMYTEQKNNKKLKALYEQALHIKSAIPHPLI  229 (440)
T ss_pred             hHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhhHhhhhhhhcccHHHHHHHHHHHHhhccCCchHH
Confidence            355666666666666666665542            0   1245666777787777777777777776642 23454444


Q ss_pred             HHHHHHH-----hcCCCChHHHHHHHHHHHHHc---CCCCCch--HHHHHHHHHhhcC----ChHHHHHHHHhccCCCCh
Q 011249          349 FIGVLTA-----CSHGGLVEDGCKQFELMTRVF---GIKPLTE--HLTCMVDLLGRSG----QLEKAHSLIMDYKDFCDA  414 (490)
Q Consensus       349 ~~~l~~~-----~~~~g~~~~a~~~~~~~~~~~---~~~~~~~--~~~~l~~~~~~~g----~~~~A~~~~~~~~~~~~~  414 (490)
                      ... ++-     ..+.|++++|..-|-++.+.+   |.+....  -|..|..++.+.|    +.++|.-    ....|..
T Consensus       230 mGv-IRECGGKMHlreg~fe~AhTDFFEAFKNYDEsGspRRttCLKYLVLANMLmkS~iNPFDsQEAKP----yKNdPEI  304 (440)
T KOG1464|consen  230 MGV-IRECGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAKP----YKNDPEI  304 (440)
T ss_pred             HhH-HHHcCCccccccchHHHHHhHHHHHHhcccccCCcchhHHHHHHHHHHHHHHcCCCCCcccccCC----CCCCHHH
Confidence            433 333     345677777765544444422   2221122  1334445555544    1112110    1123444


Q ss_pred             hhHHHHHHHHhhhCChHHHHHHHH
Q 011249          415 GTWGALLGACKVHVNAELGEIAAR  438 (490)
Q Consensus       415 ~~~~~l~~~~~~~g~~~~a~~~~~  438 (490)
                      .....++.+|.. ++..+-++++.
T Consensus       305 lAMTnlv~aYQ~-NdI~eFE~Il~  327 (440)
T KOG1464|consen  305 LAMTNLVAAYQN-NDIIEFERILK  327 (440)
T ss_pred             HHHHHHHHHHhc-ccHHHHHHHHH
Confidence            556666666643 34444444443

>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=91.25  E-value=4.8  Score=33.25  Aligned_cols=76  Identities=20%  Similarity=0.142  Sum_probs=55.3

Q ss_pred             HHhhcCChHHHHHHHHhccCCC---ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC-C---CCCchHHHHHHHHHhcCC
Q 011249          391 LLGRSGQLEKAHSLIMDYKDFC---DAGTWGALLGACKVHVNAELGEIAARHLLELG-P---EKTGNSALLANIYASMGK  463 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~~~~~~---~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-p---~~~~~~~~l~~~~~~~g~  463 (490)
                      .+.+.|+ ++|.+.|-++...|   ++.....|+ .|....|.++++.++-++++.. |   -|+..+..|+.++.+.|+
T Consensus       116 ~Wsr~~d-~~A~~~fL~~E~~~~l~t~elq~aLA-tyY~krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~  193 (203)
T PF11207_consen  116 HWSRFGD-QEALRRFLQLEGTPELETAELQYALA-TYYTKRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKN  193 (203)
T ss_pred             HhhccCc-HHHHHHHHHHcCCCCCCCHHHHHHHH-HHHHccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcc
Confidence            3455566 67777777766333   334444444 4555779999999999999865 2   268899999999999999


Q ss_pred             cchHH
Q 011249          464 WKDSE  468 (490)
Q Consensus       464 ~~~A~  468 (490)
                      ++.|-
T Consensus       194 ~e~AY  198 (203)
T PF11207_consen  194 YEQAY  198 (203)
T ss_pred             hhhhh
Confidence            98874

>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=91.08  E-value=0.57  Score=29.18  Aligned_cols=35  Identities=20%  Similarity=0.104  Sum_probs=27.3

Q ss_pred             HHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHH
Q 011249          419 ALLGACKVHVNAELGEIAARHLLELGPEKTGNSAL  453 (490)
Q Consensus       419 ~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~  453 (490)
                      .+..++.+.|++++|.+..+.+++.+|+|..+...
T Consensus         6 ~lAig~ykl~~Y~~A~~~~~~lL~~eP~N~Qa~~L   40 (53)
T PF14853_consen    6 YLAIGHYKLGEYEKARRYCDALLEIEPDNRQAQSL   40 (53)
T ss_dssp             HHHHHHHHTT-HHHHHHHHHHHHHHTTS-HHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHhhCCCcHHHHHH
Confidence            45567899999999999999999999998765443

>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=91.06  E-value=0.25  Score=25.36  Aligned_cols=24  Identities=17%  Similarity=0.093  Sum_probs=16.7

Q ss_pred             chHHHHHHHHHhcCCcchHHHHHH
Q 011249          449 GNSALLANIYASMGKWKDSEIVKM  472 (490)
Q Consensus       449 ~~~~~l~~~~~~~g~~~~A~~~~~  472 (490)
                      .....++.++...|++++|..+++
T Consensus         2 ~a~~~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    2 RARLALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHh
Confidence            345667777777777777777664

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

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=90.95  E-value=21  Score=36.67  Aligned_cols=217  Identities=10%  Similarity=-0.055  Sum_probs=120.8

Q ss_pred             HHhccCChHHHHHHHHHHHhcCCCCchh-------HHHHHH-HHHHhcCChHHHHHHHhcccC--------CChhHHHHH
Q 011249          254 ACTQLGDVEMAAILAKHVDEGCCDRTNY-------VSNALI-HMHSKCGYLDLAWREFSRIKN--------KDVISYSSM  317 (490)
Q Consensus       254 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~-------~~~~l~-~~~~~~~~~~~A~~~~~~~~~--------~~~~~~~~l  317 (490)
                      ......++++|..+..++...-..|+..       .++++- .+....|+++.|.++.+....        .....+..+
T Consensus       424 ~~~s~~r~~ea~~li~~l~~~l~~~~~~~~~~l~ae~~aL~a~val~~~~~e~a~~lar~al~~L~~~~~~~r~~~~sv~  503 (894)
T COG2909         424 LLASQHRLAEAETLIARLEHFLKAPMHSRQGDLLAEFQALRAQVALNRGDPEEAEDLARLALVQLPEAAYRSRIVALSVL  503 (894)
T ss_pred             HHHHccChHHHHHHHHHHHHHhCcCcccchhhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhcccccchhhhhhhhhh
Confidence            3456788999999888876543233221       223221 233456888888887766543        356677788


Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCCCCcHHH---HHHHHH--HhcCCCC--hHHHHHHHHHHHHHcCCCCC-----chHH
Q 011249          318 ITAFADHGKSQEALDMFLKMRNEGIEPNQVT---FIGVLT--ACSHGGL--VEDGCKQFELMTRVFGIKPL-----TEHL  385 (490)
Q Consensus       318 ~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~---~~~l~~--~~~~~g~--~~~a~~~~~~~~~~~~~~~~-----~~~~  385 (490)
                      ..+..-.|++++|..+.+...+..-.-+...   +..+..  .+..+|.  .++....+......+.....     ..++
T Consensus       504 ~~a~~~~G~~~~Al~~~~~a~~~a~~~~~~~l~~~~~~~~s~il~~qGq~~~a~~~~~~~~~~~q~l~q~~~~~f~~~~r  583 (894)
T COG2909         504 GEAAHIRGELTQALALMQQAEQMARQHDVYHLALWSLLQQSEILEAQGQVARAEQEKAFNLIREQHLEQKPRHEFLVRIR  583 (894)
T ss_pred             hHHHHHhchHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccchhHHHHH
Confidence            8888889999999988887765322233332   233322  3566773  33344444444443222222     2333


Q ss_pred             HHHHHHHhhcCChHHHHHHHHhc----c-CCCCh--h--hHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC--CchHHH-
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDY----K-DFCDA--G--TWGALLGACKVHVNAELGEIAARHLLELGPEK--TGNSAL-  453 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~----~-~~~~~--~--~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~--~~~~~~-  453 (490)
                      ..+..++.+   ++.+..-....    . ..|.+  .  .+..++......|+.++|...++++.....++  ...|.. 
T Consensus       584 ~~ll~~~~r---~~~~~~ear~~~~~~~~~~~~~~~~~~~~~~LA~l~~~~Gdl~~A~~~l~~~~~l~~~~~~~~~~~a~  660 (894)
T COG2909         584 AQLLRAWLR---LDLAEAEARLGIEVGSVYTPQPLLSRLALSMLAELEFLRGDLDKALAQLDELERLLLNGQYHVDYLAA  660 (894)
T ss_pred             HHHHHHHHH---HhhhhHHhhhcchhhhhcccchhHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCCCCchHHHH
Confidence            444455544   33333322221    1 22222  1  22366777888999999999999888744222  222221 


Q ss_pred             --H--HHHHHhcCCcchHHHHHHH
Q 011249          454 --L--ANIYASMGKWKDSEIVKMM  473 (490)
Q Consensus       454 --l--~~~~~~~g~~~~A~~~~~~  473 (490)
                        .  .......|+...+.....+
T Consensus       661 ~~~v~~~lwl~qg~~~~a~~~l~~  684 (894)
T COG2909         661 AYKVKLILWLAQGDKELAAEWLLK  684 (894)
T ss_pred             HHHhhHHHhcccCCHHHHHHHHHh
Confidence              1  2223456888877776665

>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A

Probab=90.92  E-value=0.25  Score=26.90  Aligned_cols=30  Identities=13%  Similarity=0.102  Sum_probs=26.1

Q ss_pred             hHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          450 NSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       450 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ++..++.++.+.|++++|.+.++++.+.-+
T Consensus         2 a~~~~a~~~~~~g~~~~A~~~~~~~~~~~P   31 (33)
T PF13174_consen    2 ALYRLARCYYKLGDYDEAIEYFQRLIKRYP   31 (33)
T ss_dssp             HHHHHHHHHHHHCHHHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHHCc
Confidence            467889999999999999999999987643

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=90.72  E-value=9.8  Score=36.97  Aligned_cols=152  Identities=16%  Similarity=0.156  Sum_probs=97.0

Q ss_pred             HHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHH
Q 011249          189 YGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILA  268 (490)
Q Consensus       189 ~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~  268 (490)
                      ....|+++.|..++..+.+   ...+.++..+-+.|-.++|+++         .+|+....   ....+.|+++.|.++.
T Consensus       596 ~vmrrd~~~a~~vLp~I~k---~~rt~va~Fle~~g~~e~AL~~---------s~D~d~rF---elal~lgrl~iA~~la  660 (794)
T KOG0276|consen  596 LVLRRDLEVADGVLPTIPK---EIRTKVAHFLESQGMKEQALEL---------STDPDQRF---ELALKLGRLDIAFDLA  660 (794)
T ss_pred             HhhhccccccccccccCch---hhhhhHHhHhhhccchHhhhhc---------CCChhhhh---hhhhhcCcHHHHHHHH
Confidence            3456777777776666653   3345566667777777777664         23332221   2234678888877765


Q ss_pred             HHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHH
Q 011249          269 KHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVT  348 (490)
Q Consensus       269 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~  348 (490)
                      .+.      .+..-|..|.++..+.+++..|.+.|.....     |..|+-.+...|+.+....+-....+.|. .|.  
T Consensus       661 ~e~------~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~d-----~~~LlLl~t~~g~~~~l~~la~~~~~~g~-~N~--  726 (794)
T KOG0276|consen  661 VEA------NSEVKWRQLGDAALSAGELPLASECFLRARD-----LGSLLLLYTSSGNAEGLAVLASLAKKQGK-NNL--  726 (794)
T ss_pred             Hhh------cchHHHHHHHHHHhhcccchhHHHHHHhhcc-----hhhhhhhhhhcCChhHHHHHHHHHHhhcc-cch--
Confidence            543      3456678888888888888888888876543     56667777777777766666666666542 122  


Q ss_pred             HHHHHHHhcCCCChHHHHHHHHHH
Q 011249          349 FIGVLTACSHGGLVEDGCKQFELM  372 (490)
Q Consensus       349 ~~~l~~~~~~~g~~~~a~~~~~~~  372 (490)
                         ...+|...|+++++.+++.+-
T Consensus       727 ---AF~~~~l~g~~~~C~~lLi~t  747 (794)
T KOG0276|consen  727 ---AFLAYFLSGDYEECLELLIST  747 (794)
T ss_pred             ---HHHHHHHcCCHHHHHHHHHhc
Confidence               223345578888888777655

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=90.70  E-value=0.34  Score=26.90  Aligned_cols=24  Identities=17%  Similarity=0.063  Sum_probs=13.8

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHH
Q 011249          277 DRTNYVSNALIHMHSKCGYLDLAW  300 (490)
Q Consensus       277 ~~~~~~~~~l~~~~~~~~~~~~A~  300 (490)
                      |.+...|+.+..+|...|++++|+
T Consensus        10 P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   10 PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            445555666666666666665553

>PRK10941 hypothetical protein; Provisional

Probab=90.40  E-value=1.4  Score=38.72  Aligned_cols=63  Identities=21%  Similarity=0.065  Sum_probs=51.4

Q ss_pred             HHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          417 WGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       417 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .+.+-.+|.+.+++++|.++.+.++...|+++.-+.--+-+|.+.|.+..|..-++...+..+
T Consensus       184 l~nLK~~~~~~~~~~~AL~~~e~ll~l~P~dp~e~RDRGll~~qL~c~~~A~~DL~~fl~~~P  246 (269)
T PRK10941        184 LDTLKAALMEEKQMELALRASEALLQFDPEDPYEIRDRGLIYAQLDCEHVALSDLSYFVEQCP  246 (269)
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHHHhCC
Confidence            355666778888899999999998888898888888888888888888888888877766543

>smart00028 TPR Tetratricopeptide repeats

Probab=90.30  E-value=0.66  Score=24.49  Aligned_cols=30  Identities=20%  Similarity=-0.015  Sum_probs=16.3

Q ss_pred             HHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          417 WGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       417 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      +..+...+...|+++.|...++++++..|.
T Consensus         4 ~~~~a~~~~~~~~~~~a~~~~~~~~~~~~~   33 (34)
T smart00028        4 LYNLGNAYLKLGDYDEALEYYEKALELDPN   33 (34)
T ss_pred             HHHHHHHHHHHhhHHHHHHHHHHHHccCCC
Confidence            344445555555666666666555555543

Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.

>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=90.21  E-value=8.5  Score=30.97  Aligned_cols=41  Identities=5%  Similarity=0.153  Sum_probs=21.9

Q ss_pred             HHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcC
Q 011249           90 LYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMA  144 (490)
Q Consensus        90 ~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  144 (490)
                      .+..+.+.|+.|+...+..++..              +.+.|++..-.+++..-.
T Consensus        16 YirSl~~~~i~~~~~L~~lli~l--------------Li~~~~~~~L~qllq~~V   56 (167)
T PF07035_consen   16 YIRSLNQHNIPVQHELYELLIDL--------------LIRNGQFSQLHQLLQYHV   56 (167)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHH--------------HHHcCCHHHHHHHHhhcc
Confidence            33444455666666666555554              455555555555554333

>KOG1308 consensus Hsp70-interacting protein Hip/Transient component of progesterone receptor complexes and an Hsp70-binding protein [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=89.84  E-value=0.22  Score=44.07  Aligned_cols=59  Identities=7%  Similarity=0.116  Sum_probs=28.9

Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      -.+++.+.+....|++-+..+.+++|+...-|-.-+.+....|+|++|.+.+....+.+
T Consensus       154 r~sv~lkl~kp~~airD~d~A~ein~Dsa~~ykfrg~A~rllg~~e~aa~dl~~a~kld  212 (377)
T KOG1308|consen  154 RASVFLKLKKPNAAIRDCDFAIEINPDSAKGYKFRGYAERLLGNWEEAAHDLALACKLD  212 (377)
T ss_pred             ccceeeeccCCchhhhhhhhhhccCcccccccchhhHHHHHhhchHHHHHHHHHHHhcc
Confidence            33444444455555555555555555554444444444444555555555554444443

>KOG0276 consensus Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.63  E-value=3.5  Score=39.80  Aligned_cols=99  Identities=15%  Similarity=0.195  Sum_probs=47.5

Q ss_pred             HhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCC
Q 011249          128 TKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISE  207 (490)
Q Consensus       128 ~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~  207 (490)
                      .+.|+.+.|.++..+.  .+..-|..|.++....+++..|.+.|.+..     -|..|+-.+...|+.+....+-....+
T Consensus       648 l~lgrl~iA~~la~e~--~s~~Kw~~Lg~~al~~~~l~lA~EC~~~a~-----d~~~LlLl~t~~g~~~~l~~la~~~~~  720 (794)
T KOG0276|consen  648 LKLGRLDIAFDLAVEA--NSEVKWRQLGDAALSAGELPLASECFLRAR-----DLGSLLLLYTSSGNAEGLAVLASLAKK  720 (794)
T ss_pred             hhcCcHHHHHHHHHhh--cchHHHHHHHHHHhhcccchhHHHHHHhhc-----chhhhhhhhhhcCChhHHHHHHHHHHh
Confidence            3446666666654433  344556666666666666666666665543     233344444444444332222222211


Q ss_pred             CCHHhHHHHHHHHHhcCChHHHHHHHHH
Q 011249          208 PDASCWAAMTVCYVQNGYAKAAIEMYKV  235 (490)
Q Consensus       208 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~  235 (490)
                      .  ...|.-.-+|...|+++++.+++.+
T Consensus       721 ~--g~~N~AF~~~~l~g~~~~C~~lLi~  746 (794)
T KOG0276|consen  721 Q--GKNNLAFLAYFLSGDYEECLELLIS  746 (794)
T ss_pred             h--cccchHHHHHHHcCCHHHHHHHHHh
Confidence            0  0112222345556666666555433

>KOG4279 consensus Serine/threonine protein kinase [Signal transduction mechanisms]

Probab=89.18  E-value=6.9  Score=38.98  Aligned_cols=188  Identities=18%  Similarity=0.193  Sum_probs=97.1

Q ss_pred             HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccCh----------hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCc
Q 011249          210 ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISE----------VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRT  279 (490)
Q Consensus       210 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~----------~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~  279 (490)
                      +.+...++-.|....+++..+++.+.+++.   ||.          ..|...++--.+-|+-++|....-.+.+..-+..
T Consensus       201 ~d~V~nlmlSyRDvQdY~amirLVe~Lk~i---P~t~~vve~~nv~f~YaFALNRRNr~GDRakAL~~~l~lve~eg~va  277 (1226)
T KOG4279|consen  201 PDTVSNLMLSYRDVQDYDAMIRLVEDLKRI---PDTLKVVETHNVRFHYAFALNRRNRPGDRAKALNTVLPLVEKEGPVA  277 (1226)
T ss_pred             HHHHHHHHhhhccccchHHHHHHHHHHHhC---cchhhhhccCceEEEeeehhcccCCCccHHHHHHHHHHHHHhcCCCC
Confidence            445556667777778888888888777653   222          1233333333455777777766665554432333


Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHH---HHHHHHHh
Q 011249          280 NYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVT---FIGVLTAC  356 (490)
Q Consensus       280 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~---~~~l~~~~  356 (490)
                      +..|       +-+|++      |++|-         +.+.|...+..+.|.+.|++..+  +.|+...   +..|+.+-
T Consensus       278 pDm~-------Cl~GRI------YKDmF---------~~S~ytDa~s~~~a~~WyrkaFe--veP~~~sGIN~atLL~aa  333 (1226)
T KOG4279|consen  278 PDMY-------CLCGRI------YKDMF---------IASNYTDAESLNHAIEWYRKAFE--VEPLEYSGINLATLLRAA  333 (1226)
T ss_pred             Ccee-------eeechh------hhhhh---------hccCCcchhhHHHHHHHHHHHhc--cCchhhccccHHHHHHHh
Confidence            3222       222221      22111         11123444556777778887776  5665542   33333221


Q ss_pred             cCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHH
Q 011249          357 SHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIA  436 (490)
Q Consensus       357 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~  436 (490)
                        ...++...++- .+    |        -.|-..+++.|..++-.++++-..          .+.+-.-.+|+.+|++.
T Consensus       334 --G~~Fens~Elq-~I----g--------mkLn~LlgrKG~leklq~YWdV~~----------y~~asVLAnd~~kaiqA  388 (1226)
T KOG4279|consen  334 --GEHFENSLELQ-QI----G--------MKLNSLLGRKGALEKLQEYWDVAT----------YFEASVLANDYQKAIQA  388 (1226)
T ss_pred             --hhhccchHHHH-HH----H--------HHHHHHhhccchHHHHHHHHhHHH----------hhhhhhhccCHHHHHHH
Confidence              11222222111 11    1        113344567777777766665433          23344456778888888


Q ss_pred             HHHHHhcCCCCCc
Q 011249          437 ARHLLELGPEKTG  449 (490)
Q Consensus       437 ~~~~~~~~p~~~~  449 (490)
                      .+.+.++.|..-.
T Consensus       389 ae~mfKLk~P~WY  401 (1226)
T KOG4279|consen  389 AEMMFKLKPPVWY  401 (1226)
T ss_pred             HHHHhccCCceeh
Confidence            8888887766433

>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=88.97  E-value=0.5  Score=25.99  Aligned_cols=31  Identities=16%  Similarity=0.158  Sum_probs=26.9

Q ss_pred             chHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          449 GNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       449 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .+|..++.+|...|++++|.+.|++..+...
T Consensus         2 ~~~~~lg~~y~~~~~~~~A~~~~~~a~~~~~   32 (34)
T PF13181_consen    2 EAYYNLGKIYEQLGDYEEALEYFEKALELNP   32 (34)
T ss_dssp             HHHHHHHHHHHHTTSHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            4688899999999999999999999877543

...

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=88.87  E-value=0.55  Score=27.24  Aligned_cols=29  Identities=21%  Similarity=0.233  Sum_probs=24.8

Q ss_pred             chHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          449 GNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       449 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      .++..|+.+|...|++++|..++++..+.
T Consensus         3 ~~~~~la~~~~~~g~~~~A~~~~~~al~~   31 (42)
T PF13374_consen    3 SALNNLANAYRAQGRYEEALELLEEALEI   31 (42)
T ss_dssp             HHHHHHHHHHHHCT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcchhhHHHHHHHHH
Confidence            46789999999999999999999988664

>COG4455 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]

Probab=88.54  E-value=1.5  Score=36.40  Aligned_cols=73  Identities=22%  Similarity=0.073  Sum_probs=52.1

Q ss_pred             HHHHHHHHhhcCChHHHHHHHH-hccCCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC---chHHHHHHH
Q 011249          385 LTCMVDLLGRSGQLEKAHSLIM-DYKDFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT---GNSALLANI  457 (490)
Q Consensus       385 ~~~l~~~~~~~g~~~~A~~~~~-~~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~---~~~~~l~~~  457 (490)
                      .+.-+..+.+.+.+++++...+ +++.+| +...-..++..++-.|++++|..-++-+-++.|++.   ..|..++.+
T Consensus         4 l~~t~seLL~~~sL~dai~~a~~qVkakPtda~~RhflfqLlcvaGdw~kAl~Ql~l~a~l~p~~t~~a~lyr~lir~   81 (273)
T COG4455           4 LRDTISELLDDNSLQDAIGLARDQVKAKPTDAGGRHFLFQLLCVAGDWEKALAQLNLAATLSPQDTVGASLYRHLIRC   81 (273)
T ss_pred             hHHHHHHHHHhccHHHHHHHHHHHHhcCCccccchhHHHHHHhhcchHHHHHHHHHHHhhcCcccchHHHHHHHHHHH
Confidence            3445667778888899988874 444445 445666777888889999999998888888888753   345555433

>PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional

Probab=87.99  E-value=4.3  Score=38.05  Aligned_cols=153  Identities=14%  Similarity=0.066  Sum_probs=92.4

Q ss_pred             HHHHHhcCChHHHHH-HHhcccC--CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChH
Q 011249          287 IHMHSKCGYLDLAWR-EFSRIKN--KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVE  363 (490)
Q Consensus       287 ~~~~~~~~~~~~A~~-~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  363 (490)
                      |.-....|++-.|-+ ++..+..  .++.........+...|+++.+...+...... +.....+..++++.....|+++
T Consensus       296 i~k~~~~gd~~aas~~~~~~lr~~~~~p~~i~l~~~i~~~lg~ye~~~~~~s~~~~~-~~s~~~~~~~~~r~~~~l~r~~  374 (831)
T PRK15180        296 ITKQLADGDIIAASQQLFAALRNQQQDPVLIQLRSVIFSHLGYYEQAYQDISDVEKI-IGTTDSTLRCRLRSLHGLARWR  374 (831)
T ss_pred             HHHHhhccCHHHHHHHHHHHHHhCCCCchhhHHHHHHHHHhhhHHHHHHHhhchhhh-hcCCchHHHHHHHhhhchhhHH
Confidence            333445577666644 4443333  23333333344567789999999988876553 4456678888999999999999


Q ss_pred             HHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHH
Q 011249          364 DGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLL  441 (490)
Q Consensus       364 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  441 (490)
                      +|...-..|... .+ .+++........--..|-++++...++++.  .+|....|...+..-.-.++...-.+.|..-.
T Consensus       375 ~a~s~a~~~l~~-ei-e~~ei~~iaa~sa~~l~~~d~~~~~wk~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~  452 (831)
T PRK15180        375 EALSTAEMMLSN-EI-EDEEVLTVAAGSADALQLFDKSYHYWKRVLLLNPETQSGWVNFLSSTQYFNDGNAFSEAFHAGI  452 (831)
T ss_pred             HHHHHHHHHhcc-cc-CChhheeeecccHHHHhHHHHHHHHHHHHhccCChhcccceeeeccceeccCcchHHHHHHhhh
Confidence            999988888763 22 233333333333445678899998888776  45555566555544322233333334444444


Q ss_pred             h
Q 011249          442 E  442 (490)
Q Consensus       442 ~  442 (490)
                      +
T Consensus       453 ~  453 (831)
T PRK15180        453 Q  453 (831)
T ss_pred             h
Confidence            3

>KOG2396 consensus HAT (Half-A-TPR) repeat-containing protein [General function prediction only]

Probab=87.72  E-value=26  Score=33.42  Aligned_cols=271  Identities=11%  Similarity=0.054  Sum_probs=0.0

Q ss_pred             HHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccC--CchhHHHHHHHHHhcCChhHHHHHHhhcCC----
Q 011249          134 DDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEK--NSVTWVAMIAGYGKCGEVREAKKVFDEISE----  207 (490)
Q Consensus       134 ~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----  207 (490)
                      +.|.+.++-..+.+...+...-.........+....+|++..++  +...|+..|..|...-....-..+...+.-    
T Consensus       268 ~laqr~l~i~~~tdl~~~~~~~~~~~~~~k~s~~~~v~ee~v~~l~t~sm~e~YI~~~lE~~~~~r~~~I~h~~~~~~~~  347 (568)
T KOG2396|consen  268 DLAQRELEILSQTDLQHTDNQAKAVEVGSKESRCCAVYEEAVKTLPTESMWECYITFCLERFTFLRGKRILHTMCVFRKA  347 (568)
T ss_pred             HHHHHHHHHHHHhhccchhhhhhchhcchhHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH


Q ss_pred             -----CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhcc--CChHHHHHHHHHHHhcCCCCch
Q 011249          208 -----PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQL--GDVEMAAILAKHVDEGCCDRTN  280 (490)
Q Consensus       208 -----~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~--g~~~~a~~~~~~~~~~~~~~~~  280 (490)
                           .....+......+.......++...-..+...++.-+...+..-+......  .---.-..++..+...-..+..
T Consensus       348 ~~~~~l~~~~~~~ys~~~l~~~t~~~~r~~a~~l~~e~f~~s~k~~~~kl~~~~~s~sD~q~~f~~l~n~~r~~~~s~~~  427 (568)
T KOG2396|consen  348 HELKLLSECLYKQYSVLLLCLNTLNEAREVAVKLTTELFRDSGKMWQLKLQVLIESKSDFQMLFEELFNHLRKQVCSELL  427 (568)
T ss_pred             HHhcccccchHHHHHHHHHHHhccchHhHHHHHhhHHHhcchHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHhcchhH


Q ss_pred             hHHHHHH-HHHHhcCChHHHHHHHhcccCCChhHH-HHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH---
Q 011249          281 YVSNALI-HMHSKCGYLDLAWREFSRIKNKDVISY-SSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTA---  355 (490)
Q Consensus       281 ~~~~~l~-~~~~~~~~~~~A~~~~~~~~~~~~~~~-~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~---  355 (490)
                      ..++... ..+......+.....+..+..++..++ +..+.-+.+.|-..+|...+..+... .+|+...|..+++.   
T Consensus       428 ~~w~s~~~~dsl~~~~~~~Ii~a~~s~~~~~~~tl~s~~l~~~~e~~~~~~ark~y~~l~~l-pp~sl~l~r~miq~e~~  506 (568)
T KOG2396|consen  428 ISWASASEGDSLQEDTLDLIISALLSVIGADSVTLKSKYLDWAYESGGYKKARKVYKSLQEL-PPFSLDLFRKMIQFEKE  506 (568)
T ss_pred             HHHHHHhhccchhHHHHHHHHHHHHHhcCCceeehhHHHHHHHHHhcchHHHHHHHHHHHhC-CCccHHHHHHHHHHHhh


Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhc
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDY  408 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  408 (490)
                      ....| ..-+..+++.+...+|  .++..|...+..-...|+.+.+-.++.+.
T Consensus       507 ~~sc~-l~~~r~~yd~a~~~fg--~d~~lw~~y~~~e~~~g~~en~~~~~~ra  556 (568)
T KOG2396|consen  507 QESCN-LANIREYYDRALREFG--ADSDLWMDYMKEELPLGRPENCGQIYWRA  556 (568)
T ss_pred             HhhcC-chHHHHHHHHHHHHhC--CChHHHHHHHHhhccCCCcccccHHHHHH

>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

Probab=87.63  E-value=19  Score=31.60  Aligned_cols=48  Identities=15%  Similarity=0.183  Sum_probs=26.2

Q ss_pred             HHHHHhCCChHHHHHHHHHhccC-----------CchhHHHHHHHHHhcCChhHHHHHH
Q 011249          155 VAGYANCGNMKAAKEFYDRMTEK-----------NSVTWVAMIAGYGKCGEVREAKKVF  202 (490)
Q Consensus       155 ~~~~~~~~~~~~a~~~~~~~~~~-----------~~~~~~~l~~~~~~~~~~~~A~~~~  202 (490)
                      .+-..+.+++++|+..|.++...           ...+...+...|...|+...--++.
T Consensus        10 a~~~v~~~~~~~ai~~yk~iL~kg~s~dek~~nEqE~tvlel~~lyv~~g~~~~l~~~i   68 (421)
T COG5159          10 ANNAVKSNDIEKAIGEYKRILGKGVSKDEKTLNEQEATVLELFKLYVSKGDYCSLGDTI   68 (421)
T ss_pred             HHHhhhhhhHHHHHHHHHHHhcCCCChhhhhhhHHHHHHHHHHHHHHhcCCcchHHHHH
Confidence            34445556666666666666532           1234455666666666665544444

>PRK12798 chemotaxis protein; Reviewed

Probab=87.59  E-value=24  Score=32.90  Aligned_cols=184  Identities=14%  Similarity=0.119  Sum_probs=112.5

Q ss_pred             cCChHHHHHHHhcccC----CChhHHHHHHHH-HHhcCChHHHHHHHHHHHHcCCCCcH----HHHHHHHHHhcCCCChH
Q 011249          293 CGYLDLAWREFSRIKN----KDVISYSSMITA-FADHGKSQEALDMFLKMRNEGIEPNQ----VTFIGVLTACSHGGLVE  363 (490)
Q Consensus       293 ~~~~~~A~~~~~~~~~----~~~~~~~~l~~~-~~~~~~~~~a~~~~~~~~~~~~~p~~----~~~~~l~~~~~~~g~~~  363 (490)
                      .|+.+++.+.+..+..    +....|-.|+.+ .....++.+|+++|+...-  ..|..    .....-+......|+.+
T Consensus       125 ~Gr~~~a~~~La~i~~~~l~~~lg~~laLv~a~l~~~~dP~~Al~~lD~aRL--laPGTLvEEAALRRsi~la~~~g~~~  202 (421)
T PRK12798        125 SGRGREARKLLAGVAPEYLPAELGAYLALVQGNLMVATDPATALKLLDQARL--LAPGTLVEEAALRRSLFIAAQLGDAD  202 (421)
T ss_pred             cCCHHHHHHHhhcCChhhcCchhhhHHHHHHHHHhcccCHHHHHHHHHHHHH--hCCchHHHHHHHHHhhHHHHhcCcHH
Confidence            4777777777777664    234455566554 3445678888888888765  34533    23444455567888888


Q ss_pred             HHHHHHHHHHHHcCCCCCchHHHH-HHHHHhhc---CChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHH
Q 011249          364 DGCKQFELMTRVFGIKPLTEHLTC-MVDLLGRS---GQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARH  439 (490)
Q Consensus       364 ~a~~~~~~~~~~~~~~~~~~~~~~-l~~~~~~~---g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  439 (490)
                      ++..+-......|...|-...|.. +...+.+.   -..+.-..++..|...-....|..+...-...|+.+.|.-.-++
T Consensus       203 rf~~la~~Y~rRF~~S~YA~~F~~~F~~~~~~~~d~~~~~~l~~~ls~~d~~~q~~lYL~iAR~Ali~Gk~~lA~~As~~  282 (421)
T PRK12798        203 KFEALARNYLRRFRHSPYASQFAQRFVDLVVRLDDEIRDARLVEILSFMDPERQRELYLRIARAALIDGKTELARFASER  282 (421)
T ss_pred             HHHHHHHHHHHHhccCchHHHHHHHHHHHHHhccccccHHHHHHHHHhcCchhHHHHHHHHHHHHHHcCcHHHHHHHHHH
Confidence            888877777776565555444432 22333333   23444555556665333456888888888889999999999999


Q ss_pred             HHhcCCCCCchHHHHHHHH-----HhcCCcchHHHHHHHhhhccc
Q 011249          440 LLELGPEKTGNSALLANIY-----ASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       440 ~~~~~p~~~~~~~~l~~~~-----~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +..+... ...-...+..|     .-..+.+++.+.+..+....+
T Consensus       283 A~~L~~~-~~~~~~ra~LY~aaa~v~s~~~~~al~~L~~I~~~~L  326 (421)
T PRK12798        283 ALKLADP-DSADAARARLYRGAALVASDDAESALEELSQIDRDKL  326 (421)
T ss_pred             HHHhccC-CCcchHHHHHHHHHHccCcccHHHHHHHHhcCChhhC
Confidence            8886633 22222222222     234557777777776654433

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.59  E-value=6.5  Score=34.79  Aligned_cols=95  Identities=14%  Similarity=0.133  Sum_probs=60.9

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHhcccC-C--------ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHH
Q 011249          277 DRTNYVSNALIHMHSKCGYLDLAWREFSRIKN-K--------DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV  347 (490)
Q Consensus       277 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~--------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~  347 (490)
                      +.+..+...++..-....++++++..+-++.. |        ...+|-.+   + -.-++++++.++..=+.-|+-||..
T Consensus        61 ~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irl---l-lky~pq~~i~~l~npIqYGiF~dqf  136 (418)
T KOG4570|consen   61 PVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRL---L-LKYDPQKAIYTLVNPIQYGIFPDQF  136 (418)
T ss_pred             CcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHH---H-HccChHHHHHHHhCcchhccccchh
Confidence            44444455555555556667777766665543 1        12222222   2 2335677777777777788888888


Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHH
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRV  375 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~  375 (490)
                      ++..+++.+.+.+++.+|..+...|...
T Consensus       137 ~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  137 TFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             hHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            8888888888888888887777666653

>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B

Probab=87.54  E-value=1.4  Score=31.30  Aligned_cols=55  Identities=16%  Similarity=0.029  Sum_probs=36.1

Q ss_pred             CCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC--CCchHHHHHHHHHhcCCcc
Q 011249          411 FCDAGTWGALLGACKVHVNAELGEIAARHLLELGPE--KTGNSALLANIYASMGKWK  465 (490)
Q Consensus       411 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~--~~~~~~~l~~~~~~~g~~~  465 (490)
                      +.|...-..+...+...|+++.|++.+-.+++.+|+  +...-..++.++...|.-+
T Consensus        19 P~D~~ar~~lA~~~~~~g~~e~Al~~Ll~~v~~dr~~~~~~ar~~ll~~f~~lg~~~   75 (90)
T PF14561_consen   19 PDDLDARYALADALLAAGDYEEALDQLLELVRRDRDYEDDAARKRLLDIFELLGPGD   75 (90)
T ss_dssp             TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHCC-TTCCCCHHHHHHHHHHHHH-TT-
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccccccHHHHHHHHHHHHcCCCC
Confidence            345566677777788888888888888888877654  3556677777777777654

>PF04910 Tcf25: Transcriptional repressor TCF25; InterPro: IPR006994 This entry appears to represent a novel family of basic helix-loop-helix (bHLH) proteins that control differentiation and development of a variety of organs [, ]

Probab=87.32  E-value=11  Score=35.12  Aligned_cols=57  Identities=12%  Similarity=-0.005  Sum_probs=45.5

Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCC-CCchHHHHHHHHH-hcCCcchHHHHHHHhhh
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPE-KTGNSALLANIYA-SMGKWKDSEIVKMMISE  476 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~-~~~~~~~l~~~~~-~~g~~~~A~~~~~~~~~  476 (490)
                      .+..+.+.|-+..|.++.+-+..++|. ||-.....+..|. +.++++--+++.+....
T Consensus       109 ~i~~L~~RG~~rTAlE~~KlLlsLdp~~DP~g~ll~ID~~ALrs~~y~~Li~~~~~~~~  167 (360)
T PF04910_consen  109 YIQSLGRRGCWRTALEWCKLLLSLDPDEDPLGVLLFIDYYALRSRQYQWLIDFSESPLA  167 (360)
T ss_pred             HHHHHHhcCcHHHHHHHHHHHHhcCCCCCcchhHHHHHHHHHhcCCHHHHHHHHHhHhh
Confidence            345678899999999999999999998 8877777776665 66788888888876554

Human Nulp1 (Q2MK75 from SWISSPROT) is a basic helix-loop-helix protein expressed broadly during early embryonic organogenesis. Over expression of human Nulp1 in COS-7 cells inhibits the transcriptional activity of serum response factor (SRF), suggesting that Nulp1 may act as a novel bHLH transcriptional repressor in the SRF signalling pathway to mediate cellular functions [].

>KOG2063 consensus Vacuolar assembly/sorting proteins VPS39/VAM6/VPS3 [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.31  E-value=19  Score=37.48  Aligned_cols=29  Identities=14%  Similarity=0.340  Sum_probs=24.8

Q ss_pred             HhHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011249          211 SCWAAMTVCYVQNGYAKAAIEMYKVMRQE  239 (490)
Q Consensus       211 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  239 (490)
                      .-|..|+..|...|+.++|+++|.+....
T Consensus       505 ~~y~~Li~LY~~kg~h~~AL~ll~~l~d~  533 (877)
T KOG2063|consen  505 KKYRELIELYATKGMHEKALQLLRDLVDE  533 (877)
T ss_pred             ccHHHHHHHHHhccchHHHHHHHHHHhcc
Confidence            35888999999999999999999998763

>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function

Probab=87.28  E-value=3  Score=35.29  Aligned_cols=66  Identities=11%  Similarity=-0.004  Sum_probs=43.7

Q ss_pred             hHHHHHHHHhhhCChHH-------HHHHHHHHHhcC--CC----CCchHHHHHHHHHhcCCcchHHHHHHHhhhccccc
Q 011249          416 TWGALLGACKVHVNAEL-------GEIAARHLLELG--PE----KTGNSALLANIYASMGKWKDSEIVKMMISETEKKK  481 (490)
Q Consensus       416 ~~~~l~~~~~~~g~~~~-------a~~~~~~~~~~~--p~----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  481 (490)
                      .+..+.+.|...|+.+.       |.+.|+++.+..  |.    ...+...+|.+..+.|++++|.+.|.++...+-.+
T Consensus       120 l~LrlAWlyR~~~~~~~E~~fl~~Al~~y~~a~~~e~~~~~~~~~~~l~YLigeL~rrlg~~~eA~~~fs~vi~~~~~s  198 (214)
T PF09986_consen  120 LCLRLAWLYRDLGDEENEKRFLRKALEFYEEAYENEDFPIEGMDEATLLYLIGELNRRLGNYDEAKRWFSRVIGSKKAS  198 (214)
T ss_pred             HHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCCC
Confidence            45556667777777444       444445544433  22    23567778888999999999999999887765433

>KOG4642 consensus Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones]

Probab=87.19  E-value=2.3  Score=35.89  Aligned_cols=84  Identities=8%  Similarity=-0.175  Sum_probs=45.2

Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCc-hHHHHHHHHHhhcCChHHHHHHHHhcc-CCCChh-hHHHHHHHHhhhCChHH
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLT-EHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAG-TWGALLGACKVHVNAEL  432 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~-~~~~l~~~~~~~g~~~~  432 (490)
                      |....+++.|...+.+...   +.|+. ..|..=+.++.+..+++.+..--.+.. ..|+.. ....+.........+++
T Consensus        20 ~f~~k~y~~ai~~y~raI~---~nP~~~~Y~tnralchlk~~~~~~v~~dcrralql~~N~vk~h~flg~~~l~s~~~~e   96 (284)
T KOG4642|consen   20 CFIPKRYDDAIDCYSRAIC---INPTVASYYTNRALCHLKLKHWEPVEEDCRRALQLDPNLVKAHYFLGQWLLQSKGYDE   96 (284)
T ss_pred             ccchhhhchHHHHHHHHHh---cCCCcchhhhhHHHHHHHhhhhhhhhhhHHHHHhcChHHHHHHHHHHHHHHhhccccH
Confidence            5555666666666555543   34554 334455556666666666655443333 333332 33334444555666677


Q ss_pred             HHHHHHHHHh
Q 011249          433 GEIAARHLLE  442 (490)
Q Consensus       433 a~~~~~~~~~  442 (490)
                      |+..+.++..
T Consensus        97 aI~~Lqra~s  106 (284)
T KOG4642|consen   97 AIKVLQRAYS  106 (284)
T ss_pred             HHHHHHHHHH
Confidence            7777666644

>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]

Probab=87.03  E-value=37  Score=34.39  Aligned_cols=99  Identities=8%  Similarity=0.066  Sum_probs=75.7

Q ss_pred             HHHHHhcCCHHHHHHHHhhcCC--C---CHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHH
Q 011249          124 ICGYTKIGLMDDAQRLFDSMAE--R---NVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREA  198 (490)
Q Consensus       124 ~~~~~~~g~~~~A~~~~~~~~~--~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  198 (490)
                      ++.+.+.+.+++|+...+....  +   -...+...+..+...|++++|-...-.|...+..-|...+..+...++....
T Consensus       363 i~Wll~~k~yeeAl~~~k~~~~~~~~~~i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn~~~eWe~~V~~f~e~~~l~~I  442 (846)
T KOG2066|consen  363 IDWLLEKKKYEEALDAAKASIGNEERFVIKKVGKTYIDHLLFEGKYDEAASLCPKMLGNNAAEWELWVFKFAELDQLTDI  442 (846)
T ss_pred             HHHHHHhhHHHHHHHHHHhccCCccccchHHHHHHHHHHHHhcchHHHHHhhhHHHhcchHHHHHHHHHHhccccccchh
Confidence            4557788999999999887765  2   2346788899999999999999999999988888888888888887776655


Q ss_pred             HHHHhhcCC-CCHHhHHHHHHHHHh
Q 011249          199 KKVFDEISE-PDASCWAAMTVCYVQ  222 (490)
Q Consensus       199 ~~~~~~~~~-~~~~~~~~l~~~~~~  222 (490)
                      ..++-.-.. .++..|..++..+..
T Consensus       443 a~~lPt~~~rL~p~vYemvLve~L~  467 (846)
T KOG2066|consen  443 APYLPTGPPRLKPLVYEMVLVEFLA  467 (846)
T ss_pred             hccCCCCCcccCchHHHHHHHHHHH
Confidence            544433332 456778888877776

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=86.78  E-value=5.8  Score=28.22  Aligned_cols=48  Identities=10%  Similarity=0.153  Sum_probs=34.5

Q ss_pred             hHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHh
Q 011249          226 AKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDE  273 (490)
Q Consensus       226 ~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  273 (490)
                      .-++.+-++.+....+.|++....+.+++|.+.+|+..|.++++-++.
T Consensus        23 ~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~   70 (103)
T cd00923          23 GWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKD   70 (103)
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            345556666666667777777777778888888888888887777663

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.

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=86.70  E-value=4.8  Score=28.61  Aligned_cols=61  Identities=13%  Similarity=0.110  Sum_probs=40.9

Q ss_pred             hHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHH
Q 011249          327 SQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMV  389 (490)
Q Consensus       327 ~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  389 (490)
                      .-++.+-+..+....+.|++......+++|.+.+++..|.++++-++.+.+.  +...|..++
T Consensus        23 ~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~--~~~~y~~~l   83 (103)
T cd00923          23 GWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGA--HKEIYPYIL   83 (103)
T ss_pred             HHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccC--chhhHHHHH
Confidence            3455556666666667788888888888888888888888888877754332  334555444

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.

>KOG4507 consensus Uncharacterized conserved protein, contains TPR repeats [Function unknown]

Probab=86.56  E-value=2.8  Score=40.34  Aligned_cols=98  Identities=19%  Similarity=0.077  Sum_probs=64.1

Q ss_pred             cCCCChHHHHHHHHHHHHHcCCCCC--chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHH
Q 011249          357 SHGGLVEDGCKQFELMTRVFGIKPL--TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAEL  432 (490)
Q Consensus       357 ~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~  432 (490)
                      ...|+...|.+.+..+..   ..|.  -...-.|...+.+.|....|..++.+..  ....+.++..+.+++....++++
T Consensus       618 r~~gn~~~a~~cl~~a~~---~~p~~~~v~~v~la~~~~~~~~~~da~~~l~q~l~~~~sepl~~~~~g~~~l~l~~i~~  694 (886)
T KOG4507|consen  618 RAVGNSTFAIACLQRALN---LAPLQQDVPLVNLANLLIHYGLHLDATKLLLQALAINSSEPLTFLSLGNAYLALKNISG  694 (886)
T ss_pred             eecCCcHHHHHHHHHHhc---cChhhhcccHHHHHHHHHHhhhhccHHHHHHHHHhhcccCchHHHhcchhHHHHhhhHH
Confidence            345777777777776643   2332  1223345566666677777777765443  33455567777778888888888


Q ss_pred             HHHHHHHHHhcCCCCCchHHHHHHH
Q 011249          433 GEIAARHLLELGPEKTGNSALLANI  457 (490)
Q Consensus       433 a~~~~~~~~~~~p~~~~~~~~l~~~  457 (490)
                      |++.|+++++.+|+++..-..|..+
T Consensus       695 a~~~~~~a~~~~~~~~~~~~~l~~i  719 (886)
T KOG4507|consen  695 ALEAFRQALKLTTKCPECENSLKLI  719 (886)
T ss_pred             HHHHHHHHHhcCCCChhhHHHHHHH
Confidence            8888888888888887766665443

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=86.47  E-value=4  Score=29.34  Aligned_cols=60  Identities=13%  Similarity=0.107  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHH
Q 011249          329 EALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVD  390 (490)
Q Consensus       329 ~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  390 (490)
                      +..+-+..+....+.|++......+++|.+.+++..|.++++-++.+.+  +....|..+++
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~--~~~~~Y~~~lq   87 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCG--NKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTT--T-TTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc--ChHHHHHHHHH
Confidence            4555666666666788888888888888888888888888888887544  33336666553

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 ....

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=86.08  E-value=6.1  Score=28.43  Aligned_cols=60  Identities=10%  Similarity=0.208  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 011249          228 AAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIH  288 (490)
Q Consensus       228 ~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  288 (490)
                      +..+-++.+....+.|++....+.+.+|.+.+++..|.++++-++... .+....|..+++
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~-~~~~~~Y~~~lq   87 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKC-GNKKEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHT-TT-TTHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHc-cChHHHHHHHHH
Confidence            455556666666677777777777777777777777777777775543 222225554443

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 ....

>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=85.90  E-value=17  Score=29.33  Aligned_cols=101  Identities=12%  Similarity=0.042  Sum_probs=46.7

Q ss_pred             HHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCC
Q 011249          231 EMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKD  310 (490)
Q Consensus       231 ~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~  310 (490)
                      ++++.+.+.++.|+...+..++..+.+.|++.....    +...++-+|.......+-.+.  +....+.++=-+|.++=
T Consensus        15 EYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~q----llq~~Vi~DSk~lA~~LLs~~--~~~~~~~Ql~lDMLkRL   88 (167)
T PF07035_consen   15 EYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQ----LLQYHVIPDSKPLACQLLSLG--NQYPPAYQLGLDMLKRL   88 (167)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHH----HHhhcccCCcHHHHHHHHHhH--ccChHHHHHHHHHHHHh
Confidence            444555556666666666666666666666543332    233333333322222211111  12223333333333222


Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHHH
Q 011249          311 VISYSSMITAFADHGKSQEALDMFLKM  337 (490)
Q Consensus       311 ~~~~~~l~~~~~~~~~~~~a~~~~~~~  337 (490)
                      ...+..+++.+...|++-+|+++.+..
T Consensus        89 ~~~~~~iievLL~~g~vl~ALr~ar~~  115 (167)
T PF07035_consen   89 GTAYEEIIEVLLSKGQVLEALRYARQY  115 (167)
T ss_pred             hhhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence            223444555566666666666666553

>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=85.89  E-value=12  Score=31.04  Aligned_cols=74  Identities=12%  Similarity=0.001  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcC---CCCchhHHHHHHHHHHhcCChHHHH
Q 011249          226 AKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGC---CDRTNYVSNALIHMHSKCGYLDLAW  300 (490)
Q Consensus       226 ~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~---~~~~~~~~~~l~~~~~~~~~~~~A~  300 (490)
                      -+.|.+.|-++...+.--++.....|...|. ..+.+++..++.+..+..   -.+|+..+.+|+..|.+.|+++.|.
T Consensus       122 d~~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~AY  198 (203)
T PF11207_consen  122 DQEALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQAY  198 (203)
T ss_pred             cHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhhh
Confidence            3566777777776654444444444444443 567777777777665532   2456677777777777777776664

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=85.81  E-value=26  Score=31.51  Aligned_cols=158  Identities=11%  Similarity=0.121  Sum_probs=74.1

Q ss_pred             hHHHHHHHHHHHHcCCCCcHHHHHHHHHHhc--CCC----ChHHHHHHHHHHHHHcCCC--CCchHHHHHHHHHhhcCCh
Q 011249          327 SQEALDMFLKMRNEGIEPNQVTFIGVLTACS--HGG----LVEDGCKQFELMTRVFGIK--PLTEHLTCMVDLLGRSGQL  398 (490)
Q Consensus       327 ~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~--~~g----~~~~a~~~~~~~~~~~~~~--~~~~~~~~l~~~~~~~g~~  398 (490)
                      +++.+.+++.|.+.|+.-+..+|........  ...    ...+|..+++.|++.+.+-  ++-..+..++..  ..++.
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            3455667777888877777666554332222  222    2456778888888865442  223333333221  33333


Q ss_pred             ----HHHHHHHHhcc----CCCCh-hhHHHHHHHHhhhCC--hHHHHHHHHHHHhcC-CCCCchHHHHHHHHHhcCCcch
Q 011249          399 ----EKAHSLIMDYK----DFCDA-GTWGALLGACKVHVN--AELGEIAARHLLELG-PEKTGNSALLANIYASMGKWKD  466 (490)
Q Consensus       399 ----~~A~~~~~~~~----~~~~~-~~~~~l~~~~~~~g~--~~~a~~~~~~~~~~~-p~~~~~~~~l~~~~~~~g~~~~  466 (490)
                          +++..+|+.+.    .+.+. .....++..+....+  ..++.++++.+.+.+ +-....|..+|-+-.-.+..++
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lGlLall~~~~~~  235 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLGLLALLEDPEEK  235 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHHHHHhcCCchHH
Confidence                33344444444    22233 233333333222222  346677777777655 2234445555533323333324


Q ss_pred             HHHHHHHhhhcccccCCCccc
Q 011249          467 SEIVKMMISETEKKKSPGCSW  487 (490)
Q Consensus       467 A~~~~~~~~~~~~~~~~~~~~  487 (490)
                      ..+.+..+.+. +...+|+.|
T Consensus       236 ~~~~i~ev~~~-L~~~k~~~~  255 (297)
T PF13170_consen  236 IVEEIKEVIDE-LKEQKGFGW  255 (297)
T ss_pred             HHHHHHHHHHH-HhhCcccCh
Confidence            44444444332 334444433

>KOG2471 consensus TPR repeat-containing protein [General function prediction only]

Probab=85.69  E-value=17  Score=34.44  Aligned_cols=77  Identities=16%  Similarity=0.130  Sum_probs=42.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHH-------cCCCCcH-----------HHHHHHHHHhcCCCChHHHHHHHHHHHHH
Q 011249          314 YSSMITAFADHGKSQEALDMFLKMRN-------EGIEPNQ-----------VTFIGVLTACSHGGLVEDGCKQFELMTRV  375 (490)
Q Consensus       314 ~~~l~~~~~~~~~~~~a~~~~~~~~~-------~~~~p~~-----------~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  375 (490)
                      ||.|...+.+.|.+.-+..+|.+..+       .|++|..           .+|+.-+ .|...|++-.|.+.|.+....
T Consensus       286 ~NNlGcIh~~~~~y~~~~~~F~kAL~N~c~qL~~g~~~~~~~tls~nks~eilYNcG~-~~Lh~grPl~AfqCf~~av~v  364 (696)
T KOG2471|consen  286 NNNLGCIHYQLGCYQASSVLFLKALRNSCSQLRNGLKPAKTFTLSQNKSMEILYNCGL-LYLHSGRPLLAFQCFQKAVHV  364 (696)
T ss_pred             ecCcceEeeehhhHHHHHHHHHHHHHHHHHHHhccCCCCcceehhcccchhhHHhhhH-HHHhcCCcHHHHHHHHHHHHH
Confidence            45555555555555555555555542       3444321           1233222 355667777777777777663


Q ss_pred             cCCCCCchHHHHHHHHHh
Q 011249          376 FGIKPLTEHLTCMVDLLG  393 (490)
Q Consensus       376 ~~~~~~~~~~~~l~~~~~  393 (490)
                        +..++..|..|..+|.
T Consensus       365 --fh~nPrlWLRlAEcCi  380 (696)
T KOG2471|consen  365 --FHRNPRLWLRLAECCI  380 (696)
T ss_pred             --HhcCcHHHHHHHHHHH
Confidence              4455566666666664

>KOG2063 consensus Vacuolar assembly/sorting proteins VPS39/VAM6/VPS3 [Intracellular trafficking, secretion, and vesicular transport]

Probab=85.42  E-value=51  Score=34.49  Aligned_cols=86  Identities=14%  Similarity=0.058  Sum_probs=49.8

Q ss_pred             HHhhcCChHHHHHHHHhcc---CCCChhhHHHHHHHHhhhC--------ChHHHHHH--HHHHH---h----cCCC----
Q 011249          391 LLGRSGQLEKAHSLIMDYK---DFCDAGTWGALLGACKVHV--------NAELGEIA--ARHLL---E----LGPE----  446 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~~~---~~~~~~~~~~l~~~~~~~g--------~~~~a~~~--~~~~~---~----~~p~----  446 (490)
                      .|......+-++.+++.+.   ..++....+.++..|...=        +.+++.+.  .+++.   +    ..|.    
T Consensus       600 ~~l~~~~~~l~I~YLE~li~~~~~~~~~lht~ll~ly~e~v~~~~~~~~kg~e~~E~~~rekl~~~l~~s~~Y~p~~~L~  679 (877)
T KOG2063|consen  600 NYLKSKEPKLLIPYLEHLISDNRLTSTLLHTVLLKLYLEKVLEQASTDGKGEEAPETTVREKLLDFLESSDLYDPQLLLE  679 (877)
T ss_pred             HHhhhhCcchhHHHHHHHhHhccccchHHHHHHHHHHHHHHhhccCchhccccchhhhHHHHHHHHhhhhcccCcchhhh
Confidence            4455666777777887776   2345555566665554321        12233333  22221   1    1121    


Q ss_pred             ---CCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          447 ---KTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       447 ---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                         ....|...+..+.+.|+.++|+.++-....
T Consensus       680 ~~~~~~l~ee~aill~rl~khe~aL~Iyv~~L~  712 (877)
T KOG2063|consen  680 RLNGDELYEERAILLGRLGKHEEALHIYVHELD  712 (877)
T ss_pred             hccchhHHHHHHHHHhhhhhHHHHHHHHHHHhc
Confidence               245777778888899999999998865543

>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=85.07  E-value=1.9  Score=22.03  Aligned_cols=20  Identities=20%  Similarity=0.300  Sum_probs=10.4

Q ss_pred             HHHHHHhhcCChHHHHHHHH
Q 011249          387 CMVDLLGRSGQLEKAHSLIM  406 (490)
Q Consensus       387 ~l~~~~~~~g~~~~A~~~~~  406 (490)
                      .+...+...|++++|..+++
T Consensus         6 ~la~~~~~~G~~~eA~~~l~   25 (26)
T PF07721_consen    6 ALARALLAQGDPDEAERLLR   25 (26)
T ss_pred             HHHHHHHHcCCHHHHHHHHh
Confidence            34455555555555555543

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

>smart00386 HAT HAT (Half-A-TPR) repeats

Probab=84.88  E-value=2  Score=22.98  Aligned_cols=30  Identities=17%  Similarity=-0.017  Sum_probs=24.3

Q ss_pred             CChHHHHHHHHHHHhcCCCCCchHHHHHHH
Q 011249          428 VNAELGEIAARHLLELGPEKTGNSALLANI  457 (490)
Q Consensus       428 g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  457 (490)
                      |+.+.+..+|++++...|.++.++...+..
T Consensus         1 ~~~~~~r~i~e~~l~~~~~~~~~W~~y~~~   30 (33)
T smart00386        1 GDIERARKIYERALEKFPKSVELWLKYAEF   30 (33)
T ss_pred             CcHHHHHHHHHHHHHHCCCChHHHHHHHHH
Confidence            567888999999999888888888777643

Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.

>TIGR03504 FimV_Cterm FimV C-terminal domain

Probab=83.68  E-value=1.7  Score=25.83  Aligned_cols=25  Identities=24%  Similarity=0.274  Sum_probs=18.2

Q ss_pred             HHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          453 LLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       453 ~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      .|+.+|.+.|+.+.|.++++.+...
T Consensus         4 dLA~ayie~Gd~e~Ar~lL~evl~~   28 (44)
T TIGR03504         4 DLARAYIEMGDLEGARELLEEVIEE   28 (44)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHc
Confidence            5677777777777777777777643

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.

>smart00028 TPR Tetratricopeptide repeats

Probab=82.97  E-value=1.7  Score=22.68  Aligned_cols=29  Identities=17%  Similarity=0.133  Sum_probs=25.3

Q ss_pred             chHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          449 GNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       449 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      ..+..++.++...|++++|...++...+.
T Consensus         2 ~~~~~~a~~~~~~~~~~~a~~~~~~~~~~   30 (34)
T smart00028        2 EALYNLGNAYLKLGDYDEALEYYEKALEL   30 (34)
T ss_pred             hHHHHHHHHHHHHhhHHHHHHHHHHHHcc
Confidence            46788999999999999999999987754

Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.

>PRK11619 lytic murein transglycosylase; Provisional

Probab=82.72  E-value=59  Score=33.11  Aligned_cols=336  Identities=7%  Similarity=-0.090  Sum_probs=153.8

Q ss_pred             HHHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhcc---CCchhHHHHHHHHHhcCChhHHHHHH
Q 011249          126 GYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTE---KNSVTWVAMIAGYGKCGEVREAKKVF  202 (490)
Q Consensus       126 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~A~~~~  202 (490)
                      .+.+.+++......+.. ...+...-.....+....|+.++|....+.+-.   ..+...+.++..+.+.|.+.... ++
T Consensus       108 ~La~~~~w~~~~~~~~~-~p~~~~~~c~~~~A~~~~G~~~~A~~~a~~lW~~g~~~p~~cd~l~~~~~~~g~lt~~d-~w  185 (644)
T PRK11619        108 ELARREDWRGLLAFSPE-KPKPVEARCNYYYAKWATGQQQEAWQGAKELWLTGKSLPNACDKLFSVWQQSGKQDPLA-YL  185 (644)
T ss_pred             HHHHccCHHHHHHhcCC-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCCChHHHHHHHHHHHcCCCCHHH-HH
Confidence            35567777777773322 223555555667777778887777666655532   24555666666665554433221 11


Q ss_pred             hhcC----CCCHHhHHHHHHHH-----------Hh-cCChHHHHHHHHHHHHcCcccChhhHHHHHHHH--hccCChHHH
Q 011249          203 DEIS----EPDASCWAAMTVCY-----------VQ-NGYAKAAIEMYKVMRQENVRISEVAMVGAISAC--TQLGDVEMA  264 (490)
Q Consensus       203 ~~~~----~~~~~~~~~l~~~~-----------~~-~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~--~~~g~~~~a  264 (490)
                      .++.    ..+...-..+....           .. ..++..+..++..     +.|+...-..++.++  ....+.+.|
T Consensus       186 ~R~~~al~~~~~~lA~~l~~~l~~~~~~~a~a~~al~~~p~~~~~~~~~-----~~~~~~~~~~~~~~l~Rlar~d~~~A  260 (644)
T PRK11619        186 ERIRLAMKAGNTGLVTYLAKQLPADYQTIASALIKLQNDPNTVETFART-----TGPTDFTRQMAAVAFASVARQDAENA  260 (644)
T ss_pred             HHHHHHHHCCCHHHHHHHHHhcChhHHHHHHHHHHHHHCHHHHHHHhhc-----cCCChhhHHHHHHHHHHHHHhCHHHH
Confidence            1111    11111111111111           00 0111111111111     112221111111111  123455667


Q ss_pred             HHHHHHHHhcC-CCCc--hhHHHHHHHHHHhcCChHHHHHHHhcccC--CChhHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011249          265 AILAKHVDEGC-CDRT--NYVSNALIHMHSKCGYLDLAWREFSRIKN--KDVISYSSMITAFADHGKSQEALDMFLKMRN  339 (490)
Q Consensus       265 ~~~~~~~~~~~-~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  339 (490)
                      ..++..+.... ..+.  ..+...+.......+..++|...+.....  .+......-+..-...++++.+...+..|-.
T Consensus       261 ~~~~~~~~~~~~~~~~~~~~~~~~lA~~~a~~~~~~~a~~w~~~~~~~~~~~~~~e~r~r~Al~~~dw~~~~~~i~~L~~  340 (644)
T PRK11619        261 RLMIPSLVRAQKLNEDQRQELRDIVAWRLMGNDVTDEQAKWRDDVIMRSQSTSLLERRVRMALGTGDRRGLNTWLARLPM  340 (644)
T ss_pred             HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccCCHHHHHHHHhcccccCCcHHHHHHHHHHHHccCHHHHHHHHHhcCH
Confidence            77776653332 2221  12233333333333225566666665443  2333444444444467777777777776644


Q ss_pred             cCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHH-----------cCCCCC------chH--------HHHHHHHHhh
Q 011249          340 EGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRV-----------FGIKPL------TEH--------LTCMVDLLGR  394 (490)
Q Consensus       340 ~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-----------~~~~~~------~~~--------~~~l~~~~~~  394 (490)
                      .. .-...-.--+.+++...|+.++|..+|+.+...           .|.++.      +..        -..-+..+..
T Consensus       341 ~~-~~~~rw~YW~aRa~~~~g~~~~A~~~~~~~a~~~~fYG~LAa~~Lg~~~~~~~~~~~~~~~~~~~~~~~~ra~~L~~  419 (644)
T PRK11619        341 EA-KEKDEWRYWQADLLLEQGRKAEAEEILRQLMQQRGFYPMVAAQRLGEEYPLKIDKAPKPDSALTQGPEMARVRELMY  419 (644)
T ss_pred             hh-ccCHhhHHHHHHHHHHcCCHHHHHHHHHHHhcCCCcHHHHHHHHcCCCCCCCCCCCCchhhhhccChHHHHHHHHHH
Confidence            21 112233334555555567777777777765331           011100      000        0112344556


Q ss_pred             cCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC---CCCCchHHHHHHHHHhcCCcchHHH
Q 011249          395 SGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELG---PEKTGNSALLANIYASMGKWKDSEI  469 (490)
Q Consensus       395 ~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~---p~~~~~~~~l~~~~~~~g~~~~A~~  469 (490)
                      .|+..+|...+..+....+......+.......|..+.++....+....+   -..|..|...+..+.+.-..+.++-
T Consensus       420 ~g~~~~a~~ew~~~~~~~~~~~~~~la~~A~~~g~~~~ai~~~~~~~~~~~~~~rfp~~~~~~~~~~a~~~~v~~~lv  497 (644)
T PRK11619        420 WNMDNTARSEWANLVASRSKTEQAQLARYAFNQQWWDLSVQATIAGKLWDHLEERFPLAWNDEFRRYTSGKGIPQSYA  497 (644)
T ss_pred             CCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHCCCHHHHHHHHhhchhHHHHHHhCCcchHHHHHHHHHHcCCCHHHH
Confidence            67777777776655534455555555555667777777776665443211   1123334444444444444554443

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=82.59  E-value=16  Score=26.33  Aligned_cols=59  Identities=14%  Similarity=0.160  Sum_probs=35.9

Q ss_pred             HHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhH
Q 011249          187 AGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAM  248 (490)
Q Consensus       187 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~  248 (490)
                      ..+...|++++|..+.+...-||...|..|.  -.+.|-.+.+..-+..|...| .|....|
T Consensus        47 sSLmNrG~Yq~Al~l~~~~~~pdlepw~ALc--e~rlGl~s~l~~rl~rla~sg-~p~lq~F  105 (115)
T TIGR02508        47 SSLMNRGDYQSALQLGNKLCYPDLEPWLALC--EWRLGLGSALESRLNRLAASG-DPRLQTF  105 (115)
T ss_pred             HHHHccchHHHHHHhcCCCCCchHHHHHHHH--HHhhccHHHHHHHHHHHHhCC-CHHHHHH
Confidence            3456677777777777777667777766554  335565666666666666555 3343333

YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc.

>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional

Probab=82.20  E-value=76  Score=34.02  Aligned_cols=154  Identities=11%  Similarity=0.005  Sum_probs=65.8

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHH-HHHHHHHHHHcCCCCcHHHHHHHHHHh
Q 011249          278 RTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQE-ALDMFLKMRNEGIEPNQVTFIGVLTAC  356 (490)
Q Consensus       278 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~-a~~~~~~~~~~~~~p~~~~~~~l~~~~  356 (490)
                      +|..+-...+.++.+.+..+.   +...+..++..+-...+.++...+..+. +...+..+..   .++...-...+.++
T Consensus       726 ~d~~VR~~Av~aL~~~~~~~~---l~~~l~D~~~~VR~~aa~aL~~~~~~~~~~~~~L~~ll~---D~d~~VR~aA~~aL  799 (897)
T PRK13800        726 PDHRVRIEAVRALVSVDDVES---VAGAATDENREVRIAVAKGLATLGAGGAPAGDAVRALTG---DPDPLVRAAALAAL  799 (897)
T ss_pred             CCHHHHHHHHHHHhcccCcHH---HHHHhcCCCHHHHHHHHHHHHHhccccchhHHHHHHHhc---CCCHHHHHHHHHHH
Confidence            344444444444444433221   2222333455555555555555444322 2333333332   33444444455555


Q ss_pred             cCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHH
Q 011249          357 SHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIA  436 (490)
Q Consensus       357 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~  436 (490)
                      ...|..+.+...+..+.+    .++..+-...+.++.+.+. +++...+..+...++..+-...+.++...+....+...
T Consensus       800 g~~g~~~~~~~~l~~aL~----d~d~~VR~~Aa~aL~~l~~-~~a~~~L~~~L~D~~~~VR~~A~~aL~~~~~~~~a~~~  874 (897)
T PRK13800        800 AELGCPPDDVAAATAALR----ASAWQVRQGAARALAGAAA-DVAVPALVEALTDPHLDVRKAAVLALTRWPGDPAARDA  874 (897)
T ss_pred             HhcCCcchhHHHHHHHhc----CCChHHHHHHHHHHHhccc-cchHHHHHHHhcCCCHHHHHHHHHHHhccCCCHHHHHH
Confidence            555544333333333322    2344444445555555544 33444443333344554444445555443223344444


Q ss_pred             HHHHHh
Q 011249          437 ARHLLE  442 (490)
Q Consensus       437 ~~~~~~  442 (490)
                      +..+++
T Consensus       875 L~~al~  880 (897)
T PRK13800        875 LTTALT  880 (897)
T ss_pred             HHHHHh
Confidence            444443

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=82.08  E-value=36  Score=30.14  Aligned_cols=83  Identities=8%  Similarity=0.051  Sum_probs=45.9

Q ss_pred             CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHc-CcccChhhHHHHHHHHhccCChHHHHHHHHH-----HHhcCCCCchh
Q 011249          208 PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQE-NVRISEVAMVGAISACTQLGDVEMAAILAKH-----VDEGCCDRTNY  281 (490)
Q Consensus       208 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~-----~~~~~~~~~~~  281 (490)
                      ++..+...++..++..+++..-.++++..... +..-|...|..++......|+..-..++...     +.+.+++.+..
T Consensus       200 l~~~vi~~Il~~L~~~~dW~kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~kiI~~GhLLwikR~~V~v~~~  279 (292)
T PF13929_consen  200 LTRNVIISILEILAESRDWNKLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKIIDDGHLLWIKRNNVDVTDE  279 (292)
T ss_pred             CChhHHHHHHHHHHhcccHHHHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHHhhCCCeEEeeecCCcCCHH
Confidence            44455555666666666666666666555543 3444555666666666666666655555543     34445555555


Q ss_pred             HHHHHHHHH
Q 011249          282 VSNALIHMH  290 (490)
Q Consensus       282 ~~~~l~~~~  290 (490)
                      .-..+-..+
T Consensus       280 L~~~L~~LF  288 (292)
T PF13929_consen  280 LRSQLSELF  288 (292)
T ss_pred             HHHHHHHHH
Confidence            544444433

>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex

Probab=81.11  E-value=66  Score=32.62  Aligned_cols=38  Identities=16%  Similarity=0.312  Sum_probs=19.4

Q ss_pred             HHHHHHhCCChHHHHHHHHHhcc---CCchhHHHHHHHHHh
Q 011249          154 MVAGYANCGNMKAAKEFYDRMTE---KNSVTWVAMIAGYGK  191 (490)
Q Consensus       154 l~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~l~~~~~~  191 (490)
                      ++-.|.+.|++++|.++..+...   .....+...+..|..
T Consensus       117 ~Iyy~LR~G~~~~A~~~~~~~~~~~~~~~~~f~~~l~~~~~  157 (613)
T PF04097_consen  117 LIYYCLRCGDYDEALEVANENRNQFQKIERSFPTYLKAYAS  157 (613)
T ss_dssp             HHHHHHTTT-HHHHHHHHHHTGGGS-TTTTHHHHHHHHCTT
T ss_pred             HHHHHHhcCCHHHHHHHHHHhhhhhcchhHHHHHHHHHHHh
Confidence            44555666666666666644332   233445555555544

It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.

>KOG2300 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.93  E-value=53  Score=31.37  Aligned_cols=83  Identities=18%  Similarity=0.050  Sum_probs=49.1

Q ss_pred             HHHHHHHhccCCCC-CCc-eehHHHHHHHHhcC-ChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHH
Q 011249           52 LSYARQVFDQIPKC-KTQ-FLWTSLIRNHVLHA-HFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYT  128 (490)
Q Consensus        52 ~~~A~~~~~~~~~~-~~~-~~~~~l~~~~~~~g-~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~  128 (490)
                      .+.|+.+.+.|+.- |+. ..++.|...|.... .+..+..++.+..+..-.-.......++           .++..+.
T Consensus        70 LekA~~i~~~ip~fydvKf~a~SlLa~lh~~~~~s~~~~KalLrkaielsq~~p~wsckllf-----------QLaql~~  138 (629)
T KOG2300|consen   70 LEKAWLISKSIPSFYDVKFQAASLLAHLHHQLAQSFPPAKALLRKAIELSQSVPYWSCKLLF-----------QLAQLHI  138 (629)
T ss_pred             HHHHHHHHcccccHHhhhhHHHHHHHHHHHHhcCCCchHHHHHHHHHHHhcCCchhhHHHHH-----------HHHHHHh
Confidence            34455555555532 221 35666777777665 7888888888877652221122222222           2566778


Q ss_pred             hcCCHHHHHHHHhhcCC
Q 011249          129 KIGLMDDAQRLFDSMAE  145 (490)
Q Consensus       129 ~~g~~~~A~~~~~~~~~  145 (490)
                      -..++..|.+++.--.+
T Consensus       139 idkD~~sA~elLavga~  155 (629)
T KOG2300|consen  139 IDKDFPSALELLAVGAE  155 (629)
T ss_pred             hhccchhHHHHHhcccc
Confidence            88899999888665443

>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]

Probab=80.25  E-value=49  Score=30.58  Aligned_cols=104  Identities=12%  Similarity=0.108  Sum_probs=71.9

Q ss_pred             HHHHHHHhhcCChHHHHHHHHhccCC--------CChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC-------ch
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYKDF--------CDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT-------GN  450 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~~~--------~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~-------~~  450 (490)
                      ..|...+...|+.++|..++...+..        .-....---++.|...+|+-.|.-+-++.....-+.+       ..
T Consensus       135 k~L~~ike~~Gdi~~Aa~il~el~VETygsm~~~ekV~fiLEQmrKOG~~~D~vra~i~skKI~~K~F~~~~~~~lKlky  214 (439)
T KOG1498|consen  135 KMLAKIKEEQGDIAEAADILCELQVETYGSMEKSEKVAFILEQMRLCLLRLDYVRAQIISKKINKKFFEKPDVQELKLKY  214 (439)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhHHhcCCccHHHHHHHH
Confidence            45667788889999999988877611        0111112234678889999999998888876432222       46


Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHhhhcccccCCCccccC
Q 011249          451 SALLANIYASMGKWKDSEIVKMMISETEKKKSPGCSWIS  489 (490)
Q Consensus       451 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  489 (490)
                      |..++......+.|=++-+.++.+...|.-+...-.|..
T Consensus       215 Y~lmI~l~lh~~~Yl~v~~~Yraiy~t~~vk~d~~kw~~  253 (439)
T KOG1498|consen  215 YELMIRLGLHDRAYLNVCRSYRAIYDTGNVKEDPEKWIE  253 (439)
T ss_pred             HHHHHHhcccccchhhHHHHHHHHhcccccccChhhhhh
Confidence            777888888888888999999988877765554444543

---

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	490
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	8e-09
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	1e-06
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	8e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-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 = 57.1 bits (136), Expect = 8e-09
 Identities = 30/255 (11%), Positives = 82/255 (32%), Gaps = 10/255 (3%)

Query: 236 MRQENVRISEVAMVGAISACTQLGDVEMAA-ILAKHVDEGCCDRTNYVS--NALIHMHSK 292
             Q  +   +  ++     C     + +A  +L  H  +    +   +   NA++   ++
Sbjct: 118 HSQAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWAR 177

Query: 293 CGYLDLAWREFSRIKNK----DVISYSSMITAFADHGKSQEALDMFL-KMRNEGIEPNQV 347
            G           +K+     D++SY++ +       +    ++  L +M  EG++   +
Sbjct: 178 QGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQAL 237

Query: 348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMD 407
               +L+      +++   K     +    + P       + D+  + G++      +  
Sbjct: 238 FTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPL 297

Query: 408 YKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDS 467
               C       +  A +V V +   E       E+   +     L      ++ +    
Sbjct: 298 KTLQCLFEKQLHMELASRVCVVSV--EKPTLPSKEVKHARKTLKTLRDQWEKALCRALRE 355

Query: 468 EIVKMMISETEKKKS 482
              ++     E + S
Sbjct: 356 TKNRLEREVYEGRFS 370

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 50.6 bits (119), Expect = 1e-06
 Identities = 20/192 (10%), Positives = 56/192 (29%), Gaps = 7/192 (3%)

Query: 226 AKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNA 285
            + A  +    RQ      E  +   +        +++    +    +           A
Sbjct: 73  KQMAGCLEDCTRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLA 132

Query: 286 LIHMHSKCGYLDLAWREFSRIKNK-------DVISYSSMITAFADHGKSQEALDMFLKMR 338
                     L LA         +        +  Y++++  +A  G  +E + +   ++
Sbjct: 133 FFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVK 192

Query: 339 NEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQL 398
           + G+ P+ +++   L             ++        G+K        ++    R+  L
Sbjct: 193 DAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVL 252

Query: 399 EKAHSLIMDYKD 410
           +  H +   +  
Sbjct: 253 KAVHKVKPTFSL 264

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 47.5 bits (111), Expect = 8e-06
 Identities = 14/133 (10%), Positives = 42/133 (31%), Gaps = 12/133 (9%)

Query: 120 LEAVICGYTKIGLMDDAQRLFDSMAER-------NVISWSAMVAGYANCGNMKAAKEFYD 172
           L A          +  A  L      +        +  ++A++ G+A  G  K       
Sbjct: 130 LLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLF 189

Query: 173 RMTEK----NSVTWVAMIAGYGKCGEVREA-KKVFDEISEPDASCWAAMTVCYVQNGYAK 227
            + +     + +++ A +   G+  +     ++  +++S+      A  T   +      
Sbjct: 190 MVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRA 249

Query: 228 AAIEMYKVMRQEN 240
             ++    ++   
Sbjct: 250 TVLKAVHKVKPTF 262

>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 = 46.4 bits (109), Expect = 2e-05
 Identities = 67/490 (13%), Positives = 141/490 (28%), Gaps = 146/490 (29%)

Query: 3   SKYLVPRSKTFNQLK------QVHSYLL--------KT-LT-------KPHDQYH---YY 37
           +KY V R + + +L+      +    +L        KT +        K   +     ++
Sbjct: 127 AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW 186

Query: 38  AQF--------LIRLLQLPGDNLSYARQVFDQI-PKCKTQFLWTSLIRNHVLHAHFRQSI 88
                      ++ +LQ     L Y      QI P   ++   +S I+  +         
Sbjct: 187 LNLKNCNSPETVLEMLQ----KLLY------QIDPNWTSRSDHSSNIKLRIHSIQAELRR 236

Query: 89  LLYAKMHR--LGVL--------TSGFTFSSVLNAC-----ARVPSLLEAVICGYTKIGLM 133
           LL +K +   L VL         + F  S     C      R   + + +    T    +
Sbjct: 237 LLKSKPYENCLLVLLNVQNAKAWNAFNLS-----CKILLTTRFKQVTDFLSAATTTHISL 291

Query: 134 DDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCG 193
           D             V S   ++  Y +C      +E         +   +++IA      
Sbjct: 292 DHHSMTLT---PDEVKS---LLLKYLDCRPQDLPRE-----VLTTNPRRLSIIA-----E 335

Query: 194 EVREA-------KKV-FDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISE 245
            +R+        K V  D+++    S    +     +  + + ++         +  I  
Sbjct: 336 SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV------FPPSAHIPT 389

Query: 246 VAMVGAISAC---TQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDL-AWR 301
           + +            +   ++  ++ K       ++      + I + S   YL+L    
Sbjct: 390 ILL------SLIWFDVIKSDVMVVVNKLHKYSLVEKQPK--ESTISIPS--IYLELKVKL 439

Query: 302 EFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGV-LTACSHGG 360
           E     ++ ++ + ++   F         LD +             + IG  L    H  
Sbjct: 440 ENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYF-----------YSHIGHHLKNIEHP- 487

Query: 361 LVEDGCKQFELMTRVF--------GIKPLTEHLTCMVDLLGRSGQLEK-----------A 401
                 ++  L   VF         I+  +        +L    QL+             
Sbjct: 488 ------ERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKY 541

Query: 402 HSLIMDYKDF 411
             L+    DF
Sbjct: 542 ERLVNAILDF 551

>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 = 46.4 bits (109), Expect = 2e-05
 Identities = 61/459 (13%), Positives = 121/459 (26%), Gaps = 164/459 (35%)

Query: 6   LVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPG--------DNLSYAR- 56
           L    K   Q+    +      +    + H     L RLL+            N+  A+ 
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA 258

Query: 57  -QVFDQIPKCKTQFLWTSLIRNH----VLHAHFRQSILLYAKMHRLGVLTSGFT---FSS 108
              F+    CK   L T+  R       L A     I L    H    LT          
Sbjct: 259 WNAFN--LSCKI--LLTT--RFKQVTDFLSAATTTHISL---DHHSMTLTPDEVKSLLLK 309

Query: 109 VLN-ACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAA 167
            L+     +P   E +     ++ ++ ++ R   +  +     W      + NC  +   
Sbjct: 310 YLDCRPQDLPR--EVLTTNPRRLSIIAESIRDGLATWDN----WK-----HVNCDKLTTI 358

Query: 168 -------------KEFYDRMT--EKN--------SVTWVAMIAGYGKCGEVREAKKVFDE 204
                        ++ +DR++    +        S+ W  +           +   V ++
Sbjct: 359 IESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDV--------IKSDVMVVVNK 410

Query: 205 -ISEPDASCWAAMTVCYVQNGYA-------------KAAIEMYKVMRQENVRISEVAMVG 250
                        +   + + Y              ++ ++ Y + +             
Sbjct: 411 LHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPK------------- 457

Query: 251 AISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMH-SKCG-----------YLDL 298
                    D     ++  ++D        Y  + + H H                +LD 
Sbjct: 458 ----TFDSDD-----LIPPYLD-------QYFYSHIGH-HLKNIEHPERMTLFRMVFLDF 500

Query: 299 AWREFSRIKN---------------KDVISYSSMITAFADHGKSQEAL--DM--FLKMRN 339
            + E  +I++               + +  Y   I    D+    E L   +  FL    
Sbjct: 501 RFLE-QKIRHDSTAWNASGSILNTLQQLKFYKPYIC---DNDPKYERLVNAILDFLP--- 553

Query: 340 EGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGI 378
             IE N       L    +  L+     +  LM     I
Sbjct: 554 -KIEEN-------LICSKYTDLL-----RIALMAEDEAI 579

>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 = 44.1 bits (103), Expect = 1e-04
 Identities = 46/298 (15%), Positives = 91/298 (30%), Gaps = 107/298 (35%)

Query: 266 ILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMIT------ 319
           ++ K V+E    R NY             +L    +   R  +     Y           
Sbjct: 78  MVQKFVEEV--LRINY------------KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123

Query: 320 -AFADHGKSQEALDMFLKMRN--EGIEPNQVTFIGVLTACSHG----G---LVEDGCKQF 369
             FA +  S+     +LK+R     + P +   + +      G    G   +  D C  +
Sbjct: 124 QVFAKYNVSRL--QPYLKLRQALLELRPAK--NVLI-----DGVLGSGKTWVALDVCLSY 174

Query: 370 ELMTRV-FGI-----------KPLTEHLTCMVDLLGRSGQLEKAHS-------------- 403
           ++  ++ F I           + + E L  ++  +  +      HS              
Sbjct: 175 KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234

Query: 404 -------------LIMDYKDFCDAGTWGALLGACKV-------HVNAELGEIAARHL-LE 442
                        L++   +  +A  W A   +CK+        V   L      H+ L+
Sbjct: 235 RRLLKSKPYENCLLVLL--NVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292

Query: 443 -----LGPEKTGNSALLANIYASMGKWKD--SEIVKM------MISETEKKKSPGCSW 487
                L P++    +LL   Y    + +D   E++        +I+  E  +    +W
Sbjct: 293 HHSMTLTPDEV--KSLLLK-YLDC-RPQDLPREVLTTNPRRLSIIA--ESIRDGLATW 344

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	490
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	100.0
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.96
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.95
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.95
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.95
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.95
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.94
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.94
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.93
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.91
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.91
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.89
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.89
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.89
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.88
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.87
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.86
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.86
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.86
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.86
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.85
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.84
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.84
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.84
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.84
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.84
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.82
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.82
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.82
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.82
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.79
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.76
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.76
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.76
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.75
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.73
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.73
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	99.71
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.7
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.69
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.69
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.68
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.68
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.67
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.67
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.67
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.66
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.66
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.66
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.65
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.65
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.65
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.64
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.64
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.64
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.63
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.63
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.63
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.62
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.6
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.6
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.59
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.57
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.56
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.55
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.55
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.54
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.52
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.52
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.52
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	99.51
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.51
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.48
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.48
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.47
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.46
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.46
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.45
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.44
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.38
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.37
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.34
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.32
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.32
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.31
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	99.31
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.29
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.28
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.27
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	99.27
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.27
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.25
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.23
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	99.21
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.19
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	99.19
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.17
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.13
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	99.13
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.13
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	99.12
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.12
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	99.11
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.09
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	99.08
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	99.07
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	99.06
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.05
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	99.05
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	99.05
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	99.03
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	99.03
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	99.02
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	99.02
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.01
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	99.01
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	99.0
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.99
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.97
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.97
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.97
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.97
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.97
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.96
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.94
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.93
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.92
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.92
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.91
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.9
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.89
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	98.88
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.87
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.87
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.87
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.85
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.82
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.82
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.81
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.8
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.8
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.79
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.78
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.77
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.77
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.75
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.75
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.75
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.75
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.73
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.71
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.69
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.69
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.69
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.68
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.67
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.67
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.65
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.65
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.64
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.64
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.63
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.62
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.62
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.59
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.58
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.56
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.56
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.56
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.55
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.55
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	98.54
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.54
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.54
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.54
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.52
2l6j_A	111	TPR repeat-containing protein associated with HSP;	98.5
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	98.5
3k9i_A	117	BH0479 protein; putative protein binding protein,	98.49
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.49
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.48
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.45
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.43
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	98.43
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.38
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.36
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	98.36
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	98.36
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	98.31
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	98.31
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	98.29
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	98.28
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	98.27
2kat_A	115	Uncharacterized protein; NESG, structure, structur	98.24
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	98.19
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	98.17
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	98.08
2kat_A	115	Uncharacterized protein; NESG, structure, structur	98.03
2l6j_A	111	TPR repeat-containing protein associated with HSP;	98.02
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	98.02
1klx_A	138	Cysteine rich protein B; structural genomics, heli	98.02
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	98.0
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.99
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.99
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.88
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.87
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.78
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	97.73
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.71
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	97.68
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.6
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	97.53
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.39
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	97.39
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	97.37
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	97.36
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	97.25
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	97.23
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	97.14
1pc2_A	152	Mitochondria fission protein; unknown function; NM	97.12
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	97.02
1pc2_A	152	Mitochondria fission protein; unknown function; NM	97.0
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	96.89
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.86
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	96.67
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	96.45
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	96.33
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	96.28
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.21
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	96.19
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.16
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	96.01
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	95.65
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	95.45
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	95.45
4ady_A	963	RPN2, 26S proteasome regulatory subunit RPN2; prot	95.1
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	94.91
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	93.96
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	93.58
1qsa_A	618	Protein (soluble lytic transglycosylase SLT70); al	93.43
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	93.1
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	92.71
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	92.5
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	92.33
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	92.05
1y8m_A	144	FIS1; mitochondria, unknown function; NMR {Sacchar	92.03
3o48_A	134	Mitochondria fission 1 protein; tetratricopeptide	91.87
3ltj_A	201	Alpharep-4; protein engineering, heat-like repeat,	91.64
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	91.5
3ltm_A	211	Alpha-REP4; protein engineering, heat-like repeat,	91.25
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	91.25
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	91.13
3lpz_A	336	GET4 (YOR164C homolog); protein targeting, tail-an	90.9
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	90.39
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	90.34
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	90.21
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	89.4
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	89.13
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	88.49
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	88.29
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	88.14
2wpv_A	312	GET4, UPF0363 protein YOR164C; golgi-ER traffickin	88.08
3ltm_A	211	Alpha-REP4; protein engineering, heat-like repeat,	86.79
1zbp_A	273	Hypothetical protein VPA1032; alpha-beta protein,	85.29
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	84.96
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	84.25
2p58_C	116	Putative type III secretion protein YSCG; type III	83.59
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	83.56
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	83.3
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	82.18
3esl_A	202	Checkpoint serine/threonine-protein kinase BUB1; m	81.98
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	81.61

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=1e-40  Score=332.72  Aligned_cols=424  Identities=10%  Similarity=-0.014  Sum_probs=376.5

Q ss_pred             CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHH
Q 011249           31 HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSS  108 (490)
Q Consensus        31 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~  108 (490)
                      +++.  .|+.++..|.+.|+ +++|..+|+++.  .|+. .++..++.+|.+.|++++|..+|+.+...  +++..+++.
T Consensus        82 ~~~~--~~~~~~~~~~~~g~-~~~A~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~  155 (597)
T 2xpi_A           82 SRED--YLRLWRHDALMQQQ-YKCAAFVGEKVLDITGNP-NDAFWLAQVYCCTGDYARAKCLLTKEDLY--NRSSACRYL  155 (597)
T ss_dssp             CHHH--HHHHHHHHHHHTTC-HHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHTTCHHHHHHHHHHTCGG--GTCHHHHHH
T ss_pred             HHHH--HHHHHHHHHHHccC-chHHHHHHHHHHhhCCCc-hHHHHHHHHHHHcCcHHHHHHHHHHHhcc--ccchhHHHH
Confidence            6777  89999999999999 999999999985  5666 78899999999999999999999998654  567777766


Q ss_pred             HHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCC-------------------CHhHHHHHHHHHHhCCChHHHHH
Q 011249          109 VLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAER-------------------NVISWSAMVAGYANCGNMKAAKE  169 (490)
Q Consensus       109 ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-------------------~~~~~~~l~~~~~~~~~~~~a~~  169 (490)
                      ++.              +|.+.|++++|+++|+++...                   +..+|+.++.+|.+.|++++|++
T Consensus       156 l~~--------------~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  221 (597)
T 2xpi_A          156 AAF--------------CLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKE  221 (597)
T ss_dssp             HHH--------------HHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHH--------------HHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHH
Confidence            665              489999999999999965443                   47899999999999999999999


Q ss_pred             HHHHhccCC---chhHHHH--------------------------------------HHHHHhcCChhHHHHHHhhcCC-
Q 011249          170 FYDRMTEKN---SVTWVAM--------------------------------------IAGYGKCGEVREAKKVFDEISE-  207 (490)
Q Consensus       170 ~~~~~~~~~---~~~~~~l--------------------------------------~~~~~~~~~~~~A~~~~~~~~~-  207 (490)
                      +|+++.+.+   ...+..+                                      +..|.+.|++++|.++|+++.+ 
T Consensus       222 ~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~  301 (597)
T 2xpi_A          222 CYKEALMVDAKCYEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGL  301 (597)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTG
T ss_pred             HHHHHHHhCchhhHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcC
Confidence            999998532   2333222                                      4456678999999999999988 


Q ss_pred             -CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHH
Q 011249          208 -PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNAL  286 (490)
Q Consensus       208 -~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l  286 (490)
                       ++..+|+.++.+|.+.|++++|+++|+++.+.+. .+..++..++.++.+.|++++|..+++.+.+.. +.+..+++.+
T Consensus       302 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l  379 (597)
T 2xpi_A          302 EKSSDLLLCKADTLFVRSRFIDVLAITTKILEIDP-YNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAV  379 (597)
T ss_dssp             GGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcCc-ccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHH
Confidence             8999999999999999999999999999998763 377889999999999999999999999998765 6788899999


Q ss_pred             HHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChH
Q 011249          287 IHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVE  363 (490)
Q Consensus       287 ~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  363 (490)
                      +.+|.+.|++++|.++|+++.+   .+..+|+.++.+|.+.|++++|.++|+++.+.+ +.+..++..++.+|.+.|+++
T Consensus       380 ~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~  458 (597)
T 2xpi_A          380 GIYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNIL  458 (597)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHH
Confidence            9999999999999999998864   467899999999999999999999999999853 346789999999999999999


Q ss_pred             HHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-------CCCC--hhhHHHHHHHHhhhCChHHHH
Q 011249          364 DGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-------DFCD--AGTWGALLGACKVHVNAELGE  434 (490)
Q Consensus       364 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-------~~~~--~~~~~~l~~~~~~~g~~~~a~  434 (490)
                      +|.++|+++.+.  .+.+..+|..++.+|.+.|++++|.++|+++.       ..|+  ..+|..++.+|...|++++|.
T Consensus       459 ~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~  536 (597)
T 2xpi_A          459 LANEYLQSSYAL--FQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAI  536 (597)
T ss_dssp             HHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHh--CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHH
Confidence            999999999983  45578899999999999999999999998885       2565  679999999999999999999


Q ss_pred             HHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          435 IAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       435 ~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +.++++.+.+|+++.+|..++.+|.+.|++++|.+.++++.+..+
T Consensus       537 ~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~p  581 (597)
T 2xpi_A          537 DALNQGLLLSTNDANVHTAIALVYLHKKIPGLAITHLHESLAISP  581 (597)
T ss_dssp             HHHHHHHHHSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCC
Confidence            999999999999999999999999999999999999999988654

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=100.00  E-value=6.6e-39  Score=319.57  Aligned_cols=429  Identities=9%  Similarity=0.016  Sum_probs=371.3

Q ss_pred             hhhhchhhHHHHHHHHhhhcCCCCchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChh
Q 011249            8 PRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFR   85 (490)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~   85 (490)
                      ...|+++.|..+++.+.+   ..|+..  .+..++..|.+.|+ +++|..+|+++.  .++. .+++.++.+|.+.|+++
T Consensus        95 ~~~g~~~~A~~~~~~~~~---~~p~~~--~~~~l~~~~~~~g~-~~~A~~~~~~~~~~~~~~-~~~~~l~~~~~~~g~~~  167 (597)
T 2xpi_A           95 LMQQQYKCAAFVGEKVLD---ITGNPN--DAFWLAQVYCCTGD-YARAKCLLTKEDLYNRSS-ACRYLAAFCLVKLYDWQ  167 (597)
T ss_dssp             HHTTCHHHHHHHHHHHHH---HHCCHH--HHHHHHHHHHHTTC-HHHHHHHHHHTCGGGTCH-HHHHHHHHHHHHTTCHH
T ss_pred             HHccCchHHHHHHHHHHh---hCCCch--HHHHHHHHHHHcCc-HHHHHHHHHHHhccccch-hHHHHHHHHHHHHhhHH
Confidence            345788889999988876   557778  89999999999999 999999999984  4455 89999999999999999


Q ss_pred             HHHHHHHHHHhc---------------CCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--C-C
Q 011249           86 QSILLYAKMHRL---------------GVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--R-N  147 (490)
Q Consensus        86 ~A~~~~~~m~~~---------------g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~  147 (490)
                      +|.++|+++...               |..++..++..+..              +|.+.|++++|+++|+++.+  | +
T Consensus       168 ~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~--------------~~~~~g~~~~A~~~~~~~~~~~p~~  233 (597)
T 2xpi_A          168 GALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQ--------------VYTNLSNFDRAKECYKEALMVDAKC  233 (597)
T ss_dssp             HHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHH--------------HHHHTTCHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHhccCCccccccccccccccccccchhHHHHHHHHH--------------HHHHcCCHHHHHHHHHHHHHhCchh
Confidence            999999853221               22334556655554              58999999999999999975  3 2


Q ss_pred             HhHHHHH--------------------------------------HHHHHhCCChHHHHHHHHHhcc--CCchhHHHHHH
Q 011249          148 VISWSAM--------------------------------------VAGYANCGNMKAAKEFYDRMTE--KNSVTWVAMIA  187 (490)
Q Consensus       148 ~~~~~~l--------------------------------------~~~~~~~~~~~~a~~~~~~~~~--~~~~~~~~l~~  187 (490)
                      ...+..+                                      +..|.+.|++++|.++|+++.+  ++..++..++.
T Consensus       234 ~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~  313 (597)
T 2xpi_A          234 YEAFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKAD  313 (597)
T ss_dssp             HHHHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHH
T ss_pred             hHHHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHH
Confidence            3333333                                      4556678999999999999987  69999999999


Q ss_pred             HHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHH
Q 011249          188 GYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMA  264 (490)
Q Consensus       188 ~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a  264 (490)
                      +|.+.|++++|.++|+++.+   .+..++..++.++.+.|++++|.++++++.+.. +.+..++..++..|.+.|++++|
T Consensus       314 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A  392 (597)
T 2xpi_A          314 TLFVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVGIYYLCVNKISEA  392 (597)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHhccHHHH
Confidence            99999999999999999864   577889999999999999999999999999654 44788999999999999999999


Q ss_pred             HHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 011249          265 AILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEG  341 (490)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  341 (490)
                      ..+|+++.+.. +.+..+++.++.+|.+.|++++|+++|+++.+   .+..+|..++.+|.+.|++++|.++|+++.+..
T Consensus       393 ~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  471 (597)
T 2xpi_A          393 RRYFSKSSTMD-PQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALF  471 (597)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            99999998875 56788999999999999999999999998765   478899999999999999999999999999853


Q ss_pred             CCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHc---CCCCC--chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCCh
Q 011249          342 IEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVF---GIKPL--TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDA  414 (490)
Q Consensus       342 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~---~~~~~--~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~  414 (490)
                       +.+..+|..++..|.+.|++++|.++|+++.+..   +..|+  ..+|..++.+|.+.|++++|.++++++.  .+.+.
T Consensus       472 -~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~  550 (597)
T 2xpi_A          472 -QYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAIDALNQGLLLSTNDA  550 (597)
T ss_dssp             -CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSCCH
T ss_pred             -CCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCh
Confidence             3467899999999999999999999999998742   55676  6799999999999999999999999876  45578


Q ss_pred             hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHh
Q 011249          415 GTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYAS  460 (490)
Q Consensus       415 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~  460 (490)
                      .+|..++.+|...|++++|.+.++++++.+|+++.++..++.+|..
T Consensus       551 ~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~  596 (597)
T 2xpi_A          551 NVHTAIALVYLHKKIPGLAITHLHESLAISPNEIMASDLLKRALEE  596 (597)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCChHHHHHHHHHHhc
Confidence            8999999999999999999999999999999999999999887653

>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=100.00  E-value=1.4e-30  Score=245.07  Aligned_cols=369  Identities=12%  Similarity=0.071  Sum_probs=317.3

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC---CCHhH
Q 011249           74 LIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE---RNVIS  150 (490)
Q Consensus        74 l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~---~~~~~  150 (490)
                      +...+.+.|++++|.+.++.+.+.  .|+......++..             .+...|++++|...++...+   .+..+
T Consensus         5 ~a~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~l~~-------------~~~~~~~~~~a~~~~~~a~~~~p~~~~~   69 (388)
T 1w3b_A            5 LAHREYQAGDFEAAERHCMQLWRQ--EPDNTGVLLLLSS-------------IHFQCRRLDRSAHFSTLAIKQNPLLAEA   69 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH-------------HHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHH-------------HHHHcCCHHHHHHHHHHHHhcCCCchHH
Confidence            456678899999999999988876  5666555444443             47888999999999988765   36778


Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcC
Q 011249          151 WSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNG  224 (490)
Q Consensus       151 ~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g  224 (490)
                      |..+..++.+.|++++|+..|+++.+  | +..+|..++.++...|++++|.+.|+++.+   .+...+..+...+...|
T Consensus        70 ~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g  149 (388)
T 1w3b_A           70 YSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALG  149 (388)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcc
Confidence            99999999999999999999999874  4 556789999999999999999999998765   34567788889999999


Q ss_pred             ChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHh
Q 011249          225 YAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFS  304 (490)
Q Consensus       225 ~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~  304 (490)
                      ++++|++.|+++.+.. +-+..++..+..++...|++++|...++++.+.. |.+...+..+...+...|++++|...|+
T Consensus       150 ~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~  227 (388)
T 1w3b_A          150 RLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYL  227 (388)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence            9999999999998764 2256788999999999999999999999998876 5677888899999999999999999998


Q ss_pred             cccC--C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCC
Q 011249          305 RIKN--K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKP  380 (490)
Q Consensus       305 ~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~  380 (490)
                      +...  | +..++..++.++...|++++|...|+++.+.  .| +..++..+...+...|++++|...++++.+  ..+.
T Consensus       228 ~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~--~~p~  303 (388)
T 1w3b_A          228 RALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALR--LCPT  303 (388)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH--HCTT
T ss_pred             HHHhhCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh--hCcc
Confidence            8765  3 5788999999999999999999999999985  44 466888999999999999999999999998  3566


Q ss_pred             CchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHH
Q 011249          381 LTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY  458 (490)
Q Consensus       381 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  458 (490)
                      +..++..++..+.+.|++++|.+.++++.  .+.+..++..++.++...|++++|.+.++++++..|+++.++..++.++
T Consensus       304 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~a~~~lg~~~  383 (388)
T 1w3b_A          304 HADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTL  383 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHhHHHHH
Confidence            78889999999999999999999998887  3445778999999999999999999999999999999999999999988


Q ss_pred             HhcCC
Q 011249          459 ASMGK  463 (490)
Q Consensus       459 ~~~g~  463 (490)
                      .+.|+
T Consensus       384 ~~~~~  388 (388)
T 1w3b_A          384 KEMQD  388 (388)
T ss_dssp             HHTCC
T ss_pred             HHccC
Confidence            87764

>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=100.00  E-value=1.6e-29  Score=237.74  Aligned_cols=349  Identities=14%  Similarity=0.089  Sum_probs=310.3

Q ss_pred             HHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhH
Q 011249          124 ICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVRE  197 (490)
Q Consensus       124 ~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~  197 (490)
                      ...+.+.|++++|++.++.+.+  | +...+..+...+...|++++|...++...+  | +..+|..++.++.+.|++++
T Consensus         6 a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~~a~~~~~~a~~~~p~~~~~~~~lg~~~~~~g~~~~   85 (388)
T 1w3b_A            6 AHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQE   85 (388)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHH
Confidence            3457889999999999998865  4 566788888999999999999999998875  3 67789999999999999999


Q ss_pred             HHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhc
Q 011249          198 AKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEG  274 (490)
Q Consensus       198 A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  274 (490)
                      |+..|+++.+   .+..+|..++.++.+.|++++|++.|+++.+..+ .+...+..+...+...|++++|...++++.+.
T Consensus        86 A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  164 (388)
T 1w3b_A           86 AIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNP-DLYCVRSDLGNLLKALGRLEEAKACYLKAIET  164 (388)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCT-TCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            9999998864   4566899999999999999999999999998642 24556778888899999999999999999887


Q ss_pred             CCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHH
Q 011249          275 CCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFI  350 (490)
Q Consensus       275 ~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~  350 (490)
                      . |.+..++..+...+...|++++|...|+++.+   .+...|..+...+...|++++|...++++.+.  .| +..++.
T Consensus       165 ~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~  241 (388)
T 1w3b_A          165 Q-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSL--SPNHAVVHG  241 (388)
T ss_dssp             C-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH--CTTCHHHHH
T ss_pred             C-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCCHHHHH
Confidence            5 56788899999999999999999999999875   35678999999999999999999999999884  45 467888


Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhC
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHV  428 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g  428 (490)
                      .+...+...|++++|...++++.+  ..+.++..+..++.++.+.|++++|.+.|+++.  .+.+..++..+...+...|
T Consensus       242 ~l~~~~~~~g~~~~A~~~~~~al~--~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g  319 (388)
T 1w3b_A          242 NLACVYYEQGLIDLAIDTYRRAIE--LQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQG  319 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH--TCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHh--hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcC
Confidence            999999999999999999999987  345567789999999999999999999999887  5667889999999999999


Q ss_pred             ChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          429 NAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       429 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      ++++|++.++++++..|+++.++..++.++.+.|++++|.+.++++.+..
T Consensus       320 ~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~  369 (388)
T 1w3b_A          320 NIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS  369 (388)
T ss_dssp             CHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC
Confidence            99999999999999999999999999999999999999999999998754

>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=4.7e-28  Score=231.56  Aligned_cols=183  Identities=10%  Similarity=0.124  Sum_probs=154.2

Q ss_pred             HhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCC---------hHHHHHHHHHHHhcCCCCchh
Q 011249          211 SCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGD---------VEMAAILAKHVDEGCCDRTNY  281 (490)
Q Consensus       211 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~---------~~~a~~~~~~~~~~~~~~~~~  281 (490)
                      ..++.+|.+|++.|++++|+++|++|.+.|+.||..||+.||.+|++.+.         ++.|.++|++|.+.|+.||..
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            35777888888888888888888888888888888888888888876554         577888888888888888888


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccC----CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhc
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKN----KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACS  357 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~  357 (490)
                      +|+++|.+|++.|++++|.++|++|.+    ||..+|+.+|.+|++.|++++|.++|++|.+.|+.||..||+.++.+|+
T Consensus       107 tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~~  186 (501)
T 4g26_A          107 TFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVSM  186 (501)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHh
Confidence            888888888888888888888888864    7888888888888888888888888888888888888888888888888


Q ss_pred             CCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh
Q 011249          358 HGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR  394 (490)
Q Consensus       358 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  394 (490)
                      +.|++++|.+++++|.+. +..|+..||+.++..|..
T Consensus       187 ~~g~~d~A~~ll~~Mr~~-g~~ps~~T~~~l~~~F~s  222 (501)
T 4g26_A          187 DTKNADKVYKTLQRLRDL-VRQVSKSTFDMIEEWFKS  222 (501)
T ss_dssp             HTTCHHHHHHHHHHHHHH-TSSBCHHHHHHHHHHHHS
T ss_pred             hCCCHHHHHHHHHHHHHh-CCCcCHHHHHHHHHHHhc
Confidence            888888888888888885 888888888888887765

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.95  E-value=8.7e-26  Score=220.53  Aligned_cols=265  Identities=10%  Similarity=-0.081  Sum_probs=221.6

Q ss_pred             HHhHHHHHHHHHh---cCChHHHHHHHHHHHH-----cCc--------ccChhhHHHHHHHHhccCChHHHHHHHHHHHh
Q 011249          210 ASCWAAMTVCYVQ---NGYAKAAIEMYKVMRQ-----ENV--------RISEVAMVGAISACTQLGDVEMAAILAKHVDE  273 (490)
Q Consensus       210 ~~~~~~l~~~~~~---~g~~~~A~~~~~~~~~-----~~~--------~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  273 (490)
                      ...+......+..   .|++++|+..|+++.+     ...        +.+...+..+..++...|++++|...++.+.+
T Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~  265 (514)
T 2gw1_A          186 ADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIE  265 (514)
T ss_dssp             HHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            4455555555555   8999999999999887     311        22356778888889999999999999999988


Q ss_pred             cCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHH
Q 011249          274 GCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFI  350 (490)
Q Consensus       274 ~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~  350 (490)
                      ....  ...+..++.++...|++++|...++++.+   .+...+..+...+...|++++|...++++.+.. +.+...+.
T Consensus       266 ~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  342 (514)
T 2gw1_A          266 LFPR--VNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELD-PENIFPYI  342 (514)
T ss_dssp             HCCC--HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTC-SSCSHHHH
T ss_pred             hCcc--HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-hhhHHHHH
Confidence            7633  88888899999999999999999998765   366788999999999999999999999998853 22456888


Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc----CCCC----hhhHHHHHH
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK----DFCD----AGTWGALLG  422 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~----~~~~~~l~~  422 (490)
                      .+...+...|++++|...++++.+.  .+.+...+..++..+...|++++|...++++.    ..+.    ...+..+..
T Consensus       343 ~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~  420 (514)
T 2gw1_A          343 QLACLAYRENKFDDCETLFSEAKRK--FPEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVGKAT  420 (514)
T ss_dssp             HHHHHTTTTTCHHHHHHHHHHHHHH--STTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHH--cccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHH
Confidence            8889999999999999999999873  45567888899999999999999999998776    1122    338888999


Q ss_pred             HHhh---hCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          423 ACKV---HVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       423 ~~~~---~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .+..   .|++++|.+.++++.+..|+++.++..++.++.+.|++++|.+.++++.+.++
T Consensus       421 ~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~  480 (514)
T 2gw1_A          421 LLTRNPTVENFIEATNLLEKASKLDPRSEQAKIGLAQMKLQQEDIDEAITLFEESADLAR  480 (514)
T ss_dssp             HHHTSCCTTHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS
T ss_pred             HHhhhhhcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhcc
Confidence            9999   99999999999999999999999999999999999999999999999887654

>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=5.7e-27  Score=224.09  Aligned_cols=200  Identities=14%  Similarity=0.188  Sum_probs=172.6

Q ss_pred             HHHHHHHHHHHHcCcccCh-hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCC---------h
Q 011249          227 KAAIEMYKVMRQENVRISE-VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGY---------L  296 (490)
Q Consensus       227 ~~A~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---------~  296 (490)
                      ..+..+.+++.+.+..+.+ ..++.+|.+|++.|++++|.++|++|.+.|+.||..+|++||.+|.+.+.         +
T Consensus         7 s~~e~L~~~~~~k~~~~spe~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l   86 (501)
T 4g26_A            7 SPSENLSRKAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGL   86 (501)
T ss_dssp             -----------------CHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHH
T ss_pred             chHHHHHHHHHHhcccCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchH
Confidence            3455666777777765544 46888999999999999999999999999999999999999999987665         6


Q ss_pred             HHHHHHHhcccC----CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHH
Q 011249          297 DLAWREFSRIKN----KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELM  372 (490)
Q Consensus       297 ~~A~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~  372 (490)
                      +.|.++|++|..    ||..+|+++|.+|++.|++++|.++|++|.+.|+.||..||+.+|.+|++.|++++|.++|++|
T Consensus        87 ~~A~~lf~~M~~~G~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M  166 (501)
T 4g26_A           87 SRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHM  166 (501)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHH
Confidence            889999999975    8999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc---CCCChhhHHHHHHHHhhh
Q 011249          373 TRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK---DFCDAGTWGALLGACKVH  427 (490)
Q Consensus       373 ~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---~~~~~~~~~~l~~~~~~~  427 (490)
                      .+. |+.||..+|+.|+.+|++.|+.++|.+++++|.   ..|+..||+.++..|...
T Consensus       167 ~~~-G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          167 VES-EVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HHT-TCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSH
T ss_pred             Hhc-CCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcC
Confidence            995 999999999999999999999999999999998   789999999999888653

>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=99.95  E-value=3.4e-25  Score=217.64  Aligned_cols=420  Identities=12%  Similarity=0.005  Sum_probs=299.0

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCH-hhHHHHHHHh
Q 011249           37 YAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSG-FTFSSVLNAC  113 (490)
Q Consensus        37 ~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~-~~~~~ll~~~  113 (490)
                      .+..+...+.+.|+ +++|.+.|+++.  .|+....|..+..++.+.|++++|++.|+++.+.  .|+. ..+..+    
T Consensus        27 ~~~~~g~~~~~~g~-~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l----   99 (537)
T 3fp2_A           27 QLKNRGNHFFTAKN-FNEAIKYYQYAIELDPNEPVFYSNISACYISTGDLEKVIEFTTKALEI--KPDHSKALLRR----   99 (537)
T ss_dssp             HHHHHHHHHHHTTC-CC-CHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHH----
T ss_pred             HHHHHHHHHHHhcc-HHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCchHHHHHHH----
Confidence            78889999999999 999999999885  5666588999999999999999999999999886  3443 333322    


Q ss_pred             cCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccC------CchhHHHHHH
Q 011249          114 ARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEK------NSVTWVAMIA  187 (490)
Q Consensus       114 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~~~~~l~~  187 (490)
                                ...+...|++++|+..|+.+ ..++......+..+...+....|...++++...      ........+.
T Consensus       100 ----------a~~~~~~g~~~~A~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~  168 (537)
T 3fp2_A          100 ----------ASANESLGNFTDAMFDLSVL-SLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLA  168 (537)
T ss_dssp             ----------HHHHHHHTCHHHHHHHHHHH-C-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHH
T ss_pred             ----------HHHHHHcCCHHHHHHHHHHH-hcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHH
Confidence                      33588899999999999744 333333333445566666678899999988753      2222344555


Q ss_pred             HHHhcCChhHHHHHHhhcCCCCHH---hHHHHHHHHHh--------cCChHHHHHHHHHHHHcCcccC------hhhHHH
Q 011249          188 GYGKCGEVREAKKVFDEISEPDAS---CWAAMTVCYVQ--------NGYAKAAIEMYKVMRQENVRIS------EVAMVG  250 (490)
Q Consensus       188 ~~~~~~~~~~A~~~~~~~~~~~~~---~~~~l~~~~~~--------~g~~~~A~~~~~~~~~~~~~p~------~~~~~~  250 (490)
                      .+....+.+.+...+......+..   ....+...+..        .|++++|+.+++++.+......      ..++..
T Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~  248 (537)
T 3fp2_A          169 SFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCY  248 (537)
T ss_dssp             HHHHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHH
T ss_pred             HHHHhcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHH
Confidence            566677777777777666653322   33333333322        2477888888888876532210      224666


Q ss_pred             HHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCCh
Q 011249          251 AISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKS  327 (490)
Q Consensus       251 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~  327 (490)
                      +...+...|++++|...++.+.+..  |+...+..+...+...|++++|...|+++.+   .+..+|..+...+...|++
T Consensus       249 ~g~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  326 (537)
T 3fp2_A          249 TGIFHFLKNNLLDAQVLLQESINLH--PTPNSYIFLALTLADKENSQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDY  326 (537)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhcccHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHhcCHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCH
Confidence            6677778888888888888888765  3367777788888888888888888887764   3567788888888888888


Q ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHh
Q 011249          328 QEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMD  407 (490)
Q Consensus       328 ~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  407 (490)
                      ++|...++++.+.. +.+...+..+...+...|++++|...++++.+.  .+.+...+..+..++...|++++|.+.|++
T Consensus       327 ~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  403 (537)
T 3fp2_A          327 KNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNETKLK--FPTLPEVPTFFAEILTDRGDFDTAIKQYDI  403 (537)
T ss_dssp             HHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            88888888888742 223467777888888888888888888888873  455567788888888888888888888877


Q ss_pred             cc--C--CC----ChhhHHHHHHHHhhh----------CChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHH
Q 011249          408 YK--D--FC----DAGTWGALLGACKVH----------VNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEI  469 (490)
Q Consensus       408 ~~--~--~~----~~~~~~~l~~~~~~~----------g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~  469 (490)
                      +.  .  .+    ....+......+...          |++++|...++++.+..|+++.++..++.+|.+.|++++|.+
T Consensus       404 a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~g~~~~A~~  483 (537)
T 3fp2_A          404 AKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAKIGLAQLKLQMEKIDEAIE  483 (537)
T ss_dssp             HHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHH
Confidence            65  1  11    112234445566666          888888888888888888888888888888888888888888


Q ss_pred             HHHHhhhccc
Q 011249          470 VKMMISETEK  479 (490)
Q Consensus       470 ~~~~~~~~~~  479 (490)
                      .++++.+...
T Consensus       484 ~~~~al~~~~  493 (537)
T 3fp2_A          484 LFEDSAILAR  493 (537)
T ss_dssp             HHHHHHHHC-
T ss_pred             HHHHHHHhCC
Confidence            8888776543

>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=99.95  E-value=8e-25  Score=209.99  Aligned_cols=327  Identities=10%  Similarity=0.061  Sum_probs=267.6

Q ss_pred             CHhHHHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHH
Q 011249          147 NVISWSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCY  220 (490)
Q Consensus       147 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~  220 (490)
                      +...+..++..+.+.|++++|+.+|+++.+  | +..++..++.++...|++++|+..|+++.+   .+...+..++.+|
T Consensus        25 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~  104 (450)
T 2y4t_A           25 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLL  104 (450)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHH
Confidence            556788888889999999999999998875  3 677888888999999999999999988764   4577888899999


Q ss_pred             HhcCChHHHHHHHHHHHHcCcccCh---hhHHHH------------HHHHhccCChHHHHHHHHHHHhcCCCCchhHHHH
Q 011249          221 VQNGYAKAAIEMYKVMRQENVRISE---VAMVGA------------ISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNA  285 (490)
Q Consensus       221 ~~~g~~~~A~~~~~~~~~~~~~p~~---~~~~~l------------~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  285 (490)
                      .+.|++++|.+.|+++.+.... +.   ..+..+            ...+...|++++|...++.+.+.. +.+..++..
T Consensus       105 ~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~  182 (450)
T 2y4t_A          105 LKQGKLDEAEDDFKKVLKSNPS-ENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAELREL  182 (450)
T ss_dssp             HHTTCHHHHHHHHHHHHTSCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhcCCC-ChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHH
Confidence            9999999999999998875321 22   444444            445888999999999999998876 667888999


Q ss_pred             HHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcH-HHHHHH---------
Q 011249          286 LIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQ-VTFIGV---------  352 (490)
Q Consensus       286 l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~~~~l---------  352 (490)
                      ++.+|.+.|++++|...|+++.+   .++.+|..++.+|...|++++|...|+++.+.  .|+. ..+..+         
T Consensus       183 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~p~~~~~~~~~~~~~~~~~~  260 (450)
T 2y4t_A          183 RAECFIKEGEPRKAISDLKAASKLKNDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCFAHYKQVKKLNKL  260 (450)
T ss_dssp             HHHHHHHTTCGGGGHHHHHHHHHHHCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCChHHHHHHHHHHHHHHHH
Confidence            99999999999999999998865   46789999999999999999999999999874  4443 344333         


Q ss_pred             ---HHHhcCCCChHHHHHHHHHHHHHcCCCCC-----chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHH
Q 011249          353 ---LTACSHGGLVEDGCKQFELMTRVFGIKPL-----TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLG  422 (490)
Q Consensus       353 ---~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~  422 (490)
                         ...+...|++++|...++++.+.   .|+     ...+..++.++.+.|++++|...++++.  .+.+...|..++.
T Consensus       261 ~~~~~~~~~~g~~~~A~~~~~~~l~~---~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~  337 (450)
T 2y4t_A          261 IESAEELIRDGRYTDATSKYESVMKT---EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQMEPDNVNALKDRAE  337 (450)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHH---CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhc---CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHH
Confidence               77889999999999999999874   333     3477888999999999999999999876  4557889999999


Q ss_pred             HHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHH------------HHhcC-----CcchHHHHHHH-hhhcccc
Q 011249          423 ACKVHVNAELGEIAARHLLELGPEKTGNSALLANI------------YASMG-----KWKDSEIVKMM-ISETEKK  480 (490)
Q Consensus       423 ~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~------------~~~~g-----~~~~A~~~~~~-~~~~~~~  480 (490)
                      +|...|++++|.+.++++++..|+++.++..++.+            |...|     +.+++.+.+++ ..+..+.
T Consensus       338 ~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~~~y~~lg~~~~~~~~~~~~~y~~~~l~~~pd  413 (450)
T 2y4t_A          338 AYLIEEMYDEAIQDYETAQEHNENDQQIREGLEKAQRLLKQSQKRDYYKILGVKRNAKKQEIIKAYRKLALQWHPD  413 (450)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHHHHHHSCCSGGGSCSSTTCCTTHHHHHHHHHHHHSCGG
T ss_pred             HHHHhcCHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHhhcccchhHHHHhCCCccCCHHHHHHHHHHHHHHhCCC
Confidence            99999999999999999999999999999999844            55555     45666777775 4443333

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.94  E-value=6.1e-25  Score=214.52  Aligned_cols=397  Identities=11%  Similarity=-0.020  Sum_probs=289.0

Q ss_pred             HHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCH-hhHHHHHHHh
Q 011249           37 YAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSG-FTFSSVLNAC  113 (490)
Q Consensus        37 ~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~-~~~~~ll~~~  113 (490)
                      .+..+...+.+.|+ +++|...|+++.  .|+. ..|..+..++...|++++|+..|+++.+.  .|+. ..+..+.   
T Consensus         8 ~~~~~g~~~~~~g~-~~~A~~~~~~al~~~p~~-~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~---   80 (514)
T 2gw1_A            8 ALKDKGNQFFRNKK-YDDAIKYYNWALELKEDP-VFYSNLSACYVSVGDLKKVVEMSTKALEL--KPDYSKVLLRRA---   80 (514)
T ss_dssp             HHHHHHHHHHHTSC-HHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CSCCHHHHHHHH---
T ss_pred             HHHHHHHHHHHhcc-HHHHHHHHHHHHhcCccH-HHHHhHHHHHHHHhhHHHHHHHHHHHhcc--ChHHHHHHHHHH---
Confidence            45556666666666 666666666654  3444 56666666666666666666666666654  2322 2222222   


Q ss_pred             cCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCCChHHHHHH--------------------
Q 011249          114 ARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCGNMKAAKEF--------------------  170 (490)
Q Consensus       114 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~--------------------  170 (490)
                                 .+|...|++++|...|+++.+  | +......++..+........+.+.                    
T Consensus        81 -----------~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~  149 (514)
T 2gw1_A           81 -----------SANEGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAK  149 (514)
T ss_dssp             -----------HHHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC--------------------
T ss_pred             -----------HHHHHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhh
Confidence                       235666666666666666543  1 222222222222211111111111                    


Q ss_pred             ------------------HHHhcc---------C-CchhHHHHHHHHHh---cCChhHHHHHHhhcCC------------
Q 011249          171 ------------------YDRMTE---------K-NSVTWVAMIAGYGK---CGEVREAKKVFDEISE------------  207 (490)
Q Consensus       171 ------------------~~~~~~---------~-~~~~~~~l~~~~~~---~~~~~~A~~~~~~~~~------------  207 (490)
                                        +.....         | +...+......+..   .|++++|...|+++.+            
T Consensus       150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~  229 (514)
T 2gw1_A          150 ERKDKQENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNED  229 (514)
T ss_dssp             -------CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTC
T ss_pred             HHHhhccCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccc
Confidence                              111100         1 14445555555554   8999999999987644            


Q ss_pred             -----CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhH
Q 011249          208 -----PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYV  282 (490)
Q Consensus       208 -----~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~  282 (490)
                           .+...+..+..++...|++++|+..++++.+....  ...+..+..++...|++++|...++.+.+.. +.+..+
T Consensus       230 ~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~~~--~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~  306 (514)
T 2gw1_A          230 EKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELFPR--VNSYIYMALIMADRNDSTEYYNYFDKALKLD-SNNSSV  306 (514)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHCCC--HHHHHHHHHHHHTSSCCTTGGGHHHHHHTTC-TTCTHH
T ss_pred             cccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCcc--HHHHHHHHHHHHHCCCHHHHHHHHHHHhhcC-cCCHHH
Confidence                 13457888999999999999999999999987533  7888899999999999999999999998876 567788


Q ss_pred             HHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCC
Q 011249          283 SNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHG  359 (490)
Q Consensus       283 ~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  359 (490)
                      +..+..+|...|++++|...|+++.+   .+...+..+...+...|++++|...++++.+.. +.+...+..+...+...
T Consensus       307 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~  385 (514)
T 2gw1_A          307 YYHRGQMNFILQNYDQAGKDFDKAKELDPENIFPYIQLACLAYRENKFDDCETLFSEAKRKF-PEAPEVPNFFAEILTDK  385 (514)
T ss_dssp             HHHHHHHHHHTTCTTHHHHHHHHHHHTCSSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS-TTCSHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc-ccCHHHHHHHHHHHHHC
Confidence            89999999999999999999998764   467789999999999999999999999998852 33556888899999999


Q ss_pred             CChHHHHHHHHHHHHHcCCCCC----chHHHHHHHHHhh---cCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCCh
Q 011249          360 GLVEDGCKQFELMTRVFGIKPL----TEHLTCMVDLLGR---SGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNA  430 (490)
Q Consensus       360 g~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~---~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~  430 (490)
                      |++++|...++++.+.....++    ...+..++.++..   .|++++|.+.++++.  .+.+..++..+...+...|++
T Consensus       386 ~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~  465 (514)
T 2gw1_A          386 NDFDKALKQYDLAIELENKLDGIYVGIAPLVGKATLLTRNPTVENFIEATNLLEKASKLDPRSEQAKIGLAQMKLQQEDI  465 (514)
T ss_dssp             TCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHHHHHHHHTSCCTTHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCH
T ss_pred             CCHHHHHHHHHHHHHhhhccchHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCH
Confidence            9999999999999874222232    3388899999999   999999999998876  455677889999999999999


Q ss_pred             HHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          431 ELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       431 ~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      ++|.+.++++.+..|+++..+..+.
T Consensus       466 ~~A~~~~~~a~~~~~~~~~~~~~~~  490 (514)
T 2gw1_A          466 DEAITLFEESADLARTMEEKLQAIT  490 (514)
T ss_dssp             HHHHHHHHHHHHHCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccHHHHHHHH
Confidence            9999999999999999888777664

>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=99.94  E-value=5.7e-24  Score=204.07  Aligned_cols=339  Identities=12%  Similarity=0.043  Sum_probs=276.6

Q ss_pred             HHHHHHhcCCHHHHHHHHhhcCC---CCHhHHHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChh
Q 011249          123 VICGYTKIGLMDDAQRLFDSMAE---RNVISWSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVR  196 (490)
Q Consensus       123 l~~~~~~~g~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~  196 (490)
                      ++..+.+.|++++|+.+|+++.+   .+..+|..++.++...|++++|+..|+++.+  | +..++..++.+|...|+++
T Consensus        32 ~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~  111 (450)
T 2y4t_A           32 LGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLKMDFTAARLQRGHLLLKQGKLD  111 (450)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHH
Confidence            34458999999999999999875   4788999999999999999999999999985  3 6778999999999999999


Q ss_pred             HHHHHHhhcCC--CC-H---HhHHHH------------HHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhcc
Q 011249          197 EAKKVFDEISE--PD-A---SCWAAM------------TVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQL  258 (490)
Q Consensus       197 ~A~~~~~~~~~--~~-~---~~~~~l------------~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  258 (490)
                      +|.+.|+++.+  |+ .   ..+..+            ...+...|++++|+..|+++.+.. +.+...+..+..++...
T Consensus       112 ~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~  190 (450)
T 2y4t_A          112 EAEDDFKKVLKSNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAELRELRAECFIKE  190 (450)
T ss_dssp             HHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHC
Confidence            99999999876  33 3   555555            445899999999999999999764 33678899999999999


Q ss_pred             CChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-ChhHHHHH------------HHHHHh
Q 011249          259 GDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-DVISYSSM------------ITAFAD  323 (490)
Q Consensus       259 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l------------~~~~~~  323 (490)
                      |++++|...++.+.+.. +.+..++..++.+|...|++++|...|+++.+  | +...+..+            +..+..
T Consensus       191 g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~  269 (450)
T 2y4t_A          191 GEPRKAISDLKAASKLK-NDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQVKKLNKLIESAEELIR  269 (450)
T ss_dssp             TCGGGGHHHHHHHHHHH-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999998875 66788999999999999999999999998865  3 34445444            788999


Q ss_pred             cCChHHHHHHHHHHHHcCCCCc-----HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCCh
Q 011249          324 HGKSQEALDMFLKMRNEGIEPN-----QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQL  398 (490)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~~~p~-----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  398 (490)
                      .|++++|...|+++.+.  .|+     ...+..+...+.+.|++++|...++++.+.  .+.+...+..++.+|...|++
T Consensus       270 ~g~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~--~p~~~~~~~~l~~~~~~~~~~  345 (450)
T 2y4t_A          270 DGRYTDATSKYESVMKT--EPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQM--EPDNVNALKDRAEAYLIEEMY  345 (450)
T ss_dssp             HTCHHHHHHHHHHHHHH--CCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCH
T ss_pred             cCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHhcCH
Confidence            99999999999999984  454     347888889999999999999999999873  455688999999999999999


Q ss_pred             HHHHHHHHhcc-CCC-ChhhHHHHHHH------------HhhhC-----ChHHHHHHHHH-HHhcCCCCCc---------
Q 011249          399 EKAHSLIMDYK-DFC-DAGTWGALLGA------------CKVHV-----NAELGEIAARH-LLELGPEKTG---------  449 (490)
Q Consensus       399 ~~A~~~~~~~~-~~~-~~~~~~~l~~~------------~~~~g-----~~~~a~~~~~~-~~~~~p~~~~---------  449 (490)
                      ++|...++++. ..| +...+..+..+            |...|     +.+++.+.+++ +++..|++..         
T Consensus       346 ~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~~~y~~lg~~~~~~~~~~~~~y~~~~l~~~pd~~~~~~~~~~a~  425 (450)
T 2y4t_A          346 DEAIQDYETAQEHNENDQQIREGLEKAQRLLKQSQKRDYYKILGVKRNAKKQEIIKAYRKLALQWHPDNFQNEEEKKKAE  425 (450)
T ss_dssp             HHHHHHHHHHHTTSSSCHHHHHHHHHHHHHHHHHHSCCSGGGSCSSTTCCTTHHHHHHHHHHHHSCGGGCCSHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcchHHHHHHHHHHHHHhhcccchhHHHHhCCCccCCHHHHHHHHHHHHHHhCCCCCCCchHHHHHH
Confidence            99999999886 334 45566666633            33344     66788888887 6777776432         


Q ss_pred             -hHHHHHHHHHhcCCcchH
Q 011249          450 -NSALLANIYASMGKWKDS  467 (490)
Q Consensus       450 -~~~~l~~~~~~~g~~~~A  467 (490)
                       .+..+..+|...|+.+++
T Consensus       426 ~~~~~i~~ay~~L~d~~~r  444 (450)
T 2y4t_A          426 KKFIDIAAAKEVLSDPEMR  444 (450)
T ss_dssp             HHHHHHHHHHHHSSGGGGC
T ss_pred             HHHHHHHHHHHHhCCHHHH
Confidence             445566666666655543

>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=99.93  E-value=2.1e-23  Score=204.81  Aligned_cols=421  Identities=9%  Similarity=-0.003  Sum_probs=323.0

Q ss_pred             cchhhhhhchhhHHHHHHHHhhhcCCC-CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHh
Q 011249            4 KYLVPRSKTFNQLKQVHSYLLKTLTKP-HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVL   80 (490)
Q Consensus         4 ~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~   80 (490)
                      +..+-..|+++.|...++...+   .. .++.  .+..+...|.+.|+ +++|.+.|+++.  .|+....|..+...+..
T Consensus        32 g~~~~~~g~~~~A~~~~~~al~---~~p~~~~--~~~~la~~~~~~g~-~~~A~~~~~~al~~~p~~~~~~~~la~~~~~  105 (537)
T 3fp2_A           32 GNHFFTAKNFNEAIKYYQYAIE---LDPNEPV--FYSNISACYISTGD-LEKVIEFTTKALEIKPDHSKALLRRASANES  105 (537)
T ss_dssp             HHHHHHTTCCC-CHHHHHHHHH---HCTTCHH--HHHHHHHHHHHHTC-HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhccHHHHHHHHHHHHh---hCCCCcH--HHHHHHHHHHHcCC-HHHHHHHHHHHHhcCCchHHHHHHHHHHHHH
Confidence            3445567888889988888887   55 7888  99999999999999 999999999985  56665789999999999


Q ss_pred             cCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCC------HhHHHHH
Q 011249           81 HAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERN------VISWSAM  154 (490)
Q Consensus        81 ~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~------~~~~~~l  154 (490)
                      .|++++|...|+.+ ..  .|+....  .+.              .+...+...+|...++.+...+      .......
T Consensus       106 ~g~~~~A~~~~~~~-~~--~~~~~~~--~~~--------------~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~  166 (537)
T 3fp2_A          106 LGNFTDAMFDLSVL-SL--NGDFDGA--SIE--------------PMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTS  166 (537)
T ss_dssp             HTCHHHHHHHHHHH-C-----------------------------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHH
T ss_pred             cCCHHHHHHHHHHH-hc--CCCCChH--HHH--------------HHHHHHHHHHHHHHHHHHHHhCccccccccchHhH
Confidence            99999999999643 32  3332221  111              1344566778999998887521      1122334


Q ss_pred             HHHHHhCCChHHHHHHHHHhccCCch---hHHHHHHHHHh--------cCChhHHHHHHhhcCC--CC--------HHhH
Q 011249          155 VAGYANCGNMKAAKEFYDRMTEKNSV---TWVAMIAGYGK--------CGEVREAKKVFDEISE--PD--------ASCW  213 (490)
Q Consensus       155 ~~~~~~~~~~~~a~~~~~~~~~~~~~---~~~~l~~~~~~--------~~~~~~A~~~~~~~~~--~~--------~~~~  213 (490)
                      +..+....+.+.+...+.+....+..   ....+...+..        .|++++|..+|+++.+  |+        ..++
T Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~  246 (537)
T 3fp2_A          167 LASFFGIFDSHLEVSSVNTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALAL  246 (537)
T ss_dssp             HHHHHHTSCHHHHHHTSCCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHH
T ss_pred             HHHHHHhcChHHHHHHHhhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHH
Confidence            55566677777777776666554433   33333333322        2578999999998866  33        2357


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc
Q 011249          214 AAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC  293 (490)
Q Consensus       214 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  293 (490)
                      ..+...+...|++++|+..++++.+.  .|+...+..+..++...|++++|...++.+.+.. +.+..++..+...+...
T Consensus       247 ~~~g~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~  323 (537)
T 3fp2_A          247 CYTGIFHFLKNNLLDAQVLLQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDLN-PEYPPTYYHRGQMYFIL  323 (537)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcccHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhccC-CCCHHHHHHHHHHHHhc
Confidence            77788899999999999999999986  4557888899999999999999999999998876 66788899999999999


Q ss_pred             CChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHH
Q 011249          294 GYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFE  370 (490)
Q Consensus       294 ~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~  370 (490)
                      |++++|...|+++.+   .+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++
T Consensus       324 ~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~  402 (537)
T 3fp2_A          324 QDYKNAKEDFQKAQSLNPENVYPYIQLACLLYKQGKFTESEAFFNETKLKF-PTLPEVPTFFAEILTDRGDFDTAIKQYD  402 (537)
T ss_dssp             TCHHHHHHHHHHHHHHCTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhCCHHHHHHHHH
Confidence            999999999998865   356789999999999999999999999999852 3345688888999999999999999999


Q ss_pred             HHHHHcCCCCC----chHHHHHHHHHhhc----------CChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHH
Q 011249          371 LMTRVFGIKPL----TEHLTCMVDLLGRS----------GQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGE  434 (490)
Q Consensus       371 ~~~~~~~~~~~----~~~~~~l~~~~~~~----------g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~  434 (490)
                      ++.+.....++    ...+..+..++...          |++++|...|+++.  .+.+...+..+...+...|++++|.
T Consensus       403 ~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~g~~~~A~  482 (537)
T 3fp2_A          403 IAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAIKLLTKACELDPRSEQAKIGLAQLKLQMEKIDEAI  482 (537)
T ss_dssp             HHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHH
Confidence            98874211121    22244456777777          99999999999877  4556788999999999999999999


Q ss_pred             HHHHHHHhcCCCCCchHHH
Q 011249          435 IAARHLLELGPEKTGNSAL  453 (490)
Q Consensus       435 ~~~~~~~~~~p~~~~~~~~  453 (490)
                      +.|+++++..|+++.....
T Consensus       483 ~~~~~al~~~~~~~~~~~~  501 (537)
T 3fp2_A          483 ELFEDSAILARTMDEKLQA  501 (537)
T ss_dssp             HHHHHHHHHC--CHHHHHH
T ss_pred             HHHHHHHHhCCCcHHHHHH
Confidence            9999999999998776543

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.91  E-value=7.2e-22  Score=183.20  Aligned_cols=310  Identities=9%  Similarity=0.043  Sum_probs=229.5

Q ss_pred             CHhHHHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHH
Q 011249          147 NVISWSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCY  220 (490)
Q Consensus       147 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~  220 (490)
                      |+..+..+...+...|++++|+..|+++.+  | +..++..++..+...|++++|...|+++.+   .+...+..+..++
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~   81 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIALKMDFTAARLQRGHLL   81 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCcchHHHHHHHHH
Confidence            345666677777777888888888877764  2 556777777777778888888887777654   3556777788888


Q ss_pred             HhcCChHHHHHHHHHHHHcCcc--cChhhHHHH------------HHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHH
Q 011249          221 VQNGYAKAAIEMYKVMRQENVR--ISEVAMVGA------------ISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNAL  286 (490)
Q Consensus       221 ~~~g~~~~A~~~~~~~~~~~~~--p~~~~~~~l------------~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l  286 (490)
                      ...|++++|+..|+++.+....  .+...+..+            ...+...|++++|...++.+.+.. +.+...+..+
T Consensus        82 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~  160 (359)
T 3ieg_A           82 LKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-VWDAELRELR  160 (359)
T ss_dssp             HHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCchHHHHHH
Confidence            8888888888888887765320  123333333            467778888888888888887775 5667778888


Q ss_pred             HHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc-HHHHH------------
Q 011249          287 IHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN-QVTFI------------  350 (490)
Q Consensus       287 ~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~------------  350 (490)
                      ...+...|++++|...++++.+   .+...+..+...+...|++++|...++++.+.  .|+ ...+.            
T Consensus       161 ~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~  238 (359)
T 3ieg_A          161 AECFIKEGEPRKAISDLKAASKLKSDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCFAHYKQVKKLNKLI  238 (359)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHTTCSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CccchHHHHHHHHHHHHHHHH
Confidence            8888888888888888887765   36678888888888888999998888888874  333 22222            


Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHcCCCCCc----hHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHH
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLT----EHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGAC  424 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~  424 (490)
                      .+...+...|++++|...++++.+. . +.+.    ..+..+..++...|++++|.+.+++..  .+.+..++..+...+
T Consensus       239 ~~a~~~~~~~~~~~A~~~~~~~~~~-~-~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  316 (359)
T 3ieg_A          239 ESAEELIRDGRYTDATSKYESVMKT-E-PSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQMEPDNVNALKDRAEAY  316 (359)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH-C-CSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhc-C-CCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            2255677889999999999888874 2 2222    234457788888999999999888776  444677888888888


Q ss_pred             hhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhc
Q 011249          425 KVHVNAELGEIAARHLLELGPEKTGNSALLANIYASM  461 (490)
Q Consensus       425 ~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  461 (490)
                      ...|++++|.+.++++++.+|+++.++..+..+....
T Consensus       317 ~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~  353 (359)
T 3ieg_A          317 LIEEMYDEAIQDYEAAQEHNENDQQIREGLEKAQRLL  353 (359)
T ss_dssp             HHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHH
Confidence            8899999999999999999998888888887766544

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.91  E-value=1.2e-21  Score=181.58  Aligned_cols=297  Identities=12%  Similarity=0.020  Sum_probs=251.3

Q ss_pred             CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHH
Q 011249          178 NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISA  254 (490)
Q Consensus       178 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~  254 (490)
                      |+..+..++..+...|++++|+..|+++.+   .+...+..+..++...|++++|+..++++.+.. +.+...+..+..+
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~   80 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGDPDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHL   80 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHH
Confidence            345677889999999999999999998865   567889999999999999999999999999864 2256788999999


Q ss_pred             HhccCChHHHHHHHHHHHhcCCC---CchhHHHHH------------HHHHHhcCChHHHHHHHhcccC---CChhHHHH
Q 011249          255 CTQLGDVEMAAILAKHVDEGCCD---RTNYVSNAL------------IHMHSKCGYLDLAWREFSRIKN---KDVISYSS  316 (490)
Q Consensus       255 ~~~~g~~~~a~~~~~~~~~~~~~---~~~~~~~~l------------~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~  316 (490)
                      +...|++++|...++.+.+.. +   .+...+..+            ...+...|++++|...++++.+   .+...+..
T Consensus        81 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~  159 (359)
T 3ieg_A           81 LLKQGKLDEAEDDFKKVLKSN-PSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVWDAELREL  159 (359)
T ss_dssp             HHHHTCHHHHHHHHHHHHTSC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHHcCChHHHHHHHHHHHhcC-CcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHHHHH
Confidence            999999999999999998875 3   345555544            5788999999999999998865   46788999


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHH----------
Q 011249          317 MITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLT----------  386 (490)
Q Consensus       317 l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~----------  386 (490)
                      +...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.  .+.+...+.          
T Consensus       160 ~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~  236 (359)
T 3ieg_A          160 RAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKISTLYYQLGDHELSLSEVRECLKL--DQDHKRCFAHYKQVKKLNK  236 (359)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CccchHHHHHHHHHHHHHH
Confidence            9999999999999999999999852 346678889999999999999999999999874  233333332          


Q ss_pred             --HHHHHHhhcCChHHHHHHHHhcc-CCCC-h----hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHH
Q 011249          387 --CMVDLLGRSGQLEKAHSLIMDYK-DFCD-A----GTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY  458 (490)
Q Consensus       387 --~l~~~~~~~g~~~~A~~~~~~~~-~~~~-~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  458 (490)
                        .++..+.+.|++++|.+.++++. ..|+ .    ..+..+...+...|++++|++.++++.+..|+++.++..++.++
T Consensus       237 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~  316 (359)
T 3ieg_A          237 LIESAEELIRDGRYTDATSKYESVMKTEPSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQMEPDNVNALKDRAEAY  316 (359)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence              23667899999999999998876 2333 3    23455778899999999999999999999999999999999999


Q ss_pred             HhcCCcchHHHHHHHhhhccc
Q 011249          459 ASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       459 ~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ...|++++|.+.++++.+..+
T Consensus       317 ~~~g~~~~A~~~~~~a~~~~p  337 (359)
T 3ieg_A          317 LIEEMYDEAIQDYEAAQEHNE  337 (359)
T ss_dssp             HHTTCHHHHHHHHHHHHTTCT
T ss_pred             HHcCCHHHHHHHHHHHHhcCC
Confidence            999999999999999987644

>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=99.89  E-value=1.4e-20  Score=172.33  Aligned_cols=285  Identities=13%  Similarity=-0.023  Sum_probs=203.6

Q ss_pred             CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHH
Q 011249          178 NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISA  254 (490)
Q Consensus       178 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~  254 (490)
                      +...+..++..+...|++++|+++|+++.+   .+...+..++.++...|++++|..+++++.+.. +.+...+..+...
T Consensus        21 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~   99 (330)
T 3hym_B           21 NLDVVVSLAERHYYNCDFKMCYKLTSVVMEKDPFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGCY   99 (330)
T ss_dssp             CCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHH
Confidence            444555555555555666666665555543   233455556666666677777777777766543 2245566666666


Q ss_pred             HhccC-ChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHH
Q 011249          255 CTQLG-DVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEA  330 (490)
Q Consensus       255 ~~~~g-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a  330 (490)
                      +...| ++++|...++.+.+.. +.+...+..+...+...|++++|...|+++.+   .+...+..+...+...|++++|
T Consensus       100 ~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A  178 (330)
T 3hym_B          100 YLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLA  178 (330)
T ss_dssp             HHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHH
Confidence            66777 6777777777776654 44556666777777777777777777776654   2355666677788888888888


Q ss_pred             HHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcC-------CCCCchHHHHHHHHHhhcCChHHHHH
Q 011249          331 LDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFG-------IKPLTEHLTCMVDLLGRSGQLEKAHS  403 (490)
Q Consensus       331 ~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~-------~~~~~~~~~~l~~~~~~~g~~~~A~~  403 (490)
                      ...++++.+.. +.+...+..+...+...|++++|...++++.+...       .+.....+..+..++...|++++|.+
T Consensus       179 ~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~  257 (330)
T 3hym_B          179 ERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALD  257 (330)
T ss_dssp             HHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHH
Confidence            88888887742 33456777788888888888888888888877421       14446788889999999999999999


Q ss_pred             HHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHH-HhcCCcc
Q 011249          404 LIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY-ASMGKWK  465 (490)
Q Consensus       404 ~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~-~~~g~~~  465 (490)
                      .+++..  .+.+...+..+...+...|++++|.+.++++++..|+++..+..++.++ ...|+.+
T Consensus       258 ~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~g~~~  322 (330)
T 3hym_B          258 YHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTALGLRRDDTFSVTMLGHCIEMYIGDSE  322 (330)
T ss_dssp             HHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTCSCCHHHHHHHHHHHHTTTTC--
T ss_pred             HHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHHHHHccCCCchHHHHHHHHHHHHHhCchh
Confidence            998876  4456778889999999999999999999999999999999999999888 4555543

>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=99.89  E-value=2.7e-21  Score=180.13  Aligned_cols=259  Identities=10%  Similarity=-0.093  Sum_probs=180.3

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHH
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHS  291 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  291 (490)
                      .+..+...+...|++++|+..|+++.+.. +.+...+..+..++...|++++|...++.+.+.. +.+..++..++.+|.
T Consensus        66 ~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~  143 (368)
T 1fch_A           66 QPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFT  143 (368)
T ss_dssp             SHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHH
Confidence            34444444555555555555555544432 1233444444444555555555555555544443 334444444555555


Q ss_pred             hcCChHHHHHHHhcccC--C-ChhH----------------HHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHH
Q 011249          292 KCGYLDLAWREFSRIKN--K-DVIS----------------YSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIG  351 (490)
Q Consensus       292 ~~~~~~~A~~~~~~~~~--~-~~~~----------------~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~  351 (490)
                      ..|++++|...|+++..  | +...                +..+...+ ..|++++|...++++.+..... +..++..
T Consensus       144 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~  222 (368)
T 1fch_A          144 NESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLL-SDSLFLEVKELFLAAVRLDPTSIDPDVQCG  222 (368)
T ss_dssp             HTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHH-HHHHHHHHHHHHHHHHHHSTTSCCHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHh-hcccHHHHHHHHHHHHHhCcCcccHHHHHH
Confidence            55555555555544432  1 1111                11233333 8899999999999999853221 4778889


Q ss_pred             HHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCC
Q 011249          352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVN  429 (490)
Q Consensus       352 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~  429 (490)
                      +...+...|++++|...++++.+.  .+.+...+..++.++...|++++|...|+++.  .+.+...+..+..++...|+
T Consensus       223 l~~~~~~~g~~~~A~~~~~~al~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~  300 (368)
T 1fch_A          223 LGVLFNLSGEYDKAVDCFTAALSV--RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGA  300 (368)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCC
Confidence            999999999999999999999883  45567888999999999999999999998876  45567899999999999999


Q ss_pred             hHHHHHHHHHHHhcCCCC-----------CchHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          430 AELGEIAARHLLELGPEK-----------TGNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       430 ~~~a~~~~~~~~~~~p~~-----------~~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      +++|...++++++..|++           +.++..++.+|...|++++|..++++..
T Consensus       301 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l  357 (368)
T 1fch_A          301 HREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADARDL  357 (368)
T ss_dssp             HHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHTTCH
T ss_pred             HHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHhHHHHH
Confidence            999999999999988887           7899999999999999999999987544

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.89  E-value=1.1e-19  Score=175.88  Aligned_cols=375  Identities=8%  Similarity=-0.030  Sum_probs=291.6

Q ss_pred             HHHhccCCCCCCceehHHHHHHHHh----cCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHh--
Q 011249           56 RQVFDQIPKCKTQFLWTSLIRNHVL----HAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTK--  129 (490)
Q Consensus        56 ~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~--  129 (490)
                      ...+++...++....+..|...|..    .+++++|+..|++..+.|.   ...+..              +...|..  
T Consensus        27 ~~~~~~~a~~g~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~~---~~a~~~--------------Lg~~y~~g~   89 (490)
T 2xm6_A           27 LEQLKQKAESGEAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQGY---TPAEYV--------------LGLRYMNGE   89 (490)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC---HHHHHH--------------HHHHHHHTS
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCCC---HHHHHH--------------HHHHHHcCC
Confidence            3444443333333677777777777    7888888888888877642   222222              2223566  


Q ss_pred             --cCCHHHHHHHHhhcCC-CCHhHHHHHHHHHHh----CCChHHHHHHHHHhccC-CchhHHHHHHHHHh----cCChhH
Q 011249          130 --IGLMDDAQRLFDSMAE-RNVISWSAMVAGYAN----CGNMKAAKEFYDRMTEK-NSVTWVAMIAGYGK----CGEVRE  197 (490)
Q Consensus       130 --~g~~~~A~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~-~~~~~~~l~~~~~~----~~~~~~  197 (490)
                        .++.++|...|++..+ .++..+..|...|..    .+++++|++.|++..+. ++..+..+...|..    .+++++
T Consensus        90 g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~  169 (490)
T 2xm6_A           90 GVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVM  169 (490)
T ss_dssp             SSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHH
T ss_pred             CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHH
Confidence              7888889888888766 366777778888887    78899999999888765 67788888888887    788999


Q ss_pred             HHHHHhhcCC-CCHHhHHHHHHHHHh----cCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhc----cCChHHHHHHH
Q 011249          198 AKKVFDEISE-PDASCWAAMTVCYVQ----NGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQ----LGDVEMAAILA  268 (490)
Q Consensus       198 A~~~~~~~~~-~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~a~~~~  268 (490)
                      |++.|++..+ .++..+..+...|..    .+++++|+++|++..+.|   +...+..+...+..    .+++++|..++
T Consensus       170 A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~  246 (490)
T 2xm6_A          170 AREWYSKAAEQGNVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLF  246 (490)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence            9999987654 677888888888888    889999999999988765   45667777777765    78999999999


Q ss_pred             HHHHhcCCCCchhHHHHHHHHHHh----cCChHHHHHHHhcccC-CChhHHHHHHHHHHhc-----CChHHHHHHHHHHH
Q 011249          269 KHVDEGCCDRTNYVSNALIHMHSK----CGYLDLAWREFSRIKN-KDVISYSSMITAFADH-----GKSQEALDMFLKMR  338 (490)
Q Consensus       269 ~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~-~~~~~~~~l~~~~~~~-----~~~~~a~~~~~~~~  338 (490)
                      +...+.+   ++..+..+..+|..    .+++++|..+|++..+ .++..+..+...|...     +++++|...|++..
T Consensus       247 ~~a~~~~---~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~  323 (490)
T 2xm6_A          247 SQSAEQG---NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSA  323 (490)
T ss_dssp             HHHHTTT---CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHH
T ss_pred             HHHHHCC---CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHH
Confidence            9988765   34556667777777    8899999999998876 4677788888888877     89999999999999


Q ss_pred             HcCCCCcHHHHHHHHHHhcCCC---ChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh----cCChHHHHHHHHhccCC
Q 011249          339 NEGIEPNQVTFIGVLTACSHGG---LVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR----SGQLEKAHSLIMDYKDF  411 (490)
Q Consensus       339 ~~~~~p~~~~~~~l~~~~~~~g---~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~  411 (490)
                      +.|   +...+..+...|...|   +.++|.+.|++..+.    .++..+..+..+|..    .+++++|.+.|++....
T Consensus       324 ~~~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~----~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~  396 (490)
T 2xm6_A          324 EQG---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAK----GEKAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQ  396 (490)
T ss_dssp             HTT---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             hcC---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHC----CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhC
Confidence            864   3456666777776656   788999999999873    456778888888888    89999999999988755


Q ss_pred             CChhhHHHHHHHHhh----hCChHHHHHHHHHHHhcCCC---CCchHHHHHHHHHh
Q 011249          412 CDAGTWGALLGACKV----HVNAELGEIAARHLLELGPE---KTGNSALLANIYAS  460 (490)
Q Consensus       412 ~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~p~---~~~~~~~l~~~~~~  460 (490)
                      .++..+..+...|..    .+++++|...|+++.+.+|+   ++.+...++.++..
T Consensus       397 ~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~~a~~~l~~~~~~  452 (490)
T 2xm6_A          397 GLSAAQVQLGEIYYYGLGVERDYVQAWAWFDTASTNDMNLFGTENRNITEKKLTAK  452 (490)
T ss_dssp             TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHTTSCHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCCCcCCHHHHHHHHhcCHh
Confidence            678888889888887    89999999999999999854   77777777766554

>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=99.88  E-value=3.2e-20  Score=169.96  Aligned_cols=267  Identities=10%  Similarity=-0.002  Sum_probs=234.0

Q ss_pred             CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHH
Q 011249          208 PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALI  287 (490)
Q Consensus       208 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  287 (490)
                      .+...+..++..+...|++++|+++++++.+.. +.+...+..++.++...|++++|..+++++.+.. +.+...+..+.
T Consensus        20 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~   97 (330)
T 3hym_B           20 ENLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVG   97 (330)
T ss_dssp             CCCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHH
Confidence            566678889999999999999999999999764 2355677778888999999999999999998876 66788889999


Q ss_pred             HHHHhcC-ChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChH
Q 011249          288 HMHSKCG-YLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVE  363 (490)
Q Consensus       288 ~~~~~~~-~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  363 (490)
                      ..+...| ++++|...|+++.+   .+...|..+...+...|++++|...++++.+.. +.+...+..+...+...|+++
T Consensus        98 ~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~  176 (330)
T 3hym_B           98 CYYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGLEYGLTNNSK  176 (330)
T ss_dssp             HHHHHSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHhhHH
Confidence            9999999 99999999998876   356789999999999999999999999999853 223456777888999999999


Q ss_pred             HHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccC-----------CCChhhHHHHHHHHhhhCChHH
Q 011249          364 DGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKD-----------FCDAGTWGALLGACKVHVNAEL  432 (490)
Q Consensus       364 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----------~~~~~~~~~l~~~~~~~g~~~~  432 (490)
                      +|...++++.+  ..+.+...+..++..+...|++++|...+++...           +....++..+...+...|++++
T Consensus       177 ~A~~~~~~al~--~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~  254 (330)
T 3hym_B          177 LAERFFSQALS--IAPEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAE  254 (330)
T ss_dssp             HHHHHHHHHHT--TCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHH--hCCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHH
Confidence            99999999987  4556678889999999999999999999987761           3345689999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          433 GEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       433 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      |...++++.+..|+++.++..++.++.+.|++++|.+.++++.+..+
T Consensus       255 A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p  301 (330)
T 3hym_B          255 ALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTALGLRR  301 (330)
T ss_dssp             HHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTTCS
T ss_pred             HHHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHHHHHccCC
Confidence            99999999999999999999999999999999999999999876543

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.87  E-value=2e-18  Score=167.04  Aligned_cols=335  Identities=14%  Similarity=0.032  Sum_probs=288.0

Q ss_pred             cCCHHHHHHHHhhcCC-CCHhHHHHHHHHHHh----CCChHHHHHHHHHhccC-CchhHHHHHHHHHh----cCChhHHH
Q 011249          130 IGLMDDAQRLFDSMAE-RNVISWSAMVAGYAN----CGNMKAAKEFYDRMTEK-NSVTWVAMIAGYGK----CGEVREAK  199 (490)
Q Consensus       130 ~g~~~~A~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~-~~~~~~~l~~~~~~----~~~~~~A~  199 (490)
                      .+++++|+..|++..+ .+...+..|...|..    .+++++|++.|++..+. ++..+..+...|..    .+++++|+
T Consensus        56 ~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~  135 (490)
T 2xm6_A           56 TKDLTQAMDWFRRAAEQGYTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKGLPQAQQNLGVMYHEGNGVKVDKAESV  135 (490)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHH
T ss_pred             CcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence            7999999999998876 477888999999998    99999999999999876 77888889999988    88999999


Q ss_pred             HHHhhcCC-CCHHhHHHHHHHHHh----cCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhc----cCChHHHHHHHHH
Q 011249          200 KVFDEISE-PDASCWAAMTVCYVQ----NGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQ----LGDVEMAAILAKH  270 (490)
Q Consensus       200 ~~~~~~~~-~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~a~~~~~~  270 (490)
                      +.|++..+ .++..+..|...|..    .+++++|++.|++..+.|   +...+..+...+..    .++.++|..+|++
T Consensus       136 ~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~  212 (490)
T 2xm6_A          136 KWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSCNQLGYMYSRGLGVERNDAISAQWYRK  212 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCCCcCHHHHHHHHHH
Confidence            99998765 577888889999988    889999999999998865   66778888888877    8999999999999


Q ss_pred             HHhcCCCCchhHHHHHHHHHHh----cCChHHHHHHHhcccC-CChhHHHHHHHHHHh----cCChHHHHHHHHHHHHcC
Q 011249          271 VDEGCCDRTNYVSNALIHMHSK----CGYLDLAWREFSRIKN-KDVISYSSMITAFAD----HGKSQEALDMFLKMRNEG  341 (490)
Q Consensus       271 ~~~~~~~~~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~  341 (490)
                      ..+.+   ++..+..+...|..    .+++++|..+|++..+ .++..+..+...|..    .+++++|...|++..+.|
T Consensus       213 a~~~~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~  289 (490)
T 2xm6_A          213 SATSG---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQGNSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQG  289 (490)
T ss_dssp             HHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTT
T ss_pred             HHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcC
Confidence            98875   45667778888886    7899999999999876 567788888888888    899999999999998754


Q ss_pred             CCCcHHHHHHHHHHhcCC-----CChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcC---ChHHHHHHHHhccCCCC
Q 011249          342 IEPNQVTFIGVLTACSHG-----GLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSG---QLEKAHSLIMDYKDFCD  413 (490)
Q Consensus       342 ~~p~~~~~~~l~~~~~~~-----g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~~~~~  413 (490)
                         +...+..+...|...     ++.++|...+++..+. +   +...+..+...|...|   ++++|.++|++.....+
T Consensus       290 ---~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~-~---~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~~  362 (490)
T 2xm6_A          290 ---NSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQ-G---DATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKGE  362 (490)
T ss_dssp             ---CHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTTC
T ss_pred             ---CHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhc-C---CHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCCC
Confidence               445666677777766     8999999999999883 3   4567777888888766   88999999998875678


Q ss_pred             hhhHHHHHHHHhh----hCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHh----cCCcchHHHHHHHhhhccc
Q 011249          414 AGTWGALLGACKV----HVNAELGEIAARHLLELGPEKTGNSALLANIYAS----MGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       414 ~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~  479 (490)
                      +..+..+...+..    .+++++|.+.|+++.+.+  ++.++..|+.+|..    .+++++|...+++..+.+.
T Consensus       363 ~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~A~~~~--~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~  434 (490)
T 2xm6_A          363 KAAQFNLGNALLQGKGVKKDEQQAAIWMRKAAEQG--LSAAQVQLGEIYYYGLGVERDYVQAWAWFDTASTNDM  434 (490)
T ss_dssp             HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHhCC--CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCC
Confidence            8899999999988    899999999999999864  68899999999998    8999999999999988874

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.86  E-value=5.5e-18  Score=165.65  Aligned_cols=409  Identities=11%  Similarity=0.015  Sum_probs=269.0

Q ss_pred             CCCchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhH
Q 011249           29 KPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTF  106 (490)
Q Consensus        29 ~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~  106 (490)
                      .|.+..  .|..++.. .+.|+ +++|+.+|+++.  .|+....|..++..+.+.|++++|..+|+++.+.  .|+...|
T Consensus         9 ~P~~~~--~w~~l~~~-~~~~~-~~~a~~~~e~al~~~P~~~~~w~~~~~~~~~~~~~~~a~~~~~ral~~--~p~~~lw   82 (530)
T 2ooe_A            9 NPYDLD--AWSILIRE-AQNQP-IDKARKTYERLVAQFPSSGRFWKLYIEAEIKAKNYDKVEKLFQRCLMK--VLHIDLW   82 (530)
T ss_dssp             CTTCHH--HHHHHHHH-HHSSC-HHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTT--CCCHHHH
T ss_pred             CCCCHH--HHHHHHHH-HHhCC-HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhc--CCChHHH
Confidence            557788  89999984 77888 999999999885  5666567899999999999999999999998886  4666555


Q ss_pred             HHHHHHhcCCCChHHHHHHHHHhcCCHHHHHH----HHhhcCC------CCHhHHHHHHHHHHh---------CCChHHH
Q 011249          107 SSVLNACARVPSLLEAVICGYTKIGLMDDAQR----LFDSMAE------RNVISWSAMVAGYAN---------CGNMKAA  167 (490)
Q Consensus       107 ~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~----~~~~~~~------~~~~~~~~l~~~~~~---------~~~~~~a  167 (490)
                      ...+..             .....|+.+.|.+    +|+....      ++...|...+....+         .|+++.|
T Consensus        83 ~~~~~~-------------~~~~~~~~~~a~~~~~~~~~~al~~~g~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~a  149 (530)
T 2ooe_A           83 KCYLSY-------------VRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIWVDYINFLKGVEAVGSYAENQRITAV  149 (530)
T ss_dssp             HHHHHH-------------HHHHTTTSTTHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHSCCCSSTTHHHHHHHH
T ss_pred             HHHHHH-------------HHHHccchhhHHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHhcCCCcccHHHHhHHHHH
Confidence            544432             1234577776665    6665532      355677777766554         5778888


Q ss_pred             HHHHHHhcc-CCc---hhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHH------
Q 011249          168 KEFYDRMTE-KNS---VTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMR------  237 (490)
Q Consensus       168 ~~~~~~~~~-~~~---~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~------  237 (490)
                      ..+|++..+ |+.   ..|..........|. ..+..++.                 ...+++..|..++++..      
T Consensus       150 ~~~y~~al~~P~~~~~~~~~~~~~~e~~~~~-~~~~~~l~-----------------~~~~~~~~A~~~~~~~~~~~~~l  211 (530)
T 2ooe_A          150 RRVYQRGCVNPMINIEQLWRDYNKYEEGINI-HLAKKMIE-----------------DRSRDYMNARRVAKEYETVMKGL  211 (530)
T ss_dssp             HHHHHHHTTSCCTTHHHHHHHHHHHHHHHCH-HHHHHHHH-----------------TTHHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhchhhhHHHHHHHHHHHHHhhch-hHHHHHHH-----------------HhhHHHHHHHHHHHHHHHHHHHh
Confidence            888888775 221   122221111100110 00111110                 12344555665555422      


Q ss_pred             HcC---cccC--------hhhHHHHHHHHhc----cCCh----HHHHHHHHHHHhcCCCCchhHHHHHHHHHHh------
Q 011249          238 QEN---VRIS--------EVAMVGAISACTQ----LGDV----EMAAILAKHVDEGCCDRTNYVSNALIHMHSK------  292 (490)
Q Consensus       238 ~~~---~~p~--------~~~~~~l~~~~~~----~g~~----~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~------  292 (490)
                      +..   +.|+        ...|...+.....    .++.    ..+..+|+++.... |.++..|..++..+.+      
T Consensus       212 ~~~~~~~~p~~~~~~~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~-p~~~~~w~~~~~~~~~~~~~~~  290 (530)
T 2ooe_A          212 DRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLA  290 (530)
T ss_dssp             CSSSCCCCCC--CCHHHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccccccCCCCCChhHHHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhchhhh
Confidence            111   1222        1233333322211    1232    36667788877764 5667777777777765      


Q ss_pred             -cCChH-------HHHHHHhcccC---C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc-H-HHHHHHHHHhcC
Q 011249          293 -CGYLD-------LAWREFSRIKN---K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN-Q-VTFIGVLTACSH  358 (490)
Q Consensus       293 -~~~~~-------~A~~~~~~~~~---~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~-~~~~~l~~~~~~  358 (490)
                       .|+++       +|..+|++..+   | +...|..++..+.+.|++++|..+|+++.+.  .|+ . ..|..++..+.+
T Consensus       291 ~~g~~~~a~~~~~~A~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~  368 (530)
T 2ooe_A          291 EKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAI--EDIDPTLVYIQYMKFARR  368 (530)
T ss_dssp             TTTCCHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--SSSCHHHHHHHHHHHHHH
T ss_pred             hccchhhhhhhhHHHHHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCc--cccCchHHHHHHHHHHHH
Confidence             68876       78888887764   3 4677888888888888888888888888873  554 2 467777777777


Q ss_pred             CCChHHHHHHHHHHHHHcCCCCCchHHHHHHHH-HhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHH
Q 011249          359 GGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDL-LGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEI  435 (490)
Q Consensus       359 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~  435 (490)
                      .|+.++|..+|++..+.  .+.+...+...+.. +...|+.++|..+|++..  .+.++..|..++..+...|+.++|..
T Consensus       369 ~~~~~~A~~~~~~Al~~--~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~p~~~~~~~~~~~~~~~~g~~~~Ar~  446 (530)
T 2ooe_A          369 AEGIKSGRMIFKKARED--ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRV  446 (530)
T ss_dssp             HHHHHHHHHHHHHHHTC--TTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTTTCHHHHHH
T ss_pred             hcCHHHHHHHHHHHHhc--cCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHCCCCHHHHHHHHHHHHhCCCHhhHHH
Confidence            88888888888888762  22233334332222 335788888888888765  33457788888888888889999999


Q ss_pred             HHHHHHhcCCCCCc----hHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          436 AARHLLELGPEKTG----NSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       436 ~~~~~~~~~p~~~~----~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +|++++...|.++.    ++...+......|+.+.+..+.+++.+.-+
T Consensus       447 ~~~~al~~~~~~~~~~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~~p  494 (530)
T 2ooe_A          447 LFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFR  494 (530)
T ss_dssp             HHHHHHHSCCSCGGGCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHTH
T ss_pred             HHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence            99988888776665    777777777788888888888888766543

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.86  E-value=2.8e-20  Score=173.10  Aligned_cols=261  Identities=10%  Similarity=-0.091  Sum_probs=203.4

Q ss_pred             CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 011249          209 DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIH  288 (490)
Q Consensus       209 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  288 (490)
                      +...+..+...+.+.|++++|++.|+++.+.. +.+...+..+..++...|++++|...++++.+.. +.+..++..++.
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  141 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQ-PNNLKALMALAV  141 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            34457777777788888888888888877654 2356677777777888888888888888877765 556677777888


Q ss_pred             HHHhcCChHHHHHHHhcccCCC-------------hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC-CcHHHHHHHHH
Q 011249          289 MHSKCGYLDLAWREFSRIKNKD-------------VISYSSMITAFADHGKSQEALDMFLKMRNEGIE-PNQVTFIGVLT  354 (490)
Q Consensus       289 ~~~~~~~~~~A~~~~~~~~~~~-------------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-p~~~~~~~l~~  354 (490)
                      +|...|++++|...|+++.+.+             ...+..+...+...|++++|...++++.+.... ++...+..+..
T Consensus       142 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~~  221 (365)
T 4eqf_A          142 SYTNTSHQQDACEALKNWIKQNPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLGV  221 (365)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHHH
T ss_pred             HHHccccHHHHHHHHHHHHHhCccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHHH
Confidence            8888888888888887776411             223344577889999999999999999985322 15778899999


Q ss_pred             HhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHH
Q 011249          355 ACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAEL  432 (490)
Q Consensus       355 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~  432 (490)
                      .+...|++++|...++++.+.  .+.+..++..++.+|...|++++|.+.|+++.  .+.+..++..+..++...|++++
T Consensus       222 ~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~  299 (365)
T 4eqf_A          222 LFHLSGEFNRAIDAFNAALTV--RPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPGFIRSRYNLGISCINLGAYRE  299 (365)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHH
Confidence            999999999999999999883  45568889999999999999999999998876  44567899999999999999999


Q ss_pred             HHHHHHHHHhcCCC------------CCchHHHHHHHHHhcCCcchHHHHHHH
Q 011249          433 GEIAARHLLELGPE------------KTGNSALLANIYASMGKWKDSEIVKMM  473 (490)
Q Consensus       433 a~~~~~~~~~~~p~------------~~~~~~~l~~~~~~~g~~~~A~~~~~~  473 (490)
                      |...++++++..|+            +..++..++.++...|+.+.+.++.++
T Consensus       300 A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  352 (365)
T 4eqf_A          300 AVSNFLTALSLQRKSRNQQQVPHPAISGNIWAALRIALSLMDQPELFQAANLG  352 (365)
T ss_dssp             HHHHHHHHHHHHHCC------------CHHHHHHHHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCcccCCCcccchhhhHHHHHHHHHHHHHHcCcHHHHHHHHHh
Confidence            99999999998876            367899999999999999999888765

>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=99.86  E-value=2.1e-19  Score=164.01  Aligned_cols=379  Identities=9%  Similarity=0.033  Sum_probs=183.5

Q ss_pred             cchhhhhhchhhHHHHHHHHhhhcCCCCchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCCCCCceehHHHHHHHHhcCC
Q 011249            4 KYLVPRSKTFNQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAH   83 (490)
Q Consensus         4 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~   83 (490)
                      ..|+..+|+++.|.+..+++.       ++.  +|..|+.++.+.|+ +++|++.|.+.  ++. ..|..++..+...|+
T Consensus        10 ~~ll~~~~~ld~A~~fae~~~-------~~~--vWs~La~A~l~~g~-~~eAIdsfika--~D~-~~y~~V~~~ae~~g~   76 (449)
T 1b89_A           10 QVLIEHIGNLDRAYEFAERCN-------EPA--VWSQLAKAQLQKGM-VKEAIDSYIKA--DDP-SSYMEVVQAANTSGN   76 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHccCHHHHHHHHHhCC-------ChH--HHHHHHHHHHHcCC-HHHHHHHHHcC--CCH-HHHHHHHHHHHhCCC
Confidence            456777888888887777773       356  99999999999999 99999999775  455 689999999999999


Q ss_pred             hhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCC
Q 011249           84 FRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGN  163 (490)
Q Consensus        84 ~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~  163 (490)
                      +++|+..++..++.  .+++.+.+.++.+              |.+.|+++++.++++   .|+..+|+.++..|...|.
T Consensus        77 ~EeAi~yl~~ark~--~~~~~i~~~Li~~--------------Y~Klg~l~e~e~f~~---~pn~~a~~~IGd~~~~~g~  137 (449)
T 1b89_A           77 WEELVKYLQMARKK--ARESYVETELIFA--------------LAKTNRLAELEEFIN---GPNNAHIQQVGDRCYDEKM  137 (449)
T ss_dssp             ------------------------------------------------CHHHHTTTTT---CC----------------C
T ss_pred             HHHHHHHHHHHHHh--CccchhHHHHHHH--------------HHHhCCHHHHHHHHc---CCcHHHHHHHHHHHHHcCC
Confidence            99999988777664  4455666666554              788899999887775   4777899999999999999


Q ss_pred             hHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCccc
Q 011249          164 MKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRI  243 (490)
Q Consensus       164 ~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p  243 (490)
                      +++|...|..+     ..|..++.++.+.|++++|.+.+.++.  ++.+|..++.+|...|+++.|......+     ..
T Consensus       138 yeeA~~~Y~~a-----~n~~~LA~~L~~Lg~yq~AVea~~KA~--~~~~Wk~v~~aCv~~~ef~lA~~~~l~L-----~~  205 (449)
T 1b89_A          138 YDAAKLLYNNV-----SNFGRLASTLVHLGEYQAAVDGARKAN--STRTWKEVCFACVDGKEFRLAQMCGLHI-----VV  205 (449)
T ss_dssp             TTTHHHHHHHT-----TCHHHHHHHHHTTTCHHHHHHHHHHHT--CHHHHHHHHHHHHHTTCHHHHHHTTTTT-----TT
T ss_pred             HHHHHHHHHHh-----hhHHHHHHHHHHhccHHHHHHHHHHcC--CchhHHHHHHHHHHcCcHHHHHHHHHHH-----Hh
Confidence            99999999988     589999999999999999999999994  8899999999999999999996655442     22


Q ss_pred             ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc--CChHHHHHHHhcccC--------CChhH
Q 011249          244 SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC--GYLDLAWREFSRIKN--------KDVIS  313 (490)
Q Consensus       244 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~A~~~~~~~~~--------~~~~~  313 (490)
                      .+.....++..|.+.|.+++|..+++...... +.....|+-|.-+|++-  +++.+.++.|..-..        .+...
T Consensus       206 ~ad~l~~lv~~Yek~G~~eEai~lLe~aL~le-~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~ini~k~~~~~~~~~~  284 (449)
T 1b89_A          206 HADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHL  284 (449)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHHTTTC
T ss_pred             CHhhHHHHHHHHHHCCCHHHHHHHHHHHhCCc-HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCcHHHHHHHHHHH
Confidence            33445578899999999999999999998776 55667777777777754  466667777765444        25678


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHc-CCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHH
Q 011249          314 YSSMITAFADHGKSQEALDMFLKMRNE-GIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLL  392 (490)
Q Consensus       314 ~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  392 (490)
                      |..+...|...++++.|...   |.+. ...-+...|.-++.   +..+.+--.+...-....     .+...+.|+.++
T Consensus       285 w~e~~~ly~~~~e~d~A~~t---m~~h~~~a~~~~~f~~~~~---kv~n~elyYkai~fyl~~-----~p~~l~~ll~~l  353 (449)
T 1b89_A          285 WAELVFLYDKYEEYDNAIIT---MMNHPTDAWKEGQFKDIIT---KVANVELYYRAIQFYLEF-----KPLLLNDLLMVL  353 (449)
T ss_dssp             HHHHHHHHHHTTCHHHHHHH---HHHSTTTTCCHHHHHHHHH---HCSSTHHHHHHHHHHHHH-----CGGGHHHHHHHH
T ss_pred             HHHHHHHHHhhchHHHHHHH---HHhCChhhhhhHHHHHHHh---chhHHHHHHHHHHHHHhc-----CHHHHHHHHHHH
Confidence            99999999999999988774   4443 12223344444433   334433322222222221     233345555555


Q ss_pred             hhcCChHHHHHHHHhc-------------cCCCChhhHHHHHHHHhhhCChHHHHHHHH
Q 011249          393 GRSGQLEKAHSLIMDY-------------KDFCDAGTWGALLGACKVHVNAELGEIAAR  438 (490)
Q Consensus       393 ~~~g~~~~A~~~~~~~-------------~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  438 (490)
                      ...=+...+.++|++.             ....+..+-.++-..+....|++.-....+
T Consensus       354 ~~~ld~~r~v~~~~~~~~l~l~~~yl~~v~~~n~~~vnealn~l~ieeed~~~lr~si~  412 (449)
T 1b89_A          354 SPRLDHTRAVNYFSKVKQLPLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQALRTSID  412 (449)
T ss_dssp             GGGCCHHHHHHHHHHTTCTTTTHHHHHHHHTTCCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HhccCcHHHHHHHHHcCCcHHHHHHHHHHHHhhHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence            5555555555555443             334445555566667777777776555444

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.86  E-value=4.2e-19  Score=171.26  Aligned_cols=335  Identities=10%  Similarity=-0.017  Sum_probs=201.4

Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHHHhcc-----------C-CchhHHHHHHHHHhcCChhHHHHHHhhcCC--------
Q 011249          148 VISWSAMVAGYANCGNMKAAKEFYDRMTE-----------K-NSVTWVAMIAGYGKCGEVREAKKVFDEISE--------  207 (490)
Q Consensus       148 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~-----------~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--------  207 (490)
                      ...||.|...+...|++++|++.|++..+           + ...+|+.+..+|...|++++|...+++..+        
T Consensus        51 a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nla~~y~~~g~~~~A~~~~~ka~~i~~~~~~~  130 (472)
T 4g1t_A           51 ATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNYAWVYYHMGRLSDVQIYVDKVKHVCEKFSSP  130 (472)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCS
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhHhcccc
Confidence            45678888888888888888888877652           1 345677788888888888888777766532        


Q ss_pred             ---CCHHhHHHHHHHHHh--cCChHHHHHHHHHHHHcCcccChhhHHHHHHH---HhccCChHHHHHHHHHHHhcCCCCc
Q 011249          208 ---PDASCWAAMTVCYVQ--NGYAKAAIEMYKVMRQENVRISEVAMVGAISA---CTQLGDVEMAAILAKHVDEGCCDRT  279 (490)
Q Consensus       208 ---~~~~~~~~l~~~~~~--~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~---~~~~g~~~~a~~~~~~~~~~~~~~~  279 (490)
                         ....++..+..++..  .+++++|++.|++..+..+. ++..+..+..+   +...++.++|...+++..+.. |.+
T Consensus       131 ~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~-~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p~~  208 (472)
T 4g1t_A          131 YRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPK-NPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-PDN  208 (472)
T ss_dssp             SCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTT-CHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-SSC
T ss_pred             cchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-Ccc
Confidence               224455555555544  34578888888887765321 33334333333   345567777777787777765 445


Q ss_pred             hhHHHHHHHHHHh----cCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc-HHHHHH
Q 011249          280 NYVSNALIHMHSK----CGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN-QVTFIG  351 (490)
Q Consensus       280 ~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~  351 (490)
                      ..++..+...+..    .+++++|.+.+++...   .+..++..+...|...|++++|...++++.+.  .|+ ...+..
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            5555555544443    3566778877776654   35667777888888888888888888888774  443 345555


Q ss_pred             HHHHhcCC-------------------CChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CC
Q 011249          352 VLTACSHG-------------------GLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DF  411 (490)
Q Consensus       352 l~~~~~~~-------------------g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~  411 (490)
                      +..+|...                   +..+.|...+++..+.  .+.+...+..+...|...|++++|++.|++.. ..
T Consensus       287 lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~  364 (472)
T 4g1t_A          287 IGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEA--NDNLFRVCSILASLHALADQYEEAEYYFQKEFSKE  364 (472)
T ss_dssp             HHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHH--CTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhc--CCchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcC
Confidence            54443211                   2345667777776662  34456667778888888888888888887665 23


Q ss_pred             CChh----hHHHHHH-HHhhhCChHHHHHHHHHHHh------------------------cCCCCCchHHHHHHHHHhcC
Q 011249          412 CDAG----TWGALLG-ACKVHVNAELGEIAARHLLE------------------------LGPEKTGNSALLANIYASMG  462 (490)
Q Consensus       412 ~~~~----~~~~l~~-~~~~~g~~~~a~~~~~~~~~------------------------~~p~~~~~~~~l~~~~~~~g  462 (490)
                      |+..    .+..+.. .....|++++|+..|+++++                        .+|+++.++..|+.+|...|
T Consensus       365 ~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g  444 (472)
T 4g1t_A          365 LTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKSREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELNE  444 (472)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcC
Confidence            3322    2233332 23456778888777777654                        46778899999999999999


Q ss_pred             CcchHHHHHHHhhhcccccCCCcccc
Q 011249          463 KWKDSEIVKMMISETEKKKSPGCSWI  488 (490)
Q Consensus       463 ~~~~A~~~~~~~~~~~~~~~~~~~~~  488 (490)
                      ++++|++.|++..+.+.......+|+
T Consensus       445 ~~~~A~~~y~kALe~~~~~p~a~~~~  470 (472)
T 4g1t_A          445 KMQQADEDSERGLESGSLIPSASSWN  470 (472)
T ss_dssp             HCC-----------------------
T ss_pred             CHHHHHHHHHHHHhcCCCCCcHhhcC
Confidence            99999999999999988887888885

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.85  E-value=4.1e-18  Score=166.59  Aligned_cols=396  Identities=11%  Similarity=0.065  Sum_probs=271.8

Q ss_pred             hhhchhhHHHHHHHHhhhcCCC-CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHH-HhcCCh
Q 011249            9 RSKTFNQLKQVHSYLLKTLTKP-HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNH-VLHAHF   84 (490)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~-~~~g~~   84 (490)
                      ..|+.+.+..++++..+   .. .+..  +|..++..+.+.|+ +++|+++|++..  .|+. ..|...+... ...|+.
T Consensus        24 ~~~~~~~a~~~~e~al~---~~P~~~~--~w~~~~~~~~~~~~-~~~a~~~~~ral~~~p~~-~lw~~~~~~~~~~~~~~   96 (530)
T 2ooe_A           24 QNQPIDKARKTYERLVA---QFPSSGR--FWKLYIEAEIKAKN-YDKVEKLFQRCLMKVLHI-DLWKCYLSYVRETKGKL   96 (530)
T ss_dssp             HSSCHHHHHHHHHHHHT---TCTTCHH--HHHHHHHHHHHTTC-HHHHHHHHHHHTTTCCCH-HHHHHHHHHHHHHTTTS
T ss_pred             HhCCHHHHHHHHHHHHH---HCCCCHH--HHHHHHHHHHhcCC-HHHHHHHHHHHHhcCCCh-HHHHHHHHHHHHHccch
Confidence            35788889999999887   55 7778  99999999999999 999999999986  4655 5677776533 456888


Q ss_pred             hHHHH----HHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHh---------cCCHHHHHHHHhhcCC-CCH--
Q 011249           85 RQSIL----LYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTK---------IGLMDDAQRLFDSMAE-RNV--  148 (490)
Q Consensus        85 ~~A~~----~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~---------~g~~~~A~~~~~~~~~-~~~--  148 (490)
                      +.|.+    +|+..... +..+........           ..+....+         .|+++.|+.+|++..+ |+.  
T Consensus        97 ~~a~~~~~~~~~~al~~-~g~~~~~~~~w~-----------~~~~~~~~~~~~~~~~~~~~~~~a~~~y~~al~~P~~~~  164 (530)
T 2ooe_A           97 PSYKEKMAQAYDFALDK-IGMEIMSYQIWV-----------DYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINI  164 (530)
T ss_dssp             TTHHHHHHHHHHHHHHH-TTTSTTCHHHHH-----------HHHHHHHHSCCCSSTTHHHHHHHHHHHHHHHTTSCCTTH
T ss_pred             hhHHHHHHHHHHHHHHH-CCCCcccHHHHH-----------HHHHHHhcCCCcccHHHHhHHHHHHHHHHHHHhchhhhH
Confidence            87766    55555443 223333322222           22333332         6899999999999886 432  


Q ss_pred             -hHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhh----------cC---CCC-----
Q 011249          149 -ISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDE----------IS---EPD-----  209 (490)
Q Consensus       149 -~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~----------~~---~~~-----  209 (490)
                       ..|..........|. ..+..++..                 +.++++.|..++..          ..   .|+     
T Consensus       165 ~~~~~~~~~~e~~~~~-~~~~~~l~~-----------------~~~~~~~A~~~~~~~~~~~~~l~~~~~~~~p~~~~~~  226 (530)
T 2ooe_A          165 EQLWRDYNKYEEGINI-HLAKKMIED-----------------RSRDYMNARRVAKEYETVMKGLDRNAPSVPPQNTPQE  226 (530)
T ss_dssp             HHHHHHHHHHHHHHCH-HHHHHHHHT-----------------THHHHHHHHHHHHHHHHHHHHCCSSSCCCCCC--CCH
T ss_pred             HHHHHHHHHHHHhhch-hHHHHHHHH-----------------hhHHHHHHHHHHHHHHHHHHHhccccccCCCCCChhH
Confidence             233332221111110 111111110                 12233344433322          11   122     


Q ss_pred             ---HHhHHHHHHHHHhc----CCh----HHHHHHHHHHHHcCcccChhhHHHHHHHHhc-------cCChH-------HH
Q 011249          210 ---ASCWAAMTVCYVQN----GYA----KAAIEMYKVMRQENVRISEVAMVGAISACTQ-------LGDVE-------MA  264 (490)
Q Consensus       210 ---~~~~~~l~~~~~~~----g~~----~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~-------~g~~~-------~a  264 (490)
                         ...|...+......    ++.    +++..+|++..... +-+...|...+..+.+       .|+++       +|
T Consensus       227 ~~~~~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~~-p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A  305 (530)
T 2ooe_A          227 AQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEA  305 (530)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHH
Confidence               24555555443332    232    47788899988753 3356777777777764       79987       89


Q ss_pred             HHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-Ch-hHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011249          265 AILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-DV-ISYSSMITAFADHGKSQEALDMFLKMRNE  340 (490)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~-~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  340 (490)
                      ..++++..+.-.|.+...+..++..+.+.|++++|..+|+++.+  | +. ..|...+..+.+.|++++|..+|++..+.
T Consensus       306 ~~~~~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~  385 (530)
T 2ooe_A          306 ANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED  385 (530)
T ss_dssp             HHHHHHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            99999998743366788899999999999999999999998875  3 33 47888999899999999999999999975


Q ss_pred             CCCCc-HHHHHHHHHH-hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC-C---
Q 011249          341 GIEPN-QVTFIGVLTA-CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-D---  413 (490)
Q Consensus       341 ~~~p~-~~~~~~l~~~-~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~---  413 (490)
                        .|+ ...+...+.. +...|+.++|..+|++..+.  .+.++..+..++..+.+.|+.++|..+|++.. ..| +   
T Consensus       386 --~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~--~p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~  461 (530)
T 2ooe_A          386 --ARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEK  461 (530)
T ss_dssp             --TTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGG
T ss_pred             --cCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHH--CCCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHH
Confidence              332 2333322222 33589999999999999884  34567888999999999999999999998876 212 2   


Q ss_pred             -hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          414 -AGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       414 -~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                       ...|...+......|+.+.+..+.+++.+..|+
T Consensus       462 ~~~lw~~~~~~e~~~G~~~~~~~~~~r~~~~~p~  495 (530)
T 2ooe_A          462 SGEIWARFLAFESNIGDLASILKVEKRRFTAFRE  495 (530)
T ss_dssp             CHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCch
Confidence             337888888888899999999999999998884

>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=99.84  E-value=3.8e-17  Score=165.93  Aligned_cols=369  Identities=13%  Similarity=0.099  Sum_probs=272.7

Q ss_pred             eehHHHHHHHHhcCChhHHHHHHHHHHhcCC--CCCHhhHHHHHHHhcCC--CChH-----------HHHHHHHHhcCCH
Q 011249           69 FLWTSLIRNHVLHAHFRQSILLYAKMHRLGV--LTSGFTFSSVLNACARV--PSLL-----------EAVICGYTKIGLM  133 (490)
Q Consensus        69 ~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~--~p~~~~~~~ll~~~~~~--~~~~-----------~~l~~~~~~~g~~  133 (490)
                      .--...+.+|+..|.+.+|+++|++..-.+-  .-+...-+.++..-.+.  ++..           ..+...+...|.+
T Consensus       986 eeVs~~vKaf~~aglp~EaieLLEKivl~~s~fs~n~~LqnlLi~tAIkaD~~Rv~eyI~kLd~~d~~eIA~Iai~lgly 1065 (1630)
T 1xi4_A          986 EEVSVTVKAFMTADLPNELIELLEKIVLDNSVFSEHRNLQNLLILTAIKADRTRVMEYINRLDNYDAPDIANIAISNELF 1065 (1630)
T ss_pred             HHhHHHHHHHHhCCCHHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHhChhhHHHHHHHhhhccHHHHHHHHHhCCCH
Confidence            3345667777788888888888888773311  01112222233222111  1111           3356678889999


Q ss_pred             HHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhH
Q 011249          134 DDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCW  213 (490)
Q Consensus       134 ~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~  213 (490)
                      ++|..+|++... .....+.++.   ..+++++|.++.++.  .++.+|..++.++...|++++|++.|.+.  .|...|
T Consensus      1066 EEAf~IYkKa~~-~~~A~~VLie---~i~nldrAiE~Aerv--n~p~vWsqLAKAql~~G~~kEAIdsYiKA--dD~say 1137 (1630)
T 1xi4_A         1066 EEAFAIFRKFDV-NTSAVQVLIE---HIGNLDRAYEFAERC--NEPAVWSQLAKAQLQKGMVKEAIDSYIKA--DDPSSY 1137 (1630)
T ss_pred             HHHHHHHHHcCC-HHHHHHHHHH---HHhhHHHHHHHHHhc--CCHHHHHHHHHHHHhCCCHHHHHHHHHhc--CChHHH
Confidence            999999999752 2222233322   678899999998876  45778889999999999999999999765  677888


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc
Q 011249          214 AAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC  293 (490)
Q Consensus       214 ~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  293 (490)
                      ..++.++.+.|++++|++.|...++..  +++...+.++.+|++.+++++...+.    +   .++...+..+...|...
T Consensus      1138 ~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI----~---~~n~ad~~~iGd~le~e 1208 (1630)
T 1xi4_A         1138 MEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI----N---GPNNAHIQQVGDRCYDE 1208 (1630)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH----h---CCCHHHHHHHHHHHHhc
Confidence            889999999999999999999887754  33333445888899998888644442    2   34556666799999999


Q ss_pred             CChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHH
Q 011249          294 GYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMT  373 (490)
Q Consensus       294 ~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  373 (490)
                      |++++|..+|..+     ..|..++..|.+.|++++|.+.+++.      .+..+|..+..+|...|++..|......+ 
T Consensus      1209 g~YeeA~~~Y~kA-----~ny~rLA~tLvkLge~q~AIEaarKA------~n~~aWkev~~acve~~Ef~LA~~cgl~I- 1276 (1630)
T 1xi4_A         1209 KMYDAAKLLYNNV-----SNFGRLASTLVHLGEYQAAVDGARKA------NSTRTWKEVCFACVDGKEFRLAQMCGLHI- 1276 (1630)
T ss_pred             CCHHHHHHHHHhh-----hHHHHHHHHHHHhCCHHHHHHHHHHh------CCHHHHHHHHHHHhhhhHHHHHHHHHHhh-
Confidence            9999999999985     48999999999999999999999876      35688888999999999999888766543 


Q ss_pred             HHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhh--hCChHHHHHHHHHHHhcCC----
Q 011249          374 RVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKV--HVNAELGEIAARHLLELGP----  445 (490)
Q Consensus       374 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~--~g~~~~a~~~~~~~~~~~p----  445 (490)
                           ..++..+..++..|.+.|.+++|+.+++...  .+.....|.-+..++.+  .++..++.+.|..-..+.|    
T Consensus      1277 -----iv~~deLeeli~yYe~~G~feEAI~LlE~aL~LeraH~gmftELaiLyaKy~peklmEhlk~f~~rini~k~~r~ 1351 (1630)
T 1xi4_A         1277 -----VVHADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRA 1351 (1630)
T ss_pred             -----hcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccChhHhHHHHHHHHHHHhCCHHHHHHHHHHHHHhcccchHhHH
Confidence                 3466677889999999999999999998776  33344466666666644  4566667777776666555    


Q ss_pred             -CCCchHHHHHHHHHhcCCcchHHHHH
Q 011249          446 -EKTGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       446 -~~~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                       +++..|..++..|.+.|+++.|...+
T Consensus      1352 ~e~~~lW~elv~LY~~~~e~dnA~~tm 1378 (1630)
T 1xi4_A         1352 AEQAHLWAELVFLYDKYEEYDNAIITM 1378 (1630)
T ss_pred             HHHHHHHHHHHHHHHhcccHHHHHHHH
Confidence             67888999999999999999998543

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.84  E-value=3.4e-18  Score=152.78  Aligned_cols=269  Identities=9%  Similarity=-0.026  Sum_probs=210.5

Q ss_pred             HHHHhcCChhHHHHHHhhcCCCC----HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChH
Q 011249          187 AGYGKCGEVREAKKVFDEISEPD----ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVE  262 (490)
Q Consensus       187 ~~~~~~~~~~~A~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  262 (490)
                      +-....|+++.|+..++.....+    ......+.++|...|+++.|+..++.    .-.|+..++..+...+...|+.+
T Consensus         7 ~~~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~~~~   82 (291)
T 3mkr_A            7 KNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHSRRD   82 (291)
T ss_dssp             HHHHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCSTTHH
T ss_pred             HHHHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCCcHH
Confidence            44556788888888887766532    23445677888888998888876644    13556778888888888888999


Q ss_pred             HHHHHHHHHHhcCC-CCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 011249          263 MAAILAKHVDEGCC-DRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEG  341 (490)
Q Consensus       263 ~a~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  341 (490)
                      +|.+.++.+...+. |.++..+..+..++...|++++|++.+++  ..+...+..++..+.+.|++++|.+.++++.+. 
T Consensus        83 ~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~--~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~-  159 (291)
T 3mkr_A           83 AIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ--GDSLECMAMTVQILLKLDRLDLARKELKKMQDQ-  159 (291)
T ss_dssp             HHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT--CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh-
Confidence            99999998877653 44666777788899999999999999998  567788999999999999999999999999985 


Q ss_pred             CCCcHHHH---HHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhh
Q 011249          342 IEPNQVTF---IGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGT  416 (490)
Q Consensus       342 ~~p~~~~~---~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~  416 (490)
                       .|+....   ...+..+...|++++|..+|+++.+.  .+.++..++.+..++.+.|++++|.+.|+++.  .+.++.+
T Consensus       160 -~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~  236 (291)
T 3mkr_A          160 -DEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK--CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPET  236 (291)
T ss_dssp             -CTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH--SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             -CcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH
Confidence             4554311   22334455679999999999999984  56778889999999999999999999998876  5557789


Q ss_pred             HHHHHHHHhhhCChHH-HHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHH
Q 011249          417 WGALLGACKVHVNAEL-GEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEI  469 (490)
Q Consensus       417 ~~~l~~~~~~~g~~~~-a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~  469 (490)
                      +..++..+...|+.++ +.++++++++.+|+++.+..    ...+.+.++++..
T Consensus       237 l~~l~~~~~~~g~~~eaa~~~~~~~~~~~P~~~~~~d----~~~~~~~fd~~~~  286 (291)
T 3mkr_A          237 LINLVVLSQHLGKPPEVTNRYLSQLKDAHRSHPFIKE----YRAKENDFDRLVL  286 (291)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHH----HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHHhCCCChHHHH----HHHHHHHHHHHHH
Confidence            9999999999999875 67899999999999886543    3344444444433

>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=99.84  E-value=1.1e-20  Score=172.45  Aligned_cols=304  Identities=12%  Similarity=0.073  Sum_probs=148.5

Q ss_pred             HHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcC
Q 011249          127 YTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEIS  206 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~  206 (490)
                      ..+.|++++|.+.++++..|  .+|..++.++.+.|++++|++.|.+.  +|..+|..++..+...|++++|++.++...
T Consensus        13 l~~~~~ld~A~~fae~~~~~--~vWs~La~A~l~~g~~~eAIdsfika--~D~~~y~~V~~~ae~~g~~EeAi~yl~~ar   88 (449)
T 1b89_A           13 IEHIGNLDRAYEFAERCNEP--AVWSQLAKAQLQKGMVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMAR   88 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHccCHHHHHHHHHhCCCh--HHHHHHHHHHHHcCCHHHHHHHHHcC--CCHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            34668899999999999555  59999999999999999999999764  677799999999999999999999888776


Q ss_pred             C--CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHH
Q 011249          207 E--PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSN  284 (490)
Q Consensus       207 ~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~  284 (490)
                      +  +++.+.+.++.+|.+.|+++++.++++       .|+..+|..+...|...|.+++|..+|..+         ..|.
T Consensus        89 k~~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~  152 (449)
T 1b89_A           89 KKARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFG  152 (449)
T ss_dssp             --------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT---------TCHH
T ss_pred             HhCccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHH
Confidence            5  566788999999999999999988884       367789999999999999999999999976         3688


Q ss_pred             HHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHH
Q 011249          285 ALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVED  364 (490)
Q Consensus       285 ~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~  364 (490)
                      .++.++.+.|++++|.+.+.++.  ++.+|..++.+|...|+++.|......+     ...+.....++..|.+.|++++
T Consensus       153 ~LA~~L~~Lg~yq~AVea~~KA~--~~~~Wk~v~~aCv~~~ef~lA~~~~l~L-----~~~ad~l~~lv~~Yek~G~~eE  225 (449)
T 1b89_A          153 RLASTLVHLGEYQAAVDGARKAN--STRTWKEVCFACVDGKEFRLAQMCGLHI-----VVHADELEELINYYQDRGYFEE  225 (449)
T ss_dssp             HHHHHHHTTTCHHHHHHHHHHHT--CHHHHHHHHHHHHHTTCHHHHHHTTTTT-----TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHcC--CchhHHHHHHHHHHcCcHHHHHHHHHHH-----HhCHhhHHHHHHHHHHCCCHHH
Confidence            89999999999999999999993  8899999999999999999996655542     2333445568889999999999


Q ss_pred             HHHHHHHHHHHcCCCCCchHHHHHHHHHhh--cCChHHHHHHHHhcc-CCC------ChhhHHHHHHHHhhhCChHHHHH
Q 011249          365 GCKQFELMTRVFGIKPLTEHLTCMVDLLGR--SGQLEKAHSLIMDYK-DFC------DAGTWGALLGACKVHVNAELGEI  435 (490)
Q Consensus       365 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~g~~~~A~~~~~~~~-~~~------~~~~~~~l~~~~~~~g~~~~a~~  435 (490)
                      |..+++....  .-+-....|+.+..+|++  -|+..+.++.|..-. .+|      +...|..+...|...++++.|..
T Consensus       226 ai~lLe~aL~--le~ah~~~ftel~il~~ky~p~k~~ehl~~~~~~ini~k~~~~~~~~~~w~e~~~ly~~~~e~d~A~~  303 (449)
T 1b89_A          226 LITMLEAALG--LERAHMGMFTELAILYSKFKPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAII  303 (449)
T ss_dssp             HHHHHHHHTT--STTCCHHHHHHHHHHHHTTCHHHHHHHHHHHSTTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHhC--CcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHhhchHHHHHH
Confidence            9999999875  224446677777777765  456667777664333 222      57789999999999999999987


Q ss_pred             HHHHHHhc------------CCCCCchHHHHHHHHH
Q 011249          436 AARHLLEL------------GPEKTGNSALLANIYA  459 (490)
Q Consensus       436 ~~~~~~~~------------~p~~~~~~~~l~~~~~  459 (490)
                      ..-+-...            .+.+..+|...+..|.
T Consensus       304 tm~~h~~~a~~~~~f~~~~~kv~n~elyYkai~fyl  339 (449)
T 1b89_A          304 TMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYL  339 (449)
T ss_dssp             HHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHH
T ss_pred             HHHhCChhhhhhHHHHHHHhchhHHHHHHHHHHHHH
Confidence            55443322            4566777766666665

>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=99.84  E-value=1.8e-19  Score=167.76  Aligned_cols=277  Identities=10%  Similarity=0.008  Sum_probs=185.9

Q ss_pred             hCCChHHHHH-HHHHhccC-------CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHH
Q 011249          160 NCGNMKAAKE-FYDRMTEK-------NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKA  228 (490)
Q Consensus       160 ~~~~~~~a~~-~~~~~~~~-------~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~  228 (490)
                      ..|++++|+. .|++....       +...+..++..+...|++++|...|+++.+   .+...+..+..++...|++++
T Consensus        37 ~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~  116 (368)
T 1fch_A           37 WLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELL  116 (368)
T ss_dssp             ---------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCcCHHH
Confidence            3456666665 55554421       234455666666666666666666666543   345566666666666666666


Q ss_pred             HHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHH----------------HHHHHHHh
Q 011249          229 AIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSN----------------ALIHMHSK  292 (490)
Q Consensus       229 A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~----------------~l~~~~~~  292 (490)
                      |++.|+++.+.. +.+..++..+..++...|++++|...++.+.+.. +.+...+.                .+...+ .
T Consensus       117 A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  193 (368)
T 1fch_A          117 AISALRRCLELK-PDNQTALMALAVSFTNESLQRQACEILRDWLRYT-PAYAHLVTPAEEGAGGAGLGPSKRILGSLL-S  193 (368)
T ss_dssp             HHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-TTTGGGCC---------------CTTHHHH-H
T ss_pred             HHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHHHhhhhcccHHHHHHHHHh-h
Confidence            666666666553 2245566666666666666666666666666554 22222111                233333 7


Q ss_pred             cCChHHHHHHHhcccC--C---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHH
Q 011249          293 CGYLDLAWREFSRIKN--K---DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCK  367 (490)
Q Consensus       293 ~~~~~~A~~~~~~~~~--~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~  367 (490)
                      .|++++|...|+++.+  |   +..++..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|..
T Consensus       194 ~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~g~~~~A~~  272 (368)
T 1fch_A          194 DSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVR-PNDYLLWNKLGATLANGNQSEEAVA  272 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             cccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHcCCHHHHHH
Confidence            7888888888887764  3   46778888888889999999999999888752 3346688888888888999999999


Q ss_pred             HHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCC-----------hhhHHHHHHHHhhhCChHHHH
Q 011249          368 QFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCD-----------AGTWGALLGACKVHVNAELGE  434 (490)
Q Consensus       368 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~-----------~~~~~~l~~~~~~~g~~~~a~  434 (490)
                      .++++.+.  .+.+...+..+..+|.+.|++++|...|+++.  .+.+           ..+|..+..++...|++++|.
T Consensus       273 ~~~~al~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  350 (368)
T 1fch_A          273 AYRRALEL--QPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYG  350 (368)
T ss_dssp             HHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHH
T ss_pred             HHHHHHHh--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHH
Confidence            99998873  34557788888899999999999999987765  1112           578888999999999999999


Q ss_pred             HHHHHHHh
Q 011249          435 IAARHLLE  442 (490)
Q Consensus       435 ~~~~~~~~  442 (490)
                      .++++.++
T Consensus       351 ~~~~~~l~  358 (368)
T 1fch_A          351 AADARDLS  358 (368)
T ss_dssp             HHHTTCHH
T ss_pred             HhHHHHHH
Confidence            88876654

>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=99.84  E-value=2.1e-19  Score=164.29  Aligned_cols=261  Identities=8%  Similarity=-0.084  Sum_probs=193.1

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHH
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHS  291 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~  291 (490)
                      .+..+...+...|++++|+.+|+++.+... .+...+..+..++...|++++|...++++.+.. +.+..++..+...|.
T Consensus        23 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~  100 (327)
T 3cv0_A           23 NPMEEGLSMLKLANLAEAALAFEAVCQAAP-EREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHT  100 (327)
T ss_dssp             CHHHHHHHHHHTTCHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHHHHH
Confidence            445555666666666666666666655432 244555556666666666666666666665554 445555666666666


Q ss_pred             hcCChHHHHHHHhcccC--C-ChhHHHHH--------------HH-HHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHH
Q 011249          292 KCGYLDLAWREFSRIKN--K-DVISYSSM--------------IT-AFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVL  353 (490)
Q Consensus       292 ~~~~~~~A~~~~~~~~~--~-~~~~~~~l--------------~~-~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~  353 (490)
                      ..|++++|...++++.+  | +...+..+              .. .+...|++++|...++++.+.. +.+...+..+.
T Consensus       101 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la  179 (327)
T 3cv0_A          101 NEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQLHASLG  179 (327)
T ss_dssp             HTTCHHHHHHHHHHHHHTSTTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHHHHHHH
Confidence            66666666666665543  1 11222222              22 3677889999999999998853 33667888899


Q ss_pred             HHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChH
Q 011249          354 TACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAE  431 (490)
Q Consensus       354 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~  431 (490)
                      ..+...|++++|...++++.+.  .+.+...+..++.++...|++++|.+.++++.  .+.+...+..+...+...|+++
T Consensus       180 ~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g~~~  257 (327)
T 3cv0_A          180 VLYNLSNNYDSAAANLRRAVEL--RPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYD  257 (327)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccHH
Confidence            9999999999999999999883  45567788899999999999999999998876  4456788999999999999999


Q ss_pred             HHHHHHHHHHhcCCC------------CCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          432 LGEIAARHLLELGPE------------KTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       432 ~a~~~~~~~~~~~p~------------~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      +|.+.++++.+..|+            ++.++..++.++.+.|++++|..++++..+.
T Consensus       258 ~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~  315 (327)
T 3cv0_A          258 LAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEP  315 (327)
T ss_dssp             HHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCSHH
T ss_pred             HHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            999999999999998            7889999999999999999999999876544

>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=99.82  E-value=3.9e-16  Score=158.72  Aligned_cols=430  Identities=13%  Similarity=0.083  Sum_probs=285.7

Q ss_pred             hhhhhhchhhHHHHHHHHhhhcCCC-CchhHhHHHHHHHHHhcCCCCHHHHHHH---hccC------CCCCCc-------
Q 011249            6 LVPRSKTFNQLKQVHSYLLKTLTKP-HDQYHYYAQFLIRLLQLPGDNLSYARQV---FDQI------PKCKTQ-------   68 (490)
Q Consensus         6 l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~~~~~~~~A~~~---~~~~------~~~~~~-------   68 (490)
                      |+..+......+-+...++.....| .++.  ++|+|...|-..+++++.-+.-   ++..      .+.|+-       
T Consensus       845 lv~~~ekrnrLkll~p~LE~~~~~g~~~~~--~hnalakiyid~n~npe~fL~~n~~yd~~~vgkyce~rDp~la~iay~  922 (1630)
T 1xi4_A          845 LVAEVEKRNRLKLLLPWLEARIHEGCEEPA--THNALAKIYIDSNNNPERFLRENPYYDSRVVGKYCEKRDPHLACVAYE  922 (1630)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCCCHH--HHHHHHHHHhccCCCHHHHhhccCcccHHHHHHHHHhcCcchHHHHhc
Confidence            3333333333333433333333367 8999  9999999998877656652211   1111      122220       


Q ss_pred             --eehHHHHHHHHhcCChhHHHHHH-HHHH----hcCCCCCHhhHHHHHHH-----hcCCCChH--HHHHHHHHhcCCHH
Q 011249           69 --FLWTSLIRNHVLHAHFRQSILLY-AKMH----RLGVLTSGFTFSSVLNA-----CARVPSLL--EAVICGYTKIGLMD  134 (490)
Q Consensus        69 --~~~~~l~~~~~~~g~~~~A~~~~-~~m~----~~g~~p~~~~~~~ll~~-----~~~~~~~~--~~l~~~~~~~g~~~  134 (490)
                        ..-.-||..+.+++.++.-.+.+ ++..    ..=..++...-..++..     ++...+++  ...++.|...|.+.
T Consensus       923 ~g~~d~eli~vt~~n~l~k~~arylv~r~d~~lW~~vl~~~n~~RR~Lidqv~a~aL~e~~~PeeVs~~vKaf~~aglp~ 1002 (1630)
T 1xi4_A          923 RGQCDLELINVCNENSLFKSLSRYLVRRKDPELWGSVLLESNPYRRPLIDQVVQTALSETQDPEEVSVTVKAFMTADLPN 1002 (1630)
T ss_pred             ccCCcHHHHHHHhcchhHHHHHHHHHHhcCHHHHHHHhcCCcHHHHHHHHHHHHhhcccccCHHHhHHHHHHHHhCCCHH
Confidence              11334666666666554433322 2110    00011122112222221     22222222  56788899999999


Q ss_pred             HHHHHHhhcCC-CC-----HhHHHHH---------------------------HHHHHhCCChHHHHHHHHHhccCCchh
Q 011249          135 DAQRLFDSMAE-RN-----VISWSAM---------------------------VAGYANCGNMKAAKEFYDRMTEKNSVT  181 (490)
Q Consensus       135 ~A~~~~~~~~~-~~-----~~~~~~l---------------------------~~~~~~~~~~~~a~~~~~~~~~~~~~~  181 (490)
                      +|+++++++.- |+     ...-+.+                           ...+...|.+++|..+|++... ....
T Consensus      1003 EaieLLEKivl~~s~fs~n~~LqnlLi~tAIkaD~~Rv~eyI~kLd~~d~~eIA~Iai~lglyEEAf~IYkKa~~-~~~A 1081 (1630)
T 1xi4_A         1003 ELIELLEKIVLDNSVFSEHRNLQNLLILTAIKADRTRVMEYINRLDNYDAPDIANIAISNELFEEAFAIFRKFDV-NTSA 1081 (1630)
T ss_pred             HHHHHHHHHHcCCCcccccHHHHHHHHHHHHHhChhhHHHHHHHhhhccHHHHHHHHHhCCCHHHHHHHHHHcCC-HHHH
Confidence            99999999873 22     2233333                           3445566777777777777631 1111


Q ss_pred             HHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCCh
Q 011249          182 WVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDV  261 (490)
Q Consensus       182 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~  261 (490)
                      .+.+   +...+++++|.++.++.  .++.+|..+..++...|++++|++.|.+.      -|...|..++.++.+.|++
T Consensus      1082 ~~VL---ie~i~nldrAiE~Aerv--n~p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~~~lGky 1150 (1630)
T 1xi4_A         1082 VQVL---IEHIGNLDRAYEFAERC--NEPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNW 1150 (1630)
T ss_pred             HHHH---HHHHhhHHHHHHHHHhc--CCHHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHHHHcCCH
Confidence            1222   22667777777777766  34677888999999999999999988663      3677888899999999999


Q ss_pred             HHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 011249          262 EMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEG  341 (490)
Q Consensus       262 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  341 (490)
                      ++|.+++....+..  +++...+.++.+|++.+++++...+.   ..++...|..+...|...|++++|..+|..+    
T Consensus      1151 EEAIeyL~mArk~~--~e~~Idt~LafaYAKl~rleele~fI---~~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---- 1221 (1630)
T 1xi4_A         1151 EELVKYLQMARKKA--RESYVETELIFALAKTNRLAELEEFI---NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---- 1221 (1630)
T ss_pred             HHHHHHHHHHHhhc--ccccccHHHHHHHHhhcCHHHHHHHH---hCCCHHHHHHHHHHHHhcCCHHHHHHHHHhh----
Confidence            99999998877765  33333345888888888888644443   3456677778888899999999999999874    


Q ss_pred             CCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHH
Q 011249          342 IEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALL  421 (490)
Q Consensus       342 ~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~  421 (490)
                           ..|..++.++.+.|++++|.+.+++..       +..+|..+..+|...|++..|......+.  .++..+..++
T Consensus      1222 -----~ny~rLA~tLvkLge~q~AIEaarKA~-------n~~aWkev~~acve~~Ef~LA~~cgl~Ii--v~~deLeeli 1287 (1630)
T 1xi4_A         1222 -----SNFGRLASTLVHLGEYQAAVDGARKAN-------STRTWKEVCFACVDGKEFRLAQMCGLHIV--VHADELEELI 1287 (1630)
T ss_pred             -----hHHHHHHHHHHHhCCHHHHHHHHHHhC-------CHHHHHHHHHHHhhhhHHHHHHHHHHhhh--cCHHHHHHHH
Confidence                 368888888889999999998888772       45788888888889999999988776543  4566677888


Q ss_pred             HHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhc--CCcchHHHHHH
Q 011249          422 GACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASM--GKWKDSEIVKM  472 (490)
Q Consensus       422 ~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~--g~~~~A~~~~~  472 (490)
                      ..|...|.+++|+.+++.++.++|.+..++..|+.+|.+-  ++..++.++|.
T Consensus      1288 ~yYe~~G~feEAI~LlE~aL~LeraH~gmftELaiLyaKy~peklmEhlk~f~ 1340 (1630)
T 1xi4_A         1288 NYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFKPQKMREHLELFW 1340 (1630)
T ss_pred             HHHHHcCCHHHHHHHHHHHhccChhHhHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            8999999999999999999999999999998888777764  45666666665

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.82  E-value=1.8e-17  Score=159.82  Aligned_cols=362  Identities=11%  Similarity=-0.003  Sum_probs=237.4

Q ss_pred             CCceehHHHHHHHHhcCChhHHHHHHHHHHhc-----CC--CCC-HhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHH
Q 011249           66 KTQFLWTSLIRNHVLHAHFRQSILLYAKMHRL-----GV--LTS-GFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQ  137 (490)
Q Consensus        66 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~-----g~--~p~-~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~  137 (490)
                      .....||.|...+...|++++|++.|++..+.     +.  .|+ ..+|+.+              ...|...|++++|.
T Consensus        49 ~~a~~yn~Lg~~~~~~G~~~eAl~~~~kAl~~~~~~~~~~~~~~~~~~~~nl--------------a~~y~~~g~~~~A~  114 (472)
T 4g1t_A           49 FKATMCNLLAYLKHLKGQNEAALECLRKAEELIQQEHADQAEIRSLVTWGNY--------------AWVYYHMGRLSDVQ  114 (472)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSGGGCTTTTHHHHHHH--------------HHHHHHTTCHHHHH
T ss_pred             hHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhcCccccchHHHHHHHHH--------------HHHHHHcCChHHHH
Confidence            33367999999999999999999999987542     11  222 2344433              33588899999999


Q ss_pred             HHHhhcCC-----------CCHhHHHHHHHHHHh--CCChHHHHHHHHHhcc--C-CchhHHHHHHH---HHhcCChhHH
Q 011249          138 RLFDSMAE-----------RNVISWSAMVAGYAN--CGNMKAAKEFYDRMTE--K-NSVTWVAMIAG---YGKCGEVREA  198 (490)
Q Consensus       138 ~~~~~~~~-----------~~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~---~~~~~~~~~A  198 (490)
                      ..+++..+           ....++..+..++..  .+++++|+..|++..+  | ++..+..+..+   +...++.++|
T Consensus       115 ~~~~ka~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~~~~l~~~~~~~~a  194 (472)
T 4g1t_A          115 IYVDKVKHVCEKFSSPYRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNA  194 (472)
T ss_dssp             HHHHHHHHHHHHSCCSSCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHSCCCCCT
T ss_pred             HHHHHHHHHhHhcccccchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCchHHHHH
Confidence            98887643           134567766666655  4579999999999885  4 45556555555   3456788889


Q ss_pred             HHHHhhcCC---CCHHhHHHHHHHHHh----cCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHH
Q 011249          199 KKVFDEISE---PDASCWAAMTVCYVQ----NGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHV  271 (490)
Q Consensus       199 ~~~~~~~~~---~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~  271 (490)
                      ++.+++..+   .+...+..+...+..    .|++++|.+.+++..... +.+...+..+...+...|++++|...++++
T Consensus       195 l~~~~~al~l~p~~~~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~~~~A~~~~~~a  273 (472)
T 4g1t_A          195 IDPLRQAIRLNPDNQYLKVLLALKLHKMREEGEEEGEGEKLVEEALEKA-PGVTDVLRSAAKFYRRKDEPDKAIELLKKA  273 (472)
T ss_dssp             HHHHHHHHHHCSSCHHHHHHHHHHHHHCC------CHHHHHHHHHHHHC-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHhhcCCcchHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhC-ccHHHHHHHHHHHHHHcCchHHHHHHHHHH
Confidence            988887654   455666666655544    467889999999988764 336678889999999999999999999999


Q ss_pred             HhcCCCCchhHHHHHHHHHHhc-------------------CChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHH
Q 011249          272 DEGCCDRTNYVSNALIHMHSKC-------------------GYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQE  329 (490)
Q Consensus       272 ~~~~~~~~~~~~~~l~~~~~~~-------------------~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~  329 (490)
                      .+.. |.+..++..+..+|...                   +..+.|...|++..+   .+..++..+...+...|++++
T Consensus       274 l~~~-p~~~~~~~~lg~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~~~~  352 (472)
T 4g1t_A          274 LEYI-PNNAYLHCQIGCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALADQYEE  352 (472)
T ss_dssp             HHHS-TTCHHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTCHHH
T ss_pred             HHhC-CChHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhccHHH
Confidence            8876 55677777777666432                   235667777776654   356688899999999999999


Q ss_pred             HHHHHHHHHHcCCCCcHH--HHHHHHH-HhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHH
Q 011249          330 ALDMFLKMRNEGIEPNQV--TFIGVLT-ACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIM  406 (490)
Q Consensus       330 a~~~~~~~~~~~~~p~~~--~~~~l~~-~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  406 (490)
                      |+..|++..+....|...  .+..+.. .....|+.++|+..+++..+   +.|+.......         ...+.++++
T Consensus       353 A~~~~~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~---i~~~~~~~~~~---------~~~l~~~~~  420 (472)
T 4g1t_A          353 AEYYFQKEFSKELTPVAKQLLHLRYGNFQLYQMKCEDKAIHHFIEGVK---INQKSREKEKM---------KDKLQKIAK  420 (472)
T ss_dssp             HHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHH---SCCCCHHHHHH---------HHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHh---cCcccHHHHHH---------HHHHHHHHH
Confidence            999999999854333322  2233332 24578999999999999876   34554332222         233444444


Q ss_pred             hcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          407 DYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       407 ~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      ...  .+.++.+|..+..++...|++++|++.|+++++.+|.+|.+...+|
T Consensus       421 ~~l~~~p~~~~~~~~LG~~~~~~g~~~~A~~~y~kALe~~~~~p~a~~~~G  471 (472)
T 4g1t_A          421 MRLSKNGADSEALHVLAFLQELNEKMQQADEDSERGLESGSLIPSASSWNG  471 (472)
T ss_dssp             HHHHHCC-CTTHHHHHHHHHHHHHHCC------------------------
T ss_pred             HHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCCcHhhcCC
Confidence            433  4567889999999999999999999999999999999998877665

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.82  E-value=1.5e-18  Score=155.03  Aligned_cols=250  Identities=9%  Similarity=-0.040  Sum_probs=204.9

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCh
Q 011249          217 TVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYL  296 (490)
Q Consensus       217 ~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  296 (490)
                      ++-....|++..|+..+++.......+.......+.+++...|+++.|...++.   . -+|+...+..+...+...++.
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~---~-~~~~~~a~~~la~~~~~~~~~   81 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKPSSPERDVERDVFLYRAYLAQRKYGVVLDEIKP---S-SAPELQAVRMFAEYLASHSRR   81 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCCCSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT---T-SCHHHHHHHHHHHHHHCSTTH
T ss_pred             HHHHHHHHHHHHHHHHHHhcccCCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc---c-CChhHHHHHHHHHHHcCCCcH
Confidence            345667899999999988765443222234556778999999999999876644   2 366778888999999999999


Q ss_pred             HHHHHHHhcccC----C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHH
Q 011249          297 DLAWREFSRIKN----K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFEL  371 (490)
Q Consensus       297 ~~A~~~~~~~~~----~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~  371 (490)
                      ++|++.++++..    | ++..+..+..++...|++++|+..+++      ..+...+..++..+.+.|++++|.+.+++
T Consensus        82 ~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l~~  155 (291)
T 3mkr_A           82 DAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKELKK  155 (291)
T ss_dssp             HHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            999999998642    4 566778888999999999999999987      45677888899999999999999999999


Q ss_pred             HHHHcCCCCCchHH---HHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          372 MTRVFGIKPLTEHL---TCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       372 ~~~~~~~~~~~~~~---~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      +.+.   .|+....   ..++..+...|++++|..+|+++.  .+.++..++.+..++...|++++|+..++++++.+|+
T Consensus       156 ~~~~---~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~  232 (291)
T 3mkr_A          156 MQDQ---DEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSG  232 (291)
T ss_dssp             HHHH---CTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHhh---CcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            9884   3553221   223344455699999999999887  5667889999999999999999999999999999999


Q ss_pred             CCchHHHHHHHHHhcCCcch-HHHHHHHhhhccc
Q 011249          447 KTGNSALLANIYASMGKWKD-SEIVKMMISETEK  479 (490)
Q Consensus       447 ~~~~~~~l~~~~~~~g~~~~-A~~~~~~~~~~~~  479 (490)
                      ++.++..++.++...|+.++ +.++++++.+..+
T Consensus       233 ~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~P  266 (291)
T 3mkr_A          233 HPETLINLVVLSQHLGKPPEVTNRYLSQLKDAHR  266 (291)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCT
T ss_pred             CHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCC
Confidence            99999999999999999986 5789998876543

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.82  E-value=1.2e-18  Score=162.00  Aligned_cols=234  Identities=11%  Similarity=0.027  Sum_probs=199.9

Q ss_pred             ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHH
Q 011249          244 SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITA  320 (490)
Q Consensus       244 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~  320 (490)
                      +...+..+...+.+.|++++|..+++.+.+.. |.+..++..+..+|...|++++|+..|+++.+   .+..+|..++.+
T Consensus        64 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~  142 (365)
T 4eqf_A           64 DWPGAFEEGLKRLKEGDLPVTILFMEAAILQD-PGDAEAWQFLGITQAENENEQAAIVALQRCLELQPNNLKALMALAVS  142 (365)
T ss_dssp             TCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            44568889999999999999999999999886 66788999999999999999999999998875   467899999999


Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCCcHH-----------HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHH
Q 011249          321 FADHGKSQEALDMFLKMRNEGIEPNQV-----------TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMV  389 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~~~p~~~-----------~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  389 (490)
                      |...|++++|...++++.+.  .|+..           .+..+...+...|++++|...++++.+.....++...+..++
T Consensus       143 ~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l~  220 (365)
T 4eqf_A          143 YTNTSHQQDACEALKNWIKQ--NPKYKYLVKNKKGSPGLTRRMSKSPVDSSVLEGVKELYLEAAHQNGDMIDPDLQTGLG  220 (365)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--CHHHHCC-------------------CCHHHHHHHHHHHHHHHHSCSSCCHHHHHHHH
T ss_pred             HHccccHHHHHHHHHHHHHh--CccchHHHhhhccchHHHHHHHHHHhhhhhHHHHHHHHHHHHHhCcCccCHHHHHHHH
Confidence            99999999999999999884  44432           233457788999999999999999998522222678899999


Q ss_pred             HHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchH
Q 011249          390 DLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDS  467 (490)
Q Consensus       390 ~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  467 (490)
                      ..|...|++++|.+.|+++.  .+.+..+|..+..++...|++++|+..++++++..|+++.++..++.+|.+.|++++|
T Consensus       221 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A  300 (365)
T 4eqf_A          221 VLFHLSGEFNRAIDAFNAALTVRPEDYSLWNRLGATLANGDRSEEAVEAYTRALEIQPGFIRSRYNLGISCINLGAYREA  300 (365)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHCCCHHHH
Confidence            99999999999999998876  4557889999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhcccc
Q 011249          468 EIVKMMISETEKK  480 (490)
Q Consensus       468 ~~~~~~~~~~~~~  480 (490)
                      ...++++.+....
T Consensus       301 ~~~~~~al~~~~~  313 (365)
T 4eqf_A          301 VSNFLTALSLQRK  313 (365)
T ss_dssp             HHHHHHHHHHHHC
T ss_pred             HHHHHHHHHhCcc
Confidence            9999999876543

>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=99.79  E-value=2.4e-18  Score=157.28  Aligned_cols=270  Identities=10%  Similarity=-0.010  Sum_probs=143.4

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHh
Q 011249          149 ISWSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQ  222 (490)
Q Consensus       149 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~  222 (490)
                      ..+..+...+...|++++|..+|+++.+  | +..++..++.++...|++++|.+.|+++.+   .+...+..+..++..
T Consensus        22 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~  101 (327)
T 3cv0_A           22 ENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTN  101 (327)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHH
Confidence            3455566667777777777777776653  2 445556666666666666666666665543   345556666666666


Q ss_pred             cCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHH-HH-HHHhcCChHHHH
Q 011249          223 NGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNAL-IH-MHSKCGYLDLAW  300 (490)
Q Consensus       223 ~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l-~~-~~~~~~~~~~A~  300 (490)
                      .|++++|++.++++.+.... +...+..+...+                      ++......+ .. .+...|++++|.
T Consensus       102 ~~~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~~~~~A~  158 (327)
T 3cv0_A          102 EHNANAALASLRAWLLSQPQ-YEQLGSVNLQAD----------------------VDIDDLNVQSEDFFFAAPNEYRECR  158 (327)
T ss_dssp             TTCHHHHHHHHHHHHHTSTT-TTTC------------------------------------------CCTTSHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCc-cHHHHHHHhHHH----------------------HHHHHHHHHHHhHHHHHcccHHHHH
Confidence            66666666666666654211 122222220000                      000000001 11 244445555555


Q ss_pred             HHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcC
Q 011249          301 REFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFG  377 (490)
Q Consensus       301 ~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  377 (490)
                      ..++++.+   .+...+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.  
T Consensus       159 ~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--  235 (327)
T 3cv0_A          159 TLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELR-PDDAQLWNKLGATLANGNRPQEALDAYNRALDI--  235 (327)
T ss_dssp             HHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHhhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--
Confidence            55554433   234455555555666666666666666655531 223445555666666666666666666666552  


Q ss_pred             CCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC-------------ChhhHHHHHHHHhhhCChHHHHHHHHHHHhc
Q 011249          378 IKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-------------DAGTWGALLGACKVHVNAELGEIAARHLLEL  443 (490)
Q Consensus       378 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-------------~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  443 (490)
                      .+.+...+..+..+|...|++++|.+.++++. ..|             +...+..+..++...|++++|..+++++++.
T Consensus       236 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~  315 (327)
T 3cv0_A          236 NPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEP  315 (327)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTCCSHH
T ss_pred             CCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            23345555566666666666666666665544 111             3456666666666677777777666655554


Q ss_pred             C
Q 011249          444 G  444 (490)
Q Consensus       444 ~  444 (490)
                      .
T Consensus       316 ~  316 (327)
T 3cv0_A          316 F  316 (327)
T ss_dssp             H
T ss_pred             c
Confidence            3

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.76  E-value=6.6e-17  Score=154.03  Aligned_cols=376  Identities=8%  Similarity=-0.013  Sum_probs=245.7

Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCH---HHHHHHHhhcCCCCHh
Q 011249           73 SLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLM---DDAQRLFDSMAERNVI  149 (490)
Q Consensus        73 ~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~---~~A~~~~~~~~~~~~~  149 (490)
                      .+...+.+.|++++|.++|++..+.|. |+....                +...|...|+.   ++|+.+|++..+.++.
T Consensus         8 ~la~~~~~~g~~~~A~~~~~~aa~~g~-~~A~~~----------------Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~   70 (452)
T 3e4b_A            8 RLANEALKRGDTVTAQQNYQQLAELGY-SEAQVG----------------LADIQVGTRDPAQIKQAEATYRAAADTSPR   70 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTC-CTGGGT----------------CC----------------------------
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHHCCC-HHHHHH----------------HHHHHHccCCCCCHHHHHHHHHHHHhCCHH
Confidence            356667788899999999988877653 222211                11124455666   8888888888877666


Q ss_pred             HHHHHHHHHHhCC-----ChHHHHHHHHHhccC-CchhHHHHHHHHHhcCChhHH---HHHHhhcCC-CCHHhHHHHHHH
Q 011249          150 SWSAMVAGYANCG-----NMKAAKEFYDRMTEK-NSVTWVAMIAGYGKCGEVREA---KKVFDEISE-PDASCWAAMTVC  219 (490)
Q Consensus       150 ~~~~l~~~~~~~~-----~~~~a~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A---~~~~~~~~~-~~~~~~~~l~~~  219 (490)
                      .+..+...+...+     ++++|+..|++..++ +...+..|...|...+..+++   .+.+....+ .++..+..|...
T Consensus        71 A~~~Lg~~~~~~~~~~~~~~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~Lg~~  150 (452)
T 3e4b_A           71 AQARLGRLLAAKPGATEAEHHEAESLLKKAFANGEGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAGYPEAGLAQVLL  150 (452)
T ss_dssp             CHHHHHHHHHTC--CCHHHHHHHHHHHHHHHHTTCSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHTCTTHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCcCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            7777777566655     778899999888876 666788888888876654443   333333322 456677788888


Q ss_pred             HHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccC---ChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc---
Q 011249          220 YVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLG---DVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC---  293 (490)
Q Consensus       220 ~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g---~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---  293 (490)
                      |...+.++++......+.+.-...++..+..+...+...|   +.++|...|+...+.| +++...+..+..+|...   
T Consensus       151 y~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~~y~~g~~~  229 (452)
T 3e4b_A          151 YRTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVARVLGDATLG  229 (452)
T ss_dssp             HHHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHHHHTCGGGS
T ss_pred             HHcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHhCCCCC
Confidence            8888866655554444333222234447778888888888   8889999999988887 56666556677777665   


Q ss_pred             -CChHHHHHHHhcccCCChhHHHHHHHH-H--HhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCC-----ChHH
Q 011249          294 -GYLDLAWREFSRIKNKDVISYSSMITA-F--ADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGG-----LVED  364 (490)
Q Consensus       294 -~~~~~A~~~~~~~~~~~~~~~~~l~~~-~--~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g-----~~~~  364 (490)
                       +++++|..+|++....++..+..+... +  ...+++++|...|++..+.|   +......+...|. .|     ++++
T Consensus       230 ~~d~~~A~~~~~~aa~g~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g---~~~A~~~Lg~~y~-~G~g~~~d~~~  305 (452)
T 3e4b_A          230 TPDEKTAQALLEKIAPGYPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAAD---QPRAELLLGKLYY-EGKWVPADAKA  305 (452)
T ss_dssp             SCCHHHHHHHHHHHGGGSTHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHH-HCSSSCCCHHH
T ss_pred             CCCHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHH-cCCCCCCCHHH
Confidence             788999999988874466777777776 4  46789999999999998866   5556666666665 34     8899


Q ss_pred             HHHHHHHHHHHcCCCCCchHHHHHHHHHhh----cCChHHHHHHHHhccCCCChhhHHHHHHHHhh----hCChHHHHHH
Q 011249          365 GCKQFELMTRVFGIKPLTEHLTCMVDLLGR----SGQLEKAHSLIMDYKDFCDAGTWGALLGACKV----HVNAELGEIA  436 (490)
Q Consensus       365 a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~  436 (490)
                      |...|++..     +.++..+..|..+|..    ..++++|.++|++.....++.....+...|..    ..|.++|...
T Consensus       306 A~~~~~~Aa-----~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~  380 (452)
T 3e4b_A          306 AEAHFEKAV-----GREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQNSADFAIAQLFSQGKGTKPDPLNAYVF  380 (452)
T ss_dssp             HHHHHHTTT-----TTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTCTTHHHHHHHHHHSCTTBCCCHHHHHHH
T ss_pred             HHHHHHHHh-----CCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhChHHHHHHHHHHHHhCCCCCCCHHHHHHH
Confidence            999998875     3456677777777766    44899999999888766667777777777754    4589999999


Q ss_pred             HHHHHhcCCCCCchHHHHHHHH--HhcCCcchHHHHHHHhhhc
Q 011249          437 ARHLLELGPEKTGNSALLANIY--ASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       437 ~~~~~~~~p~~~~~~~~l~~~~--~~~g~~~~A~~~~~~~~~~  477 (490)
                      |+++.+.++..  ....+..+.  ...++..+|.++.++..+.
T Consensus       381 ~~~A~~~g~~~--a~~~l~~l~~~~~~~~~~~a~~~~~~~~~~  421 (452)
T 3e4b_A          381 SQLAKAQDTPE--ANDLATQLEAPLTPAQRAEGQRLVQQELAA  421 (452)
T ss_dssp             HHHHHTTCCHH--HHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHH--HHHHHHHHHHhCCHHHHHHHHHHHHHHHHh
Confidence            99998877543  333343333  2345667777777765554

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.76  E-value=6.7e-17  Score=142.13  Aligned_cols=228  Identities=11%  Similarity=-0.026  Sum_probs=127.5

Q ss_pred             HhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCC--CchhHHHHHHH
Q 011249          211 SCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCD--RTNYVSNALIH  288 (490)
Q Consensus       211 ~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~--~~~~~~~~l~~  288 (490)
                      ..+..+...+...|++++|+..|++..+..  .+...+..+..++...|++++|...++.+.+....  ++..       
T Consensus         6 ~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~-------   76 (258)
T 3uq3_A            6 DKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYK-------   76 (258)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHH-------
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchH-------
Confidence            456666677777777777777777776655  55666666666666777777777666666543211  0100       


Q ss_pred             HHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHH
Q 011249          289 MHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQ  368 (490)
Q Consensus       289 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~  368 (490)
                                          .....+..+...+...|++++|...++++.+.  .|+..       .+...|++++|...
T Consensus        77 --------------------~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~~-------~~~~~~~~~~a~~~  127 (258)
T 3uq3_A           77 --------------------VISKSFARIGNAYHKLGDLKKTIEYYQKSLTE--HRTAD-------ILTKLRNAEKELKK  127 (258)
T ss_dssp             --------------------HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHH-------HHHHHHHHHHHHHH
T ss_pred             --------------------HHHHHHHHHHHHHHHcccHHHHHHHHHHHHhc--CchhH-------HHHHHhHHHHHHHH
Confidence                                00234444444555555555555555555542  23322       12233445555555


Q ss_pred             HHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          369 FELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      ++++..  ..+.+...+..++..+...|++++|.+.+++..  .+.+...+..+...+...|++++|+..++++++..|+
T Consensus       128 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~  205 (258)
T 3uq3_A          128 AEAEAY--VNPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPN  205 (258)
T ss_dssp             HHHHHH--CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHH--cCcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHH
Confidence            555544  222334445555555556666666666655544  2334555556666666666666666666666666666


Q ss_pred             CCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          447 KTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       447 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      ++..+..++.++...|++++|.+.+++..+..
T Consensus       206 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~  237 (258)
T 3uq3_A          206 FVRAYIRKATAQIAVKEYASALETLDAARTKD  237 (258)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC
Confidence            66666666666666666666666666655443

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.76  E-value=7.4e-17  Score=141.88  Aligned_cols=234  Identities=10%  Similarity=-0.048  Sum_probs=171.0

Q ss_pred             chhHHHHHHHHHhcCChhHHHHHHhhcCC--CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcc--cC----hhhHHH
Q 011249          179 SVTWVAMIAGYGKCGEVREAKKVFDEISE--PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVR--IS----EVAMVG  250 (490)
Q Consensus       179 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~--p~----~~~~~~  250 (490)
                      ...+..++..+...|++++|+..|++..+  .+...+..+..++...|++++|++.+++..+....  |+    ...+..
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~   84 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELHKDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSFAR   84 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhhccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHHHH
Confidence            45788899999999999999999988644  67889999999999999999999999998875321  11    467777


Q ss_pred             HHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHH
Q 011249          251 AISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEA  330 (490)
Q Consensus       251 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a  330 (490)
                      +..++...|++++|...++.+.+..  |+.                                      ..+...|++++|
T Consensus        85 l~~~~~~~~~~~~A~~~~~~a~~~~--~~~--------------------------------------~~~~~~~~~~~a  124 (258)
T 3uq3_A           85 IGNAYHKLGDLKKTIEYYQKSLTEH--RTA--------------------------------------DILTKLRNAEKE  124 (258)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHC--CCH--------------------------------------HHHHHHHHHHHH
T ss_pred             HHHHHHHcccHHHHHHHHHHHHhcC--chh--------------------------------------HHHHHHhHHHHH
Confidence            8888888888888888888877754  221                                      123344556666


Q ss_pred             HHHHHHHHHcCCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          331 LDMFLKMRNEGIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       331 ~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                      ...++++...  .|+ ...+..+...+...|++++|...++++.+.  .+.+...+..+..++...|++++|.+.+++..
T Consensus       125 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al  200 (258)
T 3uq3_A          125 LKKAEAEAYV--NPEKAEEARLEGKEYFTKSDWPNAVKAYTEMIKR--APEDARGYSNRAAALAKLMSFPEAIADCNKAI  200 (258)
T ss_dssp             HHHHHHHHHC--CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHc--CcchHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--CcccHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            6666666653  332 345666666677777777777777777663  34456667777777777777777777777665


Q ss_pred             --CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC------CCCCchHHHHHH
Q 011249          410 --DFCDAGTWGALLGACKVHVNAELGEIAARHLLELG------PEKTGNSALLAN  456 (490)
Q Consensus       410 --~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~------p~~~~~~~~l~~  456 (490)
                        .+.+...+..+...+...|++++|.+.++++.+..      |++..++..+..
T Consensus       201 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~p~~~~~~~~l~~  255 (258)
T 3uq3_A          201 EKDPNFVRAYIRKATAQIAVKEYASALETLDAARTKDAEVNNGSSAREIDQLYYK  255 (258)
T ss_dssp             HHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred             HhCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhChhhcCCCchHHHHHHHHH
Confidence              34456677788888888888888888888888877      776666665554

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.75  E-value=5.4e-17  Score=138.58  Aligned_cols=194  Identities=14%  Similarity=0.014  Sum_probs=144.6

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHH
Q 011249          277 DRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGV  352 (490)
Q Consensus       277 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l  352 (490)
                      |+++..+..+...+...|++++|...|++..+   .++..+..+..++.+.|++++|+..+++..+.  .| +...+..+
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~l   79 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKENPQDPEALYWLARTQLKLGLVNPALENGKTLVAR--TPRYLGGYMVL   79 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHH
Confidence            45566666677777777777777777776654   35567777777777788888888888887774  34 34567777


Q ss_pred             HHHhcCC-----------CChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHH
Q 011249          353 LTACSHG-----------GLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGA  419 (490)
Q Consensus       353 ~~~~~~~-----------g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~  419 (490)
                      ...+...           |++++|...+++..+.  .|.+...+..+..++...|++++|+..|++..  . .++..+..
T Consensus        80 g~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~  156 (217)
T 2pl2_A           80 SEAYVALYRQAEDRERGKGYLEQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKAEASLKQALALE-DTPEIRSA  156 (217)
T ss_dssp             HHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCHHHHHH
T ss_pred             HHHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc-cchHHHHH
Confidence            7777777           9999999999999873  34457778889999999999999999998876  5 77788999


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      +..++...|++++|+..|+++++.+|+++.++..++.++.+.|++++|+..+++..
T Consensus       157 la~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~~  212 (217)
T 2pl2_A          157 LAELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYASALLLKGKAEEAARAAALEH  212 (217)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTC---------------
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999998764

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.73  E-value=3.5e-16  Score=138.86  Aligned_cols=246  Identities=10%  Similarity=-0.017  Sum_probs=150.1

Q ss_pred             hHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCc--hhHHHHHHHH
Q 011249          212 CWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRT--NYVSNALIHM  289 (490)
Q Consensus       212 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~--~~~~~~l~~~  289 (490)
                      .+......+...|++++|+..|++..+... .+...+..+..++...|++++|...++.+.+....++  ...+..+...
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p-~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~   83 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKKY-NSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKI   83 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTTC-CCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHH
Confidence            344455566666666666666666665431 1334555566666666666666666666655221111  2235556666


Q ss_pred             HHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHH
Q 011249          290 HSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDG  365 (490)
Q Consensus       290 ~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a  365 (490)
                      +...|++++|+..|++..+   .+..+|..+...|...|++++|...+++..+.  .| +...+..+...+...+++++|
T Consensus        84 ~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~l~~~~~~~~~~~~A  161 (272)
T 3u4t_A           84 LMKKGQDSLAIQQYQAAVDRDTTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRP--TTTDPKVFYELGQAYYYNKEYVKA  161 (272)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCS--SCCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHccCHHHHHHHHHHHhhc--CCCcHHHHHHHHHHHHHHHHHHHH
Confidence            6666666666666666543   24456666666666777777777777666653  33 334555555222233477777


Q ss_pred             HHHHHHHHHHcCCCCCchHHHHHHHHHhhcCC---hHHHHHHHHhcc----CCCC------hhhHHHHHHHHhhhCChHH
Q 011249          366 CKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ---LEKAHSLIMDYK----DFCD------AGTWGALLGACKVHVNAEL  432 (490)
Q Consensus       366 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~----~~~~------~~~~~~l~~~~~~~g~~~~  432 (490)
                      ...++++.+.  .+.+...+..+..++...|+   +++|...+++..    ..|+      ...|..+...+...|++++
T Consensus       162 ~~~~~~a~~~--~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  239 (272)
T 3u4t_A          162 DSSFVKVLEL--KPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVK  239 (272)
T ss_dssp             HHHHHHHHHH--STTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHh--CccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHH
Confidence            7777777663  23335556666666666666   666776666554    1233      2467778888999999999


Q ss_pred             HHHHHHHHHhcCCCCCchHHHHHHHHHhcC
Q 011249          433 GEIAARHLLELGPEKTGNSALLANIYASMG  462 (490)
Q Consensus       433 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  462 (490)
                      |.+.++++++.+|+++.+...+..+....+
T Consensus       240 A~~~~~~al~~~p~~~~a~~~l~~~~~~~~  269 (272)
T 3u4t_A          240 ADAAWKNILALDPTNKKAIDGLKMKLEHHH  269 (272)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHC-------
T ss_pred             HHHHHHHHHhcCccHHHHHHHhhhhhcccc
Confidence            999999999999999998888877665544

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.73  E-value=2.9e-16  Score=139.51  Aligned_cols=241  Identities=9%  Similarity=-0.107  Sum_probs=188.9

Q ss_pred             hcCChHHHHHHHHHHHHcCc---ccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHH
Q 011249          222 QNGYAKAAIEMYKVMRQENV---RISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDL  298 (490)
Q Consensus       222 ~~g~~~~A~~~~~~~~~~~~---~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  298 (490)
                      ..|++++|+..++++.+...   +.+...+..+..++...|++++|...++++.+.. +.+..++..+..+|...|++++
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            45778889998888887532   1245677888888888999999999999888875 5677888888999999999999


Q ss_pred             HHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHH
Q 011249          299 AWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRV  375 (490)
Q Consensus       299 A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  375 (490)
                      |...|+++.+   .+...+..+..++...|++++|...++++.+.  .|+.......+..+...|++++|...+++....
T Consensus        96 A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~  173 (275)
T 1xnf_A           96 AYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK  173 (275)
T ss_dssp             HHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence            9999988765   36778899999999999999999999999984  455444444444556679999999999888873


Q ss_pred             cCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccC-CC-----ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          376 FGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKD-FC-----DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       376 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~-----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                        .+++...+ .++..+...++.++|.+.+++... .|     +...+..+...+...|++++|...++++++.+|++..
T Consensus       174 --~~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~  250 (275)
T 1xnf_A          174 --SDKEQWGW-NIVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNFV  250 (275)
T ss_dssp             --SCCCSTHH-HHHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTTCH
T ss_pred             --CCcchHHH-HHHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCchhHH
Confidence              44454444 477778888899999999987762 22     2568888999999999999999999999999998755


Q ss_pred             hHHHHHHHHHhcCCcchHHHHH
Q 011249          450 NSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       450 ~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      .+   +.++...|++++|++.+
T Consensus       251 ~~---~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          251 EH---RYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HH---HHHHHHHHHHHHC----
T ss_pred             HH---HHHHHHHHHHHhhHHHH
Confidence            43   66788889999998876

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=99.71  E-value=3.2e-16  Score=149.33  Aligned_cols=342  Identities=10%  Similarity=0.021  Sum_probs=236.0

Q ss_pred             HHHHHHhcCCHHHHHHHHhhcCC-CCHhHHHHHHHHHHhCCCh---HHHHHHHHHhccCCchhHHHHHHHHHhcC-----
Q 011249          123 VICGYTKIGLMDDAQRLFDSMAE-RNVISWSAMVAGYANCGNM---KAAKEFYDRMTEKNSVTWVAMIAGYGKCG-----  193 (490)
Q Consensus       123 l~~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~l~~~~~~~~~~---~~a~~~~~~~~~~~~~~~~~l~~~~~~~~-----  193 (490)
                      +...+.+.|++++|+++|++..+ .++..+..+...|...|+.   ++|++.|++..+.++..+..+...+...+     
T Consensus         9 la~~~~~~g~~~~A~~~~~~aa~~g~~~A~~~Lg~~y~~~g~~~d~~~A~~~~~~A~~~~~~A~~~Lg~~~~~~~~~~~~   88 (452)
T 3e4b_A            9 LANEALKRGDTVTAQQNYQQLAELGYSEAQVGLADIQVGTRDPAQIKQAEATYRAAADTSPRAQARLGRLLAAKPGATEA   88 (452)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCCTGGGTCC----------------------------CHHHHHHHHHTC--CCHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCCCc
Confidence            34457888999999999999876 3556667777778888888   99999999998878888888888666655     


Q ss_pred             ChhHHHHHHhhcCC-CCHHhHHHHHHHHHhcCChHH---HHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHH
Q 011249          194 EVREAKKVFDEISE-PDASCWAAMTVCYVQNGYAKA---AIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAK  269 (490)
Q Consensus       194 ~~~~A~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~---A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~  269 (490)
                      ++++|++.|++..+ .+...+..|...|...+..++   +.+.+......|   +......+...+...+.++.+.....
T Consensus        89 ~~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~~~~~~~~~~a~~~~~~a~~~g---~~~a~~~Lg~~y~~~~~~~~~~~~a~  165 (452)
T 3e4b_A           89 EHHEAESLLKKAFANGEGNTLIPLAMLYLQYPHSFPNVNAQQQISQWQAAG---YPEAGLAQVLLYRTQGTYDQHLDDVE  165 (452)
T ss_dssp             HHHHHHHHHHHHHHTTCSSCHHHHHHHHHHCGGGCTTCCHHHHHHHHHHHT---CTTHHHHHHHHHHHHTCGGGGHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcccCHHHHH
Confidence            78899999988765 445578888888888766544   455555555444   45566677777877776555544433


Q ss_pred             HHHhcCCCCchhHHHHHHHHHHhcC---ChHHHHHHHhcccC---CChhHHHHHHHHHHhc----CChHHHHHHHHHHHH
Q 011249          270 HVDEGCCDRTNYVSNALIHMHSKCG---YLDLAWREFSRIKN---KDVISYSSMITAFADH----GKSQEALDMFLKMRN  339 (490)
Q Consensus       270 ~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~----~~~~~a~~~~~~~~~  339 (490)
                      .+.+.-...++..+..|..+|...|   +.++|+..|++..+   ++...+..+...|...    +++++|...|++.. 
T Consensus       166 ~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-  244 (452)
T 3e4b_A          166 RICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-  244 (452)
T ss_dssp             HHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-
Confidence            3332222333447788999999999   99999999998765   3444446777777654    69999999999987 


Q ss_pred             cCCCCcHHHHHHHHHH-h--cCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcC-----ChHHHHHHHHhccCC
Q 011249          340 EGIEPNQVTFIGVLTA-C--SHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSG-----QLEKAHSLIMDYKDF  411 (490)
Q Consensus       340 ~~~~p~~~~~~~l~~~-~--~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-----~~~~A~~~~~~~~~~  411 (490)
                      .|   +...+..+... +  ...+++++|...|++..+. |   ++..+..|..+|. .|     ++++|.++|++.. +
T Consensus       245 ~g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~-g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~  315 (452)
T 3e4b_A          245 PG---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAA-D---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-G  315 (452)
T ss_dssp             GG---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-T
T ss_pred             CC---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-C
Confidence            43   33444455544 3  4589999999999999874 4   5667777888887 55     9999999999998 7


Q ss_pred             CChhhHHHHHHHHhh----hCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHh----cCCcchHHHHHHHhhhccc
Q 011249          412 CDAGTWGALLGACKV----HVNAELGEIAARHLLELGPEKTGNSALLANIYAS----MGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       412 ~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~  479 (490)
                      .++.....+...|..    ..|+++|.+.|+++.+  +.++.....|+.+|..    ..+.++|...+++..+.|.
T Consensus       316 g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~--~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~~g~  389 (452)
T 3e4b_A          316 REVAADYYLGQIYRRGYLGKVYPQKALDHLLTAAR--NGQNSADFAIAQLFSQGKGTKPDPLNAYVFSQLAKAQDT  389 (452)
T ss_dssp             TCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHT--TTCTTHHHHHHHHHHSCTTBCCCHHHHHHHHHHHHTTCC
T ss_pred             CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHh--hChHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHCCC
Confidence            788888888877766    3499999999999987  4568889999998875    4588999999999887764

>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=99.70  E-value=1e-14  Score=129.52  Aligned_cols=224  Identities=9%  Similarity=-0.029  Sum_probs=113.5

Q ss_pred             CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhc----cCChHHHHHHHHHHHhcCCCCchhHHH
Q 011249          209 DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQ----LGDVEMAAILAKHVDEGCCDRTNYVSN  284 (490)
Q Consensus       209 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~  284 (490)
                      ++.++..+...+...|++++|++.|++..+.+   +...+..+...+..    .+++++|...+++..+.+   ++..+.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~   78 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   78 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHHH
Confidence            45566666677777777777777777766622   34455556666666    666677776666666554   444455


Q ss_pred             HHHHHHHh----cCChHHHHHHHhcccC-CChhHHHHHHHHHHh----cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 011249          285 ALIHMHSK----CGYLDLAWREFSRIKN-KDVISYSSMITAFAD----HGKSQEALDMFLKMRNEGIEPNQVTFIGVLTA  355 (490)
Q Consensus       285 ~l~~~~~~----~~~~~~A~~~~~~~~~-~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~  355 (490)
                      .+...|..    .+++++|+..|++..+ .++..+..+...|..    .+++++|+..|++..+.+   +...+..+...
T Consensus        79 ~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~  155 (273)
T 1ouv_A           79 LLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTILGSL  155 (273)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHH
T ss_pred             HHHHHHhCCCCcccCHHHHHHHHHHHHHcCCccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHHHHH
Confidence            55555555    5555555555554443 234445555555555    555555555555555432   23333334444


Q ss_pred             hcC----CCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh----cCChHHHHHHHHhccCCCChhhHHHHHHHHhh-
Q 011249          356 CSH----GGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR----SGQLEKAHSLIMDYKDFCDAGTWGALLGACKV-  426 (490)
Q Consensus       356 ~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~-  426 (490)
                      |..    .+++++|...+++..+. +   ++..+..+..+|..    .+++++|.+.|++.....+...+..+...+.. 
T Consensus       156 ~~~~~~~~~~~~~A~~~~~~a~~~-~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~l~~~~~~g  231 (273)
T 1ouv_A          156 YDAGRGTPKDLKKALASYDKACDL-K---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELENGGGCFNLGAMQYNG  231 (273)
T ss_dssp             HHHTSSSCCCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHcCCCCCCCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHcC
Confidence            433    44555555555544441 1   22333344444444    44444444444443322223333444444444 


Q ss_pred             ---hCChHHHHHHHHHHHhcCC
Q 011249          427 ---HVNAELGEIAARHLLELGP  445 (490)
Q Consensus       427 ---~g~~~~a~~~~~~~~~~~p  445 (490)
                         .+++++|.+.++++.+.+|
T Consensus       232 ~~~~~~~~~A~~~~~~a~~~~~  253 (273)
T 1ouv_A          232 EGVTRNEKQAIENFKKGCKLGA  253 (273)
T ss_dssp             SSSSCCSTTHHHHHHHHHHHTC
T ss_pred             CCcccCHHHHHHHHHHHHHcCC
Confidence               4444444444444444443

>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=99.69  E-value=3.4e-15  Score=137.84  Aligned_cols=247  Identities=9%  Similarity=-0.006  Sum_probs=198.4

Q ss_pred             CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCC-hHHHHHHHHHHHhcCCCCchhHHHHHH
Q 011249          209 DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGD-VEMAAILAKHVDEGCCDRTNYVSNALI  287 (490)
Q Consensus       209 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~-~~~a~~~~~~~~~~~~~~~~~~~~~l~  287 (490)
                      +...|..+..++.+.|++++|++.+++..+... -+...|..+..++...|+ +++|...++++.+.. +.+...|..+.
T Consensus        96 ~~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~P-~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-P~~~~a~~~~g  173 (382)
T 2h6f_A           96 FRDVYDYFRAVLQRDERSERAFKLTRDAIELNA-ANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRR  173 (382)
T ss_dssp             HHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCc-cCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-CCCHHHHHHHH
Confidence            345677888888888999999999998887642 256778888888888886 999999999988876 66778888888


Q ss_pred             HHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcC-CCCh
Q 011249          288 HMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSH-GGLV  362 (490)
Q Consensus       288 ~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~-~g~~  362 (490)
                      .++...|++++|+..|+++.+   .+...|..+..++...|++++|+..++++++.  .| +...|..+..++.. .|..
T Consensus       174 ~~~~~~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l--~P~~~~a~~~lg~~l~~l~~~~  251 (382)
T 2h6f_A          174 VLVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE--DVRNNSVWNQRYFVISNTTGYN  251 (382)
T ss_dssp             HHHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCSC
T ss_pred             HHHHHccCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCcc
Confidence            889999999999999988875   46778888999999999999999999999985  44 55688888888887 6665


Q ss_pred             HHH-----HHHHHHHHHHcCCCCCchHHHHHHHHHhhcC--ChHHHHHHHHhccC-CCChhhHHHHHHHHhhhC------
Q 011249          363 EDG-----CKQFELMTRVFGIKPLTEHLTCMVDLLGRSG--QLEKAHSLIMDYKD-FCDAGTWGALLGACKVHV------  428 (490)
Q Consensus       363 ~~a-----~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g--~~~~A~~~~~~~~~-~~~~~~~~~l~~~~~~~g------  428 (490)
                      ++|     +..++++.+.  .+-+...|..+..++...|  ++++|.+.+.++.. +.+...+..++..+...|      
T Consensus       252 ~eA~~~~el~~~~~Al~l--~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~~~~p~~~~al~~La~~~~~~~~~~~~~  329 (382)
T 2h6f_A          252 DRAVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDN  329 (382)
T ss_dssp             SHHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHTTCSS
T ss_pred             hHHHHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHccCccchHHHHHHHHHhccCCCCHHHHHHHHHHHHHHhcccccc
Confidence            777     4778888773  3445678888888888888  68999998887742 345667888888887764      


Q ss_pred             --C-hHHHHHHHHHH-HhcCCCCCchHHHHHHHHHhc
Q 011249          429 --N-AELGEIAARHL-LELGPEKTGNSALLANIYASM  461 (490)
Q Consensus       429 --~-~~~a~~~~~~~-~~~~p~~~~~~~~l~~~~~~~  461 (490)
                        + .++|+++++++ .+.+|.....|..++..+...
T Consensus       330 ~~~~~~~A~~~~~~l~~~~DP~r~~~w~~~~~~l~~~  366 (382)
T 2h6f_A          330 KEDILNKALELCEILAKEKDTIRKEYWRYIGRSLQSK  366 (382)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHH
Confidence              3 58999999999 899999999999888777654

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.69  E-value=7.9e-16  Score=133.99  Aligned_cols=209  Identities=15%  Similarity=0.032  Sum_probs=115.3

Q ss_pred             hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHH
Q 011249          246 VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFA  322 (490)
Q Consensus       246 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~  322 (490)
                      ..+..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...|+++.+   .+...+..+...+.
T Consensus        24 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~  102 (243)
T 2q7f_A           24 MTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNVYV  102 (243)
T ss_dssp             ------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHHHH
Confidence            344445555555555555555555555543 33445555555555555555555555555443   24455566666666


Q ss_pred             hcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHH
Q 011249          323 DHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAH  402 (490)
Q Consensus       323 ~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  402 (490)
                      ..|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.  .+.+...+..++..+...|++++|.
T Consensus       103 ~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~  179 (243)
T 2q7f_A          103 VKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVEL--NENDTEARFQFGMCLANEGMLDEAL  179 (243)
T ss_dssp             HTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCHHHH
T ss_pred             HhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHcCCHHHHH
Confidence            6666677766666666542 224455666666666677777777777766652  3334556666666667777777777


Q ss_pred             HHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHH
Q 011249          403 SLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY  458 (490)
Q Consensus       403 ~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  458 (490)
                      +.++++.  .+.+..++..+...+...|++++|.+.++++.+..|+++.++..++.+.
T Consensus       180 ~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~l~  237 (243)
T 2q7f_A          180 SQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHMLALHAKKLLG  237 (243)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCTTCHHHHHHHTC--
T ss_pred             HHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHccCcchHHHHHHHHHHH
Confidence            7766554  3334556666666777777777777777777777777666666555443

>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=99.68  E-value=2.8e-14  Score=126.63  Aligned_cols=224  Identities=11%  Similarity=-0.052  Sum_probs=188.0

Q ss_pred             ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHh----cCChHHHHHHHhcccC-CChhHHHHHH
Q 011249          244 SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSK----CGYLDLAWREFSRIKN-KDVISYSSMI  318 (490)
Q Consensus       244 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~A~~~~~~~~~-~~~~~~~~l~  318 (490)
                      +...+..+...+...|++++|...|++..+.   .+...+..+...|..    .+++++|...|++..+ .++..+..+.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~---~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg   81 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDL---KENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLG   81 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT---TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHC---CCHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            4567777888888899999999999998883   345677778888888    9999999999988765 4677888888


Q ss_pred             HHHHh----cCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcC----CCChHHHHHHHHHHHHHcCCCCCchHHHHHHH
Q 011249          319 TAFAD----HGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSH----GGLVEDGCKQFELMTRVFGIKPLTEHLTCMVD  390 (490)
Q Consensus       319 ~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  390 (490)
                      ..|..    .+++++|+..|++..+.+   +...+..+...|..    .+++++|...+++..+. +   +...+..+..
T Consensus        82 ~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~-~---~~~a~~~lg~  154 (273)
T 1ouv_A           82 NLYYSGQGVSQNTNKALQYYSKACDLK---YAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDL-N---DGDGCTILGS  154 (273)
T ss_dssp             HHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHT-T---CHHHHHHHHH
T ss_pred             HHHhCCCCcccCHHHHHHHHHHHHHcC---CccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhc-C---cHHHHHHHHH
Confidence            89988    999999999999998864   66777888888887    89999999999999873 3   5567777888


Q ss_pred             HHhh----cCChHHHHHHHHhccCCCChhhHHHHHHHHhh----hCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHh--
Q 011249          391 LLGR----SGQLEKAHSLIMDYKDFCDAGTWGALLGACKV----HVNAELGEIAARHLLELGPEKTGNSALLANIYAS--  460 (490)
Q Consensus       391 ~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~--  460 (490)
                      .|..    .+++++|.+.|++.....++..+..+...+..    .+++++|++.++++.+.+|  +..+..++.+|..  
T Consensus       155 ~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~--~~a~~~l~~~~~~g~  232 (273)
T 1ouv_A          155 LYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELEN--GGGCFNLGAMQYNGE  232 (273)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHTTS
T ss_pred             HHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCC--HHHHHHHHHHHHcCC
Confidence            8887    89999999999887745567788888888888    8999999999999998866  6788889999998  


Q ss_pred             --cCCcchHHHHHHHhhhccc
Q 011249          461 --MGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       461 --~g~~~~A~~~~~~~~~~~~  479 (490)
                        .+++++|.+.+++..+.|.
T Consensus       233 ~~~~~~~~A~~~~~~a~~~~~  253 (273)
T 1ouv_A          233 GVTRNEKQAIENFKKGCKLGA  253 (273)
T ss_dssp             SSSCCSTTHHHHHHHHHHHTC
T ss_pred             CcccCHHHHHHHHHHHHHcCC
Confidence              8999999999998887764

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.68  E-value=4.3e-15  Score=131.77  Aligned_cols=232  Identities=9%  Similarity=-0.027  Sum_probs=191.1

Q ss_pred             hhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--CCh----hHHHHHH
Q 011249          245 EVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KDV----ISYSSMI  318 (490)
Q Consensus       245 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~----~~~~~l~  318 (490)
                      ...+......+...|++++|...++.+.+.. |.+...+..+..+|...|++++|+..++++.+  ++.    ..|..+.
T Consensus         3 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg   81 (272)
T 3u4t_A            3 DDVEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYG   81 (272)
T ss_dssp             --CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHH
Confidence            3456677788999999999999999998876 55666888899999999999999999998876  222    3488999


Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCCh
Q 011249          319 TAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQL  398 (490)
Q Consensus       319 ~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  398 (490)
                      ..+...|++++|+..++++.+.. +.+...+..+...+...|++++|...+++..+  ..+.+...+..+...+...+++
T Consensus        82 ~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~--~~~~~~~~~~~l~~~~~~~~~~  158 (272)
T 3u4t_A           82 KILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIR--PTTTDPKVFYELGQAYYYNKEY  158 (272)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCC--SSCCCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhh--cCCCcHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999852 23456888999999999999999999999986  3444566777777344455699


Q ss_pred             HHHHHHHHhcc--CCCChhhHHHHHHHHhhhCC---hHHHHHHHHHHHhcC---CCC-----CchHHHHHHHHHhcCCcc
Q 011249          399 EKAHSLIMDYK--DFCDAGTWGALLGACKVHVN---AELGEIAARHLLELG---PEK-----TGNSALLANIYASMGKWK  465 (490)
Q Consensus       399 ~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~---p~~-----~~~~~~l~~~~~~~g~~~  465 (490)
                      ++|.+.|+++.  .+.+...+..+..++...|+   +++|...++++.+..   |+.     ..+|..++.+|...|+++
T Consensus       159 ~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  238 (272)
T 3u4t_A          159 VKADSSFVKVLELKPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKV  238 (272)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHhCccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHH
Confidence            99999998877  44457788888888888888   889999999999865   442     258888999999999999


Q ss_pred             hHHHHHHHhhhcccc
Q 011249          466 DSEIVKMMISETEKK  480 (490)
Q Consensus       466 ~A~~~~~~~~~~~~~  480 (490)
                      +|.+.++++.+..+.
T Consensus       239 ~A~~~~~~al~~~p~  253 (272)
T 3u4t_A          239 KADAAWKNILALDPT  253 (272)
T ss_dssp             HHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHhcCcc
Confidence            999999999876553

>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=99.67  E-value=1e-14  Score=127.77  Aligned_cols=195  Identities=15%  Similarity=0.055  Sum_probs=91.5

Q ss_pred             HHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHH
Q 011249          253 SACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQE  329 (490)
Q Consensus       253 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~  329 (490)
                      ..+...|++++|...++.+.+.. +.+...+..+...|...|++++|.+.|+++.+   .+...+..+...+...|++++
T Consensus        45 ~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~  123 (252)
T 2ho1_A           45 LGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGFLYEQKRYEE  123 (252)
T ss_dssp             HHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHhHHHH
Confidence            33333334444443333333332 22233333333444444444444444433322   133344444445555555555


Q ss_pred             HHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhc
Q 011249          330 ALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDY  408 (490)
Q Consensus       330 a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  408 (490)
                      |...++++.+.+..| +...+..+...+...|++++|...++++.+.  .+.+...+..++..+...|++++|...++++
T Consensus       124 A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~  201 (252)
T 2ho1_A          124 AYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRL--NRNQPSVALEMADLLYKEREYVPARQYYDLF  201 (252)
T ss_dssp             HHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            555555554422233 2234445555555555555555555555542  2223444555555555555555555555554


Q ss_pred             c--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCch
Q 011249          409 K--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGN  450 (490)
Q Consensus       409 ~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~  450 (490)
                      .  .+.+...+..+...+...|++++|.+.++++.+..|+++..
T Consensus       202 ~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~  245 (252)
T 2ho1_A          202 AQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLYPGSLEY  245 (252)
T ss_dssp             HTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSHHH
T ss_pred             HHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCCHHH
Confidence            3  22334445555555555666666666666666666555443

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.67  E-value=3.9e-15  Score=127.02  Aligned_cols=204  Identities=15%  Similarity=-0.001  Sum_probs=92.9

Q ss_pred             HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHH
Q 011249          210 ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHM  289 (490)
Q Consensus       210 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~  289 (490)
                      ...+..+...+.+.|++++|+..|++..+.. +.+...+..+..++.+.|++++|...++++.+.. |.+...+..+..+
T Consensus         5 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~   82 (217)
T 2pl2_A            5 EQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLSEA   82 (217)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHH
Confidence            3445555555556666666666665555442 1234455555555555566666655555555554 3344445555555


Q ss_pred             HHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHH
Q 011249          290 HSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQ  368 (490)
Q Consensus       290 ~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~  368 (490)
                      +...+..           ...         .....|++++|+..+++..+.  .| +...+..+..++...|++++|+..
T Consensus        83 ~~~~~~~-----------~~~---------~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~  140 (217)
T 2pl2_A           83 YVALYRQ-----------AED---------RERGKGYLEQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKAEAS  140 (217)
T ss_dssp             HHHHHHT-----------CSS---------HHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHhhhh-----------hhh---------hcccccCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHHHHH
Confidence            5444000           000         000115555555555555542  23 233444455555555555555555


Q ss_pred             HHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHH
Q 011249          369 FELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHL  440 (490)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  440 (490)
                      |+++.+. .  .++..+..+..+|...|++++|...|++..  .+.+...+..+..++...|++++|+..+++.
T Consensus       141 ~~~al~~-~--~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~  211 (217)
T 2pl2_A          141 LKQALAL-E--DTPEIRSALAELYLSMGRLDEALAQYAKALEQAPKDLDLRVRYASALLLKGKAEEAARAAALE  211 (217)
T ss_dssp             HHHHHHH-C--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTC--------------
T ss_pred             HHHHHhc-c--cchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            5555553 2  444455555555555555555555555443  2334445555555555555555555555543

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.67  E-value=2.3e-15  Score=130.98  Aligned_cols=199  Identities=11%  Similarity=0.026  Sum_probs=159.2

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHH
Q 011249          278 RTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLT  354 (490)
Q Consensus       278 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~  354 (490)
                      .....+..+...+...|++++|...|+++.+   .+...+..+...+...|++++|...++++.+.. +.+...+..+..
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~   99 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEENKEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAGN   99 (243)
T ss_dssp             ---------------------CCTTHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHHH
Confidence            3456677788889999999999999998865   367788999999999999999999999999852 335678888999


Q ss_pred             HhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHH
Q 011249          355 ACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAEL  432 (490)
Q Consensus       355 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~  432 (490)
                      .+...|++++|...++++.+.  .+.+...+..++..+...|++++|.+.++++.  .+.+...+..+...+...|++++
T Consensus       100 ~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  177 (243)
T 2q7f_A          100 VYVVKEMYKEAKDMFEKALRA--GMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELNENDTEARFQFGMCLANEGMLDE  177 (243)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--TCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHhccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHcCCHHH
Confidence            999999999999999999884  45567788899999999999999999998876  45567889999999999999999


Q ss_pred             HHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          433 GEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       433 a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      |...++++.+..|+++.++..++.++...|++++|.+.++++.+..+
T Consensus       178 A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p  224 (243)
T 2q7f_A          178 ALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQP  224 (243)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHccCc
Confidence            99999999999999999999999999999999999999999987654

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.66  E-value=1.9e-14  Score=123.40  Aligned_cols=201  Identities=10%  Similarity=-0.038  Sum_probs=97.3

Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhc-
Q 011249          249 VGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADH-  324 (490)
Q Consensus       249 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~-  324 (490)
                      ..+...+...|++++|...++.+.+.. +.+...+..+...|...|++++|...++++.+   .+..++..++..+... 
T Consensus        12 ~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~   90 (225)
T 2vq2_A           12 TQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGWFLCGRL   90 (225)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhc
Confidence            333333444444444444444443332 22233333344444444444444444443322   1333444455555555 


Q ss_pred             CChHHHHHHHHHHHHcCCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHH
Q 011249          325 GKSQEALDMFLKMRNEGIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHS  403 (490)
Q Consensus       325 ~~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  403 (490)
                      |++++|...++++.+.+..|+ ...+..+...+...|++++|...++++.+.  .+.+...+..++.++...|++++|.+
T Consensus        91 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~~~A~~  168 (225)
T 2vq2_A           91 NRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAA--QPQFPPAFKELARTKMLAGQLGDADY  168 (225)
T ss_dssp             CCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCchHHHHHHHHHHHcCCHHHHHH
Confidence            555555555555554222232 334555555555566666666666655552  22334455555555556666666666


Q ss_pred             HHHhcc--CC-CChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHH
Q 011249          404 LIMDYK--DF-CDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSA  452 (490)
Q Consensus       404 ~~~~~~--~~-~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~  452 (490)
                      .++++.  .+ .+...+..+...+...|+.+.+..+++.+.+..|+++....
T Consensus       169 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~  220 (225)
T 2vq2_A          169 YFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQANFPYSEELQT  220 (225)
T ss_dssp             HHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHH
Confidence            555544  22 34444444445555566666666666666656666554443

>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=99.66  E-value=5e-15  Score=136.72  Aligned_cols=229  Identities=10%  Similarity=-0.019  Sum_probs=197.2

Q ss_pred             hhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCC-hHHHHHHHhcccC---CChhHHHHHHHH
Q 011249          245 EVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGY-LDLAWREFSRIKN---KDVISYSSMITA  320 (490)
Q Consensus       245 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~A~~~~~~~~~---~~~~~~~~l~~~  320 (490)
                      ...|..+..++...|++++|...++++.+.. |.+..+|+.+..++...|+ +++|+..|+++..   .+...|..+..+
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 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVL  175 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            3567778888899999999999999999987 6778899999999999997 9999999999876   467899999999


Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh-cCCh
Q 011249          321 FADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR-SGQL  398 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~g~~  398 (490)
                      +...|++++|+..|+++++.  .| +...|..+..++...|++++|+..++++.+.  .+.+...|+.+..++.. .|..
T Consensus       176 ~~~~g~~~eAl~~~~kal~l--dP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l--~P~~~~a~~~lg~~l~~l~~~~  251 (382)
T 2h6f_A          176 VEWLRDPSQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE--DVRNNSVWNQRYFVISNTTGYN  251 (382)
T ss_dssp             HHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCSC
T ss_pred             HHHccCHHHHHHHHHHHHHh--CccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCcc
Confidence            99999999999999999985  45 5678999999999999999999999999983  45567889999999999 6665


Q ss_pred             HHH-----HHHHHhcc--CCCChhhHHHHHHHHhhhC--ChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcC-------
Q 011249          399 EKA-----HSLIMDYK--DFCDAGTWGALLGACKVHV--NAELGEIAARHLLELGPEKTGNSALLANIYASMG-------  462 (490)
Q Consensus       399 ~~A-----~~~~~~~~--~~~~~~~~~~l~~~~~~~g--~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g-------  462 (490)
                      ++|     ++.|++..  .+.+...|..+...+...|  ++++|++.++++ +.+|+++.++..++.+|.+.|       
T Consensus       252 ~eA~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~-~~~p~~~~al~~La~~~~~~~~~~~~~~  330 (382)
T 2h6f_A          252 DRAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDL-QPSHSSPYLIAFLVDIYEDMLENQCDNK  330 (382)
T ss_dssp             SHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHH-TTTCCCHHHHHHHHHHHHHHHHTTCSSH
T ss_pred             hHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHccCccchHHHHHHHHHh-ccCCCCHHHHHHHHHHHHHHhcccccch
Confidence            888     47777665  4556779999999998888  689999999998 889999999999999999975       


Q ss_pred             --CcchHHHHHHHh-hhccc
Q 011249          463 --KWKDSEIVKMMI-SETEK  479 (490)
Q Consensus       463 --~~~~A~~~~~~~-~~~~~  479 (490)
                        .+++|+++++++ .+.++
T Consensus       331 ~~~~~~A~~~~~~l~~~~DP  350 (382)
T 2h6f_A          331 EDILNKALELCEILAKEKDT  350 (382)
T ss_dssp             HHHHHHHHHHHHHHHHTTCG
T ss_pred             HHHHHHHHHHHHHHHHHhCc
Confidence              258999999998 55443

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.66  E-value=1.5e-15  Score=143.40  Aligned_cols=260  Identities=13%  Similarity=-0.012  Sum_probs=131.6

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCcccCh----hhHHHHHHHHhccCChHHHHHHHHHHHhc----C-CCCchhHHHHH
Q 011249          216 MTVCYVQNGYAKAAIEMYKVMRQENVRISE----VAMVGAISACTQLGDVEMAAILAKHVDEG----C-CDRTNYVSNAL  286 (490)
Q Consensus       216 l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~-~~~~~~~~~~l  286 (490)
                      +...+...|++++|+..|+++.+.... +.    ..+..+..++...|++++|...++++.+.    + .+.....+..+
T Consensus        54 ~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l  132 (411)
T 4a1s_A           54 EGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKSSGNL  132 (411)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHHHHHH
Confidence            334444444444444444444443211 11    23444444444444444444444443322    0 01122334444


Q ss_pred             HHHHHhcCChHHHHHHHhcccC---------CChhHHHHHHHHHHhcCC-----------------hHHHHHHHHHHHHc
Q 011249          287 IHMHSKCGYLDLAWREFSRIKN---------KDVISYSSMITAFADHGK-----------------SQEALDMFLKMRNE  340 (490)
Q Consensus       287 ~~~~~~~~~~~~A~~~~~~~~~---------~~~~~~~~l~~~~~~~~~-----------------~~~a~~~~~~~~~~  340 (490)
                      ...|...|++++|...|++..+         ....++..+...|...|+                 +++|...+++..+.
T Consensus       133 ~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~~al~~  212 (411)
T 4a1s_A          133 GNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQENLKL  212 (411)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHHHHHHH
Confidence            4455555555555555444332         012344555555555555                 55665555554431


Q ss_pred             ----CCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC----chHHHHHHHHHhhcCChHHHHHHHHhcc--
Q 011249          341 ----GIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL----TEHLTCMVDLLGRSGQLEKAHSLIMDYK--  409 (490)
Q Consensus       341 ----~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~--  409 (490)
                          +..+. ...+..+...+...|++++|...+++..+.....++    ...+..+..+|...|++++|.+.+++..  
T Consensus       213 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  292 (411)
T 4a1s_A          213 MRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYKRTLAL  292 (411)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence                11111 125555556666666666666666666542111111    1245566666667777777776665544  


Q ss_pred             --CC----CChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC------CchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          410 --DF----CDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK------TGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       410 --~~----~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                        ..    ....++..+...+...|++++|.+.++++++..+..      ..++..++.+|...|++++|.+.+++..+
T Consensus       293 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  371 (411)
T 4a1s_A          293 AVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAEQHLQ  371 (411)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHH
Confidence              00    113455666666777777777777777776654322      33666677777777777777777776544

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.65  E-value=1.6e-14  Score=124.02  Aligned_cols=201  Identities=7%  Similarity=-0.092  Sum_probs=175.1

Q ss_pred             CCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHH
Q 011249          277 DRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVL  353 (490)
Q Consensus       277 ~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~  353 (490)
                      +.+...+..++..+...|++++|...|+++.+   .+...+..+...+...|++++|...++++.+.. +.+...+..+.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~   83 (225)
T 2vq2_A            5 NQVSNIKTQLAMEYMRGQDYRQATASIEDALKSDPKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYG   83 (225)
T ss_dssp             CHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHH
Confidence            44567788899999999999999999998765   457789999999999999999999999999852 33567888899


Q ss_pred             HHhcCC-CChHHHHHHHHHHHHHcCCCCC-chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCC
Q 011249          354 TACSHG-GLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVN  429 (490)
Q Consensus       354 ~~~~~~-g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~  429 (490)
                      ..+... |++++|...++++.+ .+..|+ ...+..++.++...|++++|...++++.  .+.+...+..++..+...|+
T Consensus        84 ~~~~~~~~~~~~A~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~  162 (225)
T 2vq2_A           84 WFLCGRLNRPAESMAYFDKALA-DPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQPQFPPAFKELARTKMLAGQ  162 (225)
T ss_dssp             HHHHTTTCCHHHHHHHHHHHHT-STTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHhcCcHHHHHHHHHHHHc-CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHcCC
Confidence            999999 999999999999987 233343 6778889999999999999999998876  44567889999999999999


Q ss_pred             hHHHHHHHHHHHhcCC-CCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          430 AELGEIAARHLLELGP-EKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       430 ~~~a~~~~~~~~~~~p-~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +++|.+.++++.+..| .++..+..++..+...|+.++|..+++.+.+..+
T Consensus       163 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~p  213 (225)
T 2vq2_A          163 LGDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQANFP  213 (225)
T ss_dssp             HHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCC
Confidence            9999999999999999 9999999999999999999999999999876543

>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=99.65  E-value=1.2e-14  Score=127.35  Aligned_cols=198  Identities=6%  Similarity=-0.093  Sum_probs=174.6

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHh
Q 011249          280 NYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTAC  356 (490)
Q Consensus       280 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  356 (490)
                      ...+..+...+...|++++|...|+++.+   .+...+..+...+...|++++|...++++.+.. +.+...+..+...+
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~  115 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEIDPSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGFL  115 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHH
Confidence            56678888999999999999999998765   467789999999999999999999999999853 33667888899999


Q ss_pred             cCCCChHHHHHHHHHHHHHcCCCC-CchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHH
Q 011249          357 SHGGLVEDGCKQFELMTRVFGIKP-LTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       357 ~~~g~~~~a~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      ...|++++|..+++++.+ .+..| +...+..++.++...|++++|.+.++++.  .+.+...+..++..+...|++++|
T Consensus       116 ~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  194 (252)
T 2ho1_A          116 YEQKRYEEAYQRLLEASQ-DTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLNRNQPSVALEMADLLYKEREYVPA  194 (252)
T ss_dssp             HHTTCHHHHHHHHHHHTT-CTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHhHHHHHHHHHHHHHh-CccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHcCCHHHH
Confidence            999999999999999976 23444 46677889999999999999999998876  445678899999999999999999


Q ss_pred             HHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          434 EIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       434 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ...++++.+..|+++..+..++.++...|++++|.+.++++.+..+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~p  240 (252)
T 2ho1_A          195 RQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASYGLQLKRLYP  240 (252)
T ss_dssp             HHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCC
Confidence            9999999999999999999999999999999999999999987654

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.65  E-value=3.5e-15  Score=140.58  Aligned_cols=295  Identities=12%  Similarity=0.014  Sum_probs=202.5

Q ss_pred             CchhHHHHHHHHHhcCChhHHHHHHhhcCC--C-C----HHhHHHHHHHHHhcCChHHHHHHHHHHHHc----Cccc-Ch
Q 011249          178 NSVTWVAMIAGYGKCGEVREAKKVFDEISE--P-D----ASCWAAMTVCYVQNGYAKAAIEMYKVMRQE----NVRI-SE  245 (490)
Q Consensus       178 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~p-~~  245 (490)
                      ....+......+...|++++|...|+++.+  | +    ...+..+...+...|++++|+..+++....    +-.| ..
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            344566777888888888888888887654  2 2    356777888888888888888888886542    2122 24


Q ss_pred             hhHHHHHHHHhccCChHHHHHHHHHHHhcCC----C-CchhHHHHHHHHHHhcCC--------------------hHHHH
Q 011249          246 VAMVGAISACTQLGDVEMAAILAKHVDEGCC----D-RTNYVSNALIHMHSKCGY--------------------LDLAW  300 (490)
Q Consensus       246 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~----~-~~~~~~~~l~~~~~~~~~--------------------~~~A~  300 (490)
                      ..+..+...+...|++++|...++++.+...    + ....++..+...|...|+                    +++|.
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            5677777888888888888888887755321    1 113466777788888888                    88888


Q ss_pred             HHHhcccC-----C----ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCc----HHHHHHHHHHhcCCCChHHHH
Q 011249          301 REFSRIKN-----K----DVISYSSMITAFADHGKSQEALDMFLKMRNEG-IEPN----QVTFIGVLTACSHGGLVEDGC  366 (490)
Q Consensus       301 ~~~~~~~~-----~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~----~~~~~~l~~~~~~~g~~~~a~  366 (490)
                      ..+++..+     +    ...++..+...+...|++++|...+++..+.. -.++    ...+..+...+...|++++|.
T Consensus       168 ~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  247 (406)
T 3sf4_A          168 DFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETAS  247 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHH
Confidence            77776543     1    23467777788888888888888888877631 1122    126677777788888888888


Q ss_pred             HHHHHHHHHcCCCCC----chHHHHHHHHHhhcCChHHHHHHHHhcc----CCCC----hhhHHHHHHHHhhhCChHHHH
Q 011249          367 KQFELMTRVFGIKPL----TEHLTCMVDLLGRSGQLEKAHSLIMDYK----DFCD----AGTWGALLGACKVHVNAELGE  434 (490)
Q Consensus       367 ~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~----~~~~~~l~~~~~~~g~~~~a~  434 (490)
                      ..+++........++    ..++..+...|...|++++|.+.+++..    ..++    ..++..+...+...|++++|.
T Consensus       248 ~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  327 (406)
T 3sf4_A          248 EYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQAM  327 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            888887653111111    4466677788888888888888887665    1111    446677777888888888888


Q ss_pred             HHHHHHHhcCCCCC------chHHHHHHHHHhcCCcchHHHHHH
Q 011249          435 IAARHLLELGPEKT------GNSALLANIYASMGKWKDSEIVKM  472 (490)
Q Consensus       435 ~~~~~~~~~~p~~~------~~~~~l~~~~~~~g~~~~A~~~~~  472 (490)
                      +.++++++..+...      .++..++.++...|+......-+.
T Consensus       328 ~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~  371 (406)
T 3sf4_A          328 HFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLSYSTNNSIM  371 (406)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTSCC-----
T ss_pred             HHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHhHHHHHHHH
Confidence            88888888887763      366677777777777776555444

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.64  E-value=5.9e-15  Score=134.98  Aligned_cols=265  Identities=15%  Similarity=0.033  Sum_probs=175.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCcccC----hhhHHHHHHHHhccCChHHHHHHHHHHHhc----CCC-CchhHH
Q 011249          213 WAAMTVCYVQNGYAKAAIEMYKVMRQENVRIS----EVAMVGAISACTQLGDVEMAAILAKHVDEG----CCD-RTNYVS  283 (490)
Q Consensus       213 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~----~~~-~~~~~~  283 (490)
                      +......+...|++++|+..|+++.+.... +    ...+..+...+...|++++|...++++.+.    +.+ ....++
T Consensus         8 l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~   86 (338)
T 3ro2_A            8 LALEGERLCKSGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKAS   86 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhhCcc-cHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHH
Confidence            334455566666666666666666654321 1    245556666666666776666666654332    111 123455


Q ss_pred             HHHHHHHHhcCChHHHHHHHhcccC-----CC----hhHHHHHHHHHHhcCC--------------------hHHHHHHH
Q 011249          284 NALIHMHSKCGYLDLAWREFSRIKN-----KD----VISYSSMITAFADHGK--------------------SQEALDMF  334 (490)
Q Consensus       284 ~~l~~~~~~~~~~~~A~~~~~~~~~-----~~----~~~~~~l~~~~~~~~~--------------------~~~a~~~~  334 (490)
                      ..+...|...|++++|...+++..+     ++    ..++..+...+...|+                    +++|...+
T Consensus        87 ~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~  166 (338)
T 3ro2_A           87 GNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVDLY  166 (338)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHHHH
Confidence            5666677777777777777666543     11    2366667777777777                    77777777


Q ss_pred             HHHHHc----CCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC----chHHHHHHHHHhhcCChHHHHHHH
Q 011249          335 LKMRNE----GIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL----TEHLTCMVDLLGRSGQLEKAHSLI  405 (490)
Q Consensus       335 ~~~~~~----~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~  405 (490)
                      ++..+.    +..|. ...+..+...+...|++++|...+++..+.....++    ...+..+...+...|++++|.+.+
T Consensus       167 ~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  246 (338)
T 3ro2_A          167 EENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASEYY  246 (338)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            776541    11121 236667777788888888888888887653111111    236677888888999999999988


Q ss_pred             Hhcc----CCCC----hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC------CchHHHHHHHHHhcCCcchHHHHH
Q 011249          406 MDYK----DFCD----AGTWGALLGACKVHVNAELGEIAARHLLELGPEK------TGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       406 ~~~~----~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~------~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      ++..    ..++    ..++..+...+...|++++|...++++++..|..      ..++..++.+|.+.|++++|.+.+
T Consensus       247 ~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  326 (338)
T 3ro2_A          247 KKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFA  326 (338)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             HHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHHHHH
Confidence            7765    1111    4567778888899999999999999998865432      347888999999999999999999


Q ss_pred             HHhhhcc
Q 011249          472 MMISETE  478 (490)
Q Consensus       472 ~~~~~~~  478 (490)
                      ++..+..
T Consensus       327 ~~a~~~~  333 (338)
T 3ro2_A          327 EKHLEIS  333 (338)
T ss_dssp             HHHHHC-
T ss_pred             HHHHHHH
Confidence            9887653

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.64  E-value=1.9e-16  Score=156.16  Aligned_cols=124  Identities=6%  Similarity=0.049  Sum_probs=104.1

Q ss_pred             chhHHHHHHHHHhcCChhHHHHHHhhcC-------CCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHH
Q 011249          179 SVTWVAMIAGYGKCGEVREAKKVFDEIS-------EPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGA  251 (490)
Q Consensus       179 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~-------~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l  251 (490)
                      ..+|+++|++|++.|++++|.++|++|.       .||..+||+||.+|++.|++++|.++|++|...|+.||..||+.+
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            3578888888888888888888886653       389999999999999999999999999999999999999999999


Q ss_pred             HHHHhccCCh-HHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHH
Q 011249          252 ISACTQLGDV-EMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWRE  302 (490)
Q Consensus       252 ~~~~~~~g~~-~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  302 (490)
                      |.++++.|+. ++|.+++++|.+.|+.||..+|++++..+.+.+-++.+.++
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~Vrkv  258 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKV  258 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHHGGG
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHHHHh
Confidence            9999999885 78889999999999999999999888766655433333333

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.64  E-value=2.9e-15  Score=141.10  Aligned_cols=286  Identities=10%  Similarity=-0.056  Sum_probs=216.8

Q ss_pred             CCHhHHHHHHHHHHhCCChHHHHHHHHHhcc--C-C----chhHHHHHHHHHhcCChhHHHHHHhhcCC---------CC
Q 011249          146 RNVISWSAMVAGYANCGNMKAAKEFYDRMTE--K-N----SVTWVAMIAGYGKCGEVREAKKVFDEISE---------PD  209 (490)
Q Consensus       146 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---------~~  209 (490)
                      +....+......+...|++++|+..|+++.+  | +    ...+..+...+...|++++|...+++...         ..
T Consensus         7 ~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~   86 (406)
T 3sf4_A            7 ASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGE   86 (406)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccHHH
Confidence            3456677788899999999999999999885  3 3    25688899999999999999999887643         12


Q ss_pred             HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcc-cC----hhhHHHHHHHHhccCC--------------------hHHH
Q 011249          210 ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVR-IS----EVAMVGAISACTQLGD--------------------VEMA  264 (490)
Q Consensus       210 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-p~----~~~~~~l~~~~~~~g~--------------------~~~a  264 (490)
                      ..++..+...+...|++++|+..+++..+.... ++    ..++..+...+...|+                    +++|
T Consensus        87 ~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~~A  166 (406)
T 3sf4_A           87 AKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQAA  166 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHHHH
Confidence            457888899999999999999999998764211 12    3477888888999999                    9999


Q ss_pred             HHHHHHHHhc----CC-CCchhHHHHHHHHHHhcCChHHHHHHHhcccC-----CC----hhHHHHHHHHHHhcCChHHH
Q 011249          265 AILAKHVDEG----CC-DRTNYVSNALIHMHSKCGYLDLAWREFSRIKN-----KD----VISYSSMITAFADHGKSQEA  330 (490)
Q Consensus       265 ~~~~~~~~~~----~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~----~~~~~~l~~~~~~~~~~~~a  330 (490)
                      ...++...+.    +. +....++..+...|...|++++|...+++..+     ++    ..++..+...+...|++++|
T Consensus       167 ~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  246 (406)
T 3sf4_A          167 VDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETA  246 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHH
Confidence            9999887543    11 12245677888999999999999999988764     22    23788889999999999999


Q ss_pred             HHHHHHHHHc----CCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC----chHHHHHHHHHhhcCChHHH
Q 011249          331 LDMFLKMRNE----GIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL----TEHLTCMVDLLGRSGQLEKA  401 (490)
Q Consensus       331 ~~~~~~~~~~----~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A  401 (490)
                      ...+++..+.    +..+. ..++..+...+...|++++|...+++..+.....++    ..++..+..+|...|++++|
T Consensus       247 ~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  326 (406)
T 3sf4_A          247 SEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHDQA  326 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHHHH
Confidence            9999998752    11111 347788888899999999999999998764221222    55677889999999999999


Q ss_pred             HHHHHhcc-----C--C-CChhhHHHHHHHHhhhCChH
Q 011249          402 HSLIMDYK-----D--F-CDAGTWGALLGACKVHVNAE  431 (490)
Q Consensus       402 ~~~~~~~~-----~--~-~~~~~~~~l~~~~~~~g~~~  431 (490)
                      .+.+++..     .  . ....++..+...+...|+..
T Consensus       327 ~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  364 (406)
T 3sf4_A          327 MHFAEKHLEISREVGDKSGELTARLNLSDLQMVLGLSY  364 (406)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHhhHhH
Confidence            99998765     1  1 12335555556666666554

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.63  E-value=1.9e-14  Score=119.42  Aligned_cols=166  Identities=12%  Similarity=0.033  Sum_probs=140.3

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHH
Q 011249          310 DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCM  388 (490)
Q Consensus       310 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l  388 (490)
                      ++..|..+...|...|++++|+..|++.++.  .| +...+..+..++...|++++|...+......  .+.+...+..+
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~   79 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKA--DPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVL--DTTSAEAYYIL   79 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CchhHHHHHHH
Confidence            5667888888888999999999999998884  44 4567888888888999999999999988873  44456677778


Q ss_pred             HHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcch
Q 011249          389 VDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKD  466 (490)
Q Consensus       389 ~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  466 (490)
                      ...+...++++.|.+.+.+..  .+.+...+..+...+...|++++|++.|+++++.+|+++.++..++.+|.+.|++++
T Consensus        80 ~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~  159 (184)
T 3vtx_A           80 GSANFMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDE  159 (184)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHH
Confidence            888889999999999888766  455677888888999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhccc
Q 011249          467 SEIVKMMISETEK  479 (490)
Q Consensus       467 A~~~~~~~~~~~~  479 (490)
                      |++.+++..+..+
T Consensus       160 A~~~~~~al~~~p  172 (184)
T 3vtx_A          160 AVKYFKKALEKEE  172 (184)
T ss_dssp             HHHHHHHHHHTTH
T ss_pred             HHHHHHHHHhCCc
Confidence            9999998887654

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.63  E-value=5.4e-15  Score=141.72  Aligned_cols=210  Identities=10%  Similarity=-0.075  Sum_probs=170.1

Q ss_pred             hHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCh-HHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHH
Q 011249          261 VEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYL-DLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLK  336 (490)
Q Consensus       261 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~  336 (490)
                      ++++...++...... +.+...+..+...+...|++ ++|++.|++..+   .+...|..+..+|...|++++|...|++
T Consensus        84 ~~~al~~l~~~~~~~-~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~  162 (474)
T 4abn_A           84 MEKTLQQMEEVLGSA-QVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEPELVEAWNQLGEVYWKKGDVTSAHTCFSG  162 (474)
T ss_dssp             HHHHHHHHHHHHTTC-CCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccC-chhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            344445555444432 44566666677777777777 777777776654   3466788888888889999999999999


Q ss_pred             HHHcCCCCcHHHHHHHHHHhcCC---------CChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhc--------CChH
Q 011249          337 MRNEGIEPNQVTFIGVLTACSHG---------GLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRS--------GQLE  399 (490)
Q Consensus       337 ~~~~~~~p~~~~~~~l~~~~~~~---------g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--------g~~~  399 (490)
                      ..+.  .|+...+..+...+...         |++++|...++++.+.  .+.+...+..+..+|...        |+++
T Consensus       163 al~~--~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~  238 (474)
T 4abn_A          163 ALTH--CKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQM--DVLDGRSWYILGNAYLSLYFNTGQNPKISQ  238 (474)
T ss_dssp             HHTT--CCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHhh--CCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHhhccccchHH
Confidence            8884  67777888888889888         9999999999999883  455677888899999888        9999


Q ss_pred             HHHHHHHhcc--CC---CChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          400 KAHSLIMDYK--DF---CDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       400 ~A~~~~~~~~--~~---~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      +|++.|++..  .+   .+...|..+..++...|++++|.+.|+++++.+|+++.++..++.++...|++++|.+.+.++
T Consensus       239 ~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~a~~~l~~~~~~lg~~~eAi~~~~~~  318 (474)
T 4abn_A          239 QALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAWPEPQQREQQLLEFLSRLTSLLESKGKT  318 (474)
T ss_dssp             HHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence            9999998876  33   477899999999999999999999999999999999999999999999999999999876554


Q ss_pred             h
Q 011249          475 S  475 (490)
Q Consensus       475 ~  475 (490)
                      .
T Consensus       319 ~  319 (474)
T 4abn_A          319 K  319 (474)
T ss_dssp             C
T ss_pred             c
Confidence            3

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.63  E-value=2.6e-16  Score=155.18  Aligned_cols=118  Identities=14%  Similarity=0.164  Sum_probs=96.5

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHhccc-------CCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHH
Q 011249          278 RTNYVSNALIHMHSKCGYLDLAWREFSRIK-------NKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFI  350 (490)
Q Consensus       278 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~-------~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~  350 (490)
                      ....+|++||++|++.|++++|.++|+.|.       .||+.+||+||.+|++.|++++|.++|++|.+.|+.||..||+
T Consensus       125 ~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTYn  204 (1134)
T 3spa_A          125 GQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYA  204 (1134)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHHH
Confidence            345678888888888888888888886653       3788888888888888888888888888888888888888888


Q ss_pred             HHHHHhcCCCCh-HHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcC
Q 011249          351 GVLTACSHGGLV-EDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSG  396 (490)
Q Consensus       351 ~l~~~~~~~g~~-~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  396 (490)
                      ++|.++++.|+. ++|.++|++|.+. |+.||..+|++++....+.+
T Consensus       205 tLI~glcK~G~~~e~A~~Ll~EM~~k-G~~PD~vtY~~ll~~~eR~~  250 (1134)
T 3spa_A          205 AALQCMGRQDQDAGTIERCLEQMSQE-GLKLQALFTAVLLSEEDRAT  250 (1134)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHHHH-TCCSHHHHHHSCCCHHHHHH
T ss_pred             HHHHHHHhCCCcHHHHHHHHHHHHHc-CCCCChhhcccccChhhHHH
Confidence            888888888874 6788888888886 88888888888776655543

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.62  E-value=8.5e-15  Score=130.02  Aligned_cols=236  Identities=11%  Similarity=-0.089  Sum_probs=140.8

Q ss_pred             CChhHHHHHHhhcCC-------CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHH
Q 011249          193 GEVREAKKVFDEISE-------PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAA  265 (490)
Q Consensus       193 ~~~~~A~~~~~~~~~-------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~  265 (490)
                      |++++|++.|+++.+       .+...+..+..++...|++++|+..|+++.+.. +.+...+..+..++...|++++|.
T Consensus        19 ~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~   97 (275)
T 1xnf_A           19 LQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAY   97 (275)
T ss_dssp             HHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             chHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHH
Confidence            445555555554433       123455666666666666666666666666543 224556666666666666677776


Q ss_pred             HHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC
Q 011249          266 ILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIE  343 (490)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~  343 (490)
                      ..++.+.+.. +.+..++..+..+|...|++++|...|+++.+  |+.......+..+...|++++|...+++..... +
T Consensus        98 ~~~~~al~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~  175 (275)
T 1xnf_A           98 EAFDSVLELD-PTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS-D  175 (275)
T ss_dssp             HHHHHHHHHC-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS-C
T ss_pred             HHHHHHHhcC-ccccHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-C
Confidence            6666666654 44556666666677777777777777766654  333333333344455677888888887766642 2


Q ss_pred             CcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC-----chHHHHHHHHHhhcCChHHHHHHHHhcc-CCCChhhH
Q 011249          344 PNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL-----TEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAGTW  417 (490)
Q Consensus       344 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~~~  417 (490)
                      ++...+ .++..+...++.++|...+++...   ..|.     ...+..++.+|.+.|++++|...|++.. ..|+  .+
T Consensus       176 ~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~--~~  249 (275)
T 1xnf_A          176 KEQWGW-NIVEFYLGNISEQTLMERLKADAT---DNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVH--NF  249 (275)
T ss_dssp             CCSTHH-HHHHHHTTSSCHHHHHHHHHHHCC---SHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCT--TC
T ss_pred             cchHHH-HHHHHHHHhcCHHHHHHHHHHHhc---ccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCch--hH
Confidence            333333 355556666777777777776654   1221     4666777888888888888888887766 2232  23


Q ss_pred             HHHHHHHhhhCChHHHHHHH
Q 011249          418 GALLGACKVHVNAELGEIAA  437 (490)
Q Consensus       418 ~~l~~~~~~~g~~~~a~~~~  437 (490)
                      .....++...|++++|++.+
T Consensus       250 ~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          250 VEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHHHHHHHhhHHHH
Confidence            33355666777777777665

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.60  E-value=1.7e-14  Score=134.80  Aligned_cols=164  Identities=14%  Similarity=0.061  Sum_probs=89.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHc---CC-CCCch
Q 011249          313 SYSSMITAFADHGKSQEALDMFLKMRNE----GIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVF---GI-KPLTE  383 (490)
Q Consensus       313 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~---~~-~~~~~  383 (490)
                      +++.+...|...|++++|...+++..+.    +-.+. ..++..+...|...|++++|...+++..+..   +. +....
T Consensus       186 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  265 (383)
T 3ulq_A          186 CHSLFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQ  265 (383)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHH
Confidence            4555555566666666666666555431    10010 1245555666666666666666666655411   11 22244


Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc------CCC-ChhhHHHHHHHHhhhCC---hHHHHHHHHHHHhcCCCCCchHHH
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK------DFC-DAGTWGALLGACKVHVN---AELGEIAARHLLELGPEKTGNSAL  453 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~------~~~-~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~p~~~~~~~~  453 (490)
                      ++..+..+|.+.|++++|.+.+++..      ..| ....+..+...+...|+   +++|+.++++. ...|....++..
T Consensus       266 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~-~~~~~~~~~~~~  344 (383)
T 3ulq_A          266 AYFLITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESK-MLYADLEDFAID  344 (383)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHT-TCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC-cCHHHHHHHHHH
Confidence            45566666666666666666665544      011 11223445555666666   55666665554 222334456666


Q ss_pred             HHHHHHhcCCcchHHHHHHHhhhc
Q 011249          454 LANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       454 l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      ++.+|...|++++|.+.+++..+.
T Consensus       345 la~~y~~~g~~~~A~~~~~~al~~  368 (383)
T 3ulq_A          345 VAKYYHERKNFQKASAYFLKVEQV  368 (383)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHH
Confidence            777777777777777777766554

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.60  E-value=2.1e-14  Score=135.58  Aligned_cols=270  Identities=10%  Similarity=-0.011  Sum_probs=163.0

Q ss_pred             hHHHHHHHHHHhCCChHHHHHHHHHhcc--C-Cc----hhHHHHHHHHHhcCChhHHHHHHhhcCC---------CCHHh
Q 011249          149 ISWSAMVAGYANCGNMKAAKEFYDRMTE--K-NS----VTWVAMIAGYGKCGEVREAKKVFDEISE---------PDASC  212 (490)
Q Consensus       149 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~----~~~~~l~~~~~~~~~~~~A~~~~~~~~~---------~~~~~  212 (490)
                      ..+..+...+...|++++|+..|+++.+  | +.    ..+..+...|...|++++|...|++..+         .....
T Consensus        49 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~  128 (411)
T 4a1s_A           49 LELALEGERLCNAGDCRAGVAFFQAAIQAGTEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAKS  128 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHhcccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHHH
Confidence            3455566777888888888888887764  2 22    3566666667777777777766665432         12344


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcC-----cccChhhHHHHHHHHhccCC----------hHHHHHHHHHHHhcCCC
Q 011249          213 WAAMTVCYVQNGYAKAAIEMYKVMRQEN-----VRISEVAMVGAISACTQLGD----------VEMAAILAKHVDEGCCD  277 (490)
Q Consensus       213 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~-----~~p~~~~~~~l~~~~~~~g~----------~~~a~~~~~~~~~~~~~  277 (490)
                      +..+...|...|++++|+..+++.....     .......+..+...+...|+          .+++...          
T Consensus       129 ~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~----------  198 (411)
T 4a1s_A          129 SGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEA----------  198 (411)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHH----------
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHH----------
Confidence            5556666666666666666666654321     01112244444444444455          0000000          


Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHhcccC---------CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCC-CCc--
Q 011249          278 RTNYVSNALIHMHSKCGYLDLAWREFSRIKN---------KDVISYSSMITAFADHGKSQEALDMFLKMRNEGI-EPN--  345 (490)
Q Consensus       278 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---------~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~p~--  345 (490)
                                        +++|...+++..+         .....+..+...+...|++++|...+++..+... .++  
T Consensus       199 ------------------~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  260 (411)
T 4a1s_A          199 ------------------LTRAVEFYQENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRA  260 (411)
T ss_dssp             ------------------HHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             ------------------HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcH
Confidence                              4444444433321         0223566666777777777777777777665210 011  


Q ss_pred             --HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCC----CchHHHHHHHHHhhcCChHHHHHHHHhcc----CCC---
Q 011249          346 --QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKP----LTEHLTCMVDLLGRSGQLEKAHSLIMDYK----DFC---  412 (490)
Q Consensus       346 --~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~---  412 (490)
                        ...+..+...+...|++++|...+++......-..    ....+..+..+|...|++++|.+.+++..    ..+   
T Consensus       261 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  340 (411)
T 4a1s_A          261 AERRANSNLGNSHIFLGQFEDAAEHYKRTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRI  340 (411)
T ss_dssp             HHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChH
Confidence              12566777778888888888888877765311111    14566677888888888888888887665    111   


Q ss_pred             -ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          413 -DAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       413 -~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                       ...++..+...+...|++++|.+.++++.++.+.
T Consensus       341 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~  375 (411)
T 4a1s_A          341 GEARACWSLGNAHSAIGGHERALKYAEQHLQLAXX  375 (411)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCH
T ss_pred             HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhh
Confidence             1346777888888999999999999998887654

>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=99.59  E-value=9.4e-12  Score=122.58  Aligned_cols=411  Identities=9%  Similarity=0.032  Sum_probs=282.2

Q ss_pred             hhHHHHHHHHhhhcCCCCchhHhHHHHHHHHHhcCCCCHHHHHHHhccCC--CCCCceehHHHHHHHHhcCC---hhHHH
Q 011249           14 NQLKQVHSYLLKTLTKPHDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIP--KCKTQFLWTSLIRNHVLHAH---FRQSI   88 (490)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~---~~~A~   88 (490)
                      +....+.+.+.+   .+.|..  .|..+++.+.+.+. ++.++.+|+++.  .|.....|...+..-.+.|+   ++.+.
T Consensus        50 d~i~~lE~~l~~---np~d~~--~W~~yi~~~~~~~~-~~~aR~vyEraL~~fP~~~~lW~~Yi~~E~~~~~~~~~~~v~  123 (679)
T 4e6h_A           50 DVIGKLNDMIEE---QPTDIF--LYVKLLKHHVSLKQ-WKQVYETFDKLHDRFPLMANIWCMRLSLEFDKMEELDAAVIE  123 (679)
T ss_dssp             CHHHHHHHHHHH---CTTCHH--HHHHHHHHHHHTTC-HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTC--CCCHHHHH
T ss_pred             HHHHHHHHHHHH---CcCCHH--HHHHHHHHHHhcCc-HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhhCCcchHHHHH
Confidence            345677888888   779999  99999999999999 999999999986  56655778888888888888   99999


Q ss_pred             HHHHHHHhcC-CCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCC--------HHHHHHHHhhcC------CC-CHhHHH
Q 011249           89 LLYAKMHRLG-VLTSGFTFSSVLNACARVPSLLEAVICGYTKIGL--------MDDAQRLFDSMA------ER-NVISWS  152 (490)
Q Consensus        89 ~~~~~m~~~g-~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~--------~~~A~~~~~~~~------~~-~~~~~~  152 (490)
                      ++|++..... ..|+...|..-+.-.              .+.++        .+...++|+...      .+ +...|.
T Consensus       124 ~lfeRal~~~~~~~sv~LW~~Yl~f~--------------~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~  189 (679)
T 4e6h_A          124 PVLARCLSKELGNNDLSLWLSYITYV--------------RKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWN  189 (679)
T ss_dssp             HHHHHHTCSSSCCCCHHHHHHHHHHH--------------HHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHH
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHHHH--------------HHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHH
Confidence            9999998863 137777776655521              11222        233456777643      23 456777


Q ss_pred             HHHHHHH---------hCCChHHHHHHHHHhcc-CC--c-hhHH---HHHHHH----------HhcCChhHHHHHHhhc-
Q 011249          153 AMVAGYA---------NCGNMKAAKEFYDRMTE-KN--S-VTWV---AMIAGY----------GKCGEVREAKKVFDEI-  205 (490)
Q Consensus       153 ~l~~~~~---------~~~~~~~a~~~~~~~~~-~~--~-~~~~---~l~~~~----------~~~~~~~~A~~~~~~~-  205 (490)
                      ..+....         ..++++.+..+|++++. |.  . .+|.   .+....          -...+++.|...+.++ 
T Consensus       190 ~Yi~f~~~~~~~~~~eeq~~~~~~R~iy~raL~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~  269 (679)
T 4e6h_A          190 EYLHFLEHWKPVNKFEEQQRVQYIRKLYKTLLCQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWL  269 (679)
T ss_dssp             HHHHHHHTCCCCSHHHHHHHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccccCcHHHHhHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHH
Confidence            7776543         23457788999999885 21  1 2221   111110          0011233344444331 


Q ss_pred             ------CC--C--------------C------HHhHHHHHHHHHhcC-------ChHHHHHHHHHHHHcCcccChhhHHH
Q 011249          206 ------SE--P--------------D------ASCWAAMTVCYVQNG-------YAKAAIEMYKVMRQENVRISEVAMVG  250 (490)
Q Consensus       206 ------~~--~--------------~------~~~~~~l~~~~~~~g-------~~~~A~~~~~~~~~~~~~p~~~~~~~  250 (490)
                            .+  |              +      ...|...+..-...+       ..+.+..+|++....- +-+...|..
T Consensus       270 ~~~~~l~r~~p~~~~~~~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~~-p~~~~lW~~  348 (679)
T 4e6h_A          270 NITKGLKRNLPITLNQATESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQHV-CFAPEIWFN  348 (679)
T ss_dssp             HHTTTCCCCCCSSSTTCCTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHT-TTCHHHHHH
T ss_pred             HHHHhHhhccccccccchhccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence                  11  0              0      134555554433332       1244567788887653 336677777


Q ss_pred             HHHHHhccCChHHHH-HHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC-------------CC------
Q 011249          251 AISACTQLGDVEMAA-ILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN-------------KD------  310 (490)
Q Consensus       251 l~~~~~~~g~~~~a~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-------------~~------  310 (490)
                      .+..+...|+.++|. .+|+...... |.+...+..++....+.|+++.|.++|+++.+             |+      
T Consensus       349 ya~~~~~~~~~~~a~r~il~rAi~~~-P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~  427 (679)
T 4e6h_A          349 MANYQGEKNTDSTVITKYLKLGQQCI-PNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAIN  427 (679)
T ss_dssp             HHHHHHHHSCCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHH
T ss_pred             HHHHHHhcCcHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhh
Confidence            787788889988896 9999998754 66777788888889999999999999988764             21      


Q ss_pred             ------hhHHHHHHHHHHhcCChHHHHHHHHHHHHc-CCCCcHHHHHHHHHHhcC-CCChHHHHHHHHHHHHHcCCCCCc
Q 011249          311 ------VISYSSMITAFADHGKSQEALDMFLKMRNE-GIEPNQVTFIGVLTACSH-GGLVEDGCKQFELMTRVFGIKPLT  382 (490)
Q Consensus       311 ------~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~p~~~~~~~l~~~~~~-~g~~~~a~~~~~~~~~~~~~~~~~  382 (490)
                            ...|...+....+.|+.+.|..+|.++.+. + .+....|...+..-.+ .++.+.|.++|+...+.  .+.+.
T Consensus       428 ~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~-~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~--~p~~~  504 (679)
T 4e6h_A          428 QLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKK-LVTPDIYLENAYIEYHISKDTKTACKVLELGLKY--FATDG  504 (679)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGG-GSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH--HTTCH
T ss_pred             hhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--CCCch
Confidence                  235777777778889999999999999875 2 1122333333222223 35689999999999985  44556


Q ss_pred             hHHHHHHHHHhhcCChHHHHHHHHhcc-CCC----ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          383 EHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC----DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       383 ~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                      ..+...++.....|+.+.|..+|++.. ..|    ....|...+..-...|+.+.+..+.+++.+..|+++.
T Consensus       505 ~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~~~~  576 (679)
T 4e6h_A          505 EYINKYLDFLIYVNEESQVKSLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPEVNK  576 (679)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTTCCH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCcH
Confidence            667788888888999999999998877 223    3457888888788899999999999999999998653

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.57  E-value=4.6e-14  Score=129.03  Aligned_cols=265  Identities=12%  Similarity=0.019  Sum_probs=151.5

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHhcc--C-C----chhHHHHHHHHHhcCChhHHHHHHhhcCC---------CCHHhHH
Q 011249          151 WSAMVAGYANCGNMKAAKEFYDRMTE--K-N----SVTWVAMIAGYGKCGEVREAKKVFDEISE---------PDASCWA  214 (490)
Q Consensus       151 ~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---------~~~~~~~  214 (490)
                      +......+...|++++|+..|+++.+  | +    ...+..+...+...|++++|.+.+++..+         .....+.
T Consensus         8 l~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~   87 (338)
T 3ro2_A            8 LALEGERLCKSGDCRAGVSFFEAAVQVGTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASG   87 (338)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHH
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHHHHH
Confidence            34445566666777777776666653  2 1    23444555555555555555555544322         1123344


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCcc-cChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc
Q 011249          215 AMTVCYVQNGYAKAAIEMYKVMRQENVR-ISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC  293 (490)
Q Consensus       215 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~-p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  293 (490)
                      .+...+...|++++|+..+++..+.... ++..                               ....++..+...|...
T Consensus        88 ~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~-------------------------------~~~~~~~~l~~~~~~~  136 (338)
T 3ro2_A           88 NLGNTLKVLGNFDEAIVCCQRHLDISRELNDKV-------------------------------GEARALYNLGNVYHAK  136 (338)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH-------------------------------HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHHhcCch-------------------------------HHHHHHHHHHHHHHHc
Confidence            4455555555555555555544332100 0100                               0012344444445555


Q ss_pred             CC--------------------hHHHHHHHhcccC-----C----ChhHHHHHHHHHHhcCChHHHHHHHHHHHHc----
Q 011249          294 GY--------------------LDLAWREFSRIKN-----K----DVISYSSMITAFADHGKSQEALDMFLKMRNE----  340 (490)
Q Consensus       294 ~~--------------------~~~A~~~~~~~~~-----~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----  340 (490)
                      |+                    +++|...+++...     +    ....+..+...+...|++++|...+++..+.    
T Consensus       137 ~~~~~~~~~~~~~~~~~~a~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~  216 (338)
T 3ro2_A          137 GKSFGCPGPQDTGEFPEDVRNALQAAVDLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEF  216 (338)
T ss_dssp             HHTSSSSSCC----CCHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             CcccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhc
Confidence            55                    5555555444322     1    1235666677777778888887777776642    


Q ss_pred             CCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC----chHHHHHHHHHhhcCChHHHHHHHHhcc----CC
Q 011249          341 GIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL----TEHLTCMVDLLGRSGQLEKAHSLIMDYK----DF  411 (490)
Q Consensus       341 ~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~  411 (490)
                      +..+ ....+..+...+...|++++|...+++........++    ...+..+...+...|++++|...+++..    ..
T Consensus       217 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~  296 (338)
T 3ro2_A          217 GDKAAERRAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQEL  296 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhc
Confidence            1111 1226666777777888888888888877653111111    4456677888888899998888887765    11


Q ss_pred             C----ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          412 C----DAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       412 ~----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      .    ...++..+...+...|++++|.+.++++.++.+.
T Consensus       297 ~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~  335 (338)
T 3ro2_A          297 KDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEISRE  335 (338)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHC---
T ss_pred             CCcHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHh
Confidence            1    1346777888899999999999999999887654

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.56  E-value=2.9e-12  Score=115.60  Aligned_cols=220  Identities=11%  Similarity=0.029  Sum_probs=167.2

Q ss_pred             HHHHHHHHHHHHcCcccChhhHHHHHHHHh-------ccCCh-------HHHHHHHHHHHhcCCCCchhHHHHHHHHHHh
Q 011249          227 KAAIEMYKVMRQENVRISEVAMVGAISACT-------QLGDV-------EMAAILAKHVDEGCCDRTNYVSNALIHMHSK  292 (490)
Q Consensus       227 ~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~-------~~g~~-------~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~  292 (490)
                      ++|+..|++..... +-+...|..++..+.       ..|++       ++|..+|++..+.-.|.+...|..++..+..
T Consensus        33 ~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~  111 (308)
T 2ond_A           33 KRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEES  111 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHh
Confidence            67778888887653 235566666666654       35776       8899999988884225566788888888889


Q ss_pred             cCChHHHHHHHhcccC--C-Chh-HHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH-hcCCCChHHHHH
Q 011249          293 CGYLDLAWREFSRIKN--K-DVI-SYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTA-CSHGGLVEDGCK  367 (490)
Q Consensus       293 ~~~~~~A~~~~~~~~~--~-~~~-~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~-~~~~g~~~~a~~  367 (490)
                      .|++++|..+|+++.+  | +.. .|..++..+.+.|++++|..+|+++.+.. +++...|...... +...|+.++|..
T Consensus       112 ~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~~a~~~~~~~~~~~~A~~  190 (308)
T 2ond_A          112 RMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-RTRHHVYVTAALMEYYCSKDKSVAFK  190 (308)
T ss_dssp             TTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-TCCTHHHHHHHHHHHHTSCCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHcCCHHHHHH
Confidence            9999999999988876  3 343 78888888889999999999999998753 2233444433333 223699999999


Q ss_pred             HHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccC----CC--ChhhHHHHHHHHhhhCChHHHHHHHHHHH
Q 011249          368 QFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKD----FC--DAGTWGALLGACKVHVNAELGEIAARHLL  441 (490)
Q Consensus       368 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  441 (490)
                      +|++..+.  .+.+...+..++..+.+.|++++|..+|++...    +|  ....|..++......|+.+.|..+++++.
T Consensus       191 ~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a~  268 (308)
T 2ond_A          191 IFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRRF  268 (308)
T ss_dssp             HHHHHHHH--HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHH
T ss_pred             HHHHHHHh--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            99999874  345677888888999999999999999988763    33  34578888888888999999999999999


Q ss_pred             hcCCCCCch
Q 011249          442 ELGPEKTGN  450 (490)
Q Consensus       442 ~~~p~~~~~  450 (490)
                      +..|+++..
T Consensus       269 ~~~p~~~~~  277 (308)
T 2ond_A          269 TAFREEYEG  277 (308)
T ss_dssp             HHTTTTTSS
T ss_pred             HHccccccc
Confidence            999986643

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.55  E-value=1.8e-13  Score=113.48  Aligned_cols=167  Identities=11%  Similarity=-0.001  Sum_probs=131.4

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Q 011249          279 TNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTA  355 (490)
Q Consensus       279 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~  355 (490)
                      ++.+|..+...|...|++++|++.|++..+   .++.++..+..+|...|++++|...++...... +.+...+..+...
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~   82 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKADPNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGSA   82 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHHH
Confidence            455667777777777777777777777654   356677778888888888888888888887752 2245566677777


Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHH
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      +...++++.+...+.+...  ..+.+...+..+..+|.+.|++++|++.|++..  .+.+..+|..+..++...|++++|
T Consensus        83 ~~~~~~~~~a~~~~~~a~~--~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~lg~~~~~~g~~~~A  160 (184)
T 3vtx_A           83 NFMIDEKQAAIDALQRAIA--LNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIKPGFIRAYQSIGLAYEGKGLRDEA  160 (184)
T ss_dssp             HHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHH--hCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhcchhhhHHHHHHHHHHHCCCHHHH
Confidence            8888899999999888887  345567778888889999999999999998776  455677889999999999999999


Q ss_pred             HHHHHHHHhcCCCCC
Q 011249          434 EIAARHLLELGPEKT  448 (490)
Q Consensus       434 ~~~~~~~~~~~p~~~  448 (490)
                      ++.|+++++.+|+++
T Consensus       161 ~~~~~~al~~~p~~a  175 (184)
T 3vtx_A          161 VKYFKKALEKEEKKA  175 (184)
T ss_dssp             HHHHHHHHHTTHHHH
T ss_pred             HHHHHHHHhCCccCH
Confidence            999999999998754

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.55  E-value=3.9e-13  Score=125.56  Aligned_cols=229  Identities=9%  Similarity=-0.010  Sum_probs=159.7

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHc----Cccc-ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCC------CCchhHHH
Q 011249          216 MTVCYVQNGYAKAAIEMYKVMRQE----NVRI-SEVAMVGAISACTQLGDVEMAAILAKHVDEGCC------DRTNYVSN  284 (490)
Q Consensus       216 l~~~~~~~g~~~~A~~~~~~~~~~----~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~------~~~~~~~~  284 (490)
                      ....+...|++++|+..+++..+.    +-.+ ...++..+..++...|+++.|...+.+..+...      +....+++
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            455566667777777777766542    1111 234566666667777777777777766654311      11134566


Q ss_pred             HHHHHHHhcCChHHHHHHHhcccC-----CC----hhHHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCC-cHHHHH
Q 011249          285 ALIHMHSKCGYLDLAWREFSRIKN-----KD----VISYSSMITAFADHGKSQEALDMFLKMRNE----GIEP-NQVTFI  350 (490)
Q Consensus       285 ~l~~~~~~~~~~~~A~~~~~~~~~-----~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p-~~~~~~  350 (490)
                      .+..+|...|++++|...|++..+     ++    ..++..+..+|...|++++|...+++..+.    +..| ...++.
T Consensus       189 ~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~  268 (383)
T 3ulq_A          189 LFATNFLDLKQYEDAISHFQKAYSMAEAEKQPQLMGRTLYNIGLCKNSQSQYEDAIPYFKRAIAVFEESNILPSLPQAYF  268 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhccchhHHHHHH
Confidence            677777788888888777776653     11    246778888899999999999999988762    2324 345788


Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHc---CCCCCchHHHHHHHHHhhcCC---hHHHHHHHHhccCCCC-hhhHHHHHHH
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVF---GIKPLTEHLTCMVDLLGRSGQ---LEKAHSLIMDYKDFCD-AGTWGALLGA  423 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~---~~~~~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~-~~~~~~l~~~  423 (490)
                      .+...+...|++++|...+++..+..   +.+.....+..+...+...|+   +++|..++++....|. ...+..+...
T Consensus       269 ~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~  348 (383)
T 3ulq_A          269 LITQIHYKLGKIDKAHEYHSKGMAYSQKAGDVIYLSEFEFLKSLYLSGPDEEAIQGFFDFLESKMLYADLEDFAIDVAKY  348 (383)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            88889999999999999999887631   112223335668888889998   8899999988864333 4477788899


Q ss_pred             HhhhCChHHHHHHHHHHHhcC
Q 011249          424 CKVHVNAELGEIAARHLLELG  444 (490)
Q Consensus       424 ~~~~g~~~~a~~~~~~~~~~~  444 (490)
                      +...|++++|.+.++++.+..
T Consensus       349 y~~~g~~~~A~~~~~~al~~~  369 (383)
T 3ulq_A          349 YHERKNFQKASAYFLKVEQVR  369 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHHH
Confidence            999999999999999998754

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.54  E-value=1.3e-12  Score=118.04  Aligned_cols=214  Identities=10%  Similarity=-0.029  Sum_probs=176.2

Q ss_pred             HHHHHHHHHHHhcCCCCchhHHHHHHHHHHh-------cCCh-------HHHHHHHhcccC---C-ChhHHHHHHHHHHh
Q 011249          262 EMAAILAKHVDEGCCDRTNYVSNALIHMHSK-------CGYL-------DLAWREFSRIKN---K-DVISYSSMITAFAD  323 (490)
Q Consensus       262 ~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------~~~~-------~~A~~~~~~~~~---~-~~~~~~~l~~~~~~  323 (490)
                      ++|...|+++.+.. |.++..|..++..+..       .|++       ++|..+|++..+   | +...|..++..+..
T Consensus        33 ~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~~~p~~~~~~~~~~~~~~~  111 (308)
T 2ond_A           33 KRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEES  111 (308)
T ss_dssp             HHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHHhCcccHHHHHHHHHHHHh
Confidence            67888999988875 6778888888887763       5886       899999998765   3 45689999999999


Q ss_pred             cCChHHHHHHHHHHHHcCCCCc-HH-HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHh-hcCChHH
Q 011249          324 HGKSQEALDMFLKMRNEGIEPN-QV-TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLG-RSGQLEK  400 (490)
Q Consensus       324 ~~~~~~a~~~~~~~~~~~~~p~-~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~g~~~~  400 (490)
                      .|++++|..+|+++.+  +.|+ .. .|..++..+.+.|++++|..+|+++.+  ..+++...|...+.... ..|++++
T Consensus       112 ~~~~~~A~~~~~~al~--~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~--~~p~~~~~~~~~a~~~~~~~~~~~~  187 (308)
T 2ond_A          112 RMKYEKVHSIYNRLLA--IEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARE--DARTRHHVYVTAALMEYYCSKDKSV  187 (308)
T ss_dssp             TTCHHHHHHHHHHHHT--SSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHT--STTCCTHHHHHHHHHHHHTSCCHHH
T ss_pred             cCCHHHHHHHHHHHHh--ccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHh--cCCCCHHHHHHHHHHHHHHcCCHHH
Confidence            9999999999999998  4564 33 788888889999999999999999987  33445556654444322 3799999


Q ss_pred             HHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhc---CCC-CCchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          401 AHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLEL---GPE-KTGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       401 A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~---~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      |.++|++..  .+.+...|..++..+...|++++|..+|+++++.   .|+ ...++..++..+.+.|+.++|..+++++
T Consensus       188 A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a  267 (308)
T 2ond_A          188 AFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRR  267 (308)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            999998876  4456789999999999999999999999999996   453 6678999999999999999999999999


Q ss_pred             hhcccc
Q 011249          475 SETEKK  480 (490)
Q Consensus       475 ~~~~~~  480 (490)
                      .+..+.
T Consensus       268 ~~~~p~  273 (308)
T 2ond_A          268 FTAFRE  273 (308)
T ss_dssp             HHHTTT
T ss_pred             HHHccc
Confidence            877654

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.52  E-value=3.3e-14  Score=128.62  Aligned_cols=237  Identities=13%  Similarity=0.043  Sum_probs=123.3

Q ss_pred             HHhHHHHHHHHHhcCChHHHHHHHHHHHHc-------CcccChhhHHHHHHHHhccCChHHHHHHHHHHHhc------CC
Q 011249          210 ASCWAAMTVCYVQNGYAKAAIEMYKVMRQE-------NVRISEVAMVGAISACTQLGDVEMAAILAKHVDEG------CC  276 (490)
Q Consensus       210 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~-------~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~------~~  276 (490)
                      ..++..+...+...|++++|+.+++++.+.       ........+..+..++...|++++|...++++.+.      +.
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            456777888888888888888888887763       22223456677777777788888888877776543      11


Q ss_pred             -CCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHc------CCCCc-HHH
Q 011249          277 -DRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNE------GIEPN-QVT  348 (490)
Q Consensus       277 -~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~p~-~~~  348 (490)
                       +....++..+...|...|++++|...|++                               +.+.      +..|+ ...
T Consensus       107 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~-------------------------------a~~~~~~~~~~~~~~~~~~  155 (311)
T 3nf1_A          107 HPAVAATLNNLAVLYGKRGKYKEAEPLCKR-------------------------------ALEIREKVLGKDHPDVAKQ  155 (311)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCHHHHHHHHHH-------------------------------HHHHHHHHHCTTCHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHcCcHHHHHHHHHH-------------------------------HHHHHHHhcCCCChHHHHH
Confidence             12234444555555555555555555544                               3331      11121 123


Q ss_pred             HHHHHHHhcCCCChHHHHHHHHHHHHHc-----C-CCCCchHHHHHHHHHhhcCChHHHHHHHHhccC----------CC
Q 011249          349 FIGVLTACSHGGLVEDGCKQFELMTRVF-----G-IKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKD----------FC  412 (490)
Q Consensus       349 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~-----~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~----------~~  412 (490)
                      +..+...+...|++++|..+++++.+..     + .+.....+..+..+|...|++++|.+.++++..          .+
T Consensus       156 ~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  235 (311)
T 3nf1_A          156 LNNLALLCQNQGKYEEVEYYYQRALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDD  235 (311)
T ss_dssp             HHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCc
Confidence            4444444555555555555555444320     0 111123344455555555555555555544330          00


Q ss_pred             -C------hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          413 -D------AGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       413 -~------~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                       .      ...+......+...+.+.++...++++....|..+.++..++.+|.+.|++++|.+++++..+.
T Consensus       236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l  307 (311)
T 3nf1_A          236 ENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMRS  307 (311)
T ss_dssp             --CCHHHHHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence             0      1111222223344555666666677777667777777777888888888888888877776654

>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=99.52  E-value=2.4e-13  Score=135.50  Aligned_cols=164  Identities=14%  Similarity=0.142  Sum_probs=143.2

Q ss_pred             ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHH
Q 011249          310 DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCM  388 (490)
Q Consensus       310 ~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l  388 (490)
                      +..+|+.+..+|.+.|++++|+..|++.++.  .|+ ...+..+..+|.+.|++++|+..|+++.+.  .+.+...|..+
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nL   83 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNM   83 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHH
Confidence            3567888888899999999999999998884  554 568888889999999999999999998873  34457788899


Q ss_pred             HHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcch
Q 011249          389 VDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKD  466 (490)
Q Consensus       389 ~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  466 (490)
                      ..+|.+.|++++|++.|++..  .+.+...|..+..++...|++++|++.|+++++++|+++.++..++.+|...|++++
T Consensus        84 g~~l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~  163 (723)
T 4gyw_A           84 GNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTD  163 (723)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTT
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHH
Confidence            999999999999999998876  445678999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhc
Q 011249          467 SEIVKMMISET  477 (490)
Q Consensus       467 A~~~~~~~~~~  477 (490)
                      |.+.++++.+.
T Consensus       164 A~~~~~kal~l  174 (723)
T 4gyw_A          164 YDERMKKLVSI  174 (723)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99999987654

>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=99.52  E-value=3.8e-13  Score=111.35  Aligned_cols=166  Identities=14%  Similarity=0.046  Sum_probs=104.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHh
Q 011249          314 YSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLG  393 (490)
Q Consensus       314 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  393 (490)
                      +..+...+...|++++|...++++.+.. +.+...+..+...+...|++++|...++++.+.  .+.+...+..++..+.
T Consensus        11 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~   87 (186)
T 3as5_A           11 YRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLAD--APDNVKVATVLGLTYV   87 (186)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCCCHHHHHHHHHHHH
Confidence            3344444455555555555555544321 123344555555555556666666666655552  2334455556666666


Q ss_pred             hcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHH
Q 011249          394 RSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       394 ~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      ..|++++|.+.++++.  .+.+...+..+...+...|++++|.+.++++.+..|+++.++..++.++...|++++|.+.+
T Consensus        88 ~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~  167 (186)
T 3as5_A           88 QVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEALPHF  167 (186)
T ss_dssp             HHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHHHHH
Confidence            6666666666666554  33455667777777777888888888888888888887888888888888888888888888


Q ss_pred             HHhhhcccccC
Q 011249          472 MMISETEKKKS  482 (490)
Q Consensus       472 ~~~~~~~~~~~  482 (490)
                      +++.+......
T Consensus       168 ~~~~~~~~~~~  178 (186)
T 3as5_A          168 KKANELDEGAS  178 (186)
T ss_dssp             HHHHHHHHCCC
T ss_pred             HHHHHcCCCch
Confidence            87776654333

>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=99.51  E-value=1.3e-10  Score=114.44  Aligned_cols=400  Identities=8%  Similarity=0.004  Sum_probs=273.7

Q ss_pred             CCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCC---HHHHHHHH
Q 011249           64 KCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGL---MDDAQRLF  140 (490)
Q Consensus        64 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~---~~~A~~~~  140 (490)
                      .|.....|..++..+.+.++++.+..+|+.+... .+.....|...+..              -.+.|.   ++.+..+|
T Consensus        62 np~d~~~W~~yi~~~~~~~~~~~aR~vyEraL~~-fP~~~~lW~~Yi~~--------------E~~~~~~~~~~~v~~lf  126 (679)
T 4e6h_A           62 QPTDIFLYVKLLKHHVSLKQWKQVYETFDKLHDR-FPLMANIWCMRLSL--------------EFDKMEELDAAVIEPVL  126 (679)
T ss_dssp             CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHH--------------HHTC--CCCHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHH-CCCCHHHHHHHHHH--------------HHhhCCcchHHHHHHHH
Confidence            5555488999999999999999999999999886 23344444444442              455677   99999999


Q ss_pred             hhcCC-----CCHhHHHHHHHHHHhCCCh--------HHHHHHHHHhcc------C-CchhHHHHHHHHH---------h
Q 011249          141 DSMAE-----RNVISWSAMVAGYANCGNM--------KAAKEFYDRMTE------K-NSVTWVAMIAGYG---------K  191 (490)
Q Consensus       141 ~~~~~-----~~~~~~~~l~~~~~~~~~~--------~~a~~~~~~~~~------~-~~~~~~~l~~~~~---------~  191 (490)
                      ++...     |++..|...+.-..+.++.        +.+.++|+....      + +...|...+....         .
T Consensus       127 eRal~~~~~~~sv~LW~~Yl~f~~~~~~~~~~~~~~r~~vr~~FErAl~~vG~~d~~s~~iW~~Yi~f~~~~~~~~~~ee  206 (679)
T 4e6h_A          127 ARCLSKELGNNDLSLWLSYITYVRKKNDIITGGEEARNIVIQAFQVVVDKCAIFEPKSIQFWNEYLHFLEHWKPVNKFEE  206 (679)
T ss_dssp             HHHTCSSSCCCCHHHHHHHHHHHHHHSCSTTTHHHHHHHHHHHHHHHHHHTTTTCSSCHHHHHHHHHHHHTCCCCSHHHH
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHHHHhcccccccchhHHHHHHHHHHHHHHhCcccccchHHHHHHHHHHHhccccCcHHH
Confidence            99875     6778888877766655543        334577777552      3 3456776666543         2


Q ss_pred             cCChhHHHHHHhhcCC-CC---HHhHHHHHHHHHh-------------cCChHHHHHHHHHHHH--cCcc----------
Q 011249          192 CGEVREAKKVFDEISE-PD---ASCWAAMTVCYVQ-------------NGYAKAAIEMYKVMRQ--ENVR----------  242 (490)
Q Consensus       192 ~~~~~~A~~~~~~~~~-~~---~~~~~~l~~~~~~-------------~g~~~~A~~~~~~~~~--~~~~----------  242 (490)
                      .++++.+.++|++... |.   ..+|......-..             ..+++.|...+.++..  .++.          
T Consensus       207 q~~~~~~R~iy~raL~iP~~~~~~~w~~Y~~fe~~~~~~~a~~~~~e~~~~y~~Ar~~~~e~~~~~~~l~r~~p~~~~~~  286 (679)
T 4e6h_A          207 QQRVQYIRKLYKTLLCQPMDCLESMWQRYTQWEQDVNQLTARRHIGELSAQYMNARSLYQDWLNITKGLKRNLPITLNQA  286 (679)
T ss_dssp             HHHHHHHHHHHHHHTTSCCSSHHHHHHHHHHHHHHHCTTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTCCCCCCSSSTTC
T ss_pred             HhHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHhcCcchHHHHHHHhhHHHHHHHHHHHHHHHHHHhHhhccccccccc
Confidence            3457788999998876 32   1233222111111             1223445555555432  1111          


Q ss_pred             -----c--C------hhhHHHHHHHHhccC-------ChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHH-H
Q 011249          243 -----I--S------EVAMVGAISACTQLG-------DVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAW-R  301 (490)
Q Consensus       243 -----p--~------~~~~~~l~~~~~~~g-------~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~-~  301 (490)
                           |  +      ...|...+.---..+       ..+.+..+|++..... +....+|...+..+...|+.++|. .
T Consensus       287 ~~~~~p~~~~~~~~ql~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~~-p~~~~lW~~ya~~~~~~~~~~~a~r~  365 (679)
T 4e6h_A          287 TESNLPKPNEYDVQQLLIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQHV-CFAPEIWFNMANYQGEKNTDSTVITK  365 (679)
T ss_dssp             CTTTSCCTTCCCHHHHHHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHHT-TTCHHHHHHHHHHHHHHSCCTTHHHH
T ss_pred             hhccCCCCchhHHHHHHHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHhcCcHHHHHHH
Confidence                 1  0      022333333222221       1234567788887764 668888988999999999999996 9


Q ss_pred             HHhcccC--C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCC---------CCc------------HHHHHHHHHHhc
Q 011249          302 EFSRIKN--K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGI---------EPN------------QVTFIGVLTACS  357 (490)
Q Consensus       302 ~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---------~p~------------~~~~~~l~~~~~  357 (490)
                      +|++...  | +...|...+...-..|+++.|..+|+++.+...         .|+            ...|...+....
T Consensus       366 il~rAi~~~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~er  445 (679)
T 4e6h_A          366 YLKLGQQCIPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMK  445 (679)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHH
Confidence            9988765  3 555677788888899999999999999986310         132            235777777777


Q ss_pred             CCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcC-ChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHH
Q 011249          358 HGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSG-QLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGE  434 (490)
Q Consensus       358 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~  434 (490)
                      +.|..+.|..+|.++.+. ...+....|...+..-.+.| +.+.|.++|+...  .+.+...|..++......|+.+.|.
T Consensus       446 R~~~l~~AR~vf~~A~~~-~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~p~~~~~w~~y~~fe~~~~~~~~AR  524 (679)
T 4e6h_A          446 RIQGLAASRKIFGKCRRL-KKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKYFATDGEYINKYLDFLIYVNEESQVK  524 (679)
T ss_dssp             HHHCHHHHHHHHHHHHHT-GGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHh-cCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHhCCCHHHHH
Confidence            889999999999999873 12233455554444444544 5899999998776  3446667778888888899999999


Q ss_pred             HHHHHHHhcCCC---CCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          435 IAARHLLELGPE---KTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       435 ~~~~~~~~~~p~---~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      .+|++++...|+   ...++..++..-.+.|+.+.+..+.+++.+..++
T Consensus       525 ~lferal~~~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~  573 (679)
T 4e6h_A          525 SLFESSIDKISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPE  573 (679)
T ss_dssp             HHHHHHTTTSSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTT
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            999999998873   4567888888888999999999999999887654

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.51  E-value=9.9e-14  Score=125.43  Aligned_cols=238  Identities=11%  Similarity=0.002  Sum_probs=146.4

Q ss_pred             CchhHHHHHHHHHhcCChhHHHHHHhhcCC-----------CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHc------C
Q 011249          178 NSVTWVAMIAGYGKCGEVREAKKVFDEISE-----------PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQE------N  240 (490)
Q Consensus       178 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~------~  240 (490)
                      +..++..++..+...|++++|...|+++.+           .....+..+..++...|++++|+..+++....      +
T Consensus        26 ~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~  105 (311)
T 3nf1_A           26 RLRTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGK  105 (311)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCC
Confidence            446788899999999999999999988754           12456888999999999999999999998864      2


Q ss_pred             c-ccChhhHHHHHHHHhccCChHHHHHHHHHHHhc------CC-CCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChh
Q 011249          241 V-RISEVAMVGAISACTQLGDVEMAAILAKHVDEG------CC-DRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVI  312 (490)
Q Consensus       241 ~-~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~------~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~  312 (490)
                      - ......+..+...+...|++++|...++++.+.      +. +.....+..+...+...|++++|...|+        
T Consensus       106 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~--------  177 (311)
T 3nf1_A          106 DHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQ--------  177 (311)
T ss_dssp             TCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHH--------
T ss_pred             CChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHH--------
Confidence            1 223567888999999999999999999988654      11 1123334445555555555555555544        


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHc------CCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHc------CCC
Q 011249          313 SYSSMITAFADHGKSQEALDMFLKMRNE------GIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVF------GIK  379 (490)
Q Consensus       313 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~------~~~  379 (490)
                                             ++.+.      +..|. ...+..+...+...|++++|...++++.+..      ...
T Consensus       178 -----------------------~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  234 (311)
T 3nf1_A          178 -----------------------RALEIYQTKLGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVD  234 (311)
T ss_dssp             -----------------------HHHHHHHHTSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC---
T ss_pred             -----------------------HHHHHHHHHhCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCC
Confidence                                   44331      11221 1244444555555555555555555554310      011


Q ss_pred             CC-ch------HHHHHHHHHhhcCChHHHHHHHHhcc-C-CCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          380 PL-TE------HLTCMVDLLGRSGQLEKAHSLIMDYK-D-FCDAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       380 ~~-~~------~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      +. ..      .+..+...+...+.+.+|...++... . +....++..+..++...|++++|.+.+++++++.|.
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~~~  310 (311)
T 3nf1_A          235 DENKPIWMHAEEREECKGKQKDGTSFGEYGGWYKACKVDSPTVTTTLKNLGALYRRQGKFEAAETLEEAAMRSRKQ  310 (311)
T ss_dssp             ---CCHHHHHHHHHHC-------CCSCCCC---------CHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHC-
T ss_pred             cchHHHHHHHHHHHHhcCchhhHHHHHHHHHHHhhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhc
Confidence            11 11      12222333445556666666666655 2 234567888899999999999999999999988765

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.48  E-value=2.4e-11  Score=112.91  Aligned_cols=262  Identities=9%  Similarity=-0.061  Sum_probs=123.2

Q ss_pred             HHHHHHHhcCChhHHHHHHhhcCC----CCH----HhHHHHHHHHHhcCChHHHHHHHHHHHHcCcc-cCh----hhHHH
Q 011249          184 AMIAGYGKCGEVREAKKVFDEISE----PDA----SCWAAMTVCYVQNGYAKAAIEMYKVMRQENVR-ISE----VAMVG  250 (490)
Q Consensus       184 ~l~~~~~~~~~~~~A~~~~~~~~~----~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-p~~----~~~~~  250 (490)
                      .....+...|++++|...+++...    .+.    ..++.+...+...|++++|...+++....... ++.    .++..
T Consensus        19 ~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~   98 (373)
T 1hz4_A           19 LRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQ   98 (373)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence            334445556666666666555321    111    13445555566666666666666665532111 111    22344


Q ss_pred             HHHHHhccCChHHHHHHHHHHHhc----CCC--C-chhHHHHHHHHHHhcCChHHHHHHHhcccC--C------ChhHHH
Q 011249          251 AISACTQLGDVEMAAILAKHVDEG----CCD--R-TNYVSNALIHMHSKCGYLDLAWREFSRIKN--K------DVISYS  315 (490)
Q Consensus       251 l~~~~~~~g~~~~a~~~~~~~~~~----~~~--~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~------~~~~~~  315 (490)
                      +...+...|++++|...+++..+.    +.+  | ....+..+...+...|++++|...+++...  +      ...++.
T Consensus        99 la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~  178 (373)
T 1hz4_A           99 QSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLA  178 (373)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHHHH
Confidence            555556666666666666655432    111  1 123344455555666666666666555432  1      113444


Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCCCCc--HHHHH----HHHHHhcCCCChHHHHHHHHHHHHHcCCCCC---chHHH
Q 011249          316 SMITAFADHGKSQEALDMFLKMRNEGIEPN--QVTFI----GVLTACSHGGLVEDGCKQFELMTRVFGIKPL---TEHLT  386 (490)
Q Consensus       316 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~--~~~~~----~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~  386 (490)
                      .+...+...|++++|...+++.......++  .....    ..+..+...|++++|...+++.... ...+.   ...+.
T Consensus       179 ~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~-~~~~~~~~~~~~~  257 (373)
T 1hz4_A          179 MLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKP-EFANNHFLQGQWR  257 (373)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCC-CCTTCGGGHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCC-CCCcchhhHHHHH
Confidence            555555566666666666665544211111  11111    1122244556666666665555431 11000   11233


Q ss_pred             HHHHHHhhcCChHHHHHHHHhcc----CC---CCh-hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          387 CMVDLLGRSGQLEKAHSLIMDYK----DF---CDA-GTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       387 ~l~~~~~~~g~~~~A~~~~~~~~----~~---~~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      .+...+...|++++|...+++..    ..   ++. ..+..+..++...|+.++|...++++....+.
T Consensus       258 ~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~~~~~  325 (373)
T 1hz4_A          258 NIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANR  325 (373)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhcc
Confidence            44555555566666665555443    00   011 13334444555556666666666665555443

>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=99.48  E-value=1.5e-12  Score=112.05  Aligned_cols=190  Identities=12%  Similarity=-0.031  Sum_probs=109.2

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHhcccC----CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc-HHHHHHHH
Q 011249          279 TNYVSNALIHMHSKCGYLDLAWREFSRIKN----KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN-QVTFIGVL  353 (490)
Q Consensus       279 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~l~  353 (490)
                      ++..+......+...|++++|+..|++..+    ++...+..+..++...|++++|+..+++..+.  .|+ ...+..+.
T Consensus         6 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~   83 (228)
T 4i17_A            6 DPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKK--NYNLANAYIGKS   83 (228)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TCSHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHh--CcchHHHHHHHH
Confidence            445555666666666777777666665543    34455555666666666666666666666653  343 34566666


Q ss_pred             HHhcCCCChHHHHHHHHHHHHHcCCCCCc-------hHHHHHHHHHhhcCChHHHHHHHHhcc-CCCC---hhhHHHHHH
Q 011249          354 TACSHGGLVEDGCKQFELMTRVFGIKPLT-------EHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD---AGTWGALLG  422 (490)
Q Consensus       354 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-------~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~---~~~~~~l~~  422 (490)
                      .++...|++++|...+++..+.  .+.+.       ..|..+...+...|++++|++.|++.. ..|+   ...+..+..
T Consensus        84 ~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~l~~  161 (228)
T 4i17_A           84 AAYRDMKNNQEYIATLTEGIKA--VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDVTSKKWKTDALYSLGV  161 (228)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSSCHHHHHHHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence            6666666666666666666653  22223       335555566666666666666666554 2232   344555555


Q ss_pred             HHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          423 ACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       423 ~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ++...     +...++++....+.++..|...  .....+.+++|+..+++..+..+
T Consensus       162 ~~~~~-----~~~~~~~a~~~~~~~~~~~~~~--~~~~~~~~~~A~~~~~~a~~l~p  211 (228)
T 4i17_A          162 LFYNN-----GADVLRKATPLASSNKEKYASE--KAKADAAFKKAVDYLGEAVTLSP  211 (228)
T ss_dssp             HHHHH-----HHHHHHHHGGGTTTCHHHHHHH--HHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHH-----HHHHHHHHHhcccCCHHHHHHH--HHHHHHHHHHHHHHHHHHhhcCC
Confidence            54333     3334455555554443333322  23344556999999998887654

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.47  E-value=7.6e-12  Score=116.51  Aligned_cols=228  Identities=11%  Similarity=0.016  Sum_probs=123.5

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCc-cc----ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCC--C----CchhHH
Q 011249          215 AMTVCYVQNGYAKAAIEMYKVMRQENV-RI----SEVAMVGAISACTQLGDVEMAAILAKHVDEGCC--D----RTNYVS  283 (490)
Q Consensus       215 ~l~~~~~~~g~~~~A~~~~~~~~~~~~-~p----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~----~~~~~~  283 (490)
                      .....+...|++++|+..|++..+... .+    ...++..+..++...|+++.|...+++..+...  .    ....++
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            344556677777777777777664211 11    134566666677777777777777766554311  0    113345


Q ss_pred             HHHHHHHHhcCChHHHHHHHhcccC-----CC----hhHHHHHHHHHHhcCChHHHHHHHHHHHHc----CCCCcHHHHH
Q 011249          284 NALIHMHSKCGYLDLAWREFSRIKN-----KD----VISYSSMITAFADHGKSQEALDMFLKMRNE----GIEPNQVTFI  350 (490)
Q Consensus       284 ~~l~~~~~~~~~~~~A~~~~~~~~~-----~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p~~~~~~  350 (490)
                      +.+..+|...|++++|...|++..+     ++    ..++..+..+|...|++++|...+++..+.    +.+....++.
T Consensus       186 ~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~  265 (378)
T 3q15_A          186 FVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLF  265 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHH
Confidence            5566666666666666666655443     11    234555666666667777776666666541    1111234555


Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHcCCCCC---chHHHHHHHHHhhcCC---hHHHHHHHHhccCCCC-hhhHHHHHHH
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPL---TEHLTCMVDLLGRSGQ---LEKAHSLIMDYKDFCD-AGTWGALLGA  423 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~g~---~~~A~~~~~~~~~~~~-~~~~~~l~~~  423 (490)
                      .+...+...|++++|...+++..+.....++   ...+..+...+...|+   +++|+.++++....++ ...+..+...
T Consensus       266 ~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~la~~  345 (378)
T 3q15_A          266 GLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYIEACARSAAAV  345 (378)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHHHHHHHHHHHH
Confidence            6666666666666666666666653211111   2223344444555555   5555555555432221 2234445555


Q ss_pred             HhhhCChHHHHHHHHHHHh
Q 011249          424 CKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       424 ~~~~g~~~~a~~~~~~~~~  442 (490)
                      |...|++++|.+.|+++.+
T Consensus       346 y~~~g~~~~A~~~~~~al~  364 (378)
T 3q15_A          346 FESSCHFEQAAAFYRKVLK  364 (378)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH
Confidence            5555555555555555544

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.46  E-value=1.1e-12  Score=122.17  Aligned_cols=228  Identities=10%  Similarity=-0.022  Sum_probs=173.3

Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHhcCC--C---CchhHHHHHHHHHHhcCChHHHHHHHhcccC-----CC-----hhH
Q 011249          249 VGAISACTQLGDVEMAAILAKHVDEGCC--D---RTNYVSNALIHMHSKCGYLDLAWREFSRIKN-----KD-----VIS  313 (490)
Q Consensus       249 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~--~---~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~-----~~~  313 (490)
                      ......+...|++++|...++++.+...  +   ....++..+..+|...|+++.|...+++..+     ++     ..+
T Consensus       105 ~~~g~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~  184 (378)
T 3q15_A          105 FFRGMYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQS  184 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHH
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHH
Confidence            3445567789999999999999876421  1   1245778899999999999999998887654     12     347


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHc----CCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHc---CCCCCchHH
Q 011249          314 YSSMITAFADHGKSQEALDMFLKMRNE----GIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVF---GIKPLTEHL  385 (490)
Q Consensus       314 ~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~---~~~~~~~~~  385 (490)
                      ++.+..+|...|++++|...+++..+.    +-.+ ...++..+..+|...|++++|...+++..+..   +.+....++
T Consensus       185 ~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  264 (378)
T 3q15_A          185 LFVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVL  264 (378)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHH
Confidence            888999999999999999999998762    1111 12467888889999999999999999987621   223336677


Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc----C--CC-ChhhHHHHHHHHhhhCC---hHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK----D--FC-DAGTWGALLGACKVHVN---AELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~----~--~~-~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      ..+..+|.+.|++++|...+++..    .  .+ ....+..+...+...++   +++|+..+++. ...|.....+..++
T Consensus       265 ~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~-~~~~~~~~~~~~la  343 (378)
T 3q15_A          265 FGLSWTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKK-NLHAYIEACARSAA  343 (378)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHT-TCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhC-CChhHHHHHHHHHH
Confidence            889999999999999999998765    1  12 22345555566777788   77888877762 22344556788999


Q ss_pred             HHHHhcCCcchHHHHHHHhhhc
Q 011249          456 NIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       456 ~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      .+|...|++++|.+.+++..+.
T Consensus       344 ~~y~~~g~~~~A~~~~~~al~~  365 (378)
T 3q15_A          344 AVFESSCHFEQAAAFYRKVLKA  365 (378)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHH
Confidence            9999999999999999988654

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.46  E-value=2e-12  Score=123.95  Aligned_cols=190  Identities=13%  Similarity=-0.033  Sum_probs=86.7

Q ss_pred             CHHhHHHHHHHHHhcCCh-HHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHH
Q 011249          209 DASCWAAMTVCYVQNGYA-KAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALI  287 (490)
Q Consensus       209 ~~~~~~~l~~~~~~~g~~-~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  287 (490)
                      +...+..+..++...|++ ++|++.|++..+... -+...+..+..++...|++++|...|+++.+..  |+...+..+.
T Consensus       101 ~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~p-~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~lg  177 (474)
T 4abn_A          101 EAQALMLKGKALNVTPDYSPEAEVLLSKAVKLEP-ELVEAWNQLGEVYWKKGDVTSAHTCFSGALTHC--KNKVSLQNLS  177 (474)
T ss_dssp             CHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTC--CCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccccHHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCHHHHHHHH
Confidence            444555555555555555 555555555554421 134455555555555555555555555555443  2334444455


Q ss_pred             HHHHhc---------CChHHHHHHHhcccC---CChhHHHHHHHHHHhc--------CChHHHHHHHHHHHHcCCCC---
Q 011249          288 HMHSKC---------GYLDLAWREFSRIKN---KDVISYSSMITAFADH--------GKSQEALDMFLKMRNEGIEP---  344 (490)
Q Consensus       288 ~~~~~~---------~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~--------~~~~~a~~~~~~~~~~~~~p---  344 (490)
                      .+|...         |++++|+..|++..+   .+...|..+..+|...        |++++|+..|++..+.  .|   
T Consensus       178 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~p~~~  255 (474)
T 4abn_A          178 MVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMDVLDGRSWYILGNAYLSLYFNTGQNPKISQQALSAYAQAEKV--DRKAS  255 (474)
T ss_dssp             HHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH--CGGGG
T ss_pred             HHHHHhccCChhhhhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHh--CCCcc
Confidence            555554         444444444444432   2334444444444444        4444444444444442  22   


Q ss_pred             -cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHH
Q 011249          345 -NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLI  405 (490)
Q Consensus       345 -~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~  405 (490)
                       +...+..+..+|...|++++|...|+++.+.  .+.+...+..+..++...|++++|.+.+
T Consensus       256 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l--~p~~~~a~~~l~~~~~~lg~~~eAi~~~  315 (474)
T 4abn_A          256 SNPDLHLNRATLHKYEESYGEALEGFSQAAAL--DPAWPEPQQREQQLLEFLSRLTSLLESK  315 (474)
T ss_dssp             GCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence             3334444444444444444444444444431  1222333334444444444444444433

>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=99.45  E-value=5.9e-12  Score=108.21  Aligned_cols=206  Identities=10%  Similarity=0.023  Sum_probs=162.8

Q ss_pred             cChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-ChhHHHHHHH
Q 011249          243 ISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-DVISYSSMIT  319 (490)
Q Consensus       243 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l~~  319 (490)
                      .|+..+......+...|++++|...|+.+.+...+++...+..+..++...|++++|+..|++..+  | +...|..+..
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~   84 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKNYNLANAYIGKSA   84 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCSHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhCcchHHHHHHHHH
Confidence            356788889999999999999999999999987447777777799999999999999999998875  3 5678899999


Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCc-H-------HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCC--CchHHHHHH
Q 011249          320 AFADHGKSQEALDMFLKMRNEGIEPN-Q-------VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKP--LTEHLTCMV  389 (490)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~~~p~-~-------~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~--~~~~~~~l~  389 (490)
                      ++...|++++|+..+++..+.  .|+ .       ..+..+...+...|++++|...++++.+  ..+.  +...+..+.
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~~~l~  160 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKA--VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATD--VTSKKWKTDALYSLG  160 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTT--SSCHHHHHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHh--cCCCcccHHHHHHHH
Confidence            999999999999999999985  443 3       4577788888999999999999999986  2233  356777888


Q ss_pred             HHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          390 DLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       390 ~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      .+|...|+.     +++++.  ...+...+....  ....+.+++|+..++++++.+|+++.+...+..+..
T Consensus       161 ~~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~p~~~~~~~~l~~i~~  225 (228)
T 4i17_A          161 VLFYNNGAD-----VLRKATPLASSNKEKYASEK--AKADAAFKKAVDYLGEAVTLSPNRTEIKQMQDQVKA  225 (228)
T ss_dssp             HHHHHHHHH-----HHHHHGGGTTTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHH-----HHHHHHhcccCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHH
Confidence            888765543     333333  123344444333  345677999999999999999999988888776543

>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=99.44  E-value=7.5e-12  Score=103.43  Aligned_cols=169  Identities=9%  Similarity=-0.073  Sum_probs=141.7

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHh
Q 011249          280 NYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTAC  356 (490)
Q Consensus       280 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~  356 (490)
                      ...+..+...+...|++++|...++++.+   .+...+..+...+...|++++|...++++.+.. +.+...+..+...+
T Consensus         8 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   86 (186)
T 3as5_A            8 QVYYRDKGISHAKAGRYSQAVMLLEQVYDADAFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHTTTCCTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            34566677888888999999999988876   356788888889999999999999999998752 33567788888889


Q ss_pred             cCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHH
Q 011249          357 SHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGE  434 (490)
Q Consensus       357 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~  434 (490)
                      ...|++++|...++++.+.  .+.+...+..++.++...|++++|.+.++++.  .+.+...+..++..+...|++++|.
T Consensus        87 ~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~  164 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEA--NPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLRPNEGKVHRAIAFSYEQMGRHEEAL  164 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhc--CcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcCccchHHHHHHHHHHHHcCCHHHHH
Confidence            9999999999999999873  45567788889999999999999999998876  4456778899999999999999999


Q ss_pred             HHHHHHHhcCCCCCchH
Q 011249          435 IAARHLLELGPEKTGNS  451 (490)
Q Consensus       435 ~~~~~~~~~~p~~~~~~  451 (490)
                      +.++++.+..|+++...
T Consensus       165 ~~~~~~~~~~~~~~~~~  181 (186)
T 3as5_A          165 PHFKKANELDEGASVEL  181 (186)
T ss_dssp             HHHHHHHHHHHCCCGGG
T ss_pred             HHHHHHHHcCCCchhhH
Confidence            99999999988876543

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.38  E-value=1.5e-11  Score=109.86  Aligned_cols=164  Identities=10%  Similarity=-0.046  Sum_probs=88.6

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcC---CCCc--HHHHHHHHHHhcCC-CChHHHHHHHHHHHHHcCCCCC----
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEG---IEPN--QVTFIGVLTACSHG-GLVEDGCKQFELMTRVFGIKPL----  381 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~p~--~~~~~~l~~~~~~~-g~~~~a~~~~~~~~~~~~~~~~----  381 (490)
                      .+|+.+..+|...|++++|+..+++..+..   -.+.  ..++..+...|... |++++|+..+++..+...-..+    
T Consensus        78 ~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~  157 (292)
T 1qqe_A           78 NTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALS  157 (292)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHH
Confidence            345555556666666666666666555410   0111  23555666666664 7777777777766653111111    


Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc-CCCCh--------hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCch--
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDA--------GTWGALLGACKVHVNAELGEIAARHLLELGPEKTGN--  450 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~--------~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~--  450 (490)
                      ..++..+...+.+.|++++|+..|++.. ..|+.        ..+..+..++...|++++|+..++++++++|..+..  
T Consensus       158 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~  237 (292)
T 1qqe_A          158 NKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRE  237 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHH
Confidence            2345666677777777777777776654 22211        134556666677777777777777777777765442  


Q ss_pred             ---HHHHHHHHH--hcCCcchHHHHHHHhh
Q 011249          451 ---SALLANIYA--SMGKWKDSEIVKMMIS  475 (490)
Q Consensus       451 ---~~~l~~~~~--~~g~~~~A~~~~~~~~  475 (490)
                         +..++.++.  ..+++++|+..++++.
T Consensus       238 ~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~  267 (292)
T 1qqe_A          238 SNFLKSLIDAVNEGDSEQLSEHCKEFDNFM  267 (292)
T ss_dssp             HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHhccCC
Confidence               333444443  3455666666666554

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.37  E-value=5.5e-11  Score=110.48  Aligned_cols=291  Identities=13%  Similarity=0.048  Sum_probs=199.6

Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHhccC----Cch----hHHHHHHHHHhcCChhHHHHHHhhcCC-----CCH----HhH
Q 011249          151 WSAMVAGYANCGNMKAAKEFYDRMTEK----NSV----TWVAMIAGYGKCGEVREAKKVFDEISE-----PDA----SCW  213 (490)
Q Consensus       151 ~~~l~~~~~~~~~~~~a~~~~~~~~~~----~~~----~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~~----~~~  213 (490)
                      .......+...|++++|...+++....    +..    ++..+...+...|++++|.+.+++...     .+.    .++
T Consensus        17 ~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~   96 (373)
T 1hz4_A           17 NALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSL   96 (373)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCchhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence            444556677899999999999887642    221    456777888889999999999988754     222    335


Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHc----Ccc--c-ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCC----chhH
Q 011249          214 AAMTVCYVQNGYAKAAIEMYKVMRQE----NVR--I-SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDR----TNYV  282 (490)
Q Consensus       214 ~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~--p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~----~~~~  282 (490)
                      ..+...+...|++++|...+++....    +..  | ....+..+...+...|++++|...+++..+.....    ....
T Consensus        97 ~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  176 (373)
T 1hz4_A           97 IQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQC  176 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccCcHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCcHHHHHH
Confidence            67788889999999999999888753    211  2 23456667788889999999999999887653221    2346


Q ss_pred             HHHHHHHHHhcCChHHHHHHHhcccC----CC-hhHHH-----HHHHHHHhcCChHHHHHHHHHHHHcCCCC---cHHHH
Q 011249          283 SNALIHMHSKCGYLDLAWREFSRIKN----KD-VISYS-----SMITAFADHGKSQEALDMFLKMRNEGIEP---NQVTF  349 (490)
Q Consensus       283 ~~~l~~~~~~~~~~~~A~~~~~~~~~----~~-~~~~~-----~l~~~~~~~~~~~~a~~~~~~~~~~~~~p---~~~~~  349 (490)
                      +..+...+...|++++|...+++...    ++ ...+.     ..+..+...|++++|...+++.......+   ....+
T Consensus       177 ~~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~  256 (373)
T 1hz4_A          177 LAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQW  256 (373)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHH
Confidence            67788889999999999999887643    21 12222     23344778999999999998877643221   12355


Q ss_pred             HHHHHHhcCCCChHHHHHHHHHHHHHc---CCCCCc-hHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHh
Q 011249          350 IGVLTACSHGGLVEDGCKQFELMTRVF---GIKPLT-EHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACK  425 (490)
Q Consensus       350 ~~l~~~~~~~g~~~~a~~~~~~~~~~~---~~~~~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~  425 (490)
                      ..+...+...|++++|...++......   +.+++. ..+..+..++...|+.++|...+++.......   ......+.
T Consensus       257 ~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~~~~~---~g~~~~~~  333 (373)
T 1hz4_A          257 RNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLANR---TGFISHFV  333 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHH---HCCCHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhcc---ccHHHHHH
Confidence            677788888999999999998886531   211122 35566778888999999999998876511000   01122333


Q ss_pred             hhCChHHHHHHHHHHHhcCCC
Q 011249          426 VHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       426 ~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      ..|  +....+++.+....|.
T Consensus       334 ~~g--~~~~~ll~~~~~~~~~  352 (373)
T 1hz4_A          334 IEG--EAMAQQLRQLIQLNTL  352 (373)
T ss_dssp             TTH--HHHHHHHHHHHHTTCS
T ss_pred             Hcc--HHHHHHHHHHHhCCCC
Confidence            344  6667777777777764

>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=99.34  E-value=8.5e-12  Score=110.82  Aligned_cols=164  Identities=11%  Similarity=0.102  Sum_probs=83.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHc------CCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHc-----C-CC
Q 011249          313 SYSSMITAFADHGKSQEALDMFLKMRNE------GIEPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVF-----G-IK  379 (490)
Q Consensus       313 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-----~-~~  379 (490)
                      ++..+...|...|++++|...++++.+.      .-.|+ ...+..+...+...|++++|...++++.+..     + .+
T Consensus        87 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  166 (283)
T 3edt_B           87 TLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDP  166 (283)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCH
Confidence            4455555555555555555555555442      11122 2355556666666666666666666665520     0 11


Q ss_pred             CCchHHHHHHHHHhhcCChHHHHHHHHhcc----------CCC-ChhhHHHHHHHHhhhC------ChHHHHHHHHHHHh
Q 011249          380 PLTEHLTCMVDLLGRSGQLEKAHSLIMDYK----------DFC-DAGTWGALLGACKVHV------NAELGEIAARHLLE  442 (490)
Q Consensus       380 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----------~~~-~~~~~~~l~~~~~~~g------~~~~a~~~~~~~~~  442 (490)
                      ....++..+..+|...|++++|.+.+++..          ..+ ....+..+.......+      .+..+...++....
T Consensus       167 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (283)
T 3edt_B          167 NVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKV  246 (283)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCC
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCC
Confidence            123455566666666666666666665543          011 1223333332222222      22333333333333


Q ss_pred             cCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          443 LGPEKTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       443 ~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      ..|..+..+..++.+|...|++++|..++++..+
T Consensus       247 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  280 (283)
T 3edt_B          247 DSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASR  280 (283)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            3355566777788888888888888888877654

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.32  E-value=1e-10  Score=104.54  Aligned_cols=172  Identities=8%  Similarity=-0.080  Sum_probs=108.2

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccC-----CC----hhHHHHHHHHHHhc-CChHHHHHHHHHHHHcCCCCc------
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKN-----KD----VISYSSMITAFADH-GKSQEALDMFLKMRNEGIEPN------  345 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~----~~~~~~l~~~~~~~-~~~~~a~~~~~~~~~~~~~p~------  345 (490)
                      +++.+..+|...|++++|+..|++..+     .+    ..+++.+..+|... |++++|+..|++..+.  .|+      
T Consensus        79 ~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~~lg~~~~A~~~~~~Al~~--~~~~~~~~~  156 (292)
T 1qqe_A           79 TYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEW--YAQDQSVAL  156 (292)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH--HHHTTCHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHH--HHhCCChHH
Confidence            334444444444444444444444332     01    23567777788885 8888888888887762  221      


Q ss_pred             -HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCc-----hHHHHHHHHHhhcCChHHHHHHHHhcc-CCCCh----
Q 011249          346 -QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLT-----EHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDA----  414 (490)
Q Consensus       346 -~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~----  414 (490)
                       ..++..+...+...|++++|+..++++.+...-.+..     ..+..+..++...|++++|...|++.. ..|+.    
T Consensus       157 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~  236 (292)
T 1qqe_A          157 SNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSR  236 (292)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC--------
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcH
Confidence             2467778888888999999999999888731111111     146677788888999999999998876 23321    


Q ss_pred             --hhHHHHHHHHh--hhCChHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          415 --GTWGALLGACK--VHVNAELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       415 --~~~~~l~~~~~--~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                        ..+..++.++.  ..+++++|+..|+++.+++|....++..+-
T Consensus       237 ~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~l~~~~~~~~~~~k  281 (292)
T 1qqe_A          237 ESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRLDKWKITILNKIK  281 (292)
T ss_dssp             -HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHhccCCccHHHHHHHHHHHH
Confidence              12344555553  456788888888888888876554444443

>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=99.32  E-value=1.3e-11  Score=123.01  Aligned_cols=162  Identities=12%  Similarity=0.098  Sum_probs=104.5

Q ss_pred             chhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc-HHHHHHHHH
Q 011249          279 TNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN-QVTFIGVLT  354 (490)
Q Consensus       279 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~  354 (490)
                      +...++.|..+|.+.|++++|++.|++..+   .+..+|..+..+|.+.|++++|+..|++.++.  .|+ ...+..+..
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nLg~   85 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMGN   85 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHH
Confidence            344555566666666666666666665543   24556666666666777777777777776663  443 446666677


Q ss_pred             HhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHH
Q 011249          355 ACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAEL  432 (490)
Q Consensus       355 ~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~  432 (490)
                      ++...|++++|++.|++..+.  .+-+...+..+..+|...|++++|++.|++..  .+.+...+..++.++...|++++
T Consensus        86 ~l~~~g~~~~A~~~~~kAl~l--~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~~~  163 (723)
T 4gyw_A           86 TLKEMQDVQGALQCYTRAIQI--NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTD  163 (723)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCCTT
T ss_pred             HHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccHHH
Confidence            777777777777777777652  23345666677777777777777777776655  33455677777777777777777


Q ss_pred             HHHHHHHHHhcC
Q 011249          433 GEIAARHLLELG  444 (490)
Q Consensus       433 a~~~~~~~~~~~  444 (490)
                      |.+.+++++++.
T Consensus       164 A~~~~~kal~l~  175 (723)
T 4gyw_A          164 YDERMKKLVSIV  175 (723)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC
Confidence            777777776643

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.31  E-value=4.4e-10  Score=98.39  Aligned_cols=243  Identities=8%  Similarity=-0.003  Sum_probs=161.5

Q ss_pred             HHHHhcCChhHHHHHHhhcCCCC-HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHH
Q 011249          187 AGYGKCGEVREAKKVFDEISEPD-ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAA  265 (490)
Q Consensus       187 ~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~  265 (490)
                      +-..-.|++..++.-...+...+ ...-..+.++++..|++...         ..-.|....+..+...+ ..+    +.
T Consensus        21 kn~fy~G~yq~~i~e~~~~~~~~~~~~~~~~~Rs~iAlg~~~~~---------~~~~~~~~a~~~la~~~-~~~----a~   86 (310)
T 3mv2_B           21 KQNYYTGNFVQCLQEIEKFSKVTDNTLLFYKAKTLLALGQYQSQ---------DPTSKLGKVLDLYVQFL-DTK----NI   86 (310)
T ss_dssp             HHHHTTTCHHHHTHHHHTSSCCCCHHHHHHHHHHHHHTTCCCCC---------CSSSTTHHHHHHHHHHH-TTT----CC
T ss_pred             HHHHHhhHHHHHHHHHHhcCccchHHHHHHHHHHHHHcCCCccC---------CCCCHHHHHHHHHHHHh-ccc----HH
Confidence            44456788888888666654422 23334456788888887642         11233333444444333 322    66


Q ss_pred             HHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCC-----ChhHHHHHHHHHHhcCChHHHHHHHHHHHHc
Q 011249          266 ILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNK-----DVISYSSMITAFADHGKSQEALDMFLKMRNE  340 (490)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~  340 (490)
                      ..+++..+.+ +++......+..++...|++++|++++.+....     +...+..++..+.+.|+.+.|.+.+++|.+ 
T Consensus        87 ~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~-  164 (310)
T 3mv2_B           87 EELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTN-  164 (310)
T ss_dssp             HHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH-
T ss_pred             HHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHh-
Confidence            7777776655 455555567888888889999999998887542     445677788888999999999999999887 


Q ss_pred             CCCC-----cHHHHHHHHHHh----cCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccC-
Q 011249          341 GIEP-----NQVTFIGVLTAC----SHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKD-  410 (490)
Q Consensus       341 ~~~p-----~~~~~~~l~~~~----~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-  410 (490)
                       ..|     +..+...+..++    ...++..+|..+|+++...   .|+......++.++.+.|++++|.+.++.+.. 
T Consensus       165 -~~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~---~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~  240 (310)
T 3mv2_B          165 -AIEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT---FPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSD  240 (310)
T ss_dssp             -HSCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT---SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSH
T ss_pred             -cCccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh---CCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence             366     355556666552    2334888899999998653   34422323344478888999999998876542 


Q ss_pred             -----------CCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchH
Q 011249          411 -----------FCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       411 -----------~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                                 +.++.++..++......|+  +|.++++++.+..|++|.+.
T Consensus       241 ~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~P~hp~i~  290 (310)
T 3mv2_B          241 YYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKLDHEHAFIK  290 (310)
T ss_dssp             HHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHTTCCCHHHH
T ss_pred             cccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHhCCCChHHH
Confidence                       3355666566666666676  78888999999899877644

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=99.31  E-value=2.5e-10  Score=99.99  Aligned_cols=237  Identities=11%  Similarity=0.005  Sum_probs=136.5

Q ss_pred             HHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHH
Q 011249          219 CYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDL  298 (490)
Q Consensus       219 ~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  298 (490)
                      -..-.|++..++.-..++.   .........-+.+++...|++...         ....|....+..+... ...+    
T Consensus        22 n~fy~G~yq~~i~e~~~~~---~~~~~~~~~~~~Rs~iAlg~~~~~---------~~~~~~~~a~~~la~~-~~~~----   84 (310)
T 3mv2_B           22 QNYYTGNFVQCLQEIEKFS---KVTDNTLLFYKAKTLLALGQYQSQ---------DPTSKLGKVLDLYVQF-LDTK----   84 (310)
T ss_dssp             HHHTTTCHHHHTHHHHTSS---CCCCHHHHHHHHHHHHHTTCCCCC---------CSSSTTHHHHHHHHHH-HTTT----
T ss_pred             HHHHhhHHHHHHHHHHhcC---ccchHHHHHHHHHHHHHcCCCccC---------CCCCHHHHHHHHHHHH-hccc----
Confidence            3445677777666322221   111222333444666666665531         1122333333333332 2322    


Q ss_pred             HHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Q 011249          299 AWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTR  374 (490)
Q Consensus       299 A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  374 (490)
                      |+..|++...   ++..++..+..++...|++++|++++.+.+..|..+ +...+...+..+.+.|+.+.|.+.+++|.+
T Consensus        85 a~~~l~~l~~~~~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~~  164 (310)
T 3mv2_B           85 NIEELENLLKDKQNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYTN  164 (310)
T ss_dssp             CCHHHHHTTTTSCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            5566665543   344555566777777788888888777776644322 344666677777777888888888877765


Q ss_pred             HcCCCC-----CchHHHHHHHH--HhhcC--ChHHHHHHHHhcc-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhc-
Q 011249          375 VFGIKP-----LTEHLTCMVDL--LGRSG--QLEKAHSLIMDYK-DFCDAGTWGALLGACKVHVNAELGEIAARHLLEL-  443 (490)
Q Consensus       375 ~~~~~~-----~~~~~~~l~~~--~~~~g--~~~~A~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~-  443 (490)
                      .   .|     +..+...++.+  ....|  ++++|..+|+++. ..|+..+...++.++...|++++|.+.++.+.+. 
T Consensus       165 ~---~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~~~  241 (310)
T 3mv2_B          165 A---IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQRNIAEAQGIVELLLSDY  241 (310)
T ss_dssp             H---SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHSHH
T ss_pred             c---CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence            3   44     23444445544  22233  7777777777766 2343223334444677778888888877766664 


Q ss_pred             ---------CCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          444 ---------GPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       444 ---------~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                               +|+++.++..++.+....|+  +|.++++++.+.
T Consensus       242 p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~  282 (310)
T 3mv2_B          242 YSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKL  282 (310)
T ss_dssp             HHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHT
T ss_pred             ccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHh
Confidence                     47777777777666666675  777777777654

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.29  E-value=1.2e-10  Score=102.24  Aligned_cols=82  Identities=12%  Similarity=0.016  Sum_probs=60.5

Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc-CCCC----hhhHHHHHHHHhhh----------CChHHHHHHHHHHHhcCCCCCc-
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK-DFCD----AGTWGALLGACKVH----------VNAELGEIAARHLLELGPEKTG-  449 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~-~~~~----~~~~~~l~~~~~~~----------g~~~~a~~~~~~~~~~~p~~~~-  449 (490)
                      ..+..+|.+.|++++|+..|+++. ..|+    ...+..+..++...          |++++|+..++++++..|+++. 
T Consensus       152 ~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~  231 (261)
T 3qky_A          152 YEAARLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFPDSPLL  231 (261)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCTTCTHH
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCCCChHH
Confidence            556788899999999999998876 2232    34667777777765          8899999999999999999864 


Q ss_pred             --hHHHHHHHHHhcCCcchH
Q 011249          450 --NSALLANIYASMGKWKDS  467 (490)
Q Consensus       450 --~~~~l~~~~~~~g~~~~A  467 (490)
                        +...+..++.+.|+++++
T Consensus       232 ~~a~~~l~~~~~~~~~~~~~  251 (261)
T 3qky_A          232 RTAEELYTRARQRLTELEGD  251 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHhhhh
Confidence              445556566555555443

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.28  E-value=3e-10  Score=97.19  Aligned_cols=182  Identities=12%  Similarity=-0.010  Sum_probs=112.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccC--CC----hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcH----HHHHH
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKN--KD----VISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQ----VTFIG  351 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~----~~~~~  351 (490)
                      .+..+...+...|++++|+..|+++.+  |+    ...+..++.+|.+.|++++|+..|+++.+.  .|+.    ..+..
T Consensus         6 ~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~--~P~~~~~~~a~~~   83 (225)
T 2yhc_A            6 EIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL--NPTHPNIDYVMYM   83 (225)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCCcHHHHHHH
Confidence            344456667777777777777777654  32    235666667777777777777777777763  2321    13333


Q ss_pred             HHHHhcC------------------CCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCC
Q 011249          352 VLTACSH------------------GGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCD  413 (490)
Q Consensus       352 l~~~~~~------------------~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  413 (490)
                      +..++..                  .|++++|...|+++.+.  .|-+............    ..      ..+     
T Consensus        84 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~P~~~~a~~a~~~l~~----~~------~~~-----  146 (225)
T 2yhc_A           84 RGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG--YPNSQYTTDATKRLVF----LK------DRL-----  146 (225)
T ss_dssp             HHHHHHHHHC--------------CCHHHHHHHHHHHHHHTT--CTTCTTHHHHHHHHHH----HH------HHH-----
T ss_pred             HHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH--CcCChhHHHHHHHHHH----HH------HHH-----
Confidence            3333332                  34555555555555541  2222222211110000    00      000     


Q ss_pred             hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC---chHHHHHHHHHhcCCcchHHHHHHHhhhcccccC
Q 011249          414 AGTWGALLGACKVHVNAELGEIAARHLLELGPEKT---GNSALLANIYASMGKWKDSEIVKMMISETEKKKS  482 (490)
Q Consensus       414 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~  482 (490)
                      ......+...+...|++++|+..|+++++..|+++   .++..++.++.+.|++++|.+.++.+...++...
T Consensus       147 ~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~~~~  218 (225)
T 2yhc_A          147 AKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNTL  218 (225)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCSCCC
T ss_pred             HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCch
Confidence            00113456678899999999999999999999976   5789999999999999999999999887766443

>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=99.27  E-value=9.2e-12  Score=99.00  Aligned_cols=142  Identities=6%  Similarity=-0.128  Sum_probs=100.5

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCCCCcH-HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcC
Q 011249          318 ITAFADHGKSQEALDMFLKMRNEGIEPNQ-VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSG  396 (490)
Q Consensus       318 ~~~~~~~~~~~~a~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  396 (490)
                      ...+...|++++|+..++....  ..|+. ..+..+...|...|++++|++.|+++.+.  .+.+...|..+..+|...|
T Consensus         4 G~~~~~~~~~e~ai~~~~~a~~--~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~   79 (150)
T 4ga2_A            4 GSMRRSKADVERYIASVQGSTP--SPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINV--QERDPKAHRFLGLLYELEE   79 (150)
T ss_dssp             ---CCCHHHHHHHHHHHHHHSC--SHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHcChHHHHHHHHHHhcc--cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcC
Confidence            3444556677777777776654  23332 24556677777788888888888887763  3445677777888888888


Q ss_pred             ChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHH-HHHHHhcCCCCCchHHHHHHHHHhcCC
Q 011249          397 QLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIA-ARHLLELGPEKTGNSALLANIYASMGK  463 (490)
Q Consensus       397 ~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~-~~~~~~~~p~~~~~~~~l~~~~~~~g~  463 (490)
                      ++++|+..|++..  .+.++..+..+...+...|++++|.+. ++++++++|+++.+|.....++...|+
T Consensus        80 ~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P~~~~~~~l~~~ll~~~G~  149 (150)
T 4ga2_A           80 NTDKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFPGSPAVYKLKEQLLDCEGE  149 (150)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHSTTCHHHHHHHHHHHHTCCC
T ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCc
Confidence            8888888887765  344567788888888888888765554 588888888888888888888877775

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=99.27  E-value=1.5e-10  Score=101.58  Aligned_cols=185  Identities=7%  Similarity=-0.047  Sum_probs=120.5

Q ss_pred             CchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-C---hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCC-CCc-HHHH
Q 011249          278 RTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-D---VISYSSMITAFADHGKSQEALDMFLKMRNEGI-EPN-QVTF  349 (490)
Q Consensus       278 ~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~---~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~p~-~~~~  349 (490)
                      .+...+..+...+.+.|++++|+..|+++.+  | +   ...+..+..+|...|++++|...|++..+... .|. ...+
T Consensus        13 ~~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~   92 (261)
T 3qky_A           13 SSPQEAFERAMEFYNQGKYDRAIEYFKAVFTYGRTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAE   92 (261)
T ss_dssp             SSHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGCSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             CCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHH
Confidence            3445555566677777777777777777654  2 2   45566666777777777777777777776421 112 2345


Q ss_pred             HHHHHHhcC--------CCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHH
Q 011249          350 IGVLTACSH--------GGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALL  421 (490)
Q Consensus       350 ~~l~~~~~~--------~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~  421 (490)
                      ..+..++..        .|++++|...|+++.+.  .|.+......+.......++               ....+..+.
T Consensus        93 ~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~p~~~~~~~a~~~~~~~~~~---------------~~~~~~~la  155 (261)
T 3qky_A           93 YERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDR--YPNHELVDDATQKIRELRAK---------------LARKQYEAA  155 (261)
T ss_dssp             HHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHH--CTTCTTHHHHHHHHHHHHHH---------------HHHHHHHHH
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHH--CcCchhHHHHHHHHHHHHHH---------------HHHHHHHHH
Confidence            555666665        67777777777777663  22222222221111100000               011245677


Q ss_pred             HHHhhhCChHHHHHHHHHHHhcCCCCC---chHHHHHHHHHhc----------CCcchHHHHHHHhhhccc
Q 011249          422 GACKVHVNAELGEIAARHLLELGPEKT---GNSALLANIYASM----------GKWKDSEIVKMMISETEK  479 (490)
Q Consensus       422 ~~~~~~g~~~~a~~~~~~~~~~~p~~~---~~~~~l~~~~~~~----------g~~~~A~~~~~~~~~~~~  479 (490)
                      ..+...|++++|+..|+++++..|+++   .++..++.+|...          |++++|...++++.+..+
T Consensus       156 ~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~~~~~~~~~~~A~~~~~~~~~~~p  226 (261)
T 3qky_A          156 RLYERRELYEAAAVTYEAVFDAYPDTPWADDALVGAMRAYIAYAEQSVRARQPERYRRAVELYERLLQIFP  226 (261)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHTSCGGGHHHHHHHHHHHHHHHHHHCT
T ss_pred             HHHHHccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhcccchhhcccchHHHHHHHHHHHHHHCC
Confidence            889999999999999999999999854   5888999999877          889999999999987543

>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=99.27  E-value=1.7e-10  Score=102.31  Aligned_cols=162  Identities=13%  Similarity=0.006  Sum_probs=91.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccC-------C----ChhHHHHHHHHHHhcCChHHHHHHHHHHHHc------CCCC
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKN-------K----DVISYSSMITAFADHGKSQEALDMFLKMRNE------GIEP  344 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~-------~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~------~~~p  344 (490)
                      ++..+..+|...|++++|...|++..+       +    ...++..+...+...|++++|...++++.+.      +-.|
T Consensus        87 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  166 (283)
T 3edt_B           87 TLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDP  166 (283)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCH
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCH
Confidence            344444444445555554444444322       1    1345566666777777777777777776653      1133


Q ss_pred             c-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHc------CCCC-CchHHHHHHHHHhhcCC------hHHHHHHHHhcc-
Q 011249          345 N-QVTFIGVLTACSHGGLVEDGCKQFELMTRVF------GIKP-LTEHLTCMVDLLGRSGQ------LEKAHSLIMDYK-  409 (490)
Q Consensus       345 ~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~------~~~~-~~~~~~~l~~~~~~~g~------~~~A~~~~~~~~-  409 (490)
                      + ..++..+...+...|++++|...++++.+..      ...+ ....+..+...+...+.      +.++...++... 
T Consensus       167 ~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (283)
T 3edt_B          167 NVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKV  246 (283)
T ss_dssp             HHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCC
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCC
Confidence            2 3466777777778888888888887776531      1122 23333333333333332      344444444444 


Q ss_pred             CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhc
Q 011249          410 DFC-DAGTWGALLGACKVHVNAELGEIAARHLLEL  443 (490)
Q Consensus       410 ~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  443 (490)
                      ..| ...++..+...+...|++++|...++++++.
T Consensus       247 ~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  281 (283)
T 3edt_B          247 DSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASRN  281 (283)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            222 3457788889999999999999999998875

>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=99.25  E-value=1.2e-10  Score=90.33  Aligned_cols=126  Identities=15%  Similarity=0.093  Sum_probs=74.5

Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhC
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHV  428 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g  428 (490)
                      .+...+...|++++|..+++++.+.  .+.+...+..++..+...|++++|..+++++.  .+.+...+..+...+...|
T Consensus         6 ~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~   83 (136)
T 2fo7_A            6 NLGNAYYKQGDYDEAIEYYQKALEL--DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQG   83 (136)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHcCcHHHHHHHHHHHHHc--CCcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHhc
Confidence            3344444445555555555555442  12233444445555555555555555555443  2334455566666667777


Q ss_pred             ChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          429 NAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       429 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      ++++|.+.++++.+..|.++..+..++.++.+.|++++|.+.++++.+.+
T Consensus        84 ~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~  133 (136)
T 2fo7_A           84 DYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD  133 (136)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHHccC
Confidence            77777777777777777777777777777777777777777777666543

>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=99.23  E-value=6e-11  Score=118.83  Aligned_cols=168  Identities=10%  Similarity=-0.093  Sum_probs=108.7

Q ss_pred             HhcCChHHHHHHHhccc--------C---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcC
Q 011249          291 SKCGYLDLAWREFSRIK--------N---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSH  358 (490)
Q Consensus       291 ~~~~~~~~A~~~~~~~~--------~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~  358 (490)
                      ...|++++|++.+++..        +   .+...+..+..++...|++++|+..|+++.+.  .| +...+..+..++..
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDFSESVELPLMEVRALLDLGDVAKATRKLDDLAER--VGWRWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CCTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--HCCCHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHhcc--CcchHHHHHHHHHHHHH
Confidence            55667777777776655        2   34556666666777777777777777777663  33 44566666666777


Q ss_pred             CCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHH
Q 011249          359 GGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIA  436 (490)
Q Consensus       359 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~  436 (490)
                      .|++++|...|+++.+.  .+.+...+..+..+|.+.|++++ ++.|++..  .+.+...|..+..++...|++++|++.
T Consensus       480 ~g~~~~A~~~~~~al~l--~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~  556 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDT--FPGELAPKLALAATAELAGNTDE-HKFYQTVWSTNDGVISAAFGLARARSAEGDRVGAVRT  556 (681)
T ss_dssp             HTCHHHHHHHHHHHHHH--STTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhCCchHHHHHHHHHHHHHcCCHHHHHHH
Confidence            77777777777777662  33345666667777777777777 77776655  344556667777777777777777777


Q ss_pred             HHHHHhcCCCCCchHHHHHHHHHhcCC
Q 011249          437 ARHLLELGPEKTGNSALLANIYASMGK  463 (490)
Q Consensus       437 ~~~~~~~~p~~~~~~~~l~~~~~~~g~  463 (490)
                      |+++++.+|+++.++..++.++...|+
T Consensus       557 ~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          557 LDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             HHhhcccCcccHHHHHHHHHHHHccCC
Confidence            777777777777777777777655444

>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=99.21  E-value=2.8e-11  Score=96.15  Aligned_cols=126  Identities=12%  Similarity=-0.020  Sum_probs=104.9

Q ss_pred             HHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCC
Q 011249          352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVN  429 (490)
Q Consensus       352 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~  429 (490)
                      |...+...|++++|+..++....  ..+.+...+..+...|.+.|++++|++.|++..  .+.++.+|..+..++...|+
T Consensus         3 LG~~~~~~~~~e~ai~~~~~a~~--~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A            3 LGSMRRSKADVERYIASVQGSTP--SPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQERDPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             ----CCCHHHHHHHHHHHHHHSC--SHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHcChHHHHHHHHHHhcc--cCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCc
Confidence            45567778899999999988865  222235566678999999999999999999877  55678899999999999999


Q ss_pred             hHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHH-HHHhhhccc
Q 011249          430 AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIV-KMMISETEK  479 (490)
Q Consensus       430 ~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~-~~~~~~~~~  479 (490)
                      +++|+..|+++++++|+++.++..++.+|.+.|++++|.+. +++..+..+
T Consensus        81 ~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~l~P  131 (150)
T 4ga2_A           81 TDKAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAKLFP  131 (150)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHHHST
T ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHHhCc
Confidence            99999999999999999999999999999999999987765 588776544

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.19  E-value=4.9e-10  Score=99.66  Aligned_cols=175  Identities=9%  Similarity=-0.109  Sum_probs=140.1

Q ss_pred             HHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHH
Q 011249          297 DLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRV  375 (490)
Q Consensus       297 ~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  375 (490)
                      +.....+......+...+..+...+...|++++|...|+++.+.  .| +...+..+...+...|++++|...++++...
T Consensus       103 ~~l~~~l~~~lp~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~  180 (287)
T 3qou_A          103 EAIRALLDXVLPREEELXAQQAMQLMQESNYTDALPLLXDAWQL--SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ  180 (287)
T ss_dssp             HHHHHHHHHHSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG
T ss_pred             HHHHHHHHHHcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh
Confidence            34444555555455667777888889999999999999999885  45 4567888888999999999999999988763


Q ss_pred             cCCCCCchHHH-HHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC--Cch
Q 011249          376 FGIKPLTEHLT-CMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK--TGN  450 (490)
Q Consensus       376 ~~~~~~~~~~~-~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~--~~~  450 (490)
                         .|+..... .....+...++.++|...+++..  .+.+...+..+...+...|++++|+..++++++.+|++  ..+
T Consensus       181 ---~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a  257 (287)
T 3qou_A          181 ---DQDTRYQGLVAQIELLXQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQT  257 (287)
T ss_dssp             ---GCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHH
T ss_pred             ---hcchHHHHHHHHHHHHhhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchH
Confidence               34433322 23334667788888998888776  55677899999999999999999999999999999988  889


Q ss_pred             HHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          451 SALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       451 ~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      +..++.++...|+.++|...+++...
T Consensus       258 ~~~l~~~~~~~g~~~~a~~~~r~al~  283 (287)
T 3qou_A          258 RXTFQEILAALGTGDALASXYRRQLY  283 (287)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence            99999999999999999999987653

>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=99.19  E-value=1.7e-09  Score=91.36  Aligned_cols=172  Identities=8%  Similarity=-0.080  Sum_probs=125.7

Q ss_pred             HHHHHhcccC-CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCC----ChHHHHHHHHHHH
Q 011249          299 AWREFSRIKN-KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGG----LVEDGCKQFELMT  373 (490)
Q Consensus       299 A~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g----~~~~a~~~~~~~~  373 (490)
                      |.+.|++..+ .++..+..+...|...+++++|...|++..+.|   +...+..+...|.. +    +.++|..+|++..
T Consensus         5 A~~~~~~aa~~g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~   80 (212)
T 3rjv_A            5 PGSQYQQQAEAGDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAV   80 (212)
T ss_dssp             TTHHHHHHHHTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHH
Confidence            3444444433 466677777777777788888888888887754   45566666666766 5    7888888888886


Q ss_pred             HHcCCCCCchHHHHHHHHHhh----cCChHHHHHHHHhccCCCC----hhhHHHHHHHHhh----hCChHHHHHHHHHHH
Q 011249          374 RVFGIKPLTEHLTCMVDLLGR----SGQLEKAHSLIMDYKDFCD----AGTWGALLGACKV----HVNAELGEIAARHLL  441 (490)
Q Consensus       374 ~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~----~~~~~~l~~~~~~----~g~~~~a~~~~~~~~  441 (490)
                      +.    .++..+..|..+|..    .+++++|.++|++.....+    +..+..|...|..    .+++++|++.|+++.
T Consensus        81 ~~----g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~  156 (212)
T 3rjv_A           81 EA----GSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSS  156 (212)
T ss_dssp             HT----TCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHH
T ss_pred             HC----CCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence            62    355666777777776    7788888888887763333    6777788888877    778889999999888


Q ss_pred             hcCCCCCchHHHHHHHHHhc-C-----CcchHHHHHHHhhhccc
Q 011249          442 ELGPEKTGNSALLANIYASM-G-----KWKDSEIVKMMISETEK  479 (490)
Q Consensus       442 ~~~p~~~~~~~~l~~~~~~~-g-----~~~~A~~~~~~~~~~~~  479 (490)
                      +. |.++..+..|+.+|... |     ++++|.+.+++..+.|.
T Consensus       157 ~~-~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~g~  199 (212)
T 3rjv_A          157 SL-SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVSCLEGF  199 (212)
T ss_dssp             HT-SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHHHHHTC
T ss_pred             Hc-CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHcCC
Confidence            87 66677888888888754 3     78888888888877764

>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=99.17  E-value=1.1e-09  Score=84.74  Aligned_cols=131  Identities=15%  Similarity=0.141  Sum_probs=103.1

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHH
Q 011249          313 SYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLL  392 (490)
Q Consensus       313 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  392 (490)
                      .|..++..+...|++++|..+++++.+.. +.+...+..+...+...|++++|..+++++...  .+.+...+..++..+
T Consensus         3 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~   79 (136)
T 2fo7_A            3 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL--DPRSAEAWYNLGNAY   79 (136)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHH--CCCchHHHHHHHHHH
Confidence            46667777888888888888888887753 235567777777788888888888888888773  344566777888888


Q ss_pred             hhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          393 GRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       393 ~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      ...|++++|.+.++++.  .+.+...+..++..+...|++++|...++++.+.+|+
T Consensus        80 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~  135 (136)
T 2fo7_A           80 YKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR  135 (136)
T ss_dssp             HTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHSTT
T ss_pred             HHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHHccCCC
Confidence            88899999988887766  3445677888888889999999999999999888876

>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=99.13  E-value=1.2e-09  Score=98.30  Aligned_cols=219  Identities=12%  Similarity=-0.003  Sum_probs=145.2

Q ss_pred             cCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHH
Q 011249          223 NGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWRE  302 (490)
Q Consensus       223 ~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~  302 (490)
                      .|++++|.+++++..+... ..   +      +...++++.|...|..+               +..|...|++++|...
T Consensus         4 ~~~~~eA~~~~~~a~k~~~-~~---~------~~~~~~~~~A~~~~~~a---------------~~~~~~~g~~~~A~~~   58 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEKYLK-TS---F------MKWKPDYDSAASEYAKA---------------AVAFKNAKQLEQAKDA   58 (307)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-CC---S------SSCSCCHHHHHHHHHHH---------------HHHHHHTTCHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHcc-cc---c------cCCCCCHHHHHHHHHHH---------------HHHHHHcCCHHHHHHH
Confidence            4677788888877765311 11   0      11146677777666654               3456667777777777


Q ss_pred             HhcccC-----CC----hhHHHHHHHHHHhcCChHHHHHHHHHHHHcC---CCCc--HHHHHHHHHHhcCCCChHHHHHH
Q 011249          303 FSRIKN-----KD----VISYSSMITAFADHGKSQEALDMFLKMRNEG---IEPN--QVTFIGVLTACSHGGLVEDGCKQ  368 (490)
Q Consensus       303 ~~~~~~-----~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~p~--~~~~~~l~~~~~~~g~~~~a~~~  368 (490)
                      |.+..+     .+    ..+|+.+...|...|++++|+..|++..+.-   -.|.  ..++..+...|.. |++++|+..
T Consensus        59 ~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~  137 (307)
T 2ifu_A           59 YLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHL  137 (307)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHH
Confidence            766543     11    3467778888888888988888888876521   1222  2467777888888 999999999


Q ss_pred             HHHHHHHcCCCCC----chHHHHHHHHHhhcCChHHHHHHHHhcc-C---CCC----hhhHHHHHHHHhhhCChHHHHHH
Q 011249          369 FELMTRVFGIKPL----TEHLTCMVDLLGRSGQLEKAHSLIMDYK-D---FCD----AGTWGALLGACKVHVNAELGEIA  436 (490)
Q Consensus       369 ~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~---~~~----~~~~~~l~~~~~~~g~~~~a~~~  436 (490)
                      +++..+...-..+    ..++..+..+|.+.|++++|+..|++.. .   .+.    ...+..++.++...|++++|...
T Consensus       138 ~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~  217 (307)
T 2ifu_A          138 YQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKC  217 (307)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            9888763211111    4567788889999999999999988766 1   111    22556666677778999999999


Q ss_pred             HHHHHhcCCCCCch-----HHHHHHHHHhcCCcchHHH
Q 011249          437 ARHLLELGPEKTGN-----SALLANIYASMGKWKDSEI  469 (490)
Q Consensus       437 ~~~~~~~~p~~~~~-----~~~l~~~~~~~g~~~~A~~  469 (490)
                      |++++ ..|.....     ...++.++ ..|+.+.+.+
T Consensus       218 ~~~al-~~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~  253 (307)
T 2ifu_A          218 VRESY-SIPGFSGSEDCAALEDLLQAY-DEQDEEQLLR  253 (307)
T ss_dssp             HHHHT-TSTTSTTSHHHHHHHHHHHHH-HTTCHHHHHH
T ss_pred             HHHHh-CCCCCCCCHHHHHHHHHHHHH-HhcCHHHHHH
Confidence            99999 88875543     33445444 4566555554

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=99.13  E-value=5.5e-10  Score=85.55  Aligned_cols=114  Identities=9%  Similarity=-0.065  Sum_probs=84.0

Q ss_pred             CCCcH-HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHH
Q 011249          342 IEPNQ-VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWG  418 (490)
Q Consensus       342 ~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~  418 (490)
                      +.|+. ..+......|.+.|++++|+..|++..+.  .+.+...|..+..+|.+.|++++|+..+++..  .+.+...|.
T Consensus         8 inP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~   85 (126)
T 4gco_A            8 INPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKR--DPENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYI   85 (126)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHH
Confidence            44543 35666777777788888888888877762  34456677777778888888888888877665  445667777


Q ss_pred             HHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHH
Q 011249          419 ALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANI  457 (490)
Q Consensus       419 ~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  457 (490)
                      .+..++...|++++|++.|+++++++|+++.++..|+.+
T Consensus        86 ~lg~~~~~~~~~~~A~~~~~~al~l~P~~~~a~~~l~~~  124 (126)
T 4gco_A           86 RKAACLVAMREWSKAQRAYEDALQVDPSNEEAREGVRNC  124 (126)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCcCCHHHHHHHHHh
Confidence            888888888888888888888888888888777777654

>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=99.13  E-value=5.9e-10  Score=109.72  Aligned_cols=159  Identities=9%  Similarity=-0.036  Sum_probs=125.0

Q ss_pred             cCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHH
Q 011249          293 CGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQ  368 (490)
Q Consensus       293 ~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~  368 (490)
                      .|++++|.+.|++..+   .+...|..+...+...|++++|...+++..+.  .| +...+..+...+...|++++|.+.
T Consensus         2 ~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLAL--HPGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             -------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTT--STTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            4788999999998876   35778999999999999999999999999984  44 466888899999999999999999


Q ss_pred             HHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhh---CChHHHHHHHHHHHhc
Q 011249          369 FELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVH---VNAELGEIAARHLLEL  443 (490)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~---g~~~~a~~~~~~~~~~  443 (490)
                      +++..+.  .+.+...+..+..+|.+.|++++|.+.+++..  .+.+...+..+...+...   |++++|.+.++++++.
T Consensus        80 ~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A           80 LQQASDA--APEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             HHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             HHHHHhc--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence            9999884  34557788899999999999999999998876  445677888999999999   9999999999999999


Q ss_pred             CCCCCchHHHHH
Q 011249          444 GPEKTGNSALLA  455 (490)
Q Consensus       444 ~p~~~~~~~~l~  455 (490)
                      +|.+...+..++
T Consensus       158 ~p~~~~~~~~l~  169 (568)
T 2vsy_A          158 GVGAVEPFAFLS  169 (568)
T ss_dssp             TCCCSCHHHHTT
T ss_pred             CCcccChHHHhC
Confidence            999988887776

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=99.12  E-value=2.2e-10  Score=90.50  Aligned_cols=98  Identities=8%  Similarity=0.010  Sum_probs=80.7

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ...+..+...+.+.|++++|...|++..  .+.++..|..+..++...|++++|+..|+++++++|+++.++..++.+|.
T Consensus        36 ~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~lg~~~~  115 (151)
T 3gyz_A           36 MDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQL  115 (151)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHHHHHHHH
Confidence            4566677778888888888888887776  45567788888888888888888888888888888888888888888888


Q ss_pred             hcCCcchHHHHHHHhhhccc
Q 011249          460 SMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       460 ~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +.|++++|...|++..+...
T Consensus       116 ~lg~~~eA~~~~~~al~l~~  135 (151)
T 3gyz_A          116 RLKAPLKAKECFELVIQHSN  135 (151)
T ss_dssp             HTTCHHHHHHHHHHHHHHCC
T ss_pred             HcCCHHHHHHHHHHHHHhCC
Confidence            88888888888888877543

>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=99.12  E-value=5.5e-10  Score=91.46  Aligned_cols=155  Identities=8%  Similarity=-0.041  Sum_probs=92.9

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHH-Hhh
Q 011249          317 MITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDL-LGR  394 (490)
Q Consensus       317 l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~  394 (490)
                      +...+...|++++|...|++..+.  .| +...+..+...+...|++++|...++++...   .|++..+..+... +..
T Consensus        12 ~a~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~---~p~~~~~~~~~~~~~~~   86 (176)
T 2r5s_A           12 QVSELLQQGEHAQALNVIQTLSDE--LQSRGDVKLAKADCLLETKQFELAQELLATIPLE---YQDNSYKSLIAKLELHQ   86 (176)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTSCHH--HHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGG---GCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhc---cCChHHHHHHHHHHHHh
Confidence            333444455555555555544432  22 2234444444555555555555555554432   1122221111111 111


Q ss_pred             cCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC--CchHHHHHHHHHhcCCcchHHHH
Q 011249          395 SGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK--TGNSALLANIYASMGKWKDSEIV  470 (490)
Q Consensus       395 ~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~--~~~~~~l~~~~~~~g~~~~A~~~  470 (490)
                      .+...+|...+++..  .+.+...+..+..++...|++++|+..|+++++.+|+.  +.++..++.++...|+.++|...
T Consensus        87 ~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~  166 (176)
T 2r5s_A           87 QAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASK  166 (176)
T ss_dssp             HHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHH
T ss_pred             hcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHH
Confidence            122234566665554  34467788888888999999999999999999999875  55889999999999999999999


Q ss_pred             HHHhhh
Q 011249          471 KMMISE  476 (490)
Q Consensus       471 ~~~~~~  476 (490)
                      +++...
T Consensus       167 y~~al~  172 (176)
T 2r5s_A          167 YRRQLY  172 (176)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            987654

>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=99.11  E-value=3.3e-09  Score=106.25  Aligned_cols=168  Identities=8%  Similarity=-0.063  Sum_probs=123.6

Q ss_pred             hccCChHHHHHHHHHHH--------hcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhc
Q 011249          256 TQLGDVEMAAILAKHVD--------EGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADH  324 (490)
Q Consensus       256 ~~~g~~~~a~~~~~~~~--------~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~  324 (490)
                      ...|++++|...++++.        +.. +.+...+..+..++...|++++|+..|+++.+   .+...|..+..++...
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVDF-SESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------CC-TTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhccccccccc-ccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHc
Confidence            67788888888888877        433 55667777788888888888888888887765   3667788888888888


Q ss_pred             CChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHH
Q 011249          325 GKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHS  403 (490)
Q Consensus       325 ~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  403 (490)
                      |++++|+..|+++.+.  .| +...+..+..++...|++++ ...|+++.+.  .+.+...+..+..++.+.|++++|.+
T Consensus       481 g~~~~A~~~~~~al~l--~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~--~P~~~~a~~~lg~~~~~~g~~~~A~~  555 (681)
T 2pzi_A          481 GDYDSATKHFTEVLDT--FPGELAPKLALAATAELAGNTDE-HKFYQTVWST--NDGVISAAFGLARARSAEGDRVGAVR  555 (681)
T ss_dssp             TCHHHHHHHHHHHHHH--STTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHh--CCchHHHHHHHHHHHHHcCCHHHHHH
Confidence            8888888888888874  44 34577777788888888888 8888888773  34456677788888888888888888


Q ss_pred             HHHhcc-CCC-ChhhHHHHHHHHhhhCC
Q 011249          404 LIMDYK-DFC-DAGTWGALLGACKVHVN  429 (490)
Q Consensus       404 ~~~~~~-~~~-~~~~~~~l~~~~~~~g~  429 (490)
                      .|++.. ..| +...+..+..++...++
T Consensus       556 ~~~~al~l~P~~~~a~~~~~~~~~~~~~  583 (681)
T 2pzi_A          556 TLDEVPPTSRHFTTARLTSAVTLLSGRS  583 (681)
T ss_dssp             HHHTSCTTSTTHHHHHHHHHHHTC----
T ss_pred             HHHhhcccCcccHHHHHHHHHHHHccCC
Confidence            888876 334 34566667766655444

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.09  E-value=1.1e-09  Score=92.29  Aligned_cols=160  Identities=9%  Similarity=-0.040  Sum_probs=119.9

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccC--C-ChhHHHH----------------HHHHHHhcCChHHHHHHHHHHHHcCC
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKN--K-DVISYSS----------------MITAFADHGKSQEALDMFLKMRNEGI  342 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~----------------l~~~~~~~~~~~~a~~~~~~~~~~~~  342 (490)
                      ........+...|++++|+..|++..+  | ++..|..                +..+|...|++++|+..|++.++.  
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--   83 (208)
T 3urz_A            6 EMLQKVSAAIEAGQNGQAVSYFRQTIALNIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQK--   83 (208)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--
Confidence            344456677889999999999998876  3 3456666                888899999999999999999885  


Q ss_pred             CC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCC--hHHHHHHHHhccCCCCh--hhH
Q 011249          343 EP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ--LEKAHSLIMDYKDFCDA--GTW  417 (490)
Q Consensus       343 ~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~--~~~A~~~~~~~~~~~~~--~~~  417 (490)
                      .| +...+..+..++...|++++|...|+++.+.  .|.+...+..+..+|...|+  .+.+...++... .|++  ..+
T Consensus        84 ~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~a~  160 (208)
T 3urz_A           84 APNNVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLTAEQEKKKLETDYKKLS-SPTKMQYAR  160 (208)
T ss_dssp             CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC----CCCHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh-CCCchhHHH
Confidence            45 5568888888899999999999999999873  44557778888888766554  445566666665 3333  234


Q ss_pred             HHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          418 GALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       418 ~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      .....++...|++++|+..|++++++.|+
T Consensus       161 ~~~g~~~~~~~~~~~A~~~~~~al~l~P~  189 (208)
T 3urz_A          161 YRDGLSKLFTTRYEKARNSLQKVILRFPS  189 (208)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHHHHTTTSCC
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHhCCC
Confidence            44556677788999999999999999997

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=99.08  E-value=1.7e-09  Score=91.11  Aligned_cols=123  Identities=7%  Similarity=-0.104  Sum_probs=51.9

Q ss_pred             HHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCC
Q 011249          352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVN  429 (490)
Q Consensus       352 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~  429 (490)
                      +..++...|++++|...+++..+.  .|.+...+..+..++...|++++|+..|++..  .+.+...+..+..++...|+
T Consensus        60 lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~~~  137 (208)
T 3urz_A           60 LALAYKKNRNYDKAYLFYKELLQK--APNNVDCLEACAEMQVCRGQEKDALRMYEKILQLEADNLAANIFLGNYYYLTAE  137 (208)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhH
Confidence            444445555555555555555442  22234444445555555555555555554443  22334444444444433322


Q ss_pred             --hHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          430 --AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       430 --~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                        .+.+...++++....|. ...+..++.++...|++++|+..+++..+.
T Consensus       138 ~~~~~~~~~~~~~~~~~~~-~~a~~~~g~~~~~~~~~~~A~~~~~~al~l  186 (208)
T 3urz_A          138 QEKKKLETDYKKLSSPTKM-QYARYRDGLSKLFTTRYEKARNSLQKVILR  186 (208)
T ss_dssp             HHHHHHHHHHC---CCCHH-HHHHHHHHHHHHHHHTHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHhCCCch-hHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence              22333333333221111 112333444444455555555555544443

>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=99.07  E-value=2.6e-09  Score=105.12  Aligned_cols=148  Identities=7%  Similarity=-0.053  Sum_probs=107.6

Q ss_pred             cCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHH
Q 011249          258 LGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMF  334 (490)
Q Consensus       258 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~  334 (490)
                      .|++++|...++++.+.. +.+...+..+...|...|++++|.+.|++..+   .+...+..+..+|...|++++|...+
T Consensus         2 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~   80 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRVRWTQQRHAEAAVLL   80 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTSTTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            478889999999887765 55677888889999999999999999988776   35678888899999999999999999


Q ss_pred             HHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhc---CChHHHHHHHHhcc
Q 011249          335 LKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRS---GQLEKAHSLIMDYK  409 (490)
Q Consensus       335 ~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~---g~~~~A~~~~~~~~  409 (490)
                      ++..+.. +.+...+..+..++...|++++|.+.+++..+.  .+.+...+..+..++...   |++++|.+.+++..
T Consensus        81 ~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al  155 (568)
T 2vsy_A           81 QQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL--LPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAV  155 (568)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHH
T ss_pred             HHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHH
Confidence            9988852 234568888888899999999999999998873  344567788888899988   99999999998776

>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=99.06  E-value=1.7e-09  Score=97.34  Aligned_cols=197  Identities=11%  Similarity=-0.000  Sum_probs=150.4

Q ss_pred             ccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHH
Q 011249          257 QLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLK  336 (490)
Q Consensus       257 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~  336 (490)
                      ..|++++|..++++..+... ..         .+...++++.|...|.+           .+..|...|++++|...|.+
T Consensus         3 ~~~~~~eA~~~~~~a~k~~~-~~---------~~~~~~~~~~A~~~~~~-----------a~~~~~~~g~~~~A~~~~~~   61 (307)
T 2ifu_A            3 AAQKISEAHEHIAKAEKYLK-TS---------FMKWKPDYDSAASEYAK-----------AAVAFKNAKQLEQAKDAYLQ   61 (307)
T ss_dssp             CHHHHHHHHHHHHHHHHHHC-CC---------SSSCSCCHHHHHHHHHH-----------HHHHHHHTTCHHHHHHHHHH
T ss_pred             ccchHHHHHHHHHHHHHHcc-cc---------ccCCCCCHHHHHHHHHH-----------HHHHHHHcCCHHHHHHHHHH
Confidence            35778899999988876531 11         01114788888887765           35678889999999999998


Q ss_pred             HHHcC--C-CC-c-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCC--C--CchHHHHHHHHHhhcCChHHHHHHHHh
Q 011249          337 MRNEG--I-EP-N-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIK--P--LTEHLTCMVDLLGRSGQLEKAHSLIMD  407 (490)
Q Consensus       337 ~~~~~--~-~p-~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~--~--~~~~~~~l~~~~~~~g~~~~A~~~~~~  407 (490)
                      ..+..  . .+ . ..+|..+...|...|++++|...+++..+.+.-.  +  ...++..+..+|.. |++++|++.|++
T Consensus        62 al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg~~~~~-g~~~~A~~~~~~  140 (307)
T 2ifu_A           62 EAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAGKLMEP-LDLSKAVHLYQQ  140 (307)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHTT-TCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHc-CCHHHHHHHHHH
Confidence            87631  1 11 1 3478888899999999999999999987642111  1  14567788899988 999999999987


Q ss_pred             cc-CCC-------ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC------chHHHHHHHHHhcCCcchHHHHHHH
Q 011249          408 YK-DFC-------DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT------GNSALLANIYASMGKWKDSEIVKMM  473 (490)
Q Consensus       408 ~~-~~~-------~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~------~~~~~l~~~~~~~g~~~~A~~~~~~  473 (490)
                      .. ..+       ...++..+...+...|++++|++.|+++++..|.+.      ..+..++.++...|++++|...+++
T Consensus       141 Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g~~~~~~g~~~~A~~~~~~  220 (307)
T 2ifu_A          141 AAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQVLVQLHRADYVAAQKCVRE  220 (307)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            76 111       145788889999999999999999999999876543      3677788888899999999999999


Q ss_pred             hh
Q 011249          474 IS  475 (490)
Q Consensus       474 ~~  475 (490)
                      ..
T Consensus       221 al  222 (307)
T 2ifu_A          221 SY  222 (307)
T ss_dssp             HT
T ss_pred             Hh
Confidence            87

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.05  E-value=2.4e-07  Score=82.00  Aligned_cols=231  Identities=6%  Similarity=-0.045  Sum_probs=153.1

Q ss_pred             HhcCC-hHHHHHHHHHHHHcCcccChhhHHHHHHHHhccC--ChHHHHHHHHHHHhcCCCCchhHHHHHHHHH----Hhc
Q 011249          221 VQNGY-AKAAIEMYKVMRQENVRISEVAMVGAISACTQLG--DVEMAAILAKHVDEGCCDRTNYVSNALIHMH----SKC  293 (490)
Q Consensus       221 ~~~g~-~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~----~~~  293 (490)
                      .+.|. .++|+++++.+...+.. +...++.-..++...|  +++++..+++.+.... |.+..+|+.-..++    ...
T Consensus        43 ~~~~e~s~~aL~~t~~~L~~nP~-~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n-Pk~y~aW~~R~~iL~~~~~~l  120 (306)
T 3dra_A           43 MKAEEYSERALHITELGINELAS-HYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN-EKNYQIWNYRQLIIGQIMELN  120 (306)
T ss_dssp             HHTTCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC-TTCCHHHHHHHHHHHHHHHHT
T ss_pred             HHcCCCCHHHHHHHHHHHHHCcH-HHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC-cccHHHHHHHHHHHHHHHHhc
Confidence            34444 46888888888876422 4455666666677777  8888888888888776 45555555443333    344


Q ss_pred             ---CChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChH--HHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCC----
Q 011249          294 ---GYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQ--EALDMFLKMRNEGIEPNQVTFIGVLTACSHGGL----  361 (490)
Q Consensus       294 ---~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~--~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~----  361 (490)
                         +++++++.+++++.+   ++..+|+.-.-++.+.|.++  ++++.++++++.. .-|...|+.-...+...+.    
T Consensus       121 ~~~~~~~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d-~~N~sAW~~R~~ll~~l~~~~~~  199 (306)
T 3dra_A          121 NNDFDPYREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTD-LKNNSAWSHRFFLLFSKKHLATD  199 (306)
T ss_dssp             TTCCCTHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHSSGGGCCH
T ss_pred             cccCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccchh
Confidence               677888888877765   45666766666667777777  8888888888753 2245556555555555555    


Q ss_pred             --hHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHH-HHHHHHhccC-----CCChhhHHHHHHHHhhhCChHHH
Q 011249          362 --VEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEK-AHSLIMDYKD-----FCDAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       362 --~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~-A~~~~~~~~~-----~~~~~~~~~l~~~~~~~g~~~~a  433 (490)
                        ++++++.++++..  ..+-+...|+.+...+.+.|+..+ +..+..++..     ..++..+..++..+.+.|+.++|
T Consensus       200 ~~~~eEl~~~~~aI~--~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A  277 (306)
T 3dra_A          200 NTIDEELNYVKDKIV--KCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNES  277 (306)
T ss_dssp             HHHHHHHHHHHHHHH--HCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHH
T ss_pred             hhHHHHHHHHHHHHH--hCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHH
Confidence              7777777777776  345567777777777777776444 4455565541     33556777777777777888888


Q ss_pred             HHHHHHHHh-cCCCCCchHHHHHH
Q 011249          434 EIAARHLLE-LGPEKTGNSALLAN  456 (490)
Q Consensus       434 ~~~~~~~~~-~~p~~~~~~~~l~~  456 (490)
                      +++++.+.+ .+|.....+...+.
T Consensus       278 ~~~~~~l~~~~Dpir~~yW~~~~~  301 (306)
T 3dra_A          278 RTVYDLLKSKYNPIRSNFWDYQIS  301 (306)
T ss_dssp             HHHHHHHHHTTCGGGHHHHHHHHH
T ss_pred             HHHHHHHHhccChHHHHHHHHHHh
Confidence            888888775 67776666665543

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=99.05  E-value=8.4e-09  Score=88.10  Aligned_cols=186  Identities=13%  Similarity=0.008  Sum_probs=134.2

Q ss_pred             ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCC--chhHHHHHHHHHHhcCChHHHHHHHhcccC--CCh----hHHH
Q 011249          244 SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDR--TNYVSNALIHMHSKCGYLDLAWREFSRIKN--KDV----ISYS  315 (490)
Q Consensus       244 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~----~~~~  315 (490)
                      +...+..+...+...|++++|...|+.+.+.....  ....+..++.+|.+.|++++|+..|+++.+  |+.    ..+.
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~P~~~~~~~a~~   82 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVMY   82 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCcHHHHHH
Confidence            44566677788999999999999999998865221  235677789999999999999999999875  332    2455


Q ss_pred             HHHHHHHh------------------cCChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCCChHHHHHHHHHHHHHc
Q 011249          316 SMITAFAD------------------HGKSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGGLVEDGCKQFELMTRVF  376 (490)
Q Consensus       316 ~l~~~~~~------------------~~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  376 (490)
                      .+..++..                  .|++++|...|+++++.  .|+.. .......          ...+...+..  
T Consensus        83 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~--~P~~~~a~~a~~~----------l~~~~~~~~~--  148 (225)
T 2yhc_A           83 MRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG--YPNSQYTTDATKR----------LVFLKDRLAK--  148 (225)
T ss_dssp             HHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTT--CTTCTTHHHHHHH----------HHHHHHHHHH--
T ss_pred             HHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH--CcCChhHHHHHHH----------HHHHHHHHHH--
Confidence            55656554                  57899999999999984  45432 2211111          0011111111  


Q ss_pred             CCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCC-h---hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCch
Q 011249          377 GIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD-A---GTWGALLGACKVHVNAELGEIAARHLLELGPEKTGN  450 (490)
Q Consensus       377 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~-~---~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~  450 (490)
                             ....+...|.+.|++++|+..|+++. ..|+ +   ..+..+..++.+.|++++|++.++++....|++...
T Consensus       149 -------~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~~~~~~  220 (225)
T 2yhc_A          149 -------YEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNTLEH  220 (225)
T ss_dssp             -------HHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCSCCCCC
T ss_pred             -------HHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCCCchhh
Confidence                   22356788899999999999998877 3343 2   467888899999999999999999999998887653

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=99.05  E-value=1.6e-09  Score=83.00  Aligned_cols=102  Identities=10%  Similarity=0.004  Sum_probs=91.7

Q ss_pred             CCCC-chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHH
Q 011249          378 IKPL-TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALL  454 (490)
Q Consensus       378 ~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l  454 (490)
                      +.|+ ...+......|.+.|++++|++.|++..  .+.+...|..+..++...|++++|+..++++++++|+++.+|..+
T Consensus         8 inP~~a~~~~~~G~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~l   87 (126)
T 4gco_A            8 INPELAQEEKNKGNEYFKKGDYPTAMRHYNEAVKRDPENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIRK   87 (126)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHHH
Confidence            3444 4567778899999999999999998876  556788999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCcchHHHHHHHhhhccc
Q 011249          455 ANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       455 ~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +.++...|++++|++.+++..+..+
T Consensus        88 g~~~~~~~~~~~A~~~~~~al~l~P  112 (126)
T 4gco_A           88 AACLVAMREWSKAQRAYEDALQVDP  112 (126)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHCc
Confidence            9999999999999999999987654

>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=99.03  E-value=4.8e-10  Score=88.67  Aligned_cols=101  Identities=11%  Similarity=-0.092  Sum_probs=53.8

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHh
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACK  425 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~  425 (490)
                      .+..+...+...|++++|...|+++...  .+.+...+..+..+|...|++++|+..|++..  .+.++..+..+..++.
T Consensus        23 ~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~  100 (148)
T 2vgx_A           23 QLYSLAFNQYQSGXYEDAHXVFQALCVL--DHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAECLL  100 (148)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHHc--CcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHH
Confidence            4444455555555566665555555542  23344455555555555555555555555544  2334445555555555


Q ss_pred             hhCChHHHHHHHHHHHhcCCCCCch
Q 011249          426 VHVNAELGEIAARHLLELGPEKTGN  450 (490)
Q Consensus       426 ~~g~~~~a~~~~~~~~~~~p~~~~~  450 (490)
                      ..|++++|++.|+++++..|+++..
T Consensus       101 ~~g~~~~A~~~~~~al~~~p~~~~~  125 (148)
T 2vgx_A          101 QXGELAEAESGLFLAQELIANXPEF  125 (148)
T ss_dssp             HTTCHHHHHHHHHHHHHHHTTCGGG
T ss_pred             HcCCHHHHHHHHHHHHHHCcCCCcc
Confidence            5555555555555555555555443

>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=99.03  E-value=4.8e-09  Score=88.74  Aligned_cols=132  Identities=13%  Similarity=-0.040  Sum_probs=109.0

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHH
Q 011249          311 VISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVD  390 (490)
Q Consensus       311 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  390 (490)
                      ...+..+...+...|++++|...|++..    .|+...+..+...+...|++++|...+++..+.  .+.+...+..+..
T Consensus         6 ~~~~~~~g~~~~~~~~~~~A~~~~~~a~----~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~~~~~~~~~~lg~   79 (213)
T 1hh8_A            6 AISLWNEGVLAADKKDWKGALDAFSAVQ----DPHSRICFNIGCMYTILKNMTEAEKAFTRSINR--DKHLAVAYFQRGM   79 (213)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHTSS----SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHc----CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CccchHHHHHHHH
Confidence            3455667778889999999999998773    567888888999999999999999999999873  3556778888999


Q ss_pred             HHhhcCChHHHHHHHHhcc--CCCCh----------------hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC
Q 011249          391 LLGRSGQLEKAHSLIMDYK--DFCDA----------------GTWGALLGACKVHVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~~~--~~~~~----------------~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      +|...|++++|.+.|++..  .+.+.                ..+..+..++...|++++|.+.++++++..|++.
T Consensus        80 ~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~  155 (213)
T 1hh8_A           80 LYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEPR  155 (213)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSGG
T ss_pred             HHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCcccc
Confidence            9999999999999998776  22222                6778888889999999999999999999998863

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=99.02  E-value=7.5e-08  Score=85.22  Aligned_cols=215  Identities=12%  Similarity=-0.003  Sum_probs=171.3

Q ss_pred             cCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcC--ChHHHHHHHhcccC---CChhHHHHHHHHH----Hhc---C
Q 011249          258 LGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCG--YLDLAWREFSRIKN---KDVISYSSMITAF----ADH---G  325 (490)
Q Consensus       258 ~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~--~~~~A~~~~~~~~~---~~~~~~~~l~~~~----~~~---~  325 (490)
                      ....++|..+++.++..+ |.+..+++.-..++...|  +++++++.++.+..   .+..+|+.-...+    ...   +
T Consensus        46 ~e~s~~aL~~t~~~L~~n-P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~  124 (306)
T 3dra_A           46 EEYSERALHITELGINEL-ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDF  124 (306)
T ss_dssp             TCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCC
T ss_pred             CCCCHHHHHHHHHHHHHC-cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccC
Confidence            344568999999999887 666777888788888888  99999999999876   3556666655554    455   7


Q ss_pred             ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChH--HHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCC------
Q 011249          326 KSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVE--DGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ------  397 (490)
Q Consensus       326 ~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~--~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~------  397 (490)
                      ++++++.+++++.+.. +-+...|..-...+.+.|.++  ++++.++++.+.  .+-+...|+.-...+.+.|+      
T Consensus       125 ~~~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~--d~~N~sAW~~R~~ll~~l~~~~~~~~  201 (306)
T 3dra_A          125 DPYREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDT--DLKNNSAWSHRFFLLFSKKHLATDNT  201 (306)
T ss_dssp             CTHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHSSGGGCCHHH
T ss_pred             CHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHhccccchhhh
Confidence            8999999999999852 335567776666667778887  999999999984  45567777777777777776      


Q ss_pred             hHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCCh-HHHHHHHHHHHhcC---CCCCchHHHHHHHHHhcCCcchHHHHH
Q 011249          398 LEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNA-ELGEIAARHLLELG---PEKTGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       398 ~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~-~~a~~~~~~~~~~~---p~~~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      ++++++.++++.  .+.|...|+.+...+...|.. +....+.+++.+.+   |.++.++..++.+|.+.|+.++|.+++
T Consensus       202 ~~eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~  281 (306)
T 3dra_A          202 IDEELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVY  281 (306)
T ss_dssp             HHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Confidence            889999998776  566888999888888888874 44667888888776   888999999999999999999999999


Q ss_pred             HHhhh
Q 011249          472 MMISE  476 (490)
Q Consensus       472 ~~~~~  476 (490)
                      +.+.+
T Consensus       282 ~~l~~  286 (306)
T 3dra_A          282 DLLKS  286 (306)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            99875

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=99.02  E-value=2.3e-08  Score=89.23  Aligned_cols=165  Identities=8%  Similarity=-0.106  Sum_probs=122.0

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc-H----HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC----c
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN-Q----VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL----T  382 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~-~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~  382 (490)
                      ..+...+..+...|++++|...+++..+...... .    ..+..+...+...|++++|...+++..+......+    .
T Consensus        76 ~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~  155 (293)
T 2qfc_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNL  155 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHHH
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHHH
Confidence            3445566778889999999999988887432211 1    12344556677889999999999988753111112    3


Q ss_pred             hHHHHHHHHHhhcCChHHHHHHHHhcc----CCCC-----hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC------C
Q 011249          383 EHLTCMVDLLGRSGQLEKAHSLIMDYK----DFCD-----AGTWGALLGACKVHVNAELGEIAARHLLELGPE------K  447 (490)
Q Consensus       383 ~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~-----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~------~  447 (490)
                      .+++.+...|...|++++|...|++..    ..|+     ..++..+...|...|++++|+..++++++..++      -
T Consensus       156 ~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~~  235 (293)
T 2qfc_A          156 YIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSSH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHHH
Confidence            477888999999999999999997765    1222     257888889999999999999999999875432      1


Q ss_pred             CchHHHHHHHHHhcCCcchH-HHHHHHhhh
Q 011249          448 TGNSALLANIYASMGKWKDS-EIVKMMISE  476 (490)
Q Consensus       448 ~~~~~~l~~~~~~~g~~~~A-~~~~~~~~~  476 (490)
                      ..+|..++.+|.+.|++++| ...+++...
T Consensus       236 ~~~~~~lg~~y~~~g~~~~Ai~~~~~~Al~  265 (293)
T 2qfc_A          236 GQLYYQRGECLRKLEYEEAEIEDAYKKASF  265 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence            56788999999999999999 777776653

>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=99.01  E-value=2.3e-08  Score=89.28  Aligned_cols=162  Identities=9%  Similarity=-0.112  Sum_probs=123.2

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcC-CCCcHH----HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC----chHHH
Q 011249          316 SMITAFADHGKSQEALDMFLKMRNEG-IEPNQV----TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL----TEHLT  386 (490)
Q Consensus       316 ~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~~----~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~  386 (490)
                      ..+..+...|++++|..++++..+.. ..|+..    .+..+...+...|++++|...++++.......++    ..+++
T Consensus        80 ~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~  159 (293)
T 3u3w_A           80 DQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIEN  159 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHH
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHH
Confidence            34667888999999999999988732 223322    3334666778888999999999999873122222    22688


Q ss_pred             HHHHHHhhcCChHHHHHHHHhcc-----C-C--C-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC------CchH
Q 011249          387 CMVDLLGRSGQLEKAHSLIMDYK-----D-F--C-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEK------TGNS  451 (490)
Q Consensus       387 ~l~~~~~~~g~~~~A~~~~~~~~-----~-~--~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~------~~~~  451 (490)
                      .+..+|...|++++|...|+++.     . .  + ...++..+...|...|++++|++.++++++..+..      +.+|
T Consensus       160 ~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~  239 (293)
T 3u3w_A          160 AIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLY  239 (293)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHH
Confidence            89999999999999999998766     1 1  1 12377888899999999999999999999865332      5689


Q ss_pred             HHHHHHHHhcCC-cchHHHHHHHhhhc
Q 011249          452 ALLANIYASMGK-WKDSEIVKMMISET  477 (490)
Q Consensus       452 ~~l~~~~~~~g~-~~~A~~~~~~~~~~  477 (490)
                      ..++.+|.+.|+ +++|.+.+++....
T Consensus       240 ~~lg~~~~~~g~~~~~A~~~~~~Al~i  266 (293)
T 3u3w_A          240 YQRGECLRKLEYEEAEIEDAYKKASFF  266 (293)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCcHHHHHHHHHHHHHH
Confidence            999999999995 59999999887643

>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=99.01  E-value=8.9e-09  Score=84.14  Aligned_cols=151  Identities=11%  Similarity=0.015  Sum_probs=63.8

Q ss_pred             HHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHH-HhccCC
Q 011249          185 MIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISA-CTQLGD  260 (490)
Q Consensus       185 l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~-~~~~g~  260 (490)
                      ....+...|++++|+..|++..+   .+...+..+..++...|++++|+..+++.....  |+......+... +...++
T Consensus        12 ~a~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~~~~~~~~~~~   89 (176)
T 2r5s_A           12 QVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEY--QDNSYKSLIAKLELHQQAA   89 (176)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTSCHHHHTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGG--CCHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhcc--CChHHHHHHHHHHHHhhcc
Confidence            33444444444444444444443   233444444444445555555555444443321  122111111101 011111


Q ss_pred             hHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--CC---hhHHHHHHHHHHhcCChHHHHHHHH
Q 011249          261 VEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KD---VISYSSMITAFADHGKSQEALDMFL  335 (490)
Q Consensus       261 ~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~---~~~~~~l~~~~~~~~~~~~a~~~~~  335 (490)
                      ...+...+++..+.. |.+...+..+..++...|++++|...|+++.+  |+   ...+..+..++...|+.++|...|+
T Consensus        90 ~~~a~~~~~~al~~~-P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A~~~y~  168 (176)
T 2r5s_A           90 ESPELKRLEQELAAN-PDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYR  168 (176)
T ss_dssp             SCHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHHHHHHH
T ss_pred             cchHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcHHHHHH
Confidence            222344444444433 33344444455555555555555555554433  11   2244455555555555555555555


Q ss_pred             HHH
Q 011249          336 KMR  338 (490)
Q Consensus       336 ~~~  338 (490)
                      +..
T Consensus       169 ~al  171 (176)
T 2r5s_A          169 RQL  171 (176)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=99.00  E-value=2.4e-08  Score=88.65  Aligned_cols=161  Identities=10%  Similarity=-0.049  Sum_probs=102.0

Q ss_pred             ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--CChhHHHHH-HHH
Q 011249          244 SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--KDVISYSSM-ITA  320 (490)
Q Consensus       244 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~l-~~~  320 (490)
                      +...+..+...+...|++++|...++++.+.. |.+...+..+..++...|++++|...++++..  |+....... ...
T Consensus       116 ~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~~~  194 (287)
T 3qou_A          116 EEELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRYQGLVAQIE  194 (287)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHHHHHHHHHH
T ss_pred             chhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHHHHHHHHHH
Confidence            34555666666777777777777777777665 55666677777777777777777777777765  433322222 223


Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChH
Q 011249          321 FADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLE  399 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  399 (490)
                      +...++.+.|...+++..+.  .| +...+..+...+...|++++|...+.++.+...-..+...+..++..+...|+.+
T Consensus       195 l~~~~~~~~a~~~l~~al~~--~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~  272 (287)
T 3qou_A          195 LLXQAADTPEIQQLQQQVAE--NPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTGD  272 (287)
T ss_dssp             HHHHHTSCHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTTC
T ss_pred             HHhhcccCccHHHHHHHHhc--CCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCCC
Confidence            55566667777777777664  33 4456666677777777777777777777664111112455666666666667666


Q ss_pred             HHHHHHHh
Q 011249          400 KAHSLIMD  407 (490)
Q Consensus       400 ~A~~~~~~  407 (490)
                      +|...|++
T Consensus       273 ~a~~~~r~  280 (287)
T 3qou_A          273 ALASXYRR  280 (287)
T ss_dssp             HHHHHHHH
T ss_pred             cHHHHHHH
Confidence            66666654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.99  E-value=9.9e-08  Score=91.29  Aligned_cols=77  Identities=14%  Similarity=0.018  Sum_probs=36.0

Q ss_pred             ChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHH
Q 011249          361 LVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHL  440 (490)
Q Consensus       361 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  440 (490)
                      +.+.|..+|+...+.+  +.++..+...++...+.|+.+.|..+|+.+.  .....|...+..-...|+.+.+..+++++
T Consensus       335 d~~~ar~ife~al~~~--~~~~~~~~~yid~e~~~~~~~~aR~l~er~~--k~~~lw~~~~~fE~~~G~~~~~r~v~~~~  410 (493)
T 2uy1_A          335 SRATPYNIFSSGLLKH--PDSTLLKEEFFLFLLRIGDEENARALFKRLE--KTSRMWDSMIEYEFMVGSMELFRELVDQK  410 (493)
T ss_dssp             CSHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHSC--CBHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH--HHHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            3555555555555432  1122333334444445555555555555542  23344444444444445555555555554


Q ss_pred             H
Q 011249          441 L  441 (490)
Q Consensus       441 ~  441 (490)
                      .
T Consensus       411 ~  411 (493)
T 2uy1_A          411 M  411 (493)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=98.97  E-value=7.8e-09  Score=83.40  Aligned_cols=127  Identities=5%  Similarity=-0.159  Sum_probs=97.0

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHh
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACK  425 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~  425 (490)
                      .+..+...+...|++++|...+++..+.  .+.+...+..+..++...|++++|.+.+++..  .+.+...+..+..++.
T Consensus        15 ~~~~~a~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~   92 (166)
T 1a17_A           15 ELKTQANDYFKAKDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNM   92 (166)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            4555666677777888888888777763  34456677777788888888888888887665  3446677888888888


Q ss_pred             hhCChHHHHHHHHHHHhcCCCCCchHHHHHHH--HHhcCCcchHHHHHHHhhh
Q 011249          426 VHVNAELGEIAARHLLELGPEKTGNSALLANI--YASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       426 ~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~--~~~~g~~~~A~~~~~~~~~  476 (490)
                      ..|++++|...++++.+..|.++..+..+..+  +...|++++|++.+++...
T Consensus        93 ~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           93 ALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            99999999999999999999888877554444  7788999999998887654

>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=98.97  E-value=1.7e-09  Score=95.75  Aligned_cols=189  Identities=9%  Similarity=-0.072  Sum_probs=98.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccC--C-ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhc
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKN--K-DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACS  357 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~  357 (490)
                      .+..+...+...|++++|+..|++..+  | +...|..+..+|...|++++|...+++..+.  .| +...+..+..++.
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~   83 (281)
T 2c2l_A            6 ELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALEL--DGQSVKAHFFLGQCQL   83 (281)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--CTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHH
Confidence            344444445555555555555554432  2 3445555555555566666666666655542  33 3345555555566


Q ss_pred             CCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHH
Q 011249          358 HGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAA  437 (490)
Q Consensus       358 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  437 (490)
                      ..|++++|...++++.+...  .+...+...+....+..+...... ......+.+......+. .+ ..|+.++|++.+
T Consensus        84 ~~g~~~~A~~~~~~al~l~p--~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~~~l~-~l-~~~~~~~A~~~~  158 (281)
T 2c2l_A           84 EMESYDEAIANLQRAYSLAK--EQRLNFGDDIPSALRIAKKKRWNS-IEERRIHQESELHSYLT-RL-IAAERERELEEC  158 (281)
T ss_dssp             HTTCHHHHHHHHHHHHHHHH--HTTCCCCSHHHHHHHHHHHHHHHH-HHHTCCCCCCHHHHHHH-HH-HHHHHHHHHTTT
T ss_pred             HcCCHHHHHHHHHHHHHhCc--cchhhHHHHHHHHHHHHHHHHHHH-HHHHHHhhhHHHHHHHH-HH-HHHHHHHHHHHH
Confidence            66666666666665554210  000011111111111111111111 11112233333333332 22 368888888888


Q ss_pred             HHHHhcCCCCCchHHHHHHHHHhc-CCcchHHHHHHHhhhc
Q 011249          438 RHLLELGPEKTGNSALLANIYASM-GKWKDSEIVKMMISET  477 (490)
Q Consensus       438 ~~~~~~~p~~~~~~~~l~~~~~~~-g~~~~A~~~~~~~~~~  477 (490)
                      +++.+.+|++......+...+.+. +++++|.++|+++.+.
T Consensus       159 ~~al~~~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          159 QRNHEGHEDDGHIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             SGGGTTTSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             HhhhccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            888888888777777777777666 6788888888877654

>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=98.97  E-value=1.7e-08  Score=85.15  Aligned_cols=158  Identities=11%  Similarity=-0.031  Sum_probs=78.9

Q ss_pred             CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccC----ChHHHHHHHHHHHhcCCCCchhHH
Q 011249          208 PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLG----DVEMAAILAKHVDEGCCDRTNYVS  283 (490)
Q Consensus       208 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g----~~~~a~~~~~~~~~~~~~~~~~~~  283 (490)
                      .++..+..+...|...+++++|+++|++..+.|   +...+..+...+.. +    ++++|..+|++..+.+   ++..+
T Consensus        16 g~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~~~A~~~g---~~~a~   88 (212)
T 3rjv_A           16 GDRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLAEKAVEAG---SKSGE   88 (212)
T ss_dssp             TCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHCC---CHHHH
Confidence            344445555555555555555555555555433   33344444444444 3    5555555555554433   33344


Q ss_pred             HHHHHHHHh----cCChHHHHHHHhcccCCC-----hhHHHHHHHHHHh----cCChHHHHHHHHHHHHcCCCCcHHHHH
Q 011249          284 NALIHMHSK----CGYLDLAWREFSRIKNKD-----VISYSSMITAFAD----HGKSQEALDMFLKMRNEGIEPNQVTFI  350 (490)
Q Consensus       284 ~~l~~~~~~----~~~~~~A~~~~~~~~~~~-----~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~  350 (490)
                      ..|..+|..    .+++++|+.+|++..+.+     +..+..|...|..    .+++++|...|++..+.  ..+...+.
T Consensus        89 ~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~--~~~~~a~~  166 (212)
T 3rjv_A           89 IVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSSSL--SRTGYAEY  166 (212)
T ss_dssp             HHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHT--SCTTHHHH
T ss_pred             HHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHc--CCCHHHHH
Confidence            444555544    455555555555555421     3455555555555    55566666666666553  12223344


Q ss_pred             HHHHHhcCC------CChHHHHHHHHHHHH
Q 011249          351 GVLTACSHG------GLVEDGCKQFELMTR  374 (490)
Q Consensus       351 ~l~~~~~~~------g~~~~a~~~~~~~~~  374 (490)
                      .+...|...      .+.++|...|++..+
T Consensus       167 ~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~  196 (212)
T 3rjv_A          167 WAGMMFQQGEKGFIEPNKQKALHWLNVSCL  196 (212)
T ss_dssp             HHHHHHHHCBTTTBCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCCCCHHHHHHHHHHHHH
Confidence            444444321      256666666666655

>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=98.97  E-value=2.3e-09  Score=87.75  Aligned_cols=128  Identities=9%  Similarity=0.046  Sum_probs=82.3

Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHH-HhhcCCh-
Q 011249          321 FADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDL-LGRSGQL-  398 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~g~~-  398 (490)
                      +...|++++|...+++..+.. +.+...+..+...|...|++++|...++++.+.  .+.+...+..+..+ +...|++ 
T Consensus        20 ~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~la~~l~~~~~~~~   96 (177)
T 2e2e_A           20 FASQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQL--RGENAELYAALATVLYYQASQHM   96 (177)
T ss_dssp             CC-----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HCSCHHHHHHHHHHHHHHTTTCC
T ss_pred             hhhccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHhcCCcc
Confidence            344567777777777776642 234556777777777777777777777777663  23345566666666 6677776 


Q ss_pred             -HHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchH
Q 011249          399 -EKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       399 -~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                       ++|...+++..  .+.+...+..+...+...|++++|...++++++..|+++...
T Consensus        97 ~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~  152 (177)
T 2e2e_A           97 TAQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDLNSPRINRT  152 (177)
T ss_dssp             CHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTSCHH
T ss_pred             hHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCCCccHH
Confidence             77777776665  334456666777777777777777777777777777765533

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.97  E-value=1.1e-08  Score=78.71  Aligned_cols=118  Identities=9%  Similarity=-0.077  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHH
Q 011249          346 QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGA  423 (490)
Q Consensus       346 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~  423 (490)
                      ...+..+...+...|++++|...++++...  .+.+...+..+..++...|++++|.+.+++..  .+.+...+..+...
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~   89 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIEL--NPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLA   89 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHHH
Confidence            346666777777888888888888888773  34456677788888888888888888887766  34457788888889


Q ss_pred             HhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcc
Q 011249          424 CKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWK  465 (490)
Q Consensus       424 ~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~  465 (490)
                      +...|++++|...++++.+..|+++..+..++.++.+.|+++
T Consensus        90 ~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~  131 (131)
T 2vyi_A           90 LSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLREAP  131 (131)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhcCC
Confidence            999999999999999999999999999999999999888764

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.96  E-value=1.1e-08  Score=79.06  Aligned_cols=117  Identities=6%  Similarity=-0.087  Sum_probs=87.5

Q ss_pred             cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHH
Q 011249          345 NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLG  422 (490)
Q Consensus       345 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~  422 (490)
                      +...+..+...+...|++++|...+++..+  ..+.+...+..+..++...|++++|.+.+++..  .+.+...+..+..
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~--~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~   92 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIK--RNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRKAA   92 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHT--TCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--cCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCchHHHHHHHH
Confidence            344666666677777777777777777765  233456666777777777777777777776665  3445677888888


Q ss_pred             HHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCC
Q 011249          423 ACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGK  463 (490)
Q Consensus       423 ~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  463 (490)
                      ++...|++++|.+.++++.+..|.++..+..++.++...|+
T Consensus        93 ~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~  133 (133)
T 2lni_A           93 ALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQYN  133 (133)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHHHHHTC
T ss_pred             HHHHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhcC
Confidence            88888999999999999999999888888888888877664

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.94  E-value=1.4e-08  Score=77.26  Aligned_cols=115  Identities=15%  Similarity=0.105  Sum_probs=89.9

Q ss_pred             HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHH
Q 011249          346 QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGA  423 (490)
Q Consensus       346 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~  423 (490)
                      ...+..+...+...|++++|...++++.+.  .+.+...+..++..+...|++++|..+++++.  .+.+..++..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALEL--DPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHH--CcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHH
Confidence            346666777777788888888888887763  33456667777888888888888888887765  34566778888888


Q ss_pred             HhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcC
Q 011249          424 CKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMG  462 (490)
Q Consensus       424 ~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  462 (490)
                      +...|++++|...++++.+..|+++..+..++.++.+.|
T Consensus        87 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g  125 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQKQG  125 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHC
T ss_pred             HHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcc
Confidence            999999999999999999999999988888888876654

>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=98.93  E-value=3.9e-08  Score=83.01  Aligned_cols=147  Identities=10%  Similarity=-0.046  Sum_probs=119.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCC
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGL  361 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~  361 (490)
                      .+..+...+...|++++|...|++...++...|..+...+...|++++|+..+++..+.. +.+...+..+..++...|+
T Consensus         8 ~~~~~g~~~~~~~~~~~A~~~~~~a~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg~~~~~~~~   86 (213)
T 1hh8_A            8 SLWNEGVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEK   86 (213)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHccc
Confidence            455678888999999999999999998899999999999999999999999999999853 3356788889999999999


Q ss_pred             hHHHHHHHHHHHHHcCCCCCc----------------hHHHHHHHHHhhcCChHHHHHHHHhcc-CCCChhhHHHHHHHH
Q 011249          362 VEDGCKQFELMTRVFGIKPLT----------------EHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAGTWGALLGAC  424 (490)
Q Consensus       362 ~~~a~~~~~~~~~~~~~~~~~----------------~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~~~~~l~~~~  424 (490)
                      +++|...++++.+.  .+.+.                ..+..+..+|...|++++|.+.|++.. ..|+.          
T Consensus        87 ~~~A~~~~~~al~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~----------  154 (213)
T 1hh8_A           87 YDLAIKDLKEALIQ--LRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP----------  154 (213)
T ss_dssp             HHHHHHHHHHHHHT--TTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG----------
T ss_pred             HHHHHHHHHHHHHh--CCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCccc----------
Confidence            99999999999883  33333                678889999999999999999998876 34443          


Q ss_pred             hhhCChHHHHHHHHHHHh
Q 011249          425 KVHVNAELGEIAARHLLE  442 (490)
Q Consensus       425 ~~~g~~~~a~~~~~~~~~  442 (490)
                       ..+..+.+...+.+...
T Consensus       155 -~~~~~~~a~~~~~~~~~  171 (213)
T 1hh8_A          155 -RHSKIDKAMECVWKQKL  171 (213)
T ss_dssp             -GGGHHHHHHHHHHTTCC
T ss_pred             -ccchHHHHHHHHHhccc
Confidence             22445556655554433

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.92  E-value=2.7e-09  Score=83.76  Aligned_cols=99  Identities=10%  Similarity=-0.092  Sum_probs=46.0

Q ss_pred             HHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhh
Q 011249          350 IGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVH  427 (490)
Q Consensus       350 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~  427 (490)
                      ..+...+...|++++|...|+++...  .+.+...+..+..+|.+.|++++|+..|++..  .+.++..+..+..++...
T Consensus        22 ~~~a~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~   99 (142)
T 2xcb_A           22 YALGFNQYQAGKWDDAQKIFQALCML--DHYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECHLQL   99 (142)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHccHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHc
Confidence            33344444555555555555555441  22234444444445555555555555554443  223334444444444555


Q ss_pred             CChHHHHHHHHHHHhcCCCCCch
Q 011249          428 VNAELGEIAARHLLELGPEKTGN  450 (490)
Q Consensus       428 g~~~~a~~~~~~~~~~~p~~~~~  450 (490)
                      |++++|.+.|+++++..|+++..
T Consensus       100 g~~~~A~~~~~~al~~~p~~~~~  122 (142)
T 2xcb_A          100 GDLDGAESGFYSARALAAAQPAH  122 (142)
T ss_dssp             TCHHHHHHHHHHHHHHHHTCGGG
T ss_pred             CCHHHHHHHHHHHHHhCCCCcch
Confidence            55555555555555544444443

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.92  E-value=1.2e-08  Score=75.93  Aligned_cols=100  Identities=14%  Similarity=-0.016  Sum_probs=87.8

Q ss_pred             CchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC--CCchHHHHHH
Q 011249          381 LTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPE--KTGNSALLAN  456 (490)
Q Consensus       381 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~--~~~~~~~l~~  456 (490)
                      +...+..+...+...|++++|...+++..  .+.+...+..+...+...|++++|.+.++++++..|.  ++.++..++.
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~   84 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKAD   84 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHH
Confidence            45667778888999999999999998776  4456778888999999999999999999999999999  9999999999


Q ss_pred             HHHhc-CCcchHHHHHHHhhhcccc
Q 011249          457 IYASM-GKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       457 ~~~~~-g~~~~A~~~~~~~~~~~~~  480 (490)
                      ++... |++++|.+.++++.+....
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~~p~  109 (112)
T 2kck_A           85 ALRYIEGKEVEAEIAEARAKLEHHH  109 (112)
T ss_dssp             HHTTCSSCSHHHHHHHHHHGGGCCC
T ss_pred             HHHHHhCCHHHHHHHHHHHhhcccC
Confidence            99999 9999999999999876653

>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=98.91  E-value=5.1e-09  Score=82.73  Aligned_cols=99  Identities=15%  Similarity=0.035  Sum_probs=85.4

Q ss_pred             CchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHH
Q 011249          381 LTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY  458 (490)
Q Consensus       381 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  458 (490)
                      +...+..+...+...|++++|...|++..  .+.+...|..+..++...|++++|+..|+++++.+|+++.++..++.+|
T Consensus        20 ~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~   99 (148)
T 2vgx_A           20 TLEQLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMDIXEPRFPFHAAECL   99 (148)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHH
Confidence            45566778888899999999999998876  4557778888888999999999999999999999999999999999999


Q ss_pred             HhcCCcchHHHHHHHhhhccc
Q 011249          459 ASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       459 ~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ...|++++|.+.+++..+...
T Consensus       100 ~~~g~~~~A~~~~~~al~~~p  120 (148)
T 2vgx_A          100 LQXGELAEAESGLFLAQELIA  120 (148)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHT
T ss_pred             HHcCCHHHHHHHHHHHHHHCc
Confidence            999999999999998877654

>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=98.90  E-value=1.5e-09  Score=90.72  Aligned_cols=96  Identities=8%  Similarity=-0.088  Sum_probs=75.1

Q ss_pred             hHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHh
Q 011249          383 EHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYAS  460 (490)
Q Consensus       383 ~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~  460 (490)
                      ..+..+..+|...|++++|+..+++..  .+.+...+..+..++...|++++|++.|+++++..|+++.++..++.++..
T Consensus        89 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~  168 (198)
T 2fbn_A           89 SCNLNLATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNK  168 (198)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence            567778888899999999999998776  455677888999999999999999999999999999999999999999999


Q ss_pred             cCCcchHH-HHHHHhhhcc
Q 011249          461 MGKWKDSE-IVKMMISETE  478 (490)
Q Consensus       461 ~g~~~~A~-~~~~~~~~~~  478 (490)
                      .|+.+++. ..++.|...+
T Consensus       169 ~~~~~~~~~~~~~~~f~~~  187 (198)
T 2fbn_A          169 LKEARKKDKLTFGGMFDKG  187 (198)
T ss_dssp             HHHHHC-------------
T ss_pred             HHHHHHHHHHHHHHHhccc
Confidence            99888887 5566665443

>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=98.89  E-value=1e-08  Score=93.34  Aligned_cols=94  Identities=11%  Similarity=-0.056  Sum_probs=81.7

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ...+..+..+|.+.|++++|+..+++..  .+.+...+..+..++...|++++|+..|+++++++|+++.++..++.++.
T Consensus       196 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~  275 (336)
T 1p5q_A          196 LASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQ  275 (336)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence            3577888889999999999999998876  45577889999999999999999999999999999999999999999999


Q ss_pred             hcCCcchH-HHHHHHhh
Q 011249          460 SMGKWKDS-EIVKMMIS  475 (490)
Q Consensus       460 ~~g~~~~A-~~~~~~~~  475 (490)
                      +.|++++| ..++++|.
T Consensus       276 ~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          276 RIRRQLAREKKLYANMF  292 (336)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            99999998 44555553

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=98.88  E-value=3.1e-06  Score=80.90  Aligned_cols=123  Identities=7%  Similarity=-0.202  Sum_probs=83.7

Q ss_pred             HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcC-ChHHHHHHHHhcc--CCCChhhHHHHHHH
Q 011249          347 VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSG-QLEKAHSLIMDYK--DFCDAGTWGALLGA  423 (490)
Q Consensus       347 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~--~~~~~~~~~~l~~~  423 (490)
                      ..|...+....+.+..+.|..+|+++ ..  .+.+...|...+..-...| +.+.|..+|+...  .+.++..|...+..
T Consensus       287 ~lw~~y~~~~~r~~~~~~AR~i~~~A-~~--~~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~~~~~~~~yid~  363 (493)
T 2uy1_A          287 LLRINHLNYVLKKRGLELFRKLFIEL-GN--EGVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPDSTLLKEEFFLF  363 (493)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHHH-TT--SCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHh-hC--CCCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            35556666665667788899999888 31  1234444543333333334 6889999997765  22334556667776


Q ss_pred             HhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          424 CKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       424 ~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      ....|+.+.|..+|+++    +.+...+...+..-...|+.+.+..+++++.+
T Consensus       364 e~~~~~~~~aR~l~er~----~k~~~lw~~~~~fE~~~G~~~~~r~v~~~~~~  412 (493)
T 2uy1_A          364 LLRIGDEENARALFKRL----EKTSRMWDSMIEYEFMVGSMELFRELVDQKMD  412 (493)
T ss_dssp             HHHHTCHHHHHHHHHHS----CCBHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHH----HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            77889999999999987    33566777777777778998888888877764

>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=98.87  E-value=1e-08  Score=78.55  Aligned_cols=93  Identities=8%  Similarity=-0.104  Sum_probs=51.2

Q ss_pred             HHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcC
Q 011249          385 LTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMG  462 (490)
Q Consensus       385 ~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g  462 (490)
                      +..+...+.+.|++++|+..|++..  .+.+...|..+..++...|++++|+..++++++.+|+++.++..++.++...|
T Consensus         7 ~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~   86 (126)
T 3upv_A            7 ARLEGKEYFTKSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVK   86 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHh
Confidence            3444455555555555555555443  23344555555555555555555555555555555555555555555555555


Q ss_pred             CcchHHHHHHHhhhc
Q 011249          463 KWKDSEIVKMMISET  477 (490)
Q Consensus       463 ~~~~A~~~~~~~~~~  477 (490)
                      ++++|...+++..+.
T Consensus        87 ~~~~A~~~~~~al~~  101 (126)
T 3upv_A           87 EYASALETLDAARTK  101 (126)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHh
Confidence            555555555555443

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.87  E-value=7.9e-09  Score=78.41  Aligned_cols=97  Identities=14%  Similarity=-0.033  Sum_probs=84.9

Q ss_pred             hHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHh
Q 011249          383 EHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYAS  460 (490)
Q Consensus       383 ~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~  460 (490)
                      ..+..+...+.+.|++++|+..|++..  .+.+...|..+..++...|++++|+..++++++.+|+++.++..++.++..
T Consensus        18 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~   97 (121)
T 1hxi_A           18 ENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTN   97 (121)
T ss_dssp             SCHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            345567788899999999999998877  455778899999999999999999999999999999999999999999999


Q ss_pred             cCCcchHHHHHHHhhhccc
Q 011249          461 MGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       461 ~g~~~~A~~~~~~~~~~~~  479 (490)
                      .|++++|+..+++..+..+
T Consensus        98 ~g~~~~A~~~~~~al~~~P  116 (121)
T 1hxi_A           98 EHNANAALASLRAWLLSQP  116 (121)
T ss_dssp             HHHHHHHHHHHHHHHC---
T ss_pred             cCCHHHHHHHHHHHHHhCc
Confidence            9999999999999876544

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.87  E-value=1.7e-08  Score=79.66  Aligned_cols=104  Identities=7%  Similarity=-0.096  Sum_probs=80.6

Q ss_pred             CCcH-HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHH
Q 011249          343 EPNQ-VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGA  419 (490)
Q Consensus       343 ~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~  419 (490)
                      .|+. ..+..+...+...|++++|...|+++...  .|.++..|..+..+|...|++++|++.|++..  .+.++..|..
T Consensus        32 ~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l~P~~~~~~~~  109 (151)
T 3gyz_A           32 PDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIY--DFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFALGKNDYTPVFH  109 (151)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSSSCCHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCCCCcHHHHH
Confidence            4433 36666777778888888888888888773  44557777788888888888888888887776  4556778888


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCC
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      +..++...|++++|+..|+++++..|+++
T Consensus       110 lg~~~~~lg~~~eA~~~~~~al~l~~~~~  138 (151)
T 3gyz_A          110 TGQCQLRLKAPLKAKECFELVIQHSNDEK  138 (151)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHCCCHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCCHH
Confidence            88888888999999999999988888754

>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=98.85  E-value=3e-07  Score=81.98  Aligned_cols=203  Identities=9%  Similarity=-0.086  Sum_probs=136.5

Q ss_pred             HHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhH---HHHHHHHHHhcCChHHHHHHHhcccC
Q 011249          232 MYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYV---SNALIHMHSKCGYLDLAWREFSRIKN  308 (490)
Q Consensus       232 ~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~---~~~l~~~~~~~~~~~~A~~~~~~~~~  308 (490)
                      .+.++......|+..+...+...+.-.-+         .+.......+...   +...+..+...|++++|...+++..+
T Consensus        33 ~~s~~e~g~~~~~~~~l~~i~~~l~~~~~---------~~~~~~~~~~~~~~~~l~~~i~~~~~~~~y~~a~~~~~~~l~  103 (293)
T 3u3w_A           33 EVSRIESGAVYPSMDILQGIAAKLQIPII---------HFYEVLIYSDIERKKQFKDQVIMLCKQKRYKEIYNKVWNELK  103 (293)
T ss_dssp             HHHHHHTTSCCCCHHHHHHHHHHHTCCTH---------HHHHTTTSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHCCCCCCCHHHHHHHHHHhCcCHH---------HHhCCCCCCcchhHHHHHHHHHHHHHHhhHHHHHHHHHHHhc
Confidence            34444444446666666666655533211         1111111222222   22346677888999999999988765


Q ss_pred             C-----C----hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCC-Cc----HHHHHHHHHHhcCCCChHHHHHHHHHHHH
Q 011249          309 K-----D----VISYSSMITAFADHGKSQEALDMFLKMRNEGIE-PN----QVTFIGVLTACSHGGLVEDGCKQFELMTR  374 (490)
Q Consensus       309 ~-----~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~-p~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  374 (490)
                      .     +    ...+..+...+...|++++|+..++++.+.... ++    ..+++.+...|...|++++|..+++++.+
T Consensus       104 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~  183 (293)
T 3u3w_A          104 KEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILK  183 (293)
T ss_dssp             TCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             cccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            1     1    113344666777788999999999999873222 22    23688888999999999999999999885


Q ss_pred             HcC----CCC-CchHHHHHHHHHhhcCChHHHHHHHHhcc-------CCC-ChhhHHHHHHHHhhhCC-hHHHHHHHHHH
Q 011249          375 VFG----IKP-LTEHLTCMVDLLGRSGQLEKAHSLIMDYK-------DFC-DAGTWGALLGACKVHVN-AELGEIAARHL  440 (490)
Q Consensus       375 ~~~----~~~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-------~~~-~~~~~~~l~~~~~~~g~-~~~a~~~~~~~  440 (490)
                      ...    ..+ ...++..+..+|.+.|++++|.+.+++..       ..+ -...|..+..++...|+ +++|.+.++++
T Consensus       184 ~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~A  263 (293)
T 3u3w_A          184 QLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence            321    111 13467788999999999999999997765       111 25688888899999994 69999999999


Q ss_pred             Hhc
Q 011249          441 LEL  443 (490)
Q Consensus       441 ~~~  443 (490)
                      +.+
T Consensus       264 l~i  266 (293)
T 3u3w_A          264 SFF  266 (293)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            874

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.82  E-value=1.1e-07  Score=82.11  Aligned_cols=136  Identities=11%  Similarity=-0.034  Sum_probs=87.1

Q ss_pred             HHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC--chHHHHHHHHH
Q 011249          315 SSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL--TEHLTCMVDLL  392 (490)
Q Consensus       315 ~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~~l~~~~  392 (490)
                      ......+...|++++|.++|+.+...  .|+......+...+.+.+++++|+..|+.....  ..|.  ...+..+..++
T Consensus       106 LayA~~L~~~g~y~eA~~~l~~~~~~--~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~--~d~~~~~~a~~~LG~al  181 (282)
T 4f3v_A          106 MGFAACEAAQGNYADAMEALEAAPVA--GSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKW--PDKFLAGAAGVAHGVAA  181 (282)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHTSSCCT--TCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGC--SCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhc--CCchHHHHHHHHHHHHcCCHHHHHHHHHHhhcc--CCcccHHHHHHHHHHHH
Confidence            34455666677777777777766653  344434444444567777777777777755331  1111  23556677777


Q ss_pred             hhcCChHHHHHHHHhccCCC-----ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          393 GRSGQLEKAHSLIMDYKDFC-----DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       393 ~~~g~~~~A~~~~~~~~~~~-----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      .+.|++++|+..|++....|     ..........++.+.|+.++|...|+++...+|+ +.+...|.
T Consensus       182 ~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~-~~~~~aL~  248 (282)
T 4f3v_A          182 ANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE-PKVAAALK  248 (282)
T ss_dssp             HHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCC-HHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc-HHHHHHHh
Confidence            78888888888887765222     2235556666778888888888888888888887 66555554

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.82  E-value=2e-08  Score=80.96  Aligned_cols=110  Identities=13%  Similarity=-0.070  Sum_probs=94.4

Q ss_pred             cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHH
Q 011249          345 NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLG  422 (490)
Q Consensus       345 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~  422 (490)
                      +...+..+...+...|++++|+..|++..+.  .+.+...+..+..+|.+.|++++|+..|++..  .+.+...|..+..
T Consensus        10 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~   87 (164)
T 3sz7_A           10 ESDKLKSEGNAAMARKEYSKAIDLYTQALSI--APANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGL   87 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            4557888888899999999999999999883  34567888899999999999999999998876  4556788999999


Q ss_pred             HHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHH
Q 011249          423 ACKVHVNAELGEIAARHLLELGPEKTGNSALLAN  456 (490)
Q Consensus       423 ~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~  456 (490)
                      ++...|++++|++.|+++++++|+++..+...+.
T Consensus        88 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~l  121 (164)
T 3sz7_A           88 ARFDMADYKGAKEAYEKGIEAEGNGGSDAMKRGL  121 (164)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHSSSCCHHHHHHH
T ss_pred             HHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHH
Confidence            9999999999999999999999999986655543

>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=98.81  E-value=3.1e-08  Score=76.96  Aligned_cols=96  Identities=11%  Similarity=-0.056  Sum_probs=47.8

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ...+..+...+...|++++|...|++..  .+.+...+..+..++...|++++|+..++++++.+|+++.++..++.++.
T Consensus         9 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~   88 (137)
T 3q49_B            9 AQELKEQGNRLFVGRKYPEAAACYGRAITRNPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQL   88 (137)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHhhCcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHHHHHH
Confidence            3344444444555555555555554433  22234444445555555555555555555555555555555555555555


Q ss_pred             hcCCcchHHHHHHHhhhc
Q 011249          460 SMGKWKDSEIVKMMISET  477 (490)
Q Consensus       460 ~~g~~~~A~~~~~~~~~~  477 (490)
                      ..|++++|...+++..+.
T Consensus        89 ~~~~~~~A~~~~~~a~~~  106 (137)
T 3q49_B           89 EMESYDEAIANLQRAYSL  106 (137)
T ss_dssp             HTTCHHHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHHHH
Confidence            555555555555554443

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.80  E-value=2.1e-07  Score=82.89  Aligned_cols=161  Identities=9%  Similarity=-0.056  Sum_probs=109.0

Q ss_pred             HHHHHHHHHhcCChHHHHHHHhcccC--C-Ch------hHHHHHHHHHHhcCChHHHHHHHHHHHHcCC---CCc--HHH
Q 011249          283 SNALIHMHSKCGYLDLAWREFSRIKN--K-DV------ISYSSMITAFADHGKSQEALDMFLKMRNEGI---EPN--QVT  348 (490)
Q Consensus       283 ~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~~------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~---~p~--~~~  348 (490)
                      +...+..+...|++++|.+.+++..+  + ..      ..+..+...+...|++++|+..+++..+...   .+.  ..+
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            34456666777777777777765433  1 11      2234455567777888888888888775311   111  347


Q ss_pred             HHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC-----chHHHHHHHHHhhcCChHHHHHHHHhcc-CCC-------Chh
Q 011249          349 FIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL-----TEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-------DAG  415 (490)
Q Consensus       349 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-------~~~  415 (490)
                      +..+...|...|++++|...++++.+.....|+     ..++..++.+|...|++++|.+.+++.. ..+       ...
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            777888888888888888888888732111222     2477788888888899999888887665 111       155


Q ss_pred             hHHHHHHHHhhhCChHHH-HHHHHHHHhc
Q 011249          416 TWGALLGACKVHVNAELG-EIAARHLLEL  443 (490)
Q Consensus       416 ~~~~l~~~~~~~g~~~~a-~~~~~~~~~~  443 (490)
                      ++..+...+...|++++| ...++++..+
T Consensus       238 ~~~~lg~~y~~~g~~~~Ai~~~~~~Al~~  266 (293)
T 2qfc_A          238 LYYQRGECLRKLEYEEAEIEDAYKKASFF  266 (293)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence            777888888889999999 7778887763

>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=98.80  E-value=8.7e-08  Score=71.93  Aligned_cols=109  Identities=9%  Similarity=-0.073  Sum_probs=66.8

Q ss_pred             HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHH
Q 011249          347 VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGAC  424 (490)
Q Consensus       347 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~  424 (490)
                      ..+..+...+...|++++|...+++....  .+.+...+..+..++...|++++|...+++..  .+.+...+..+..++
T Consensus         5 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~   82 (118)
T 1elw_A            5 NELKEKGNKALSVGNIDDALQCYSEAIKL--DPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAAL   82 (118)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHH
Confidence            34445555556666666666666666552  23345555566666666666666666665554  233455666666667


Q ss_pred             hhhCChHHHHHHHHHHHhcCCCCCchHHHHHHH
Q 011249          425 KVHVNAELGEIAARHLLELGPEKTGNSALLANI  457 (490)
Q Consensus       425 ~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  457 (490)
                      ...|++++|.+.++++.+.+|+++..+..++.+
T Consensus        83 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~  115 (118)
T 1elw_A           83 EFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNM  115 (118)
T ss_dssp             HHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHh
Confidence            777777777777777777777766666665544

>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=98.79  E-value=2.4e-08  Score=76.51  Aligned_cols=91  Identities=10%  Similarity=-0.054  Sum_probs=43.7

Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc-------hHHHHHH
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG-------NSALLAN  456 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~-------~~~~l~~  456 (490)
                      ..+...+.+.|++++|++.|++..  .+.+...|..+..++...|++++|++.++++++++|+++.       +|..++.
T Consensus        12 ~~lG~~~~~~~~~~~A~~~y~~Al~~~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~   91 (127)
T 4gcn_A           12 KDLGNAAYKQKDFEKAHVHYDKAIELDPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMSRAGN   91 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHHHHHH
Confidence            334444445555555555554433  2233444445555555555555555555555554444332       3444444


Q ss_pred             HHHhcCCcchHHHHHHHhhh
Q 011249          457 IYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       457 ~~~~~g~~~~A~~~~~~~~~  476 (490)
                      ++...|++++|++.+++..+
T Consensus        92 ~~~~~~~~~~A~~~~~kal~  111 (127)
T 4gcn_A           92 AFQKQNDLSLAVQWFHRSLS  111 (127)
T ss_dssp             HHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHh
Confidence            45555555555555554443

>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=98.78  E-value=5.9e-08  Score=74.17  Aligned_cols=111  Identities=6%  Similarity=-0.199  Sum_probs=85.9

Q ss_pred             HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHH
Q 011249          347 VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGAC  424 (490)
Q Consensus       347 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~  424 (490)
                      ..+......+...|++++|...|++..+.  .+.+...+..+..+|.+.|++++|+..+++..  .+.+...|..+..++
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~   82 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKR--APEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHH
Confidence            45566666777788888888888888763  34456777788888888888888888887766  445677888888888


Q ss_pred             hhhCChHHHHHHHHHHHhcC------CCCCchHHHHHHHHH
Q 011249          425 KVHVNAELGEIAARHLLELG------PEKTGNSALLANIYA  459 (490)
Q Consensus       425 ~~~g~~~~a~~~~~~~~~~~------p~~~~~~~~l~~~~~  459 (490)
                      ...|++++|+..++++++.+      |.++.+...+..+..
T Consensus        83 ~~~~~~~~A~~~~~~al~~~p~~~~~p~~~~~~~~l~~~~~  123 (126)
T 3upv_A           83 IAVKEYASALETLDAARTKDAEVNNGSSAREIDQLYYKASQ  123 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHHHHhCcccCCchhHHHHHHHHHHHHH
Confidence            99999999999999999988      887777777765543

>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=98.77  E-value=6.8e-08  Score=78.90  Aligned_cols=123  Identities=9%  Similarity=-0.042  Sum_probs=93.7

Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHH-HhhhCCh--
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGA-CKVHVNA--  430 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~-~~~~g~~--  430 (490)
                      +...|++++|...+++..+.  .+.+...+..+..+|...|++++|...|++..  .+.+...+..+..+ +...|++  
T Consensus        20 ~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~   97 (177)
T 2e2e_A           20 FASQQNPEAQLQALQDKIRA--NPQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMT   97 (177)
T ss_dssp             CC-----CCCCHHHHHHHHH--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCC
T ss_pred             hhhccCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcch
Confidence            45677888888888888773  34556778888888888888888888887766  34466677777777 6778887  


Q ss_pred             HHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          431 ELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       431 ~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      ++|+..++++++.+|+++.++..++.++...|++++|...++++.+..+.
T Consensus        98 ~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~  147 (177)
T 2e2e_A           98 AQTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDLNSP  147 (177)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCT
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhhCCC
Confidence            88888888888888888888888888888888888888888888776543

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.77  E-value=5e-08  Score=76.43  Aligned_cols=98  Identities=12%  Similarity=-0.046  Sum_probs=80.9

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ...+..+...+.+.|++++|...|++..  .+.+...|..+..++...|++++|+..|+++++.+|+++.++..++.+|.
T Consensus        18 ~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~   97 (142)
T 2xcb_A           18 LEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECHL   97 (142)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHH
Confidence            4455667778888899999998888776  45567788888888888899999999999999888988888888888899


Q ss_pred             hcCCcchHHHHHHHhhhccc
Q 011249          460 SMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       460 ~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ..|++++|.+.+++..+..+
T Consensus        98 ~~g~~~~A~~~~~~al~~~p  117 (142)
T 2xcb_A           98 QLGDLDGAESGFYSARALAA  117 (142)
T ss_dssp             HTTCHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHhCC
Confidence            99999999988888876654

>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=98.75  E-value=6.8e-08  Score=72.52  Aligned_cols=98  Identities=9%  Similarity=-0.010  Sum_probs=88.4

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ...+..++..+...|++++|...+++..  .+.+...+..+...+...|++++|...++++.+..|+++..+..++.++.
T Consensus         4 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~   83 (118)
T 1elw_A            4 VNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALE   83 (118)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            4567778889999999999999998876  44577888999999999999999999999999999999999999999999


Q ss_pred             hcCCcchHHHHHHHhhhccc
Q 011249          460 SMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       460 ~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ..|++++|.+.+++..+.++
T Consensus        84 ~~~~~~~A~~~~~~~~~~~~  103 (118)
T 1elw_A           84 FLNRFEEAKRTYEEGLKHEA  103 (118)
T ss_dssp             HTTCHHHHHHHHHHHHTTCT
T ss_pred             HHhhHHHHHHHHHHHHHcCC
Confidence            99999999999999887544

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.75  E-value=3.6e-08  Score=85.19  Aligned_cols=129  Identities=11%  Similarity=-0.053  Sum_probs=104.1

Q ss_pred             HHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCC----hhhHHHHHHHH
Q 011249          349 FIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCD----AGTWGALLGAC  424 (490)
Q Consensus       349 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~----~~~~~~l~~~~  424 (490)
                      ...+...+...|++++|.+.|+.+..  + .|+......+...+.+.|++++|+..|+.....|+    ...+..+..++
T Consensus       105 ~LayA~~L~~~g~y~eA~~~l~~~~~--~-~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~al  181 (282)
T 4f3v_A          105 TMGFAACEAAQGNYADAMEALEAAPV--A-GSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVAA  181 (282)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHTSSCC--T-TCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHh--c-CCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHHH
Confidence            34456667889999999999998875  2 34333666777789999999999999987764342    23677888999


Q ss_pred             hhhCChHHHHHHHHHHHhcC--CC-CCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          425 KVHVNAELGEIAARHLLELG--PE-KTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       425 ~~~g~~~~a~~~~~~~~~~~--p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      ...|++++|+..|+++....  |. .+.....++.++.+.|+.++|...|+++...++.
T Consensus       182 ~~LG~~~eAl~~l~~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~  240 (282)
T 4f3v_A          182 ANLALFTEAERRLTEANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPE  240 (282)
T ss_dssp             HHTTCHHHHHHHHHHHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCC
T ss_pred             HHCCCHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCc
Confidence            99999999999999998533  44 4568889999999999999999999999887653

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.75  E-value=5.8e-08  Score=74.81  Aligned_cols=100  Identities=11%  Similarity=0.019  Sum_probs=89.8

Q ss_pred             CCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHH
Q 011249          380 PLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANI  457 (490)
Q Consensus       380 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~  457 (490)
                      .+...+..+...+...|++++|.+.|++..  .+.+...+..+...+...|++++|++.++++++..|+++.++..++.+
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~   93 (133)
T 2lni_A           14 DLALMVKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLEPTFIKGYTRKAAA   93 (133)
T ss_dssp             CHHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCchHHHHHHHHH
Confidence            346677888999999999999999998876  344678899999999999999999999999999999999999999999


Q ss_pred             HHhcCCcchHHHHHHHhhhccc
Q 011249          458 YASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       458 ~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +.+.|++++|.+.+++..+...
T Consensus        94 ~~~~~~~~~A~~~~~~~~~~~p  115 (133)
T 2lni_A           94 LEAMKDYTKAMDVYQKALDLDS  115 (133)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCG
T ss_pred             HHHHhhHHHHHHHHHHHHHhCC
Confidence            9999999999999999887654

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.75  E-value=1e-07  Score=76.66  Aligned_cols=95  Identities=16%  Similarity=0.048  Sum_probs=61.6

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHH
Q 011249          311 VISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMV  389 (490)
Q Consensus       311 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  389 (490)
                      ...+..+...+...|++++|+..|++.++.  .| +...+..+..+|...|++++|+..++++.+.  .+.+...+..+.
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~lg   86 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSI--APANPIYLSNRAAAYSASGQHEKAAEDAELATVV--DPKYSKAWSRLG   86 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence            445666666667777777777777776663  33 4456666666677777777777777776662  233455666666


Q ss_pred             HHHhhcCChHHHHHHHHhcc
Q 011249          390 DLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       390 ~~~~~~g~~~~A~~~~~~~~  409 (490)
                      .+|...|++++|.+.|++..
T Consensus        87 ~~~~~~g~~~~A~~~~~~al  106 (164)
T 3sz7_A           87 LARFDMADYKGAKEAYEKGI  106 (164)
T ss_dssp             HHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHccCHHHHHHHHHHHH
Confidence            77777777777777776654

>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=98.73  E-value=1.1e-05  Score=72.27  Aligned_cols=176  Identities=9%  Similarity=-0.060  Sum_probs=117.4

Q ss_pred             HHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccC-ChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhc-C-
Q 011249          218 VCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLG-DVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKC-G-  294 (490)
Q Consensus       218 ~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~-~-  294 (490)
                      ....+.+..++|+++++++...... +...++.--.++...| +++++..+++.+.... +.+..+|+.-..++... + 
T Consensus        62 ~~~~~~e~se~AL~lt~~~L~~nP~-~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL~~l~~~  139 (349)
T 3q7a_A           62 AIAAKEEKSERALELTEIIVRMNPA-HYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-LKSYQVWHHRLLLLDRISPQ  139 (349)
T ss_dssp             HHHHTTCCSHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-CCCHHHHHHHHHHHHHHCCS
T ss_pred             HHHHhCCCCHHHHHHHHHHHHhCch-hHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHhcCC
Confidence            3344455567888888888876422 4455666666666667 5888888888888776 56667777666666655 6 


Q ss_pred             ChHHHHHHHhcccCC---ChhHHHHHHHHHHhcCChH--------HHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCC--
Q 011249          295 YLDLAWREFSRIKNK---DVISYSSMITAFADHGKSQ--------EALDMFLKMRNEGIEPNQVTFIGVLTACSHGGL--  361 (490)
Q Consensus       295 ~~~~A~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~--------~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~--  361 (490)
                      ++++++++++++.+.   +..+|+--.-++.+.|.++        ++++.++++++.. .-|...|+.....+.+.+.  
T Consensus       140 ~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~d-p~N~SAW~~R~~lL~~l~~~~  218 (349)
T 3q7a_A          140 DPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVD-GRNNSAWGWRWYLRVSRPGAE  218 (349)
T ss_dssp             CCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHTTSTTCC
T ss_pred             ChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHhccccc
Confidence            788888888888773   4556655555555555555        8888888888753 2255667666666666665  


Q ss_pred             -----hHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCCh
Q 011249          362 -----VEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQL  398 (490)
Q Consensus       362 -----~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  398 (490)
                           ++++++.++++..  ..+-|...|+.+-..+.+.|+.
T Consensus       219 ~~~~~~~eELe~~~~aI~--~~P~n~SaW~Ylr~Ll~~~~~~  258 (349)
T 3q7a_A          219 TSSRSLQDELIYILKSIH--LIPHNVSAWNYLRGFLKHFSLP  258 (349)
T ss_dssp             CCHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHTTCC
T ss_pred             cchHHHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHhcCCC
Confidence                 5777777777776  3455566676666666665553

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.71  E-value=1.2e-07  Score=71.95  Aligned_cols=98  Identities=17%  Similarity=0.124  Sum_probs=88.7

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ...+..+...+...|++++|.+.++++.  .+.+..++..+...+...|++++|...++++.+..|.++..+..++.++.
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~   88 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYY   88 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHH
Confidence            4677788899999999999999998876  44567788999999999999999999999999999999999999999999


Q ss_pred             hcCCcchHHHHHHHhhhccc
Q 011249          460 SMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       460 ~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ..|++++|...++++.+..+
T Consensus        89 ~~~~~~~A~~~~~~~~~~~~  108 (125)
T 1na0_A           89 KQGDYDEAIEYYQKALELDP  108 (125)
T ss_dssp             HTTCHHHHHHHHHHHHHHCT
T ss_pred             HhcCHHHHHHHHHHHHHhCC
Confidence            99999999999999887654

>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=98.69  E-value=1.7e-07  Score=82.81  Aligned_cols=188  Identities=10%  Similarity=-0.078  Sum_probs=101.3

Q ss_pred             hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHH
Q 011249          246 VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFA  322 (490)
Q Consensus       246 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~  322 (490)
                      ..+..+...+...|++++|...|+.+.+.. +.+...+..+..+|.+.|++++|...+++..+   .+...+..+..++.
T Consensus         5 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~   83 (281)
T 2c2l_A            5 QELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQCQL   83 (281)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            344445555555566666666665555543 33555566666666666666666666666554   24456666777777


Q ss_pred             hcCChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHH
Q 011249          323 DHGKSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKA  401 (490)
Q Consensus       323 ~~~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  401 (490)
                      ..|++++|...|++..+.  .|+.. .+...+....   ....+ ..+...... ..+.+......+...  ..|++++|
T Consensus        84 ~~g~~~~A~~~~~~al~l--~p~~~~~~~~~~~~~~---~~~~~-~~~~~~~~~-~~~~~~~i~~~l~~l--~~~~~~~A  154 (281)
T 2c2l_A           84 EMESYDEAIANLQRAYSL--AKEQRLNFGDDIPSAL---RIAKK-KRWNSIEER-RIHQESELHSYLTRL--IAAERERE  154 (281)
T ss_dssp             HTTCHHHHHHHHHHHHHH--HHHTTCCCCSHHHHHH---HHHHH-HHHHHHHHT-CCCCCCHHHHHHHHH--HHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHh--CccchhhHHHHHHHHH---HHHHH-HHHHHHHHH-HHhhhHHHHHHHHHH--HHHHHHHH
Confidence            777777777777776652  22210 0000111110   01111 122223331 445555554444333  26888888


Q ss_pred             HHHHHhcc-CCCCh-hhHHHHHHHHhhh-CChHHHHHHHHHHHhc
Q 011249          402 HSLIMDYK-DFCDA-GTWGALLGACKVH-VNAELGEIAARHLLEL  443 (490)
Q Consensus       402 ~~~~~~~~-~~~~~-~~~~~l~~~~~~~-g~~~~a~~~~~~~~~~  443 (490)
                      .+.++... ..|+. .....+...+... +.+++|.++|+++.+.
T Consensus       155 ~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~~a~~~f~~a~~~  199 (281)
T 2c2l_A          155 LEECQRNHEGHEDDGHIRAQQACIEAKHDKYMADMDELFSQVDEK  199 (281)
T ss_dssp             HTTTSGGGTTTSCHHHHTHHHHHHHHHHHHHHHHHHHHHHHSSCT
T ss_pred             HHHHHhhhccccchhhhhhHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence            88887665 33433 3333343334444 6678888888888763

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.69  E-value=2.1e-07  Score=77.71  Aligned_cols=115  Identities=11%  Similarity=0.030  Sum_probs=53.6

Q ss_pred             hcCChhHHHH---HHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHc----Ccc-cChhhHHHHHHHHhccCChH
Q 011249          191 KCGEVREAKK---VFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQE----NVR-ISEVAMVGAISACTQLGDVE  262 (490)
Q Consensus       191 ~~~~~~~A~~---~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~-p~~~~~~~l~~~~~~~g~~~  262 (490)
                      ..|++++|.+   .+..-.......+..+...+...|++++|+..+++....    +.. .....+..+...+...|+++
T Consensus         4 ~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~   83 (203)
T 3gw4_A            4 EAHDYALAERQAQALLAHPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWD   83 (203)
T ss_dssp             ---CHHHHHHHHHHHHTSTTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             ccccHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHH
Confidence            3455555555   333322233445566666666666666666666665541    111 12234555555555666666


Q ss_pred             HHHHHHHHHHhc----CCC--CchhHHHHHHHHHHhcCChHHHHHHHhc
Q 011249          263 MAAILAKHVDEG----CCD--RTNYVSNALIHMHSKCGYLDLAWREFSR  305 (490)
Q Consensus       263 ~a~~~~~~~~~~----~~~--~~~~~~~~l~~~~~~~~~~~~A~~~~~~  305 (490)
                      +|...+++..+.    +..  .....+..+...+...|++++|...+++
T Consensus        84 ~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~  132 (203)
T 3gw4_A           84 AARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEK  132 (203)
T ss_dssp             HHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence            666655554332    101  0122334444444445555555444444

>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=98.69  E-value=5.4e-07  Score=72.36  Aligned_cols=128  Identities=7%  Similarity=-0.098  Sum_probs=95.6

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHH
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDL  391 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  391 (490)
                      ..+..+...+...|++++|...|++..+.. +.+...+..+..++...|++++|...+++..+.  .+.+...+..+..+
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~a~~   90 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIEL--DKKYIKGYYRRAAS   90 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHHHHHH
Confidence            456667777888888888888888888742 235667777888888888899998888888873  34556778888888


Q ss_pred             HhhcCChHHHHHHHHhcc--CCCChhhHHHH--HHHHhhhCChHHHHHHHHHHHh
Q 011249          392 LGRSGQLEKAHSLIMDYK--DFCDAGTWGAL--LGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       392 ~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l--~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                      +...|++++|.+.+++..  .+.+...+..+  +..+...|++++|++.+++...
T Consensus        91 ~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  145 (166)
T 1a17_A           91 NMALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRS  145 (166)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccchHH
Confidence            888999999998887766  33344455333  3346778899999998887765

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.68  E-value=2.2e-07  Score=77.54  Aligned_cols=133  Identities=12%  Similarity=-0.007  Sum_probs=70.3

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHHHHH----cCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCC-C---
Q 011249          311 VISYSSMITAFADHGKSQEALDMFLKMRN----EGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKP-L---  381 (490)
Q Consensus       311 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~----~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~-~---  381 (490)
                      ...+..+...+...|++++|...+++..+    .+..| ....+..+...+...|++++|...+++..+.....+ +   
T Consensus        26 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~  105 (203)
T 3gw4_A           26 SGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGNWDAARRCFLEERELLASLPEDPLA  105 (203)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHH
T ss_pred             HHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCccHHH
Confidence            34455555555666666666666655544    11111 123455555566666666666666666554211111 1   


Q ss_pred             -chHHHHHHHHHhhcCChHHHHHHHHhcc----CCCC----hhhHHHHHHHHhhhCChHHHHHHHHHHHhc
Q 011249          382 -TEHLTCMVDLLGRSGQLEKAHSLIMDYK----DFCD----AGTWGALLGACKVHVNAELGEIAARHLLEL  443 (490)
Q Consensus       382 -~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  443 (490)
                       ...+..+...+...|++++|...+++..    ..++    ..++..+...+...|++++|.+.++++.+.
T Consensus       106 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  176 (203)
T 3gw4_A          106 ASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEKNLLEAQQHWLRARDI  176 (203)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence             2334555566666666666666665543    1111    123455556666667777777777666654

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.67  E-value=3.9e-07  Score=71.60  Aligned_cols=111  Identities=10%  Similarity=-0.072  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC----chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHH
Q 011249          346 QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL----TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGA  419 (490)
Q Consensus       346 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~  419 (490)
                      ...+..+...+...|++++|...|++..+   ..|+    ...+..+..+|...|++++|...+++..  .+.+...+..
T Consensus        28 ~~~~~~~a~~~~~~~~~~~A~~~~~~a~~---~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~  104 (148)
T 2dba_A           28 VEQLRKEGNELFKCGDYGGALAAYTQALG---LDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKALYR  104 (148)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHT---SCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHH---HcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHHHHH
Confidence            34555555556666666666666666654   2233    4555666666677777777777766554  3335566777


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      +..++...|++++|...++++++.+|+++.++..+..+..
T Consensus       105 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~  144 (148)
T 2dba_A          105 RSQALEKLGRLDQAVLDLQRCVSLEPKNKVFQEALRNISG  144 (148)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHh
Confidence            7777888888888888888888888887777776665543

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.67  E-value=1e-07  Score=73.04  Aligned_cols=99  Identities=11%  Similarity=-0.033  Sum_probs=89.2

Q ss_pred             CchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHH
Q 011249          381 LTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY  458 (490)
Q Consensus       381 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  458 (490)
                      +...+..+...+...|++++|...+++..  .+.+...+..+...+...|++++|++.++++.+..|+++..+..++.++
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~   90 (131)
T 2vyi_A           11 EAERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICIDPAYSKAYGRMGLAL   90 (131)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcCccCHHHHHHHHHHH
Confidence            45667788899999999999999998876  4456788899999999999999999999999999999999999999999


Q ss_pred             HhcCCcchHHHHHHHhhhccc
Q 011249          459 ASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       459 ~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ...|++++|...+++..+..+
T Consensus        91 ~~~~~~~~A~~~~~~~~~~~p  111 (131)
T 2vyi_A           91 SSLNKHVEAVAYYKKALELDP  111 (131)
T ss_dssp             HHTTCHHHHHHHHHHHHHHST
T ss_pred             HHhCCHHHHHHHHHHHHhcCc
Confidence            999999999999999887654

>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=98.65  E-value=1.5e-07  Score=72.97  Aligned_cols=112  Identities=9%  Similarity=-0.174  Sum_probs=83.5

Q ss_pred             cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHH
Q 011249          345 NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLG  422 (490)
Q Consensus       345 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~  422 (490)
                      +...+..+...+...|++++|...|++....  .+.+...+..+..++...|++++|...+++..  .+.+...+..+..
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~   85 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITR--NPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQ   85 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhh--CcCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHHH
Confidence            4566777777777888888888888887763  34456677778888888888888888887765  4446678888888


Q ss_pred             HHhhhCChHHHHHHHHHHHhcCCC-----CCchHHHHHHHH
Q 011249          423 ACKVHVNAELGEIAARHLLELGPE-----KTGNSALLANIY  458 (490)
Q Consensus       423 ~~~~~g~~~~a~~~~~~~~~~~p~-----~~~~~~~l~~~~  458 (490)
                      ++...|++++|+..++++++..|+     +..+...+..+.
T Consensus        86 ~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~l~~~~  126 (137)
T 3q49_B           86 CQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIAK  126 (137)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHHHHTTCCCTTHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHHHHHChhHHHHHHHHHHHHHHHHH
Confidence            888889999999999999888877     444444444443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.65  E-value=2.3e-07  Score=72.98  Aligned_cols=100  Identities=11%  Similarity=-0.052  Sum_probs=89.4

Q ss_pred             CCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCC----hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHH
Q 011249          380 PLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCD----AGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALL  454 (490)
Q Consensus       380 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l  454 (490)
                      .+...+..+...+...|++++|.+.|++.. ..|+    ...+..+...+...|++++|+..++++++..|+++.++..+
T Consensus        26 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~  105 (148)
T 2dba_A           26 SSVEQLRKEGNELFKCGDYGGALAAYTQALGLDATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKDGGDVKALYRR  105 (148)
T ss_dssp             CCHHHHHHHHHHHHTTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHcccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhCccCHHHHHHH
Confidence            346677888899999999999999998876 4455    67888888999999999999999999999999999999999


Q ss_pred             HHHHHhcCCcchHHHHHHHhhhccc
Q 011249          455 ANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       455 ~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +.++...|++++|...+++..+...
T Consensus       106 a~~~~~~~~~~~A~~~~~~al~~~p  130 (148)
T 2dba_A          106 SQALEKLGRLDQAVLDLQRCVSLEP  130 (148)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHCS
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHcCC
Confidence            9999999999999999999887654

>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=98.64  E-value=2.8e-07  Score=87.65  Aligned_cols=94  Identities=9%  Similarity=-0.048  Sum_probs=76.9

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ...|..+..+|.+.|++++|+..+++..  .+.+...|..+..++...|++++|+..|+++++++|++..++..++.++.
T Consensus       317 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~  396 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQISMCQK  396 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC----CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Confidence            4577788899999999999999998876  45577889999999999999999999999999999999999999999999


Q ss_pred             hcCCcchHHH-HHHHhh
Q 011249          460 SMGKWKDSEI-VKMMIS  475 (490)
Q Consensus       460 ~~g~~~~A~~-~~~~~~  475 (490)
                      +.|+++++.+ .+++|.
T Consensus       397 ~~~~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          397 KAKEHNERDRRIYANMF  413 (457)
T ss_dssp             HHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            9999988774 345443

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.64  E-value=2.1e-07  Score=71.29  Aligned_cols=101  Identities=11%  Similarity=-0.021  Sum_probs=58.8

Q ss_pred             HHHHhcCCCChHHHHHHHHHHHHHcCCCCCc---hHHHHHHHHHhhcCChHHHHHHHHhcc--CCCC---hhhHHHHHHH
Q 011249          352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLT---EHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCD---AGTWGALLGA  423 (490)
Q Consensus       352 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~---~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~---~~~~~~l~~~  423 (490)
                      +...+...|++++|...++.+.+.  .+.+.   ..+..+..++...|++++|...|+++.  .+.+   +..+..+..+
T Consensus         8 ~a~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~   85 (129)
T 2xev_A            8 VAFDALKNGKYDDASQLFLSFLEL--YPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLS   85 (129)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--CSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHH--CCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHH
Confidence            444555666677777766666653  12222   355556666666666666666666554  2222   3445556666


Q ss_pred             HhhhCChHHHHHHHHHHHhcCCCCCchHHHH
Q 011249          424 CKVHVNAELGEIAARHLLELGPEKTGNSALL  454 (490)
Q Consensus       424 ~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l  454 (490)
                      +...|++++|...++++++..|+++......
T Consensus        86 ~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~  116 (129)
T 2xev_A           86 QYGEGKNTEAQQTLQQVATQYPGSDAARVAQ  116 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTSHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHHCCCChHHHHHH
Confidence            6666666666666666666666655544433

>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=98.63  E-value=1.3e-07  Score=90.26  Aligned_cols=119  Identities=5%  Similarity=-0.157  Sum_probs=96.3

Q ss_pred             HHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCC
Q 011249          352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVN  429 (490)
Q Consensus       352 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~  429 (490)
                      +...+...|++++|.+.++++.+.  .+.+...+..+..+|.+.|++++|++.+++..  .+.+...+..+..++...|+
T Consensus        12 lg~~~~~~g~~~~A~~~~~~Al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~lg~~~~~~g~   89 (477)
T 1wao_1           12 QANDYFKAKDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGK   89 (477)
T ss_dssp             SSSSTTTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCC
Confidence            344567788899999999988873  34457788888899999999999999998776  34467788889999999999


Q ss_pred             hHHHHHHHHHHHhcCCCCCchHHHHHHH--HHhcCCcchHHHHHH
Q 011249          430 AELGEIAARHLLELGPEKTGNSALLANI--YASMGKWKDSEIVKM  472 (490)
Q Consensus       430 ~~~a~~~~~~~~~~~p~~~~~~~~l~~~--~~~~g~~~~A~~~~~  472 (490)
                      +++|++.++++++..|+++.++..++.+  +.+.|++++|++.++
T Consensus        90 ~~eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           90 FRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999999999999999998888  888899999999988

>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=98.62  E-value=3.3e-06  Score=75.50  Aligned_cols=216  Identities=13%  Similarity=-0.011  Sum_probs=156.8

Q ss_pred             hccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcC-ChHHHHHHHhcccC---CChhHHHHHHHHHHhc-C-ChHH
Q 011249          256 TQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCG-YLDLAWREFSRIKN---KDVISYSSMITAFADH-G-KSQE  329 (490)
Q Consensus       256 ~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~-~-~~~~  329 (490)
                      .+.+..++|..+++.+...+ |.+..+++.-..++...| .+++++..++.+..   ++..+|+.-...+... + ++++
T Consensus        65 ~~~e~se~AL~lt~~~L~~n-P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~nPKny~aW~hR~wlL~~l~~~~~~~  143 (349)
T 3q7a_A           65 AKEEKSERALELTEIIVRMN-PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQNLKSYQVWHHRLLLLDRISPQDPVS  143 (349)
T ss_dssp             HTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHCCSCCHH
T ss_pred             HhCCCCHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCCChHH
Confidence            34455678999999999887 666777877777777788 59999999999876   4667787777777666 6 8999


Q ss_pred             HHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChH--------HHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCC---
Q 011249          330 ALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVE--------DGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ---  397 (490)
Q Consensus       330 a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~--------~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---  397 (490)
                      ++.+++++.+.  .| |...|..-...+.+.|.++        ++++.++++.+.  .+-+...|+.....+.+.++   
T Consensus       144 EL~~~~k~L~~--dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~--dp~N~SAW~~R~~lL~~l~~~~~  219 (349)
T 3q7a_A          144 EIEYIHGSLLP--DPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRV--DGRNNSAWGWRWYLRVSRPGAET  219 (349)
T ss_dssp             HHHHHHHHTSS--CTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHTTSTTCCC
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHhcccccc
Confidence            99999999975  34 4556655444444444444        899999999883  45677788888888888876   


Q ss_pred             ----hHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCCh--------------------HHHHHHHHHHHhcC------C
Q 011249          398 ----LEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNA--------------------ELGEIAARHLLELG------P  445 (490)
Q Consensus       398 ----~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~--------------------~~a~~~~~~~~~~~------p  445 (490)
                          ++++++.++++.  .+.|...|+.+-..+...|..                    ....++...+....      +
T Consensus       220 ~~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  299 (349)
T 3q7a_A          220 SSRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPL  299 (349)
T ss_dssp             CHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCCS
T ss_pred             chHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccCC
Confidence                688888887766  556777888777777666654                    23333333333322      4


Q ss_pred             CCCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          446 EKTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       446 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      .++.++..|+.+|.+.|+.++|.++++.+.+
T Consensus       300 ~s~~al~~l~d~~~~~~~~~~a~~~~~~l~~  330 (349)
T 3q7a_A          300 PVPLALEYLADSFIEQNRVDDAAKVFEKLSS  330 (349)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            6677889999999999999999999999864

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.62  E-value=1.6e-07  Score=85.38  Aligned_cols=152  Identities=8%  Similarity=-0.082  Sum_probs=84.5

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHH
Q 011249          311 VISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVD  390 (490)
Q Consensus       311 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  390 (490)
                      ...+..+...+.+.|++++|...|++.++.  .|+...       +...++.+++...+   .        ...|..+..
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~-------~~~~~~~~~~~~~l---~--------~~~~~nla~  238 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFM-------FQLYGKYQDMALAV---K--------NPCHLNIAA  238 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHH-------HTCCHHHHHHHHHH---H--------THHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchh-------hhhcccHHHHHHHH---H--------HHHHHHHHH
Confidence            345666777777888888888888887763  454432       22334444433222   1        237788999


Q ss_pred             HHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHH-HhcCCcchH
Q 011249          391 LLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY-ASMGKWKDS  467 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~-~~~g~~~~A  467 (490)
                      +|.+.|++++|+..+++..  .+.+...|..+..++...|++++|+..|+++++++|+++.++..+..+. ...+..+++
T Consensus       239 ~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a  318 (338)
T 2if4_A          239 CLIKLKRYDEAIGHCNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQ  318 (338)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC--------------------------
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999998876  4557789999999999999999999999999999999999999998884 456778889


Q ss_pred             HHHHHHhhhcccccC
Q 011249          468 EIVKMMISETEKKKS  482 (490)
Q Consensus       468 ~~~~~~~~~~~~~~~  482 (490)
                      ..++++|........
T Consensus       319 ~~~~~~~l~~~p~~~  333 (338)
T 2if4_A          319 KEMYKGIFKGKDEGG  333 (338)
T ss_dssp             ---------------
T ss_pred             HHHHHHhhCCCCCCC
Confidence            999999877655443

>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=98.59  E-value=8.5e-06  Score=72.54  Aligned_cols=116  Identities=9%  Similarity=-0.026  Sum_probs=52.5

Q ss_pred             hcCCh-HHHHHHHHHHHHcCcccChhhHHHHHHHHhccCC----------hHHHHHHHHHHHhcCCCCchhHHHHHHHHH
Q 011249          222 QNGYA-KAAIEMYKVMRQENVRISEVAMVGAISACTQLGD----------VEMAAILAKHVDEGCCDRTNYVSNALIHMH  290 (490)
Q Consensus       222 ~~g~~-~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~----------~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~  290 (490)
                      +.|.+ ++|+++++.+...++. +...++.--.++...+.          ++++..+++.+.... |.+..+|+.-.-++
T Consensus        41 ~~~e~s~eaL~~t~~~L~~nP~-~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~-PKny~aW~hR~wlL  118 (331)
T 3dss_A           41 QAGELDESVLELTSQILGANPD-FATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLL  118 (331)
T ss_dssp             HTTCCSHHHHHHHHHHHTTCTT-CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHCch-hHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC-CCCHHHHHHHHHHH
Confidence            44554 3567777776654321 22233332222222222          344555555555443 34444444444444


Q ss_pred             HhcC--ChHHHHHHHhcccC---CChhHHHHHHHHHHhcCC-hHHHHHHHHHHHH
Q 011249          291 SKCG--YLDLAWREFSRIKN---KDVISYSSMITAFADHGK-SQEALDMFLKMRN  339 (490)
Q Consensus       291 ~~~~--~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~-~~~a~~~~~~~~~  339 (490)
                      ...+  .+++++.+++++.+   .|..+|+--.-++...|. ++++++.+.++++
T Consensus       119 ~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~  173 (331)
T 3dss_A          119 SRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLIT  173 (331)
T ss_dssp             HHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             hccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence            4444  24555555555443   234444444444444444 3455555555554

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.58  E-value=4.7e-08  Score=73.63  Aligned_cols=92  Identities=13%  Similarity=-0.015  Sum_probs=53.5

Q ss_pred             CCChHHHHHHHHHHHHHcC--CCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHH
Q 011249          359 GGLVEDGCKQFELMTRVFG--IKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGE  434 (490)
Q Consensus       359 ~g~~~~a~~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~  434 (490)
                      .|++++|+..|+++.+. +  .+.+...+..+..+|...|++++|++.|++..  .+.+...+..+..++...|++++|+
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            46666666777666651 2  12234555666666666666666666666654  3334556666666666666666666


Q ss_pred             HHHHHHHhcCCCCCchH
Q 011249          435 IAARHLLELGPEKTGNS  451 (490)
Q Consensus       435 ~~~~~~~~~~p~~~~~~  451 (490)
                      ..++++++..|+++...
T Consensus        82 ~~~~~al~~~p~~~~~~   98 (117)
T 3k9i_A           82 ELLLKIIAETSDDETIQ   98 (117)
T ss_dssp             HHHHHHHHHHCCCHHHH
T ss_pred             HHHHHHHHhCCCcHHHH
Confidence            66666666666665543

>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=98.56  E-value=2.9e-07  Score=71.73  Aligned_cols=63  Identities=11%  Similarity=-0.076  Sum_probs=45.2

Q ss_pred             hHHHHHHHHhhhCChHHHHHHHHHHHhc-------CCCCCchH----HHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          416 TWGALLGACKVHVNAELGEIAARHLLEL-------GPEKTGNS----ALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       416 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~-------~p~~~~~~----~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      .|..+..++...|++++|+..+++++++       +|+++..|    ...+.++...|++++|+..|++..+..
T Consensus        59 a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~  132 (159)
T 2hr2_A           59 CHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMI  132 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            6666666677777777777777777777       77777777    777777777777777777777766543

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.56  E-value=3.5e-07  Score=69.17  Aligned_cols=98  Identities=13%  Similarity=-0.032  Sum_probs=71.5

Q ss_pred             HHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhh
Q 011249          349 FIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKV  426 (490)
Q Consensus       349 ~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~  426 (490)
                      +..+...+.+.|++++|...++++.+.  .+.+...+..+..++...|++++|+..|++..  .+.+...+..+..++..
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~   97 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTN   97 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            344555667788888888888888773  44467777778888888888888888887766  44466788888888888


Q ss_pred             hCChHHHHHHHHHHHhcCCCCC
Q 011249          427 HVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       427 ~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      .|++++|+..++++++.+|+++
T Consensus        98 ~g~~~~A~~~~~~al~~~P~~~  119 (121)
T 1hxi_A           98 EHNANAALASLRAWLLSQPQYE  119 (121)
T ss_dssp             HHHHHHHHHHHHHHHC------
T ss_pred             cCCHHHHHHHHHHHHHhCcCCC
Confidence            9999999999999998888754

>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=98.56  E-value=3.4e-07  Score=70.11  Aligned_cols=111  Identities=7%  Similarity=-0.102  Sum_probs=74.2

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-C----CCC----hhhHH
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-D----FCD----AGTWG  418 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~----~~~----~~~~~  418 (490)
                      .+..+...+...|++++|...+++..+.  .+.+...+..+..++...|++++|...+++.. .    .++    ..++.
T Consensus         6 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            6 KEKELGNDAYKKKDFDTALKHYDKAKEL--DPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHhc--CCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            4555556666667777777777766652  23445566666777777777777777776654 1    111    55677


Q ss_pred             HHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhc
Q 011249          419 ALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASM  461 (490)
Q Consensus       419 ~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  461 (490)
                      .+..++...|++++|.+.++++.+..| ++.....+..+....
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~~~~-~~~~~~~l~~~~~~~  125 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLAEHR-TPDVLKKCQQAEKIL  125 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhCC-CHHHHHHHHHHHHHH
Confidence            777888888888888888888888887 466666666555443

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.55  E-value=7.3e-07  Score=84.33  Aligned_cols=163  Identities=8%  Similarity=-0.141  Sum_probs=109.2

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHc-CCCCcH----HHHHHHHHHhcCCCChHHHHHHHHHHHHHc---CCCC-CchH
Q 011249          314 YSSMITAFADHGKSQEALDMFLKMRNE-GIEPNQ----VTFIGVLTACSHGGLVEDGCKQFELMTRVF---GIKP-LTEH  384 (490)
Q Consensus       314 ~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~p~~----~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~---~~~~-~~~~  384 (490)
                      +..++..|...|++++|.+.+..+... +..++.    ...+.+...+...|+.+.|..+++......   +..+ ...+
T Consensus        58 l~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  137 (434)
T 4b4t_Q           58 ILELGQLYVTMGAKDKLREFIPHSTEYMMQFAKSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSL  137 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCHHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHH
Confidence            556777777788888888777776542 111222    123334444566788888888887765421   1122 2446


Q ss_pred             HHHHHHHHhhcCChHHHHHHHHhcc-------CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC---CCC----Cc
Q 011249          385 LTCMVDLLGRSGQLEKAHSLIMDYK-------DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELG---PEK----TG  449 (490)
Q Consensus       385 ~~~l~~~~~~~g~~~~A~~~~~~~~-------~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~---p~~----~~  449 (490)
                      +..++..|...|++++|..+++++.       ..+ ...++..++..|...|++++|..+++++....   |..    ..
T Consensus       138 ~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~  217 (434)
T 4b4t_Q          138 SIKLATLHYQKKQYKDSLALINDLLREFKKLDDKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAE  217 (434)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSCSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHH
T ss_pred             HHHHHHHHHHccChHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHH
Confidence            6778888888889888888887654       112 23467777888888999999999998887753   222    24


Q ss_pred             hHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          450 NSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       450 ~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      .+..++..+...|++++|...+.+..+
T Consensus       218 ~~~~~g~~~~~~~~y~~A~~~~~~a~~  244 (434)
T 4b4t_Q          218 LDLMSGILHCEDKDYKTAFSYFFESFE  244 (434)
T ss_dssp             HHHHHHHHTTSSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            566777788888899988888776654

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.55  E-value=5.1e-07  Score=66.89  Aligned_cols=99  Identities=12%  Similarity=-0.067  Sum_probs=69.2

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCC--ChhhHHHHHHH
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFC--DAGTWGALLGA  423 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~--~~~~~~~l~~~  423 (490)
                      .+..+...+...|++++|...++++.+.  .+.+...+..+..++...|++++|.+.+++..  .+.  +...+..+..+
T Consensus         8 ~~~~~~~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~l~~~   85 (112)
T 2kck_A            8 EYYLEGVLQYDAGNYTESIDLFEKAIQL--DPEESKYWLMKGKALYNLERYEEAVDCYNYVINVIEDEYNKDVWAAKADA   85 (112)
T ss_dssp             GGGGHHHHHHSSCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSCCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccchHHHHHHHHHH
Confidence            4455566666777777777777777663  33445566677777777777777777776665  233  46677777778


Q ss_pred             Hhhh-CChHHHHHHHHHHHhcCCCCC
Q 011249          424 CKVH-VNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       424 ~~~~-g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      +... |++++|.+.++++....|.++
T Consensus        86 ~~~~~~~~~~A~~~~~~~~~~~p~~~  111 (112)
T 2kck_A           86 LRYIEGKEVEAEIAEARAKLEHHHHH  111 (112)
T ss_dssp             HTTCSSCSHHHHHHHHHHGGGCCCCC
T ss_pred             HHHHhCCHHHHHHHHHHHhhcccCCC
Confidence            8888 888888888888888887654

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=98.54  E-value=1.4e-06  Score=66.52  Aligned_cols=93  Identities=15%  Similarity=0.085  Sum_probs=66.5

Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc-CCC-Ch---hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC---CchHHHHHHH
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK-DFC-DA---GTWGALLGACKVHVNAELGEIAARHLLELGPEK---TGNSALLANI  457 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~---~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~---~~~~~~l~~~  457 (490)
                      ..+...+...|++++|.+.|+++. ..| +.   ..+..+..++...|++++|+..++++++..|++   +.++..++.+
T Consensus         6 ~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~la~~   85 (129)
T 2xev_A            6 YNVAFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRYPTHDKAAGGLLKLGLS   85 (129)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHCCCCcccHHHHHHHHHH
Confidence            345666777788888887777665 223 23   366667777777788888888888888777777   5667777778


Q ss_pred             HHhcCCcchHHHHHHHhhhcc
Q 011249          458 YASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       458 ~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      +...|++++|...++++.+..
T Consensus        86 ~~~~g~~~~A~~~~~~~~~~~  106 (129)
T 2xev_A           86 QYGEGKNTEAQQTLQQVATQY  106 (129)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHcCCHHHHHHHHHHHHHHC
Confidence            888888888888877776653

>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=98.54  E-value=5.3e-07  Score=68.84  Aligned_cols=101  Identities=7%  Similarity=-0.127  Sum_probs=58.9

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC----C----hhhHH
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC----D----AGTWG  418 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~----~----~~~~~  418 (490)
                      .+..+...+.+.|++++|+..|++..+.  .|.+...|..+..+|...|++++|++.+++.. ..|    +    ..+|.
T Consensus        10 a~~~lG~~~~~~~~~~~A~~~y~~Al~~--~p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~   87 (127)
T 4gcn_A           10 AEKDLGNAAYKQKDFEKAHVHYDKAIEL--DPSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAMS   87 (127)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHHH
Confidence            3444555555555666666666555542  23334455555566666666666666555443 111    1    12556


Q ss_pred             HHHHHHhhhCChHHHHHHHHHHHhcCCCCCchH
Q 011249          419 ALLGACKVHVNAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       419 ~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                      .+..++...|++++|++.|+++++..|+ +...
T Consensus        88 ~lg~~~~~~~~~~~A~~~~~kal~~~~~-~~~~  119 (127)
T 4gcn_A           88 RAGNAFQKQNDLSLAVQWFHRSLSEFRD-PELV  119 (127)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHSCC-HHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHhhCcC-HHHH
Confidence            6667777888888888888888887765 4433

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.54  E-value=2.4e-07  Score=74.38  Aligned_cols=80  Identities=11%  Similarity=-0.036  Sum_probs=63.4

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC-chHHHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT-GNSALLANIY  458 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~-~~~~~l~~~~  458 (490)
                      ...|..+..+|.+.|++++|+..+++..  .+.+...|..+..++...|++++|...|+++++++|+++ .+...+..+.
T Consensus        63 ~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p~~~~~~~~~l~~~~  142 (162)
T 3rkv_A           63 IPLYANMSQCYLNIGDLHEAEETSSEVLKREETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNHPAAASVVAREMKIVT  142 (162)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            4567788888888999999998887776  455677888888899999999999999999999999887 5555555554


Q ss_pred             Hhc
Q 011249          459 ASM  461 (490)
Q Consensus       459 ~~~  461 (490)
                      .+.
T Consensus       143 ~~~  145 (162)
T 3rkv_A          143 ERR  145 (162)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=98.54  E-value=2.5e-07  Score=70.86  Aligned_cols=98  Identities=12%  Similarity=-0.009  Sum_probs=86.8

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC-------CchHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK-------TGNSA  452 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~-------~~~~~  452 (490)
                      ...+..+...+...|++++|...|++..  .+.+...+..+...+...|++++|...++++.+..|++       +.++.
T Consensus         4 ~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            4 ALKEKELGNDAYKKKDFDTALKHYDKAKELDPTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            3467778899999999999999998876  45577788899999999999999999999999988776       78899


Q ss_pred             HHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          453 LLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       453 ~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .++.++...|++++|.+.++++.+...
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~~~~  110 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLAEHR  110 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHhCC
Confidence            999999999999999999999887643

>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=98.52  E-value=1.6e-06  Score=78.84  Aligned_cols=144  Identities=8%  Similarity=-0.063  Sum_probs=107.5

Q ss_pred             ChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCc----------------HHHHHHHHHH
Q 011249          295 YLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPN----------------QVTFIGVLTA  355 (490)
Q Consensus       295 ~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~----------------~~~~~~l~~~  355 (490)
                      ++++|...|+...+   .+...+..+...+.+.|++++|+..|++.++.  .|+                ...+..+..+
T Consensus       128 ~~~~A~~~~~~a~~~~p~~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~~~~~~~~~~~~~~~~~~nla~~  205 (336)
T 1p5q_A          128 SFEKAKESWEMNSEEKLEQSTIVKERGTVYFKEGKYKQALLQYKKIVSW--LEYESSFSNEEAQKAQALRLASHLNLAMC  205 (336)
T ss_dssp             EEECCCCGGGCCHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--TTTCCCCCSHHHHHHHHHHHHHHHHHHHH
T ss_pred             ecccccchhcCCHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--hhccccCChHHHHHHHHHHHHHHHHHHHH
Confidence            34444444444332   24456777788888888888888888888874  333                3678888888


Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHH
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      +.+.|++++|+..++++.+.  .+.+...+..+..+|...|++++|...|++..  .+.+...+..+..++...|+.++|
T Consensus       206 ~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~l~~~~~~~~~~~~a  283 (336)
T 1p5q_A          206 HLKLQAFSAAIESCNKALEL--DSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAR  283 (336)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            88999999999999998873  44567788888899999999999999998776  445667888888888888888888


Q ss_pred             -HHHHHHHHh
Q 011249          434 -EIAARHLLE  442 (490)
Q Consensus       434 -~~~~~~~~~  442 (490)
                       ...++++..
T Consensus       284 ~~~~~~~~~~  293 (336)
T 1p5q_A          284 EKKLYANMFE  293 (336)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence             446666654

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=98.50  E-value=9.5e-08  Score=70.98  Aligned_cols=95  Identities=8%  Similarity=-0.127  Sum_probs=81.4

Q ss_pred             CchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC------CchHH
Q 011249          381 LTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK------TGNSA  452 (490)
Q Consensus       381 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~------~~~~~  452 (490)
                      +...+..+...+...|++++|++.|++..  .+.+...+..+..++...|++++|++.++++++.+|++      ...+.
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~   82 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTSTAEHVAIRSKLQY   82 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSSTTSHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCccHHHHHHHHHH
Confidence            34567778888899999999999998776  45567888899999999999999999999999999998      78889


Q ss_pred             HHHHHHHhcCCcchHHHHHHHhh
Q 011249          453 LLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       453 ~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      .++.++...|++++|.+.++++.
T Consensus        83 ~~~~~~~~~~~~~~a~~~~~~~~  105 (111)
T 2l6j_A           83 RLELAQGAVGSVQIPVVEVDELP  105 (111)
T ss_dssp             HHHHHHHHHHCCCCCSSSSSSCS
T ss_pred             HHHHHHHHHHhHhhhHhHHHHhH
Confidence            99999999999999888776543

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=98.50  E-value=4.1e-07  Score=72.97  Aligned_cols=67  Identities=7%  Similarity=-0.046  Sum_probs=62.1

Q ss_pred             ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          413 DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       413 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +...|..+..++...|++++|+..++++++++|+++.+|..++.+|...|++++|...+++..+..+
T Consensus        62 ~~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~p  128 (162)
T 3rkv_A           62 NIPLYANMSQCYLNIGDLHEAEETSSEVLKREETNEKALFRRAKARIAAWKLDEAEEDLKLLLRNHP  128 (162)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCG
T ss_pred             HHHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHhcCC
Confidence            3467888899999999999999999999999999999999999999999999999999999887654

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=98.49  E-value=1.7e-07  Score=70.56  Aligned_cols=85  Identities=11%  Similarity=0.010  Sum_probs=63.2

Q ss_pred             hcCChHHHHHHHHhccCC----C-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHH
Q 011249          394 RSGQLEKAHSLIMDYKDF----C-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSE  468 (490)
Q Consensus       394 ~~g~~~~A~~~~~~~~~~----~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~  468 (490)
                      ..|++++|+..|++....    | +...+..+..++...|++++|+..++++++.+|+++.++..++.++...|++++|+
T Consensus         2 ~~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            2 VLGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQFPNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             -----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHcCCHHHHH
Confidence            357788888888776622    3 34577777788888888888888888888888888888888888888888888888


Q ss_pred             HHHHHhhhcc
Q 011249          469 IVKMMISETE  478 (490)
Q Consensus       469 ~~~~~~~~~~  478 (490)
                      ..+++..+..
T Consensus        82 ~~~~~al~~~   91 (117)
T 3k9i_A           82 ELLLKIIAET   91 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhC
Confidence            8888776654

>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=98.49  E-value=3e-07  Score=76.59  Aligned_cols=151  Identities=8%  Similarity=-0.034  Sum_probs=99.0

Q ss_pred             HHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCC-CCc--------------HHHHH
Q 011249          289 MHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGI-EPN--------------QVTFI  350 (490)
Q Consensus       289 ~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~p~--------------~~~~~  350 (490)
                      .....|+++++.+.++...+   .....+..+...+...|++++|...|++..+... .|+              ...+.
T Consensus        13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (198)
T 2fbn_A           13 GRENLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNL   92 (198)
T ss_dssp             ---------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHH
Confidence            33444566666665554332   2345677778888889999999999998887321 110              26777


Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhC
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHV  428 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g  428 (490)
                      .+..++...|++++|...++++.+.  .+.+...+..+..+|...|++++|.+.|++..  .+.+...+..+..++...+
T Consensus        93 ~la~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~  170 (198)
T 2fbn_A           93 NLATCYNKNKDYPKAIDHASKVLKI--DKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNKLK  170 (198)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHH
Confidence            8888889999999999999999883  45567788889999999999999999998876  3445667777777777776


Q ss_pred             ChHHHH-HHHHHHH
Q 011249          429 NAELGE-IAARHLL  441 (490)
Q Consensus       429 ~~~~a~-~~~~~~~  441 (490)
                      +.+++. ..+..+.
T Consensus       171 ~~~~~~~~~~~~~f  184 (198)
T 2fbn_A          171 EARKKDKLTFGGMF  184 (198)
T ss_dssp             HHHC----------
T ss_pred             HHHHHHHHHHHHHh
Confidence            666655 4444443

>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=98.48  E-value=4.3e-05  Score=68.05  Aligned_cols=131  Identities=11%  Similarity=0.011  Sum_probs=67.5

Q ss_pred             hcCChh-HHHHHHhhcCCC---CHHhHHHHHHHHHhcCC----------hHHHHHHHHHHHHcCcccChhhHHHHHHHHh
Q 011249          191 KCGEVR-EAKKVFDEISEP---DASCWAAMTVCYVQNGY----------AKAAIEMYKVMRQENVRISEVAMVGAISACT  256 (490)
Q Consensus       191 ~~~~~~-~A~~~~~~~~~~---~~~~~~~l~~~~~~~g~----------~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~  256 (490)
                      +.|.++ +|+++++.+...   +..+|+.--.++...+.          +++++.+++.+....++ +..+|..-..++.
T Consensus        41 ~~~e~s~eaL~~t~~~L~~nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PK-ny~aW~hR~wlL~  119 (331)
T 3dss_A           41 QAGELDESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLLS  119 (331)
T ss_dssp             HTTCCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHHHHHHCchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHh
Confidence            444444 566666665542   23334433333332222          45566666666654322 4455555555555


Q ss_pred             ccC--ChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCC-hHHHHHHHhcccC---CChhHHHHHHHHHHh
Q 011249          257 QLG--DVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGY-LDLAWREFSRIKN---KDVISYSSMITAFAD  323 (490)
Q Consensus       257 ~~g--~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~-~~~A~~~~~~~~~---~~~~~~~~l~~~~~~  323 (490)
                      ..|  +++++..+++.+.+.. +.+...|+.-.-++...|. ++++++.++++.+   .|..+|+-....+..
T Consensus       120 ~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p~N~SAW~~R~~ll~~  191 (331)
T 3dss_A          120 RLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQ  191 (331)
T ss_dssp             HCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHH
T ss_pred             ccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH
Confidence            555  3566666666666654 4455555554555555555 3666666666554   344555555444443

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.45  E-value=1.6e-05  Score=75.12  Aligned_cols=194  Identities=9%  Similarity=-0.010  Sum_probs=101.0

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCcccCh----------------hhHHHHHHHHhccCChHHHHHHHHHHHhcCCC-C
Q 011249          216 MTVCYVQNGYAKAAIEMYKVMRQENVRISE----------------VAMVGAISACTQLGDVEMAAILAKHVDEGCCD-R  278 (490)
Q Consensus       216 l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~----------------~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~-~  278 (490)
                      -...+.+.|++++|++.|.++.+.......                ..+..+...|...|++++|..++..+.+.... +
T Consensus        10 ~a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~   89 (434)
T 4b4t_Q           10 EARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFA   89 (434)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence            345677888888888888888865322111                12556666677777777777776665432111 1


Q ss_pred             ch----hHHHHHHHHHHhcCChHHHHHHHhcccC-----C----ChhHHHHHHHHHHhcCChHHHHHHHHHHHHc--CC-
Q 011249          279 TN----YVSNALIHMHSKCGYLDLAWREFSRIKN-----K----DVISYSSMITAFADHGKSQEALDMFLKMRNE--GI-  342 (490)
Q Consensus       279 ~~----~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~----~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~-  342 (490)
                      +.    .+.+.+...+...|+++.|..+++....     .    -..++..+...|...|++++|..+++++...  +. 
T Consensus        90 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~  169 (434)
T 4b4t_Q           90 KSKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLD  169 (434)
T ss_dssp             HHHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSS
T ss_pred             chHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhcc
Confidence            11    1222333344445666666666554432     0    1234555566666666666666666655431  11 


Q ss_pred             -CCc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC-----chHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          343 -EPN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL-----TEHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       343 -~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                       .|. ...+..++..|...|++++|..++++......-.++     ...+..++..+...|++++|...|.+..
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a~  243 (434)
T 4b4t_Q          170 DKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFESF  243 (434)
T ss_dssp             CSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence             111 124555555666666666666666555432111111     1233444455555566666665554443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.43  E-value=6.6e-07  Score=71.37  Aligned_cols=94  Identities=13%  Similarity=0.034  Sum_probs=56.8

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc----CCC----ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCC------CCCc
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK----DFC----DAGTWGALLGACKVHVNAELGEIAARHLLELGP------EKTG  449 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p------~~~~  449 (490)
                      .+..+...+...|++++|.+.+++..    ..+    ....+..+...+...|++++|.+.++++++..+      ..+.
T Consensus        51 ~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  130 (164)
T 3ro3_A           51 AYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGR  130 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHH
Confidence            34444555555555555555554433    001    133455566667777777777777777765421      1234


Q ss_pred             hHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          450 NSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       450 ~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      .+..++.++...|++++|.+.+++..+.
T Consensus       131 ~~~~la~~~~~~g~~~~A~~~~~~a~~~  158 (164)
T 3ro3_A          131 ACWSLGNAYTALGNHDQAMHFAEKHLEI  158 (164)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            6677788888888888888888776553

>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=98.43  E-value=7.8e-07  Score=81.79  Aligned_cols=138  Identities=9%  Similarity=-0.031  Sum_probs=100.5

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHH
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDL  391 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  391 (490)
                      ..+..+...+.+.|++++|+..|++.++.  .++..      .    ....       +....  ..+.+...|..+..+
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~--~~~~~------~----~~~~-------~~~~~--~~~~~~~~~~nla~~  282 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRY--VEGSR------A----AAED-------ADGAK--LQPVALSCVLNIGAC  282 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--HHHHH------H----HSCH-------HHHGG--GHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHH--hhcCc------c----ccCh-------HHHHH--HHHHHHHHHHHHHHH
Confidence            34666666777777777777777776652  11110      0    0000       11100  112235677888999


Q ss_pred             HhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHH
Q 011249          392 LGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEI  469 (490)
Q Consensus       392 ~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~  469 (490)
                      |.+.|++++|++.+++..  .+.+...+..+..++...|++++|++.|++++++.|+++.++..++.++...++.+++.+
T Consensus       283 ~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l~P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          283 KLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             HHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999998876  344677889999999999999999999999999999999999999999999888887765


Q ss_pred             H
Q 011249          470 V  470 (490)
Q Consensus       470 ~  470 (490)
                      .
T Consensus       363 ~  363 (370)
T 1ihg_A          363 A  363 (370)
T ss_dssp             C
T ss_pred             H
Confidence            4

>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=98.38  E-value=2.1e-05  Score=76.40  Aligned_cols=167  Identities=5%  Similarity=-0.117  Sum_probs=128.2

Q ss_pred             hHHHHHHHhcccC---CChhHHHHHHHHHHhcCC----------hHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCC-
Q 011249          296 LDLAWREFSRIKN---KDVISYSSMITAFADHGK----------SQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGG-  360 (490)
Q Consensus       296 ~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~----------~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g-  360 (490)
                      .++|++.++++..   .+..+|+.-..++...|+          +++++..++++.+.  .| +...|..-...+.+.+ 
T Consensus        45 ~eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~--~pK~y~aW~hR~w~l~~l~~  122 (567)
T 1dce_A           45 DESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRV--NPKSYGTWHHRCWLLSRLPE  122 (567)
T ss_dssp             SHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTCSS
T ss_pred             CHHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHccc
Confidence            4556677766654   234556655555555555          88899999998885  34 4557777777777778 


Q ss_pred             -ChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcC-ChHHHHHHHHhcc--CCCChhhHHHHHHHHhhh---------
Q 011249          361 -LVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSG-QLEKAHSLIMDYK--DFCDAGTWGALLGACKVH---------  427 (490)
Q Consensus       361 -~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~---------  427 (490)
                       +++++++.++++.+.  .+-+...|+.-..++.+.| .++++++.++++.  .+.+...|+....++...         
T Consensus       123 ~~~~~el~~~~k~l~~--d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~~~~~  200 (567)
T 1dce_A          123 PNWARELELCARFLEA--DERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQ  200 (567)
T ss_dssp             CCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSC
T ss_pred             ccHHHHHHHHHHHHhh--ccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhhccccccccc
Confidence             679999999999883  4556777877777778888 8899999998887  445677888777776553         


Q ss_pred             -----CChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcch
Q 011249          428 -----VNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKD  466 (490)
Q Consensus       428 -----g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  466 (490)
                           +.++++++.++++++.+|++..+|..+..++.+.+++++
T Consensus       201 ~~~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          201 GRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCCSC
T ss_pred             ccccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCCCccc
Confidence                 567999999999999999999999999999999998666

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.36  E-value=2.7e-06  Score=67.69  Aligned_cols=132  Identities=11%  Similarity=-0.004  Sum_probs=79.0

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcCC-CCc----HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC----ch
Q 011249          313 SYSSMITAFADHGKSQEALDMFLKMRNEGI-EPN----QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL----TE  383 (490)
Q Consensus       313 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~-~p~----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~----~~  383 (490)
                      ++..+...+...|++++|...+++..+... .++    ...+..+...+...|++++|...+++..+.....++    ..
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            444555556666666666666666554210 011    124555566666677777777777666542111111    33


Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc----CCC----ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK----DFC----DAGTWGALLGACKVHVNAELGEIAARHLLELG  444 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  444 (490)
                      .+..+...+...|++++|.+.+++..    ...    ....+..+...+...|++++|.+.++++.+..
T Consensus        91 ~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~  159 (164)
T 3ro3_A           91 SCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAMHFAEKHLEIS  159 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHccchHhHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHH
Confidence            45566677777777777777776554    111    13456677778888899999999988887754

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=98.36  E-value=3.5e-06  Score=79.95  Aligned_cols=124  Identities=11%  Similarity=0.011  Sum_probs=97.1

Q ss_pred             HhcCCCChHHHHHHHHHHHHHcC--CCC----CchHHHHHHHHHhhcCChHHHHHHHHhcc---------CCCC-hhhHH
Q 011249          355 ACSHGGLVEDGCKQFELMTRVFG--IKP----LTEHLTCMVDLLGRSGQLEKAHSLIMDYK---------DFCD-AGTWG  418 (490)
Q Consensus       355 ~~~~~g~~~~a~~~~~~~~~~~~--~~~----~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---------~~~~-~~~~~  418 (490)
                      .+..+|++++|+.++++..+...  +.|    ...+++.|+.+|...|++++|..++++..         ..|+ ..+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            35578999999988888776421  122    25567888999999999999999887755         2233 34788


Q ss_pred             HHHHHHhhhCChHHHHHHHHHHHh-----cCCCCCc---hHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          419 ALLGACKVHVNAELGEIAARHLLE-----LGPEKTG---NSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       419 ~l~~~~~~~g~~~~a~~~~~~~~~-----~~p~~~~---~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                      .|...|...|++++|+.+++++++     .+|++|.   ....+..++.+.|++++|+.++.++++.-
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~~  465 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREAA  465 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            899999999999999999999987     5687765   44577888889999999999999998754

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=98.36  E-value=1.5e-06  Score=79.07  Aligned_cols=153  Identities=9%  Similarity=-0.067  Sum_probs=83.3

Q ss_pred             hhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCC
Q 011249          280 NYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHG  359 (490)
Q Consensus       280 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  359 (490)
                      ...+..+...+.+.|++++|...|++....++...     .+...++++++...+.          ...+..+..++.+.
T Consensus       179 a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~-----~~~~~~~~~~~~~~l~----------~~~~~nla~~~~~~  243 (338)
T 2if4_A          179 ADRRKMDGNSLFKEEKLEEAMQQYEMAIAYMGDDF-----MFQLYGKYQDMALAVK----------NPCHLNIAACLIKL  243 (338)
T ss_dssp             HHHHHHHHHHTCSSSCCHHHHHHHHHHHHHSCHHH-----HHTCCHHHHHHHHHHH----------THHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhccch-----hhhhcccHHHHHHHHH----------HHHHHHHHHHHHHc
Confidence            34567788889999999999999998765222111     1223333444332221          13677888889999


Q ss_pred             CChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHH-HhhhCChHHHHHH
Q 011249          360 GLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGA-CKVHVNAELGEIA  436 (490)
Q Consensus       360 g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~-~~~~g~~~~a~~~  436 (490)
                      |++++|+..++++.+.  .+.+...+..+..+|...|++++|...|++.. ..| +...+..+... ....+..+++...
T Consensus       244 g~~~~A~~~~~~al~~--~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~l~p~~~~a~~~L~~l~~~~~~~~~~a~~~  321 (338)
T 2if4_A          244 KRYDEAIGHCNIVLTE--EEKNPKALFRRGKAKAELGQMDSARDDFRKAQKYAPDDKAIRRELRALAEQEKALYQKQKEM  321 (338)
T ss_dssp             TCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC-----------------------------
T ss_pred             CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999873  34567788899999999999999999998886 334 44555555554 2445678889999


Q ss_pred             HHHHHhcCCCCCc
Q 011249          437 ARHLLELGPEKTG  449 (490)
Q Consensus       437 ~~~~~~~~p~~~~  449 (490)
                      |.+++...|+++.
T Consensus       322 ~~~~l~~~p~~~~  334 (338)
T 2if4_A          322 YKGIFKGKDEGGA  334 (338)
T ss_dssp             -------------
T ss_pred             HHHhhCCCCCCCC
Confidence            9999998887653

>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=98.31  E-value=3.9e-06  Score=80.07  Aligned_cols=113  Identities=8%  Similarity=-0.119  Sum_probs=48.8

Q ss_pred             HhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHH
Q 011249          322 ADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEK  400 (490)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  400 (490)
                      .+.|++++|...+++..+.  .| +...+..+..++.+.|++++|...++++.+  ..+.+...+..+..+|...|++++
T Consensus        17 ~~~g~~~~A~~~~~~Al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~--l~p~~~~~~~~lg~~~~~~g~~~e   92 (477)
T 1wao_1           17 FKAKDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIE--LDKKYIKGYYRRAASNMALGKFRA   92 (477)
T ss_dssp             TTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--SCTTCHHHHHHHHHHHHHHTCHHH
T ss_pred             HHhCCHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHcCCHHH
Confidence            3444555555555554442  22 233444444455555555555555555544  222334444445555555555555


Q ss_pred             HHHHHHhcc--CCCChhhHHHHHHH--HhhhCChHHHHHHHH
Q 011249          401 AHSLIMDYK--DFCDAGTWGALLGA--CKVHVNAELGEIAAR  438 (490)
Q Consensus       401 A~~~~~~~~--~~~~~~~~~~l~~~--~~~~g~~~~a~~~~~  438 (490)
                      |.+.|++..  .+.+...+..+..+  +...|++++|++.++
T Consensus        93 A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           93 ALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            555554433  12222333333333  444455555555555

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=98.31  E-value=2.7e-06  Score=60.24  Aligned_cols=81  Identities=19%  Similarity=0.142  Sum_probs=66.4

Q ss_pred             chHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          382 TEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       382 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ...+..+...+...|++++|...+++..  .+.+...+..+..++...|++++|...++++.+.+|+++.++..++.++.
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~   88 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAKQNLGNAKQ   88 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence            4566677788888888888888887765  34466778888888999999999999999999999999999999888887


Q ss_pred             hcC
Q 011249          460 SMG  462 (490)
Q Consensus       460 ~~g  462 (490)
                      +.|
T Consensus        89 ~~g   91 (91)
T 1na3_A           89 KQG   91 (91)
T ss_dssp             HHC
T ss_pred             hcC
Confidence            654

>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=98.29  E-value=6.3e-07  Score=69.71  Aligned_cols=83  Identities=12%  Similarity=0.027  Sum_probs=44.1

Q ss_pred             CChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCC----------hHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcC-
Q 011249          396 GQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVN----------AELGEIAARHLLELGPEKTGNSALLANIYASMG-  462 (490)
Q Consensus       396 g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~----------~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g-  462 (490)
                      +.+++|.+.++...  .+.+...|..+..++...++          +++|+..|+++++++|+++.+|..++.+|...| 
T Consensus        16 ~~feeA~~~~~~Ai~l~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~~lg~   95 (158)
T 1zu2_A           16 LLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAF   95 (158)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhcc
Confidence            33444444444333  22334444444444444433          346666666666666666666666666666553 


Q ss_pred             ----------CcchHHHHHHHhhhcc
Q 011249          463 ----------KWKDSEIVKMMISETE  478 (490)
Q Consensus       463 ----------~~~~A~~~~~~~~~~~  478 (490)
                                ++++|++.|++..+.+
T Consensus        96 l~P~~~~a~g~~~eA~~~~~kAl~l~  121 (158)
T 1zu2_A           96 LTPDETEAKHNFDLATQFFQQAVDEQ  121 (158)
T ss_dssp             HCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             cCcchhhhhccHHHHHHHHHHHHHhC
Confidence                      5666666666665543

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=98.28  E-value=2.6e-06  Score=61.77  Aligned_cols=66  Identities=23%  Similarity=0.118  Sum_probs=48.7

Q ss_pred             CChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          412 CDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       412 ~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      .++..+..+..++...|++++|+..|+++++.+|+++.+|..++.+|...|++++|.+.+++..+.
T Consensus         5 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l   70 (100)
T 3ma5_A            5 EDPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEV   70 (100)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            345566777777777777777777777777777777777777777777777777777777766544

>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=98.27  E-value=2.2e-06  Score=66.81  Aligned_cols=74  Identities=9%  Similarity=-0.008  Sum_probs=59.5

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc-C-------CC-ChhhH----HHHHHHHhhhCChHHHHHHHHHHHhcCCCCCch
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK-D-------FC-DAGTW----GALLGACKVHVNAELGEIAARHLLELGPEKTGN  450 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~-~-------~~-~~~~~----~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~  450 (490)
                      .|..+..++.+.|++++|+..+++.. .       .| +...|    .....++...|++++|+..|++++++.|++..+
T Consensus        59 a~~n~g~al~~Lgr~~eAl~~~~kAL~l~n~~~e~~pd~~~A~~~~~~~rG~aL~~lgr~eEAl~~y~kAlel~p~d~~~  138 (159)
T 2hr2_A           59 CHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKLWISAVYSRALALDGLGRGAEAMPEFKKVVEMIEERKGE  138 (159)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCCSC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHhHHHHHHHCCCHHHHHHHHHHHHhcCCCcHHH
Confidence            67777777788888888877776655 3       55 44577    889999999999999999999999999999887


Q ss_pred             HHHHHHH
Q 011249          451 SALLANI  457 (490)
Q Consensus       451 ~~~l~~~  457 (490)
                      +..+..+
T Consensus       139 ~~~~~~~  145 (159)
T 2hr2_A          139 TPGKERM  145 (159)
T ss_dssp             CTTHHHH
T ss_pred             HHHHHHH
Confidence            7666544

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=98.24  E-value=2.7e-06  Score=63.56  Aligned_cols=81  Identities=11%  Similarity=-0.082  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHH
Q 011249          364 DGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLL  441 (490)
Q Consensus       364 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  441 (490)
                      .|+..+++..+  ..+.+...+..+..+|...|++++|...|++..  .+.+...|..+..++...|++++|...|++++
T Consensus         3 ~a~~~~~~al~--~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLA--QGTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHT--TTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH--hCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            45566666654  233445666667777777777777777776655  33445566666777777777777777777777


Q ss_pred             hcCCC
Q 011249          442 ELGPE  446 (490)
Q Consensus       442 ~~~p~  446 (490)
                      +..|.
T Consensus        81 ~~~~~   85 (115)
T 2kat_A           81 AAAQS   85 (115)
T ss_dssp             HHHHH
T ss_pred             Hhccc
Confidence            66654

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=98.19  E-value=6.5e-06  Score=58.33  Aligned_cols=70  Identities=11%  Similarity=0.048  Sum_probs=60.6

Q ss_pred             CCChhhHHHHHHHHhhhCC---hHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          411 FCDAGTWGALLGACKVHVN---AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       411 ~~~~~~~~~l~~~~~~~g~---~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      ++++..+..+..++...++   .++|..+++++++.+|+++.+...++..+.+.|++++|+..|+++.+..+.
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~   75 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDP   75 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCT
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence            4567778888887765554   799999999999999999999999999999999999999999999887665

>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=98.17  E-value=6.5e-06  Score=78.17  Aligned_cols=66  Identities=8%  Similarity=-0.089  Sum_probs=61.5

Q ss_pred             hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          414 AGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       414 ~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ...|..+..++.+.|++++|+..++++++++|+++.+|..++.+|...|++++|+..|+++.+..+
T Consensus       317 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l~P  382 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNP  382 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCC
Confidence            468888999999999999999999999999999999999999999999999999999999987654

>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=98.08  E-value=3.3e-05  Score=75.13  Aligned_cols=152  Identities=9%  Similarity=-0.044  Sum_probs=124.1

Q ss_pred             CChHHHHHHHHHHHHcCCCCcHH-HHHHHHHHhcCCCC----------hHHHHHHHHHHHHHcCCCCCchHHHHHHHHHh
Q 011249          325 GKSQEALDMFLKMRNEGIEPNQV-TFIGVLTACSHGGL----------VEDGCKQFELMTRVFGIKPLTEHLTCMVDLLG  393 (490)
Q Consensus       325 ~~~~~a~~~~~~~~~~~~~p~~~-~~~~l~~~~~~~g~----------~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~  393 (490)
                      ...++|++.++++.+.  .|+.. .|+.-..++...|+          ++++++.++.+.+  ..+.+...|..-..++.
T Consensus        43 ~~~eeal~~~~~~l~~--nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~--~~pK~y~aW~hR~w~l~  118 (567)
T 1dce_A           43 ELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLR--VNPKSYGTWHHRCWLLS  118 (567)
T ss_dssp             CCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHH
Confidence            3456889999999984  66544 55555555555555          8999999999998  45667778888888888


Q ss_pred             hcC--ChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhC-ChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhc-------
Q 011249          394 RSG--QLEKAHSLIMDYK--DFCDAGTWGALLGACKVHV-NAELGEIAARHLLELGPEKTGNSALLANIYASM-------  461 (490)
Q Consensus       394 ~~g--~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g-~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~-------  461 (490)
                      +.|  +++++++.++++.  .+.+...|+.-..++...| .++++++.++++++.+|.+..+|...+.++.+.       
T Consensus       119 ~l~~~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~~~  198 (567)
T 1dce_A          119 RLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSG  198 (567)
T ss_dssp             TCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSS
T ss_pred             HcccccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhhccccccc
Confidence            899  7799999999988  5667889998888888888 899999999999999999999999999998874       


Q ss_pred             -------CCcchHHHHHHHhhhcccc
Q 011249          462 -------GKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       462 -------g~~~~A~~~~~~~~~~~~~  480 (490)
                             ++++++++.+++.....+.
T Consensus       199 ~~~~~~~~~~~eel~~~~~ai~~~P~  224 (567)
T 1dce_A          199 PQGRLPENVLLKELELVQNAFFTDPN  224 (567)
T ss_dssp             SCCSSCHHHHHHHHHHHHHHHHHCSS
T ss_pred             ccccccHHHHHHHHHHHHHHHhhCCC
Confidence                   5678899999888776543

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=98.03  E-value=1.4e-05  Score=59.54  Aligned_cols=78  Identities=9%  Similarity=-0.088  Sum_probs=49.5

Q ss_pred             HHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhc
Q 011249          400 KAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       400 ~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      +|++.|++..  .+.+...+..+...+...|++++|+..++++++.+|+++..+..++.+|...|++++|...+++..+.
T Consensus         3 ~a~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~   82 (115)
T 2kat_A            3 AITERLEAMLAQGTDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGLAA   82 (115)
T ss_dssp             CHHHHHHHHHTTTCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            3444554443  23345566666666666777777777777777777766666777777777777777777776666543

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=98.02  E-value=1.3e-05  Score=59.01  Aligned_cols=68  Identities=6%  Similarity=-0.122  Sum_probs=62.4

Q ss_pred             ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          413 DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       413 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      +...+..+...+...|++++|++.|+++++..|+++.++..++.++.+.|++++|++.+++..+..+.
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~   70 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQPQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTST   70 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCSS
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCC
Confidence            45678888899999999999999999999999999999999999999999999999999999876543

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=98.02  E-value=1.9e-08  Score=90.96  Aligned_cols=392  Identities=9%  Similarity=0.012  Sum_probs=228.1

Q ss_pred             CchhHhHHHHHHHHHhcCCCCHHHHHHHhccCCCCCCceehHHHHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHH
Q 011249           31 HDQYHYYAQFLIRLLQLPGDNLSYARQVFDQIPKCKTQFLWTSLIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVL  110 (490)
Q Consensus        31 ~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll  110 (490)
                      ..+.  +|+.|..+..+.+. +.+|++-|=+...|   ..|..+|....+.|.+++-++.+.-.++..-.|..  =+.++
T Consensus        52 n~p~--VWs~LgkAqL~~~~-v~eAIdsyIkA~Dp---s~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~~I--DteLi  123 (624)
T 3lvg_A           52 NEPA--VWSQLAKAQLQKGM-VKEAIDSYIKADDP---SSYMEVVQAANTSGNWEELVKYLQMARKKARESYV--ETELI  123 (624)
T ss_dssp             CCCC--CSSSHHHHTTTSSS-CTTTTTSSCCCSCC---CSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCSTTT--THHHH
T ss_pred             CCcc--HHHHHHHHHHccCc-hHHHHHHHHhCCCh---HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhccccc--HHHHH
Confidence            6777  88999999999988 88888777665554   55888999999999999988888766654333322  23344


Q ss_pred             HHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHH
Q 011249          111 NACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYG  190 (490)
Q Consensus       111 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~  190 (490)
                      -              +|++.++..+-.+.+   ..||..-...+..-|...|.++.|.-+|..+     ..|..|...++
T Consensus       124 ~--------------ayAk~~rL~elEefl---~~~N~A~iq~VGDrcf~e~lYeAAKilys~i-----sN~akLAstLV  181 (624)
T 3lvg_A          124 F--------------ALAKTNRLAELEEFI---NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-----SNFGRLASTLV  181 (624)
T ss_dssp             H--------------HHHTSCSSSTTTSTT---SCCSSSCTHHHHHHHHHSCCSTTSSTTGGGS-----CCCTTTSSSSS
T ss_pred             H--------------HHHhhCcHHHHHHHH---cCCCcccHHHHHHHHHHccCHHHHHHHHHhC-----ccHHHHHHHHH
Confidence            3              467777765432221   2366666667778888888888877766544     33444555566


Q ss_pred             hcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHH
Q 011249          191 KCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKH  270 (490)
Q Consensus       191 ~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~  270 (490)
                      +.|++..|.+.-++.  .++.+|..+-.+|...+.+..|.-.--.++-     .+.....++..|...|.+++.+.+++.
T Consensus       182 ~L~~yq~AVdaArKA--ns~ktWKeV~~ACvd~~EfrLAqicGLniIv-----hadeL~elv~~YE~~G~f~ELIsLlEa  254 (624)
T 3lvg_A          182 HLGEYQAAVDGARKA--NSTRTWKEVCFACVDGKEFRLAQMCGLHIVV-----HADELEELINYYQDRGYFEELITMLEA  254 (624)
T ss_dssp             SCSGGGSSTTTTTTC--CSSCSHHHHTHHHHHSCTTTTTTHHHHHHHC-----CSSCCSGGGSSSSTTCCCTTSTTTHHH
T ss_pred             HHHHHHHHHHHHHhc--CChhHHHHHHHHHhCchHHHHHHHhcchhcc-----cHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            777777665443332  5677888888899999988877554333331     222233456678888999988888888


Q ss_pred             HHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC----C-------ChhHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011249          271 VDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN----K-------DVISYSSMITAFADHGKSQEALDMFLKMRN  339 (490)
Q Consensus       271 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~-------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  339 (490)
                      ..... ......|+-|.-.|++- ++++..+.++....    |       ....|.-++-.|.+-.++|.|...   |.+
T Consensus       255 glglE-rAHmGmFTELaILYsKY-~PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA~lt---Mi~  329 (624)
T 3lvg_A          255 ALGLE-RAHMGMFTELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIIT---MMN  329 (624)
T ss_dssp             HTTST-TCCHHHHHHHHHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHHHHT---TTS
T ss_pred             HhCCC-chhHHHHHHHHHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHHHHH---HHh
Confidence            76543 45667788888888775 45555555554332    2       455688888888888888876532   221


Q ss_pred             cCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHh------------
Q 011249          340 EGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMD------------  407 (490)
Q Consensus       340 ~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~------------  407 (490)
                      +  +|+...-..+.....+..+.+---+.+.-.     +.-.+...+.|+.++...=+...+.++|++            
T Consensus       330 h--~~~Aw~h~~Fkdii~KVaN~EiyYKAi~FY-----L~e~P~lL~DLL~vL~prlDh~RvV~~~~k~~~LpLIkpYL~  402 (624)
T 3lvg_A          330 H--PTDAWKEGQFKDIITKVANVELYYRAIQFY-----LEFKPLLLNDLLMVLSPRLDHTRAVNYFSKVKQLPLVKPYLR  402 (624)
T ss_dssp             C--HHHHCCGGGGTTTGGGCSCSHHHHHHHHHH-----TTSCCTTSHHHHHHHCTTCCSTTTHHHHHTTTCGGGGTGGGT
T ss_pred             C--ChhhccHHHHHHHHHHcchHHHHHHHHHHH-----HHhChHHHHHHHHhccccCChHHHHHHHHhcCCchhhHHHHH
Confidence            1  111111111222233333333222222111     112222334444444444444444444433            


Q ss_pred             -ccCCCChhhHHHHHHHHhhhCChHHHHHHHHHH---------HhcC-CCCCchHHHHHHHHHhcCCcchHHHHH
Q 011249          408 -YKDFCDAGTWGALLGACKVHVNAELGEIAARHL---------LELG-PEKTGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       408 -~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~---------~~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                       .....+..+-.++-..+....|++.-....+..         .++. .+-..+...-+..|.+.++|+++..+.
T Consensus       403 ~Vq~~N~~aVNeAln~L~IEEEDy~~LR~SId~ydNFD~i~LA~rLEkHeL~eFRrIAA~LYkkn~rw~qsi~l~  477 (624)
T 3lvg_A          403 SVQNHNNKSVNESLNNLFITEEDYQALRTSIDAYDNFDNISLAQRLEKHELIEFRRIAAYLFKGNNRWKQSVELC  477 (624)
T ss_dssp             SCCCSCCHHHHHHHHHHHHHTTCCHHHHHTTSSCCCSCTTHHHHHHHTCSSHHHHHHHHHHHHTTCHHHHHSSCS
T ss_pred             HHHHhhHHHHHHHHHHHHhhhhhHHHHHHHHHHhccccHHHHHHHHhhCchHHHHHHHHHHHHhcccHHHHHHHH
Confidence             333344555556666677777766443322110         0010 112344445566677777777776654

>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=98.02  E-value=5.5e-05  Score=58.38  Aligned_cols=109  Identities=10%  Similarity=-0.047  Sum_probs=57.2

Q ss_pred             ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh----cCChHHH
Q 011249          326 KSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR----SGQLEKA  401 (490)
Q Consensus       326 ~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A  401 (490)
                      ++++|...|++..+.| .|+..    +...|...+.+++|.+.|++..+.    -++..+..|..+|..    .+++++|
T Consensus        10 d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~----g~~~a~~~Lg~~y~~G~g~~~d~~~A   80 (138)
T 1klx_A           10 DLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACEL----NSGNGCRFLGDFYENGKYVKKDLRKA   80 (138)
T ss_dssp             HHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHT----TCHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             CHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcC----CCHHHHHHHHHHHHcCCCCCccHHHH
Confidence            4566666666666654 22222    445555555566666666666552    234444555555554    4555555


Q ss_pred             HHHHHhccCCCChhhHHHHHHHHhh----hCChHHHHHHHHHHHhc
Q 011249          402 HSLIMDYKDFCDAGTWGALLGACKV----HVNAELGEIAARHLLEL  443 (490)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~  443 (490)
                      .++|++.....++..+..+...|..    .+|.++|.+.|+++.+.
T Consensus        81 ~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~  126 (138)
T 1klx_A           81 AQYYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRL  126 (138)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHC
Confidence            5555554433444455555555544    45555555555555554

>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=98.00  E-value=8.5e-06  Score=63.34  Aligned_cols=91  Identities=15%  Similarity=0.011  Sum_probs=59.8

Q ss_pred             ChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCC----------hHHHHHHHHhcc--CCCChhhHHHHHHHHhhh-
Q 011249          361 LVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ----------LEKAHSLIMDYK--DFCDAGTWGALLGACKVH-  427 (490)
Q Consensus       361 ~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~----------~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~-  427 (490)
                      .+++|.+.++...+.  -+.+...|..+..++...|+          +++|+..|++..  .+.+...|..+..+|... 
T Consensus        17 ~feeA~~~~~~Ai~l--~P~~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~ldP~~~~A~~~LG~ay~~lg   94 (158)
T 1zu2_A           17 LFEQIRQDAENTYKS--NPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTSFA   94 (158)
T ss_dssp             HHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHhc
Confidence            455555555555552  23345555555555555544          347777776665  344566777777777765 


Q ss_pred             ----------CChHHHHHHHHHHHhcCCCCCchHHH
Q 011249          428 ----------VNAELGEIAARHLLELGPEKTGNSAL  453 (490)
Q Consensus       428 ----------g~~~~a~~~~~~~~~~~p~~~~~~~~  453 (490)
                                |++++|++.|+++++++|++......
T Consensus        95 ~l~P~~~~a~g~~~eA~~~~~kAl~l~P~~~~y~~a  130 (158)
T 1zu2_A           95 FLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKS  130 (158)
T ss_dssp             HHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             ccCcchhhhhccHHHHHHHHHHHHHhCCCCHHHHHH
Confidence                      58999999999999999997644333

>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=97.99  E-value=5.6e-05  Score=69.39  Aligned_cols=92  Identities=9%  Similarity=0.033  Sum_probs=49.8

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHhcccCC-------------------ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC
Q 011249          281 YVSNALIHMHSKCGYLDLAWREFSRIKNK-------------------DVISYSSMITAFADHGKSQEALDMFLKMRNEG  341 (490)
Q Consensus       281 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~-------------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~  341 (490)
                      ..+..+...+.+.|++++|+..|++..+-                   +...|..+..+|.+.|++++|+..++++++. 
T Consensus       224 ~~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~-  302 (370)
T 1ihg_A          224 EDLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEI-  302 (370)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-
Confidence            45677888999999999999999876640                   1233444444444444444444444444432 


Q ss_pred             CCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Q 011249          342 IEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTR  374 (490)
Q Consensus       342 ~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  374 (490)
                       .| +...+..+..+|...|++++|...|+++.+
T Consensus       303 -~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~  335 (370)
T 1ihg_A          303 -DPSNTKALYRRAQGWQGLKEYDQALADLKKAQE  335 (370)
T ss_dssp             -CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             -CchhHHHHHHHHHHHHHccCHHHHHHHHHHHHH
Confidence             22 223344444444444444444444444443

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.99  E-value=1.5e-05  Score=57.48  Aligned_cols=82  Identities=12%  Similarity=0.016  Sum_probs=65.2

Q ss_pred             HHHHHhhcCChHHHHHHHHhcc--CCCChh-hHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCc
Q 011249          388 MVDLLGRSGQLEKAHSLIMDYK--DFCDAG-TWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKW  464 (490)
Q Consensus       388 l~~~~~~~g~~~~A~~~~~~~~--~~~~~~-~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  464 (490)
                      .+..+.+.|++++|.+.+++..  .+.+.. .+..+..++...|++++|++.|+++++.+|+++.++..        +.+
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~--------~~~   77 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNPDSPALQAR--------KMV   77 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTHHHHH--------HHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHH--------HHH
Confidence            4567788899999999998876  444567 88888899999999999999999999999998887633        455


Q ss_pred             chHHHHHHHhhhc
Q 011249          465 KDSEIVKMMISET  477 (490)
Q Consensus       465 ~~A~~~~~~~~~~  477 (490)
                      .++...+++..+.
T Consensus        78 ~~a~~~~~~~~~~   90 (99)
T 2kc7_A           78 MDILNFYNKDMYN   90 (99)
T ss_dssp             HHHHHHHCCTTHH
T ss_pred             HHHHHHHHHHhcc
Confidence            6667777665543

>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=97.88  E-value=0.00031  Score=54.06  Aligned_cols=112  Identities=4%  Similarity=-0.087  Sum_probs=93.6

Q ss_pred             CChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhh----hCChHHHHH
Q 011249          360 GLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKV----HVNAELGEI  435 (490)
Q Consensus       360 g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~  435 (490)
                      +++++|...|++..+. + .|.  ..  +...|...+..++|.++|++.....++..+..+...|..    .+|+++|.+
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-EMF--GC--LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQ   82 (138)
T ss_dssp             HHHHHHHHHHHHHHHT-T-CTT--HH--HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHH
T ss_pred             cCHHHHHHHHHHHHcC-C-CHh--hh--HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHH
Confidence            4678899999999884 4 222  33  788888888899999999888766788888888888887    789999999


Q ss_pred             HHHHHHhcCCCCCchHHHHHHHHHh----cCCcchHHHHHHHhhhccc
Q 011249          436 AARHLLELGPEKTGNSALLANIYAS----MGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       436 ~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~  479 (490)
                      .|+++.+.  .++..+..|+.+|..    .+++++|.+.+++..+.|.
T Consensus        83 ~~~~Aa~~--g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~  128 (138)
T 1klx_A           83 YYSKACGL--NDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  128 (138)
T ss_dssp             HHHHHHHT--TCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHcC--CCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCCC
Confidence            99999886  578889999999998    8999999999999888764

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.87  E-value=3.7e-05  Score=54.15  Aligned_cols=67  Identities=19%  Similarity=0.153  Sum_probs=61.2

Q ss_pred             ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          413 DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       413 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +...+..+...+...|++++|+..++++++..|+++.++..++.++.+.|++++|...+++..+..+
T Consensus         8 ~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~p   74 (91)
T 1na3_A            8 SAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP   74 (91)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             cHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC
Confidence            3557788888999999999999999999999999999999999999999999999999999887643

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.78  E-value=0.00011  Score=69.69  Aligned_cols=123  Identities=10%  Similarity=-0.075  Sum_probs=86.3

Q ss_pred             HHHhcCChHHHHHHHHHHHHcC---CC---Cc-HHHHHHHHHHhcCCCChHHHHHHHHHHHHHc--CCCC----CchHHH
Q 011249          320 AFADHGKSQEALDMFLKMRNEG---IE---PN-QVTFIGVLTACSHGGLVEDGCKQFELMTRVF--GIKP----LTEHLT  386 (490)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~---~~---p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~--~~~~----~~~~~~  386 (490)
                      .+..+|++++|+.++++..+..   +-   |+ ..+++.|...|...|++++|..++++..+..  -+.|    ...+++
T Consensus       318 ~~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~  397 (490)
T 3n71_A          318 KARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVM  397 (490)
T ss_dssp             HHHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence            3556788888888888776521   12   22 2477888888888888888888888776531  1222    245677


Q ss_pred             HHHHHHhhcCChHHHHHHHHhcc---------CCCCh-hhHHHHHHHHhhhCChHHHHHHHHHHHh
Q 011249          387 CMVDLLGRSGQLEKAHSLIMDYK---------DFCDA-GTWGALLGACKVHVNAELGEIAARHLLE  442 (490)
Q Consensus       387 ~l~~~~~~~g~~~~A~~~~~~~~---------~~~~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~  442 (490)
                      .|...|...|++++|..++++..         ..|+. .+...+..++...+.+++|+..|.++.+
T Consensus       398 nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~  463 (490)
T 3n71_A          398 RAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMRE  463 (490)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            88888999999999988887655         22322 2445556677788899999999998876

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=97.73  E-value=0.0001  Score=53.19  Aligned_cols=67  Identities=12%  Similarity=-0.060  Sum_probs=48.4

Q ss_pred             CCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          380 PLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       380 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      .+...+..+..+|...|++++|++.|++..  .+.+...|..+..++...|++++|++.+++++++.|.
T Consensus         5 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~~~   73 (100)
T 3ma5_A            5 EDPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEVARE   73 (100)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhhc
Confidence            345566677777777788888888777665  3445667777777788888888888888888776543

>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=97.71  E-value=6.4e-05  Score=70.07  Aligned_cols=84  Identities=7%  Similarity=-0.069  Sum_probs=62.4

Q ss_pred             hcCChHHHHHHHHhcc---------CCCC-hhhHHHHHHHHhhhCChHHHHHHHHHHHh-----cCCCCC---chHHHHH
Q 011249          394 RSGQLEKAHSLIMDYK---------DFCD-AGTWGALLGACKVHVNAELGEIAARHLLE-----LGPEKT---GNSALLA  455 (490)
Q Consensus       394 ~~g~~~~A~~~~~~~~---------~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-----~~p~~~---~~~~~l~  455 (490)
                      ..|++++|..++++..         ..|+ ..+++.++.+|...|++++|+.+++++++     .+|++|   ..++.|+
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            3467777777776543         1222 34778888888888999999988888876     346555   4677888


Q ss_pred             HHHHhcCCcchHHHHHHHhhhc
Q 011249          456 NIYASMGKWKDSEIVKMMISET  477 (490)
Q Consensus       456 ~~~~~~g~~~~A~~~~~~~~~~  477 (490)
                      .+|..+|++++|+.++++..+.
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~i  411 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIAI  411 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHHH
Confidence            8899999999999998877653

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=97.68  E-value=4.4e-05  Score=54.90  Aligned_cols=61  Identities=16%  Similarity=0.173  Sum_probs=55.9

Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCc-hHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTG-NSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~-~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      ....+...|++++|++.++++++.+|+++. ++..++.+|...|++++|.+.+++..+.++.
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~   67 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELNPD   67 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCC
Confidence            456778899999999999999999999999 9999999999999999999999999877553

>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=97.60  E-value=0.00015  Score=67.77  Aligned_cols=87  Identities=8%  Similarity=-0.033  Sum_probs=58.3

Q ss_pred             HHHhhcCChHHHHHHHHhcc------CCC----ChhhHHHHHHHHhhhCChHHHHHHHHHHHh-----cCCCCC---chH
Q 011249          390 DLLGRSGQLEKAHSLIMDYK------DFC----DAGTWGALLGACKVHVNAELGEIAARHLLE-----LGPEKT---GNS  451 (490)
Q Consensus       390 ~~~~~~g~~~~A~~~~~~~~------~~~----~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~-----~~p~~~---~~~  451 (490)
                      ..+.+.|++++|..++++..      ..|    ...+++.++.+|...|++++|+.+++++++     .+|++|   ..+
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            34456677777777765543      111    134667777777778888888888887775     345554   356


Q ss_pred             HHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          452 ALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       452 ~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      +.|+.+|...|++++|+.++++..+
T Consensus       375 ~nLa~~~~~~g~~~eA~~~~~~Al~  399 (429)
T 3qwp_A          375 MKVGKLQLHQGMFPQAMKNLRLAFD  399 (429)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            7778888888888888888777654

>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=97.53  E-value=0.00054  Score=63.85  Aligned_cols=95  Identities=15%  Similarity=-0.018  Sum_probs=72.1

Q ss_pred             CCCChHHHHHHHHHHHHHc--CCCCC----chHHHHHHHHHhhcCChHHHHHHHHhcc---------CCCC-hhhHHHHH
Q 011249          358 HGGLVEDGCKQFELMTRVF--GIKPL----TEHLTCMVDLLGRSGQLEKAHSLIMDYK---------DFCD-AGTWGALL  421 (490)
Q Consensus       358 ~~g~~~~a~~~~~~~~~~~--~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~---------~~~~-~~~~~~l~  421 (490)
                      ..|++++|+.++++..+..  -+.|+    ..+++.|+.+|...|++++|..++++..         ..|+ ..+++.|.
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            4678888888888876632  12222    4567888899999999999999887765         2333 34788899


Q ss_pred             HHHhhhCChHHHHHHHHHHHh-----cCCCCCchHH
Q 011249          422 GACKVHVNAELGEIAARHLLE-----LGPEKTGNSA  452 (490)
Q Consensus       422 ~~~~~~g~~~~a~~~~~~~~~-----~~p~~~~~~~  452 (490)
                      ..|...|++++|+.+++++++     .+|++|.+-.
T Consensus       390 ~~~~~qg~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~  425 (433)
T 3qww_A          390 RLYMGLENKAAGEKALKKAIAIMEVAHGKDHPYISE  425 (433)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHH
T ss_pred             HHHHhccCHHHHHHHHHHHHHHHHHHcCCCChHHHH
Confidence            999999999999999999987     5688776443

>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=97.39  E-value=0.0039  Score=55.77  Aligned_cols=137  Identities=9%  Similarity=-0.063  Sum_probs=72.5

Q ss_pred             ChhHHHHHHHHH--HhcC---ChHHHHHHHHHHHHcCCCCcH-HHHHHHHHHhc----CCC----ChHHHHHHHHHHHHH
Q 011249          310 DVISYSSMITAF--ADHG---KSQEALDMFLKMRNEGIEPNQ-VTFIGVLTACS----HGG----LVEDGCKQFELMTRV  375 (490)
Q Consensus       310 ~~~~~~~l~~~~--~~~~---~~~~a~~~~~~~~~~~~~p~~-~~~~~l~~~~~----~~g----~~~~a~~~~~~~~~~  375 (490)
                      +...|...+.+.  ...+   +..+|..+|++.++.  .|+. ..+..+..+|.    ..+    ........++.....
T Consensus       193 ~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~l--DP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a~  270 (372)
T 3ly7_A          193 RGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQS--SPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVTL  270 (372)
T ss_dssp             SGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHhc
Confidence            555565555543  2222   357788888888873  6653 34443333332    000    011111111111110


Q ss_pred             cCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCC
Q 011249          376 FGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKT  448 (490)
Q Consensus       376 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~  448 (490)
                      ...+.++..+..+...+...|++++|...+++.. ..|+...|..+...+...|++++|.+.++++..++|..+
T Consensus       271 ~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~P~~~  344 (372)
T 3ly7_A          271 PELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLEMSWLNYVLLGKVYEMKGMNREAADAYLTAFNLRPGAN  344 (372)
T ss_dssp             GGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCSHH
T ss_pred             ccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcC
Confidence            1224455566666555556677777777776665 335555555566666677777777777777777777643

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=97.39  E-value=0.00099  Score=48.23  Aligned_cols=75  Identities=13%  Similarity=0.053  Sum_probs=58.0

Q ss_pred             CchHHHHHHHHHhhcCChHHHHHHHHhcc---------CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchH
Q 011249          381 LTEHLTCMVDLLGRSGQLEKAHSLIMDYK---------DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       381 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~---------~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                      +..-+..++..+...|+++.|...|+...         ..+...++..+..++.+.|+++.|...++++++..|+++.+.
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P~~~~~~   83 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRAN   83 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCCCHHHH
Confidence            33445567777777777777777776544         123456888999999999999999999999999999998876


Q ss_pred             HHHH
Q 011249          452 ALLA  455 (490)
Q Consensus       452 ~~l~  455 (490)
                      ..+.
T Consensus        84 ~n~~   87 (104)
T 2v5f_A           84 GNLK   87 (104)
T ss_dssp             HHHH
T ss_pred             hhHH
Confidence            6665

>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=97.37  E-value=0.00079  Score=62.81  Aligned_cols=101  Identities=12%  Similarity=-0.081  Sum_probs=76.4

Q ss_pred             HHHhcCCCChHHHHHHHHHHHHHc--CCCCC----chHHHHHHHHHhhcCChHHHHHHHHhcc---------CCCC-hhh
Q 011249          353 LTACSHGGLVEDGCKQFELMTRVF--GIKPL----TEHLTCMVDLLGRSGQLEKAHSLIMDYK---------DFCD-AGT  416 (490)
Q Consensus       353 ~~~~~~~g~~~~a~~~~~~~~~~~--~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~---------~~~~-~~~  416 (490)
                      +..+...|++++|+..+++..+..  -+.|+    ..+++.++.+|...|++++|+.++++..         ..|+ ..+
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            444556789999999998887531  12232    4567888899999999999999987765         2233 347


Q ss_pred             HHHHHHHHhhhCChHHHHHHHHHHHh-----cCCCCCchHHH
Q 011249          417 WGALLGACKVHVNAELGEIAARHLLE-----LGPEKTGNSAL  453 (490)
Q Consensus       417 ~~~l~~~~~~~g~~~~a~~~~~~~~~-----~~p~~~~~~~~  453 (490)
                      ++.|...|...|++++|+.+++++++     .+|++|.+-..
T Consensus       374 l~nLa~~~~~~g~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~  415 (429)
T 3qwp_A          374 VMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDL  415 (429)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhcCCCChHHHHH
Confidence            88899999999999999999999987     57888765544

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=97.36  E-value=0.011  Score=60.66  Aligned_cols=152  Identities=14%  Similarity=0.076  Sum_probs=104.0

Q ss_pred             HHhcCCHHHHHH-HHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhc
Q 011249          127 YTKIGLMDDAQR-LFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEI  205 (490)
Q Consensus       127 ~~~~g~~~~A~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~  205 (490)
                      ....+++++|.+ ++..+.  +......++..+.+.|..+.|+++.+.     .   ..-.......|++++|.++.+.+
T Consensus       609 ~~~~~~~~~a~~~~l~~i~--~~~~~~~~~~~l~~~~~~~~a~~~~~~-----~---~~~f~~~l~~~~~~~A~~~~~~~  678 (814)
T 3mkq_A          609 LTLRGEIEEAIENVLPNVE--GKDSLTKIARFLEGQEYYEEALNISPD-----Q---DQKFELALKVGQLTLARDLLTDE  678 (814)
T ss_dssp             HHHTTCHHHHHHHTGGGCC--CHHHHHHHHHHHHHTTCHHHHHHHCCC-----H---HHHHHHHHHHTCHHHHHHHHTTC
T ss_pred             HHHhCCHHHHHHHHHhcCC--chHHHHHHHHHHHhCCChHHheecCCC-----c---chheehhhhcCCHHHHHHHHHhh
Confidence            456789999988 664443  122337778888889999998876632     1   12244567789999999998776


Q ss_pred             CCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHH
Q 011249          206 SEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNA  285 (490)
Q Consensus       206 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~  285 (490)
                        .+...|..+...+.+.++++.|.+.|.++..         |..+...+...|+.+...++.+.....|.      ++.
T Consensus       679 --~~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~~~------~~~  741 (814)
T 3mkq_A          679 --SAEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAETTGK------FNL  741 (814)
T ss_dssp             --CCHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHHHTTC------HHH
T ss_pred             --CcHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHHHcCc------hHH
Confidence              4668999999999999999999999998753         23344445557777776666655555441      233


Q ss_pred             HHHHHHhcCChHHHHHHHhc
Q 011249          286 LIHMHSKCGYLDLAWREFSR  305 (490)
Q Consensus       286 l~~~~~~~~~~~~A~~~~~~  305 (490)
                      ...+|.+.|++++|.+++.+
T Consensus       742 A~~~~~~~g~~~~a~~~~~~  761 (814)
T 3mkq_A          742 AFNAYWIAGDIQGAKDLLIK  761 (814)
T ss_dssp             HHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHH
Confidence            34456667777777765543

>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=97.25  E-value=0.0009  Score=59.84  Aligned_cols=135  Identities=10%  Similarity=-0.054  Sum_probs=92.9

Q ss_pred             CCcHHHHHHHHHHh--cCC---CChHHHHHHHHHHHHHcCCCCC-chHHHHHHHHHhh---cC-----Ch---HHHHHHH
Q 011249          343 EPNQVTFIGVLTAC--SHG---GLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDLLGR---SG-----QL---EKAHSLI  405 (490)
Q Consensus       343 ~p~~~~~~~l~~~~--~~~---g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~---~g-----~~---~~A~~~~  405 (490)
                      +.+...|...+++.  ...   ....+|..+|+++.+.   .|+ ...+..+..+|.-   .+     ..   ..+.+..
T Consensus       191 p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~l---DP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~  267 (372)
T 3ly7_A          191 PHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQS---SPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNI  267 (372)
T ss_dssp             CSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHH
Confidence            44556666666553  333   3457899999999874   554 3445444444421   11     11   1122211


Q ss_pred             Hhcc-CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccccc
Q 011249          406 MDYK-DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKKK  481 (490)
Q Consensus       406 ~~~~-~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~  481 (490)
                      ..+. .+.++.++..+...+...|++++|...+++++.++|+ ...|..++.++.-.|++++|.+.+++....++..
T Consensus       268 ~a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln~s-~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~P~~  343 (372)
T 3ly7_A          268 VTLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLEMS-WLNYVLLGKVYEMKGMNREAADAYLTAFNLRPGA  343 (372)
T ss_dssp             HTCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCSH
T ss_pred             HhcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCC-HHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCc
Confidence            2222 4567778888887788889999999999999999975 6777889999999999999999999988776633

>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=97.23  E-value=0.0012  Score=56.42  Aligned_cols=87  Identities=10%  Similarity=0.026  Sum_probs=60.8

Q ss_pred             HHHHHHHHhcc-CCCC---hhhHHHHHHHHhh-----hCChHHHHHHHHHHHhcCCCC-CchHHHHHHHHHhc-CCcchH
Q 011249          399 EKAHSLIMDYK-DFCD---AGTWGALLGACKV-----HVNAELGEIAARHLLELGPEK-TGNSALLANIYASM-GKWKDS  467 (490)
Q Consensus       399 ~~A~~~~~~~~-~~~~---~~~~~~l~~~~~~-----~g~~~~a~~~~~~~~~~~p~~-~~~~~~l~~~~~~~-g~~~~A  467 (490)
                      .+|...+++.. ..|+   ...|..+...|..     -|+.++|.+.|+++++++|+. +.++..++..++.. |++++|
T Consensus       180 ~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a  259 (301)
T 3u64_A          180 HAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGF  259 (301)
T ss_dssp             HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHH
T ss_pred             HHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHH
Confidence            34444454444 3333   4566677766766     488888888888888888864 88888888888774 888888


Q ss_pred             HHHHHHhhhcccccCCCc
Q 011249          468 EIVKMMISETEKKKSPGC  485 (490)
Q Consensus       468 ~~~~~~~~~~~~~~~~~~  485 (490)
                      .+.+++.....+...|+.
T Consensus       260 ~~~L~kAL~a~p~~~P~~  277 (301)
T 3u64_A          260 DEALDRALAIDPESVPHN  277 (301)
T ss_dssp             HHHHHHHHHCCGGGCSSC
T ss_pred             HHHHHHHHcCCCCCCCCh
Confidence            888888877766655653

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=97.14  E-value=0.0044  Score=43.56  Aligned_cols=71  Identities=7%  Similarity=-0.042  Sum_probs=55.4

Q ss_pred             CCCchHHHHHHHHHhhcCC---hHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          379 KPLTEHLTCMVDLLGRSGQ---LEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       379 ~~~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                      +.++..+..+..++...++   .++|..++++..  .+.++.....+...+...|++++|+..|+++++.+|.++.
T Consensus         3 p~~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p~~~~   78 (93)
T 3bee_A            3 AVTATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSNDPNLD   78 (93)
T ss_dssp             CCCHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCCTTCC
T ss_pred             CCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCcc
Confidence            4566777777777754444   688888888776  5566778888888899999999999999999999888443

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=97.12  E-value=0.0026  Score=48.82  Aligned_cols=91  Identities=15%  Similarity=-0.063  Sum_probs=63.9

Q ss_pred             hHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcC---ChHHHHHHHHhcc-CC-C--ChhhHHHHHHHHhhhCChHHHH
Q 011249          362 VEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSG---QLEKAHSLIMDYK-DF-C--DAGTWGALLGACKVHVNAELGE  434 (490)
Q Consensus       362 ~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~-~~-~--~~~~~~~l~~~~~~~g~~~~a~  434 (490)
                      ...+.+.|.+..+  .-+++..+...+..++.+.+   +.++++.+++.+. .. |  ....+-.+..++.+.|++++|.
T Consensus        14 l~~~~~~y~~e~~--~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~   91 (152)
T 1pc2_A           14 LLKFEKKFQSEKA--AGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKAL   91 (152)
T ss_dssp             HHHHHHHHHHHHH--TTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHHc--cCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHH
Confidence            3445555555554  23366677777777777777   5567887777665 22 3  3456666777889999999999


Q ss_pred             HHHHHHHhcCCCCCchHHHH
Q 011249          435 IAARHLLELGPEKTGNSALL  454 (490)
Q Consensus       435 ~~~~~~~~~~p~~~~~~~~l  454 (490)
                      +.++.+++.+|++..+....
T Consensus        92 ~y~~~lL~ieP~n~QA~~Lk  111 (152)
T 1pc2_A           92 KYVRGLLQTEPQNNQAKELE  111 (152)
T ss_dssp             HHHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHhcCCCCHHHHHHH
Confidence            99999999999887655443

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=97.02  E-value=0.03  Score=41.30  Aligned_cols=140  Identities=10%  Similarity=0.063  Sum_probs=91.5

Q ss_pred             HhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHH
Q 011249          322 ADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKA  401 (490)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A  401 (490)
                      .-.|..++..++..+....   .+..-++.++.-....-+-+-..+.++.+-+-+.+              ..+|+....
T Consensus        18 ildG~v~qGveii~k~~~s---sni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDi--------------s~C~NlKrV   80 (172)
T 1wy6_A           18 LLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDL--------------DKCQNLKSV   80 (172)
T ss_dssp             HHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCG--------------GGCSCTHHH
T ss_pred             HHhhhHHHHHHHHHHHcCC---CCccccceeeeecchhhchhHHHHHHHHHhhhcCc--------------HhhhcHHHH
Confidence            4467788888888887763   24445555554444444555555666665442222              123444444


Q ss_pred             HHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          402 HSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      ...+-.+.  .+....+..+......|.-+.-.+++..++...|.+|.++..++.+|.+.|+..+|.+++++.-++|++
T Consensus        81 i~C~~~~n--~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           81 VECGVINN--TLNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHHHTT--CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhc--chHHHHHHHHHHHHHhccHhHHHHHHHHHhccCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            44443332  344555666677788888888888888877777777889999999999999999999999988888763

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=97.00  E-value=0.0013  Score=50.49  Aligned_cols=81  Identities=15%  Similarity=-0.016  Sum_probs=66.2

Q ss_pred             HHHHHHHHhcc--CCCChhhHHHHHHHHhhhC---ChHHHHHHHHHHHhcC-C-CCCchHHHHHHHHHhcCCcchHHHHH
Q 011249          399 EKAHSLIMDYK--DFCDAGTWGALLGACKVHV---NAELGEIAARHLLELG-P-EKTGNSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       399 ~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g---~~~~a~~~~~~~~~~~-p-~~~~~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      ..+.+.|.+..  ..++..+...+.+++.+.+   +.++++.+++.+.+.+ | ++...+..|+-++.+.|++++|.+++
T Consensus        15 ~~~~~~y~~e~~~~~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~~y~   94 (152)
T 1pc2_A           15 LKFEKKFQSEKAAGSVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYV   94 (152)
T ss_dssp             HHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHHHHH
Confidence            44455554432  3567888888999998877   7779999999999988 7 56889999999999999999999999


Q ss_pred             HHhhhccc
Q 011249          472 MMISETEK  479 (490)
Q Consensus       472 ~~~~~~~~  479 (490)
                      +.+.+..+
T Consensus        95 ~~lL~ieP  102 (152)
T 1pc2_A           95 RGLLQTEP  102 (152)
T ss_dssp             HHHHHHCT
T ss_pred             HHHHhcCC
Confidence            99987644

>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=96.89  E-value=0.36  Score=46.99  Aligned_cols=314  Identities=8%  Similarity=-0.027  Sum_probs=175.9

Q ss_pred             HHhcCCHHHHHHHHhhcCCCCHh---HHHHHHHHHHhCCChHHHHHHHHHhccC--CchhHHHHHHHHHhcCChhHHHHH
Q 011249          127 YTKIGLMDDAQRLFDSMAERNVI---SWSAMVAGYANCGNMKAAKEFYDRMTEK--NSVTWVAMIAGYGKCGEVREAKKV  201 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~~~~~~~~~---~~~~l~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~  201 (490)
                      ..+.|+++.+..+...+..-...   .|..+...+ .....+++..++++-...  ....-...+..+.+.+++...+.+
T Consensus        16 a~~~~~~~~~~~l~~~l~~~pL~~yl~y~~l~~~l-~~~~~~ev~~Fl~~~~~~p~~~~Lr~~~l~~l~~~~~w~~~l~~   94 (618)
T 1qsa_A           16 AWDNRQMDVVEQMMPGLKDYPLYPYLEYRQITDDL-MNQPAVTVTNFVRANPTLPPARTLQSRFVNELARREDWRGLLAF   94 (618)
T ss_dssp             HHHTTCHHHHHHHSGGGTTSTTHHHHHHHHHHHTG-GGCCHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHhhcCCCcHHHHHHHHHHhCc-ccCCHHHHHHHHHHCCCChhHHHHHHHHHHHHHhCCCHHHHHHh
Confidence            35678998888887777542122   343333222 222456666666554321  122234556667778899999998


Q ss_pred             HhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHH--HHHHHHHHHhcC----
Q 011249          202 FDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEM--AAILAKHVDEGC----  275 (490)
Q Consensus       202 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~--a~~~~~~~~~~~----  275 (490)
                      +.. ...+...-.....+....|+..+|......+-..| ...+..+..++..+.+.|.+..  ...-++.+...+    
T Consensus        95 ~~~-~p~~~~~~c~~~~A~~~~G~~~~a~~~~~~lW~~~-~~~p~~c~~l~~~~~~~g~lt~~~~~~R~~~al~~~~~~~  172 (618)
T 1qsa_A           95 SPE-KPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTG-KSQPNACDKLFSVWRASGKQDPLAYLERIRLAMKAGNTGL  172 (618)
T ss_dssp             CCS-CCSSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCS-SCCCTHHHHHHHHHHHTTCSCHHHHHHHHHHHHHTTCHHH
T ss_pred             ccC-CCCCHHHHHHHHHHHHHcCChhHHHHHHHHHHhCC-CCCcHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHH
Confidence            877 44556666667778888899888877777766554 3345566677777776665433  222222333322    


Q ss_pred             -------CCCchh-HHHHHHHHHHhcCChHHHHHHHhcccCCChh---HHHHHHHHHHhcCChHHHHHHHHHHHHcC-CC
Q 011249          276 -------CDRTNY-VSNALIHMHSKCGYLDLAWREFSRIKNKDVI---SYSSMITAFADHGKSQEALDMFLKMRNEG-IE  343 (490)
Q Consensus       276 -------~~~~~~-~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~---~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~  343 (490)
                             ++++.. ....++..+.+   ...+....... .++..   .+...+.-+.+ .+.+.|...+....+.+ +.
T Consensus       173 a~~l~~~l~~~~~~~a~~~~al~~~---p~~~~~~~~~~-~~~~~~~~~~~~~~~rlar-~d~~~A~~~~~~~~~~~~~~  247 (618)
T 1qsa_A          173 VTVLAGQMPADYQTIASAIISLANN---PNTVLTFARTT-GATDFTRQMAAVAFASVAR-QDAENARLMIPSLAQAQQLN  247 (618)
T ss_dssp             HHHHHHTCCGGGHHHHHHHHHHHHC---GGGHHHHHHHS-CCCHHHHHHHHHHHHHHHH-HCHHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHhC---hHhHHHHHhcc-CCChhhHHHHHHHHHHHHh-cCHHHHHHHHHhhhhccCCC
Confidence                   111111 11222222221   22222222221 11211   11112222333 47899999999887543 33


Q ss_pred             CcHH--HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCC--ChhhHHH
Q 011249          344 PNQV--TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFC--DAGTWGA  419 (490)
Q Consensus       344 p~~~--~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~~~~~~  419 (490)
                      +...  ....+.......+...++...+.....   ..++.....-.+....+.|+++.|...|+.|...+  ...-.--
T Consensus       248 ~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~e~~~r~Alr~~d~~~a~~~~~~l~~~~~~~~r~~YW  324 (618)
T 1qsa_A          248 EDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIM---RSQSTSLIERRVRMALGTGDRRGLNTWLARLPMEAKEKDEWRYW  324 (618)
T ss_dssp             HHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHH---TCCCHHHHHHHHHHHHHHTCHHHHHHHHHHSCTTGGGSHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCChHHHHHHHhccc---cCCChHHHHHHHHHHHHCCCHHHHHHHHHHccccccccHhHHHH
Confidence            2222  333444455566645566677776544   22343344445555667899999999999998432  2333344


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      +..+....|+.++|..+|+++.+  +  .++|..++
T Consensus       325 ~~ra~~~~g~~~~a~~~~~~~a~--~--~~fYg~lA  356 (618)
T 1qsa_A          325 QADLLLERGREAEAKEILHQLMQ--Q--RGFYPMVA  356 (618)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHT--S--CSHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHhc--C--CChHHHHH
Confidence            55677888999999999999976  3  34555553

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.86  E-value=0.023  Score=58.19  Aligned_cols=155  Identities=13%  Similarity=0.071  Sum_probs=85.1

Q ss_pred             HHHhcCChHHHHH-HHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChH
Q 011249          219 CYVQNGYAKAAIE-MYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLD  297 (490)
Q Consensus       219 ~~~~~g~~~~A~~-~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  297 (490)
                      .....+++++|.+ ++..      .|+......++..+.+.|.++.|.++.+.         ..   .-.......|+++
T Consensus       608 ~~~~~~~~~~a~~~~l~~------i~~~~~~~~~~~~l~~~~~~~~a~~~~~~---------~~---~~f~~~l~~~~~~  669 (814)
T 3mkq_A          608 TLTLRGEIEEAIENVLPN------VEGKDSLTKIARFLEGQEYYEEALNISPD---------QD---QKFELALKVGQLT  669 (814)
T ss_dssp             HHHHTTCHHHHHHHTGGG------CCCHHHHHHHHHHHHHTTCHHHHHHHCCC---------HH---HHHHHHHHHTCHH
T ss_pred             HHHHhCCHHHHHHHHHhc------CCchHHHHHHHHHHHhCCChHHheecCCC---------cc---hheehhhhcCCHH
Confidence            3345666666655 3311      11012225555556666666666655421         11   1123345668888


Q ss_pred             HHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcC
Q 011249          298 LAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFG  377 (490)
Q Consensus       298 ~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  377 (490)
                      .|.++.+.+.  +...|..+...+.+.++++.|++.|.++..         |..+...+...|+.+...++-+..... |
T Consensus       670 ~A~~~~~~~~--~~~~W~~la~~al~~~~~~~A~~~y~~~~d---------~~~l~~l~~~~~~~~~~~~~~~~a~~~-~  737 (814)
T 3mkq_A          670 LARDLLTDES--AEMKWRALGDASLQRFNFKLAIEAFTNAHD---------LESLFLLHSSFNNKEGLVTLAKDAETT-G  737 (814)
T ss_dssp             HHHHHHTTCC--CHHHHHHHHHHHHHTTCHHHHHHHHHHHTC---------HHHHHHHHHHTTCHHHHHHHHHHHHHT-T
T ss_pred             HHHHHHHhhC--cHhHHHHHHHHHHHcCCHHHHHHHHHHccC---------hhhhHHHHHHcCCHHHHHHHHHHHHHc-C
Confidence            8888776653  456788888888888888888888887653         223333344456665544444444331 1


Q ss_pred             CCCCchHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          378 IKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       378 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                            .++....+|...|++++|++++.++.
T Consensus       738 ------~~~~A~~~~~~~g~~~~a~~~~~~~~  763 (814)
T 3mkq_A          738 ------KFNLAFNAYWIAGDIQGAKDLLIKSQ  763 (814)
T ss_dssp             ------CHHHHHHHHHHHTCHHHHHHHHHHTT
T ss_pred             ------chHHHHHHHHHcCCHHHHHHHHHHcC
Confidence                  12333344555666666666655543

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=96.67  E-value=0.00014  Score=66.47  Aligned_cols=258  Identities=12%  Similarity=0.071  Sum_probs=146.2

Q ss_pred             HhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCC--CCHHhHHHHHHHHHhcCC
Q 011249          148 VISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISE--PDASCWAAMTVCYVQNGY  225 (490)
Q Consensus       148 ~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~~~~~l~~~~~~~g~  225 (490)
                      +..|..|..+....+.+.+|++.|=  +..|+..|..++....+.|.+++-.+.+....+  .++..=+.|+.+|++.++
T Consensus        54 p~VWs~LgkAqL~~~~v~eAIdsyI--kA~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~ke~~IDteLi~ayAk~~r  131 (624)
T 3lvg_A           54 PAVWSQLAKAQLQKGMVKEAIDSYI--KADDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNR  131 (624)
T ss_dssp             CCCSSSHHHHTTTSSSCTTTTTSSC--CCSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCCSTTTTHHHHHHHHTSCS
T ss_pred             ccHHHHHHHHHHccCchHHHHHHHH--hCCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccHHHHHHHHHhhCc
Confidence            3456777777777777777766552  234666677777777777777777777776665  455555677777777777


Q ss_pred             hHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhc
Q 011249          226 AKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSR  305 (490)
Q Consensus       226 ~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  305 (490)
                      ..+-.+++       ..|+..-...+..-|...|.++.|.-+|..+...         .-|...+.+.|++..|.+.-++
T Consensus       132 L~elEefl-------~~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~---------akLAstLV~L~~yq~AVdaArK  195 (624)
T 3lvg_A          132 LAELEEFI-------NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNF---------GRLASTLVHLGEYQAAVDGARK  195 (624)
T ss_dssp             SSTTTSTT-------SCCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCC---------TTTSSSSSSCSGGGSSTTTTTT
T ss_pred             HHHHHHHH-------cCCCcccHHHHHHHHHHccCHHHHHHHHHhCccH---------HHHHHHHHHHHHHHHHHHHHHh
Confidence            65543332       1356656666777777777777766666544221         1233334444554444332222


Q ss_pred             ccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHH
Q 011249          306 IKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHL  385 (490)
Q Consensus       306 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~  385 (490)
                      .  .++.+|..+-.+|...+.+.-|.-.--.++-   .|+  ....++..|...|.+++-+.+++....  .-.....+|
T Consensus       196 A--ns~ktWKeV~~ACvd~~EfrLAqicGLniIv---had--eL~elv~~YE~~G~f~ELIsLlEaglg--lErAHmGmF  266 (624)
T 3lvg_A          196 A--NSTRTWKEVCFACVDGKEFRLAQMCGLHIVV---HAD--ELEELINYYQDRGYFEELITMLEAALG--LERAHMGMF  266 (624)
T ss_dssp             C--CSSCSHHHHTHHHHHSCTTTTTTHHHHHHHC---CSS--CCSGGGSSSSTTCCCTTSTTTHHHHTT--STTCCHHHH
T ss_pred             c--CChhHHHHHHHHHhCchHHHHHHHhcchhcc---cHH--HHHHHHHHHHhCCCHHHHHHHHHHHhC--CCchhHHHH
Confidence            2  3556777777777777776665544444431   222  122345556677777776666666542  122345556


Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc----CC------CChhhHHHHHHHHhhhCChHHH
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK----DF------CDAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~----~~------~~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      +-|.-.|++- ++++.++.++..-    .+      .....|.-+...|....+++.|
T Consensus       267 TELaILYsKY-~PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA  323 (624)
T 3lvg_A          267 TELAILYSKF-KPQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNA  323 (624)
T ss_dssp             HHHHHHHHSS-CTTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHhc-CHHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHH
Confidence            6666555543 4455555443322    11      1334555555555555555554

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=96.45  E-value=0.0087  Score=43.11  Aligned_cols=67  Identities=12%  Similarity=-0.004  Sum_probs=55.8

Q ss_pred             ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC-------CCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          413 DAGTWGALLGACKVHVNAELGEIAARHLLELG-------PEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       413 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-------p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +..-...++..+...|+++.|..-++++++..       +..+.++..|+.++.+.|++++|..+++++.+..+
T Consensus         4 sa~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~P   77 (104)
T 2v5f_A            4 TAEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDP   77 (104)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             CHHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcCC
Confidence            34455678888999999999999999998853       34467899999999999999999999999876543

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=96.33  E-value=1.1  Score=45.53  Aligned_cols=249  Identities=11%  Similarity=-0.047  Sum_probs=128.6

Q ss_pred             HHhcCChhHHHHHHhhcCC----CCH--HhHHHHHHHHHhcCChHHHHHHHHHHHHcCc-------ccChhhHH--HHHH
Q 011249          189 YGKCGEVREAKKVFDEISE----PDA--SCWAAMTVCYVQNGYAKAAIEMYKVMRQENV-------RISEVAMV--GAIS  253 (490)
Q Consensus       189 ~~~~~~~~~A~~~~~~~~~----~~~--~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~-------~p~~~~~~--~l~~  253 (490)
                      .+..|+.++++.+++....    .+.  ..-..+.-+.+..|..+++..++.......-       .+....-.  .|.-
T Consensus       384 lIh~g~~~~gl~~L~~yL~~~~s~~~~ik~GAllaLGli~ag~~~~~~~lL~~~L~~~~~~~~~~~~~~ir~gAaLGLGl  463 (963)
T 4ady_A          384 VIHKGNLLEGKKVMAPYLPGSRASSRFIKGGSLYGLGLIYAGFGRDTTDYLKNIIVENSGTSGDEDVDVLLHGASLGIGL  463 (963)
T ss_dssp             HHTSSCTTTHHHHHTTTSTTSCCSCHHHHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHSSCCSCHHHHHHHHHHHHHHHH
T ss_pred             hhccCchHHHHHHHHHhccccCCCcHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHcCccccccccccHHHHHHHHHHHHH
Confidence            3445666677777766543    121  2233344555666666677777766554321       01111111  2222


Q ss_pred             HHhccCChHHHHHHHHHHHhcCCCCch--hHHHHHHHHHHhcCChHHHHHHHhcccC-CChh--HHHHHHHHHHhcCChH
Q 011249          254 ACTQLGDVEMAAILAKHVDEGCCDRTN--YVSNALIHMHSKCGYLDLAWREFSRIKN-KDVI--SYSSMITAFADHGKSQ  328 (490)
Q Consensus       254 ~~~~~g~~~~a~~~~~~~~~~~~~~~~--~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~~~--~~~~l~~~~~~~~~~~  328 (490)
                      ++.-.++ +++...+..+.... ....  ..-.+|...+...|+-+....++..+.+ .+..  -...+.-++...|+.+
T Consensus       464 a~~GS~~-eev~e~L~~~L~dd-~~~~~~~AalALGli~vGTgn~~ai~~LL~~~~e~~~e~vrR~aalgLGll~~g~~e  541 (963)
T 4ady_A          464 AAMGSAN-IEVYEALKEVLYND-SATSGEAAALGMGLCMLGTGKPEAIHDMFTYSQETQHGNITRGLAVGLALINYGRQE  541 (963)
T ss_dssp             HSTTCCC-HHHHHHHHHHHHTC-CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCGG
T ss_pred             HhcCCCC-HHHHHHHHHHHhcC-CHHHHHHHHHHHhhhhcccCCHHHHHHHHHHHhccCcHHHHHHHHHHHHhhhCCChH
Confidence            2333333 34445555444322 1111  1222344455666777666666665443 2222  2233334555778888


Q ss_pred             HHHHHHHHHHHcCCCCcHH--HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHH
Q 011249          329 EALDMFLKMRNEGIEPNQV--TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIM  406 (490)
Q Consensus       329 ~a~~~~~~~~~~~~~p~~~--~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  406 (490)
                      .+..+.+.+... ..|...  ....+.-+|+..|+.....+++..+..  ....+..-...+.-++...|+.+.+.++++
T Consensus       542 ~~~~li~~L~~~-~dp~vRygaa~alglAyaGTGn~~aIq~LL~~~~~--d~~d~VRraAViaLGlI~~g~~e~v~rlv~  618 (963)
T 4ady_A          542 LADDLITKMLAS-DESLLRYGGAFTIALAYAGTGNNSAVKRLLHVAVS--DSNDDVRRAAVIALGFVLLRDYTTVPRIVQ  618 (963)
T ss_dssp             GGHHHHHHHHHC-SCHHHHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH--CSCHHHHHHHHHHHHHHTSSSCSSHHHHTT
T ss_pred             HHHHHHHHHHhC-CCHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcc--CCcHHHHHHHHHHHHhhccCCHHHHHHHHH
Confidence            888888887763 122222  222345568888888777778888876  333333333344445556777777777777


Q ss_pred             hccCCCChhhHHHHHH--HHhhhCCh-HHHHHHHHHHHh
Q 011249          407 DYKDFCDAGTWGALLG--ACKVHVNA-ELGEIAARHLLE  442 (490)
Q Consensus       407 ~~~~~~~~~~~~~l~~--~~~~~g~~-~~a~~~~~~~~~  442 (490)
                      .+....++.+-.....  +....|+. .+++..+..+..
T Consensus       619 ~L~~~~d~~VR~gAalALGli~aGn~~~~aid~L~~L~~  657 (963)
T 4ady_A          619 LLSKSHNAHVRCGTAFALGIACAGKGLQSAIDVLDPLTK  657 (963)
T ss_dssp             TGGGCSCHHHHHHHHHHHHHHTSSSCCHHHHHHHHHHHT
T ss_pred             HHHhcCCHHHHHHHHHHHHHhccCCCcHHHHHHHHHHcc
Confidence            6653334433333322  23333433 567777777754

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=96.28  E-value=0.18  Score=37.33  Aligned_cols=137  Identities=11%  Similarity=0.084  Sum_probs=79.1

Q ss_pred             HhcCCHHHHHHHHhhcCCC-CHhHHHHHHHHHHhCCChHHHHHHHHHhccC-CchhHHHHHHHHHhcCChhHHHHHHhhc
Q 011249          128 TKIGLMDDAQRLFDSMAER-NVISWSAMVAGYANCGNMKAAKEFYDRMTEK-NSVTWVAMIAGYGKCGEVREAKKVFDEI  205 (490)
Q Consensus       128 ~~~g~~~~A~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~~  205 (490)
                      .-.|.+++..++..+...+ +..-||-++--....-+-+-..++++.+-+- |.          ..+|++......+-.+
T Consensus        18 ildG~v~qGveii~k~~~ssni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDi----------s~C~NlKrVi~C~~~~   87 (172)
T 1wy6_A           18 LLDGYIDEGVKIVLEITKSSTKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDL----------DKCQNLKSVVECGVIN   87 (172)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCG----------GGCSCTHHHHHHHHHT
T ss_pred             HHhhhHHHHHHHHHHHcCCCCccccceeeeecchhhchhHHHHHHHHHhhhcCc----------HhhhcHHHHHHHHHHh
Confidence            3456666666666655542 4445555555555555555555555555432 21          1223333333333332


Q ss_pred             CCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCC
Q 011249          206 SEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCC  276 (490)
Q Consensus       206 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  276 (490)
                      .. +....+.-+......|+-++-.+++..+... .+|++.....+..+|.+.|+..++..++.++-+.|+
T Consensus        88 n~-~se~vd~ALd~lv~~~KkDqLdki~~~~l~n-~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~  156 (172)
T 1wy6_A           88 NT-LNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIEACKKGE  156 (172)
T ss_dssp             TC-CCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             cc-hHHHHHHHHHHHHHhccHhHHHHHHHHHhcc-CCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhh
Confidence            22 2234455566777777777777777775442 366777777788888888888888888887777764

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.21  E-value=0.22  Score=39.17  Aligned_cols=128  Identities=14%  Similarity=0.104  Sum_probs=74.6

Q ss_pred             HHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHH
Q 011249          289 MHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQ  368 (490)
Q Consensus       289 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~  368 (490)
                      .....|+++.|.++.+.+  .+...|..+.......|+++-|.+.|++...         +..+.-.|...|+.+.-.++
T Consensus        14 LAL~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~kl   82 (177)
T 3mkq_B           14 LALEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLSKM   82 (177)
T ss_dssp             HHHHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHHHH
Confidence            345667777777776655  3566778888877788888888877776543         22333334445666555444


Q ss_pred             HHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHH
Q 011249          369 FELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHL  440 (490)
Q Consensus       369 ~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  440 (490)
                      -+..... |      -++.....+.-.|+++++.++|.+...-|..      .......|..+.|.++.+.+
T Consensus        83 a~iA~~~-g------~~n~af~~~l~lGdv~~~i~lL~~~~r~~eA------~~~A~t~g~~~~a~~~~~~~  141 (177)
T 3mkq_B           83 QNIAQTR-E------DFGSMLLNTFYNNSTKERSSIFAEGGSLPLA------YAVAKANGDEAAASAFLEQA  141 (177)
T ss_dssp             HHHHHHT-T------CHHHHHHHHHHHTCHHHHHHHHHHTTCHHHH------HHHHHHTTCHHHHHHHHHHT
T ss_pred             HHHHHHC-c------cHHHHHHHHHHcCCHHHHHHHHHHCCChHHH------HHHHHHcCcHHHHHHHHHHh
Confidence            4433331 1      2333445556678888888887666521211      11123356677777776655

>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=96.19  E-value=0.021  Score=43.22  Aligned_cols=109  Identities=8%  Similarity=-0.038  Sum_probs=78.3

Q ss_pred             cHHHHHHHHHHhcCCCCh------HHHHHHHHHHHHHcCCCCCch-HHHHHHH------HHhhcCChHHHHHHHHhcc--
Q 011249          345 NQVTFIGVLTACSHGGLV------EDGCKQFELMTRVFGIKPLTE-HLTCMVD------LLGRSGQLEKAHSLIMDYK--  409 (490)
Q Consensus       345 ~~~~~~~l~~~~~~~g~~------~~a~~~~~~~~~~~~~~~~~~-~~~~l~~------~~~~~g~~~~A~~~~~~~~--  409 (490)
                      |..+|-..+....+.|++      ++..++|+++..  .+||+.. .+...+.      .+...++.++|.++|+.+.  
T Consensus        12 ~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia--~~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~   89 (161)
T 4h7y_A           12 NPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIE--ALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARAN   89 (161)
T ss_dssp             SHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHH--HSCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHH--cCCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            556777777777777888      888899998888  6777632 1122222      2245688999999998875  


Q ss_pred             CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          410 DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       410 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      .+.=..+|.....--.+.|+..+|.+++.+++.+.|.....+...+
T Consensus        90 hKkFAKiwi~~AqFEiRqgnl~kARkILg~AiG~~~k~~~~le~a~  135 (161)
T 4h7y_A           90 CKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEMLEIAL  135 (161)
T ss_dssp             CTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCBCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHcccHHHHHHHHHHHhccCCCcHHHHHHHH
Confidence            2222667777777778899999999999999999988666555554

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.16  E-value=0.35  Score=38.09  Aligned_cols=102  Identities=13%  Similarity=0.054  Sum_probs=54.7

Q ss_pred             HHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHH
Q 011249          188 GYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAIL  267 (490)
Q Consensus       188 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~  267 (490)
                      .....|+++.|.++.+.+  .+...|..|.......|+++-|.+.|.+...         +..+.-.|...|+.+...++
T Consensus        14 LAL~lg~l~~A~e~a~~l--~~~~~Wk~Lg~~AL~~gn~~lAe~cy~~~~D---------~~~L~~Ly~~tg~~e~L~kl   82 (177)
T 3mkq_B           14 LALEYGNLDAALDEAKKL--NDSITWERLIQEALAQGNASLAEMIYQTQHS---------FDKLSFLYLVTGDVNKLSKM   82 (177)
T ss_dssp             HHHHTTCHHHHHHHHHHH--CCHHHHHHHHHHHHHTTCHHHHHHHHHHTTC---------HHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHHh--CCHHHHHHHHHHHHHcCChHHHHHHHHHhCC---------HHHHHHHHHHhCCHHHHHHH
Confidence            345566666666665554  3455677777777777777777666665432         22233334445555555555


Q ss_pred             HHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcc
Q 011249          268 AKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRI  306 (490)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~  306 (490)
                      -+.....| .     ++.....+...|+++++.++|.+.
T Consensus        83 a~iA~~~g-~-----~n~af~~~l~lGdv~~~i~lL~~~  115 (177)
T 3mkq_B           83 QNIAQTRE-D-----FGSMLLNTFYNNSTKERSSIFAEG  115 (177)
T ss_dssp             HHHHHHTT-C-----HHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             HHHHHHCc-c-----HHHHHHHHHHcCCHHHHHHHHHHC
Confidence            44444443 1     222333444456666666655443

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=96.01  E-value=0.077  Score=39.09  Aligned_cols=90  Identities=14%  Similarity=-0.070  Sum_probs=60.1

Q ss_pred             HHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHH---HHHHHHhccCC--C--ChhhHHHHHHHHhhhCChHHHHH
Q 011249          363 EDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEK---AHSLIMDYKDF--C--DAGTWGALLGACKVHVNAELGEI  435 (490)
Q Consensus       363 ~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~---A~~~~~~~~~~--~--~~~~~~~l~~~~~~~g~~~~a~~  435 (490)
                      ..+.+.+...... +. ++..+-..+..++.+..+...   ++.+++.+...  |  .....-.+.-++.+.|++++|.+
T Consensus        18 ~~~~~~y~~e~~~-~~-~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~A~~   95 (126)
T 1nzn_A           18 LKFEKKFQSEKAA-GS-VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALK   95 (126)
T ss_dssp             HHHHHHHHHHHHH-SC-CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHhcc-CC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHHHHH
Confidence            3444555544442 33 666666667777777766555   67777666522  2  22344556678899999999999


Q ss_pred             HHHHHHhcCCCCCchHHHH
Q 011249          436 AARHLLELGPEKTGNSALL  454 (490)
Q Consensus       436 ~~~~~~~~~p~~~~~~~~l  454 (490)
                      .++.+++.+|+|..+....
T Consensus        96 ~~~~lL~~eP~n~QA~~Lk  114 (126)
T 1nzn_A           96 YVRGLLQTEPQNNQAKELE  114 (126)
T ss_dssp             HHHHHHHHCTTCHHHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHHH
Confidence            9999999999987765543

>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=95.65  E-value=0.1  Score=39.45  Aligned_cols=98  Identities=9%  Similarity=0.141  Sum_probs=67.2

Q ss_pred             CChhHHHHHHHHHHhcCCh------HHHHHHHHHHHHcCCCCcHH----HHHHH-HH--HhcCCCChHHHHHHHHHHHHH
Q 011249          309 KDVISYSSMITAFADHGKS------QEALDMFLKMRNEGIEPNQV----TFIGV-LT--ACSHGGLVEDGCKQFELMTRV  375 (490)
Q Consensus       309 ~~~~~~~~l~~~~~~~~~~------~~a~~~~~~~~~~~~~p~~~----~~~~l-~~--~~~~~g~~~~a~~~~~~~~~~  375 (490)
                      .|..+|-..+...-+.|++      ++..++|++.... ++|+..    .|..+ +.  .+...++.++|.++|+.+...
T Consensus        11 ~~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~k~~~wrrYI~LWIrYA~~~ei~D~d~aR~vy~~a~~~   89 (161)
T 4h7y_A           11 NNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARAN   89 (161)
T ss_dssp             CSHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGGGGTTCHHHHHHHHHHHHHHHHHCGGGCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCccccccHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence            5778888888888877888      8888888888875 666531    11111 10  123347888889999888774


Q ss_pred             cCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          376 FGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       376 ~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                       +-.- ...|......-.+.|++..|.+++.+..
T Consensus        90 -hKkF-AKiwi~~AqFEiRqgnl~kARkILg~Ai  121 (161)
T 4h7y_A           90 -CKKF-AFVHISFAQFELSQGNVKKSKQLLQKAV  121 (161)
T ss_dssp             -CTTB-HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             -hHHH-HHHHHHHHHHHHHcccHHHHHHHHHHHh
Confidence             3222 6666666667778899999999887665

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=95.45  E-value=0.036  Score=40.81  Aligned_cols=83  Identities=16%  Similarity=-0.008  Sum_probs=63.7

Q ss_pred             ChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHH---HHHHHHHHHhcC-C-CCCchHHHHHHHHHhcCCcchHHH
Q 011249          397 QLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAEL---GEIAARHLLELG-P-EKTGNSALLANIYASMGKWKDSEI  469 (490)
Q Consensus       397 ~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~---a~~~~~~~~~~~-p-~~~~~~~~l~~~~~~~g~~~~A~~  469 (490)
                      ....+.+-|....  ..++..+--.+.+++.+..+...   ++.+++.+.+.+ | ........|+-++.+.|+|++|.+
T Consensus        16 ~l~~~~~~y~~e~~~~~~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~A~~   95 (126)
T 1nzn_A           16 DLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALK   95 (126)
T ss_dssp             HHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhccCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHHHHH
Confidence            3344445554332  35778888888889988776555   999999999877 5 456788889999999999999999


Q ss_pred             HHHHhhhccc
Q 011249          470 VKMMISETEK  479 (490)
Q Consensus       470 ~~~~~~~~~~  479 (490)
                      .++.+.+..+
T Consensus        96 ~~~~lL~~eP  105 (126)
T 1nzn_A           96 YVRGLLQTEP  105 (126)
T ss_dssp             HHHHHHHHCT
T ss_pred             HHHHHHHhCC
Confidence            9999987544

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=95.45  E-value=0.1  Score=51.84  Aligned_cols=55  Identities=11%  Similarity=-0.064  Sum_probs=51.2

Q ss_pred             HHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          421 LGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       421 ~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      ..-|...|+++.|+++.+++...-|.+...|..|+.+|...|+|+.|+-.++.+.
T Consensus       344 a~FLl~K~~~elAL~~Ak~AV~~aPseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          344 TNFLLNRGDYELALGVSNTSTELALDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             HHHHhccCcHHHHHHHHHHHHhcCchhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence            3456778999999999999999999999999999999999999999999999885

>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC repeat; 2.70A {Saccharomyces cerevisiae} PDB: 4b4t_N

Probab=95.10  E-value=3.4  Score=42.09  Aligned_cols=22  Identities=9%  Similarity=0.199  Sum_probs=11.6

Q ss_pred             HHHHHHhCCChHHHHHHHHHhc
Q 011249          154 MVAGYANCGNMKAAKEFYDRMT  175 (490)
Q Consensus       154 l~~~~~~~~~~~~a~~~~~~~~  175 (490)
                      ++.++.+.++.+.+.++|.++.
T Consensus       236 a~~~ai~LnD~~li~~if~~l~  257 (963)
T 4ady_A          236 LNKVVVNLNDAGLALQLFKKLK  257 (963)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHH
Confidence            4444455555555555555543

>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=94.91  E-value=0.31  Score=41.86  Aligned_cols=64  Identities=11%  Similarity=0.014  Sum_probs=28.2

Q ss_pred             hHHHHHHHHHhc-----CChHHHHHHHHHHHHcCcccChhhHHHHHHHHhc-cCChHHHHHHHHHHHhcC
Q 011249          212 CWAAMTVCYVQN-----GYAKAAIEMYKVMRQENVRISEVAMVGAISACTQ-LGDVEMAAILAKHVDEGC  275 (490)
Q Consensus       212 ~~~~l~~~~~~~-----g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~-~g~~~~a~~~~~~~~~~~  275 (490)
                      .|..+...|.+.     |+.++|.+.|++..+.+..-+..++......++. .|+.+++.+.+++.....
T Consensus       201 A~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~  270 (301)
T 3u64_A          201 VWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAID  270 (301)
T ss_dssp             HHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCC
Confidence            444444444442     4555555555554443221123344444444444 244555555555544443

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=93.96  E-value=0.16  Score=39.25  Aligned_cols=29  Identities=21%  Similarity=0.099  Sum_probs=24.5

Q ss_pred             CchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          448 TGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       448 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      .+.-..++.+|.+.|++++|+.+++.+..
T Consensus       122 ~Elkykia~C~~~l~~~~~Ai~~Le~Ip~  150 (167)
T 3ffl_A          122 IEVKYKLAECYTVLKQDKDAIAILDGIPS  150 (167)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHTSCG
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHhcCCc
Confidence            35667799999999999999999987643

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=93.58  E-value=0.48  Score=36.67  Aligned_cols=124  Identities=6%  Similarity=-0.106  Sum_probs=64.7

Q ss_pred             HHHHHHhcCChHHHHHHHhcccC-----CCh-------hHHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCcHH-HHHH
Q 011249          286 LIHMHSKCGYLDLAWREFSRIKN-----KDV-------ISYSSMITAFADHGKSQEALDMFLKMRNEG-IEPNQV-TFIG  351 (490)
Q Consensus       286 l~~~~~~~~~~~~A~~~~~~~~~-----~~~-------~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~~-~~~~  351 (490)
                      =+..+...|.++.|+-+.+.+..     ++.       .++..+.+++...+++..|...|++.++.. .-+... +...
T Consensus        26 qik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~s~~~~  105 (167)
T 3ffl_A           26 HVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTSKVRPS  105 (167)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC---------
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCCCcccc
Confidence            35566667777777766665432     221       245556667777777777777777765421 111111 1100


Q ss_pred             HHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccC-CCChhhHHHHHHH
Q 011249          352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKD-FCDAGTWGALLGA  423 (490)
Q Consensus       352 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~~~~~~l~~~  423 (490)
                      +.    .......         . .....+.+.-..+..+|.+.|++++|+.+++.++. ..++.+-..|.+.
T Consensus       106 ~~----~~ss~p~---------s-~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~k~Rt~kvnm~LakL  164 (167)
T 3ffl_A          106 TG----NSASTPQ---------S-QCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPSRQRTPKINMLLANL  164 (167)
T ss_dssp             -------------------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCGGGCCHHHHHHHHHH
T ss_pred             cc----ccCCCcc---------c-ccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCchhcCHHHHHHHHHH
Confidence            00    0000000         0 02233445556688889999999999999998872 3344444444433

>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=93.43  E-value=6.1  Score=38.45  Aligned_cols=170  Identities=6%  Similarity=-0.120  Sum_probs=97.6

Q ss_pred             CChHHHHHHHhcccC---CChh----HHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHH
Q 011249          294 GYLDLAWREFSRIKN---KDVI----SYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGC  366 (490)
Q Consensus       294 ~~~~~A~~~~~~~~~---~~~~----~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~  366 (490)
                      .+.+.|...+....+   -+..    .+..++..+...+...++...+......  .++.....-.+....+.|+++.|.
T Consensus       228 ~d~~~A~~~~~~~~~~~~~~~~~~~~~~~~ia~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~e~~~r~Alr~~d~~~a~  305 (618)
T 1qsa_A          228 QDAENARLMIPSLAQAQQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMR--SQSTSLIERRVRMALGTGDRRGLN  305 (618)
T ss_dssp             HCHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHT--CCCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             cCHHHHHHHHHhhhhccCCCHHHHHHHHHHHHHHHHHcCCChHHHHHHHhcccc--CCChHHHHHHHHHHHHCCCHHHHH
Confidence            478999999977643   1222    2333333344445356667777765553  344433444444445679999999


Q ss_pred             HHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          367 KQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       367 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      ..|..+...  ......-..-+.+++...|+.++|..+|+.+.. +  .+|-.++. ..+.|..-..     ......+.
T Consensus       306 ~~~~~l~~~--~~~~~r~~YW~~ra~~~~g~~~~a~~~~~~~a~-~--~~fYg~lA-a~~Lg~~~~~-----~~~~~~~~  374 (618)
T 1qsa_A          306 TWLARLPME--AKEKDEWRYWQADLLLERGREAEAKEILHQLMQ-Q--RGFYPMVA-AQRIGEEYEL-----KIDKAPQN  374 (618)
T ss_dssp             HHHHHSCTT--GGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT-S--CSHHHHHH-HHHTTCCCCC-----CCCCCCSC
T ss_pred             HHHHHcccc--ccccHhHHHHHHHHHHHcCCHHHHHHHHHHHhc-C--CChHHHHH-HHHcCCCCCC-----CCCCCChh
Confidence            999988652  112233344577888899999999999999884 3  23443332 2233321000     00011111


Q ss_pred             CCc-----hHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          447 KTG-----NSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       447 ~~~-----~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      ...     .-...+..+...|...+|...+..+.+
T Consensus       375 ~~~~~~~~~~~~r~~~L~~~g~~~~a~~ew~~~~~  409 (618)
T 1qsa_A          375 VDSALTQGPEMARVRELMYWNLDNTARSEWANLVK  409 (618)
T ss_dssp             CCCHHHHSHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHhhhccChHHHHHHHHHHCCChhhHHHHHHHHHh
Confidence            111     122345678889999999888877654

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=93.10  E-value=0.79  Score=34.40  Aligned_cols=77  Identities=13%  Similarity=-0.008  Sum_probs=54.8

Q ss_pred             CCCCCchHHHHHHHHHhhcCChH---HHHHHHHhcc-CCC--ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCch
Q 011249          377 GIKPLTEHLTCMVDLLGRSGQLE---KAHSLIMDYK-DFC--DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGN  450 (490)
Q Consensus       377 ~~~~~~~~~~~l~~~~~~~g~~~---~A~~~~~~~~-~~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~  450 (490)
                      +-.|+..+--.+..++.+..+.+   +++.+++.+. ..|  .....-.+..++.+.|++++|.++.+.+++.+|+|..+
T Consensus        34 ~~~vs~~t~F~YAw~Lv~S~~~~di~~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~~eP~n~QA  113 (144)
T 1y8m_A           34 GPTATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQV  113 (144)
T ss_dssp             STTSCHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHTCCCCHHH
T ss_pred             cCCCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHHH
Confidence            33567777777777888777544   5677777665 233  23345556678899999999999999999999998765


Q ss_pred             HHH
Q 011249          451 SAL  453 (490)
Q Consensus       451 ~~~  453 (490)
                      ...
T Consensus       114 ~~L  116 (144)
T 1y8m_A          114 GAL  116 (144)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=92.71  E-value=0.23  Score=36.78  Aligned_cols=75  Identities=12%  Similarity=-0.028  Sum_probs=51.9

Q ss_pred             CCCchHHHHHHHHHhhcCCh---HHHHHHHHhcc-CCC--ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHH
Q 011249          379 KPLTEHLTCMVDLLGRSGQL---EKAHSLIMDYK-DFC--DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSA  452 (490)
Q Consensus       379 ~~~~~~~~~l~~~~~~~g~~---~~A~~~~~~~~-~~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~  452 (490)
                      .|++.+--.+..++.+..+.   .+++.+++.+. ..|  ....+--+..++.+.|++++|.+..+.+++..|+|..+..
T Consensus        37 ~vs~qt~F~yAw~Lv~S~~~~d~~~GI~LLe~l~~~~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL~~eP~N~QA~~  116 (134)
T 3o48_A           37 TATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQVGA  116 (134)
T ss_dssp             GSCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTCTTCHHHHH
T ss_pred             CCChhhHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHHhhCCCCHHHHH
Confidence            45556666667777776654   45677776655 223  2345566677888999999999999999999998776544


Q ss_pred             H
Q 011249          453 L  453 (490)
Q Consensus       453 ~  453 (490)
                      .
T Consensus       117 L  117 (134)
T 3o48_A          117 L  117 (134)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=92.50  E-value=0.25  Score=45.27  Aligned_cols=56  Identities=13%  Similarity=0.024  Sum_probs=27.5

Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHH
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLL  441 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  441 (490)
                      ..++..+...|++++|...+..+.  .+-+...+..++.++...|+..+|++.|+++.
T Consensus       175 ~~~~~~~l~~g~~~~a~~~l~~~~~~~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r  232 (388)
T 2ff4_A          175 TAKAEAEIACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVK  232 (388)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            334444455555555555444433  23344455555555555555555555555443

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=92.33  E-value=5.5  Score=35.06  Aligned_cols=181  Identities=12%  Similarity=0.060  Sum_probs=108.2

Q ss_pred             HHHhCCCh---HHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHH--
Q 011249          157 GYANCGNM---KAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIE--  231 (490)
Q Consensus       157 ~~~~~~~~---~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~--  231 (490)
                      .....|++   =+|.+.+           .++..-|.+.+++++|++++-.           -...+.+.|+...+-+  
T Consensus        21 ~~I~~G~y~~~YEAHQ~~-----------RTi~~Ry~~~k~y~eAidLL~~-----------GA~~ll~~~Q~~sg~DL~   78 (336)
T 3lpz_A           21 RRIAEGQPEEQYEAAQET-----------RLVAARYSKQGNWAAAVDILAS-----------VSQTLLRSGQGGSGGDLA   78 (336)
T ss_dssp             HHHHHCCHHHHHHHHHHH-----------HHHHHHHHHTTCHHHHHHHHHH-----------HHHHHHHTTCHHHHHHHH
T ss_pred             HHHhCCCCccccHHHHHH-----------HHHHHHHHhhcCHHHHHHHHHH-----------HHHHHHHCCCcchHHHHH
Confidence            34455666   4555544           4566778888999998887642           3345666677655444  


Q ss_pred             --HHHHHHHcCcccChhhHHHHHHHHhccCChH-HHHHHHHHHH----hcC--CCCchhHHHHHHHHHHhcCChHHHHHH
Q 011249          232 --MYKVMRQENVRISEVAMVGAISACTQLGDVE-MAAILAKHVD----EGC--CDRTNYVSNALIHMHSKCGYLDLAWRE  302 (490)
Q Consensus       232 --~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~-~a~~~~~~~~----~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~  302 (490)
                        +++-+.+.++++|......++..+.....-+ .-..+.+.+.    +.|  ..-++.....+...|.+.+++.+|+..
T Consensus        79 ~llvevy~~~~~~~~~~~~~rL~~L~~~~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H  158 (336)
T 3lpz_A           79 VLLVDTFRQAGQRVDGASRGKLLGCLRLFQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKH  158 (336)
T ss_dssp             HHHHHHHHHHTCCCCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHH
Confidence              3455566788888888888888777655422 1122333332    222  334677888899999999999999988


Q ss_pred             HhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Q 011249          303 FSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTR  374 (490)
Q Consensus       303 ~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  374 (490)
                      |-.-.++.+..+..++--+...+...              .++...-..++. |...++...|...++...+
T Consensus       159 ~ilg~~~s~~~~a~mL~ew~~~~~~~--------------e~dlfiaRaVL~-yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          159 LVLGTKESPEVLARMEYEWYKQDESH--------------TAPLYCARAVLP-YLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             HTTSCTTHHHHHHHHHHHHHHTSCGG--------------GHHHHHHHHHHH-HHHTTCHHHHHHHHHHHHH
T ss_pred             HHhcCCchHHHHHHHHHHHHHhcCCc--------------cHHHHHHHHHHH-HHHhCCHHHHHHHHHHHHH
Confidence            85322233355655544443333211              122223333333 4456788888887776665

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.05  E-value=4.2  Score=37.91  Aligned_cols=186  Identities=9%  Similarity=0.059  Sum_probs=119.0

Q ss_pred             cCChHHHHHHHHHHHHc-----CcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHH----HHhc
Q 011249          223 NGYAKAAIEMYKVMRQE-----NVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHM----HSKC  293 (490)
Q Consensus       223 ~g~~~~A~~~~~~~~~~-----~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~----~~~~  293 (490)
                      .|+++.|++.+..+.+.     ...-.......++..|...|+++.....+..+.+..-.. ......+++.    ....
T Consensus        29 ~~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~ql-k~ai~~~V~~~~~~l~~~  107 (445)
T 4b4t_P           29 QNDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQL-KLSIQYMIQKVMEYLKSS  107 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTS-HHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhh-HHHHHHHHHHHHHHHhcC
Confidence            37889999888777653     223345667788999999999999988887765432122 2222333332    2223


Q ss_pred             CChH--HHHHHHhcccC---C-------ChhHHHHHHHHHHhcCChHHHHHHHHHHHH--cCCCCcH---HHHHHHHHHh
Q 011249          294 GYLD--LAWREFSRIKN---K-------DVISYSSMITAFADHGKSQEALDMFLKMRN--EGIEPNQ---VTFIGVLTAC  356 (490)
Q Consensus       294 ~~~~--~A~~~~~~~~~---~-------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~~~~p~~---~~~~~l~~~~  356 (490)
                      ...+  .-..+.+.+..   .       .......|...+...|++.+|..++..+..  .|..+..   ..+...++.|
T Consensus       108 ~~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~  187 (445)
T 4b4t_P          108 KSLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELS  187 (445)
T ss_dssp             CTTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHH
Confidence            3322  22333333322   1       112345678889999999999999999875  2332222   3566677789


Q ss_pred             cCCCChHHHHHHHHHHHHH-cCCCCC----chHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          357 SHGGLVEDGCKQFELMTRV-FGIKPL----TEHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       357 ~~~g~~~~a~~~~~~~~~~-~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                      ...+++..|..++.++... +...++    ...+...+..+...+++.+|-+.|.++.
T Consensus       188 l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~~  245 (445)
T 4b4t_P          188 ILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEIY  245 (445)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            9999999999999987532 122222    2345667778888899999988876654

>1y8m_A FIS1; mitochondria, unknown function; NMR {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=92.03  E-value=2.5  Score=31.76  Aligned_cols=45  Identities=11%  Similarity=0.042  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHhcCCC-CCchHHHHHHHHHhcCCcchHHHHHHHhhh
Q 011249          432 LGEIAARHLLELGPE-KTGNSALLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       432 ~a~~~~~~~~~~~p~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                      +++.+++.+....|. ....+..|+-++.+.|+|++|+++.+.+.+
T Consensus        60 ~GI~LLe~l~~~~~~~~RdcLYyLAvg~ykl~~Y~~Ar~y~d~lL~  105 (144)
T 1y8m_A           60 LGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFE  105 (144)
T ss_dssp             HHHHHHHHHHHHCCSTHHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHh
Confidence            444444444444442 223344444445555555555554444443

>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=91.87  E-value=1.2  Score=32.93  Aligned_cols=45  Identities=13%  Similarity=-0.012  Sum_probs=19.6

Q ss_pred             HHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          364 DGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       364 ~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                      +++.+++.+.+. +..-.......+.-++.+.|++++|.++.+.+.
T Consensus        61 ~GI~LLe~l~~~-~~~~~Rd~LYyLAvg~yklgdY~~Ar~y~d~lL  105 (134)
T 3o48_A           61 LGVKILTDIYKE-AESRRRECLYYLTIGCYKLGEYSMAKRYVDTLF  105 (134)
T ss_dssp             HHHHHHHHHHHH-CGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc-CcchhHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            444444444442 211123333344445555555555555554443

>3ltj_A Alpharep-4; protein engineering, heat-like repeat, protein binding; 1.80A {Synthetic}

Probab=91.64  E-value=4.5  Score=32.57  Aligned_cols=85  Identities=13%  Similarity=0.220  Sum_probs=35.9

Q ss_pred             hhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHH
Q 011249          141 DSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCY  220 (490)
Q Consensus       141 ~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~  220 (490)
                      +.+..+|...-...+..+.+.++.+....+.+.+..++...-...+.++...++.+....+.+.+..++...-...+.++
T Consensus        21 ~~L~~~~~~vr~~A~~~L~~~~~~~~~~~L~~~l~~~~~~vr~~a~~~L~~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL  100 (201)
T 3ltj_A           21 KNLQDDSYYVRRAAAYALGKIGDERAVEPLIKALKDEDAWVRRAAADALGQIGDERAVEPLIKALKDEDGWVRQSAAVAL  100 (201)
T ss_dssp             HHTTCSCHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHH
T ss_pred             HHhcCCCHHHHHHHHHHHHhcCChhHHHHHHHHHcCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            33333444444444444444444333333333333344444444444444444433333333333334444444444444


Q ss_pred             HhcCC
Q 011249          221 VQNGY  225 (490)
Q Consensus       221 ~~~g~  225 (490)
                      .+.++
T Consensus       101 ~~~~~  105 (201)
T 3ltj_A          101 GQIGD  105 (201)
T ss_dssp             HHHCC
T ss_pred             HHhCc
Confidence            44443

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=91.50  E-value=6.3  Score=41.92  Aligned_cols=157  Identities=8%  Similarity=0.002  Sum_probs=79.4

Q ss_pred             HHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChH
Q 011249          183 VAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVE  262 (490)
Q Consensus       183 ~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~  262 (490)
                      ..++..+...+..+-+.++...... ++..-..+..++...|++++|.+.|++... |+..+....          ....
T Consensus       816 ~~l~~~l~~~~~~~~~~~l~~~~~~-~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~-~~~~~~~l~----------~~~~  883 (1139)
T 4fhn_B          816 TELVEKLFLFKQYNACMQLIGWLNS-DPIAVYLKALIYLKSKEAVKAVRCFKTTSL-VLYSHTSQF----------AVLR  883 (1139)
T ss_dssp             HHHHHHHHHHSCTTHHHHHHHHSCC-CHHHHHHHHHHHHHTTCHHHHHHHHHTCCC-SCTTCCCSC----------SSHH
T ss_pred             HHHHHHHHHhhhHHHHHHHhhhccC-CcHHHHHHHHHHHhcCCHHHHHHHHHHHhh-hhcccchhh----------hhhc
Confidence            3455666677777777766655544 334445677888888888888888876532 111111000          0000


Q ss_pred             HHHHHHHHHHhcC--CCCchhHHHHHHHHHHhcCChHHHHHHHhcccC----CCh----hHHHHHHHHHHhcCChHHHHH
Q 011249          263 MAAILAKHVDEGC--CDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN----KDV----ISYSSMITAFADHGKSQEALD  332 (490)
Q Consensus       263 ~a~~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~~~----~~~~~l~~~~~~~~~~~~a~~  332 (490)
                      .    +..+....  ...-...|..++..+.+.+.++.+.++-....+    .+.    ..|..+...+...|++++|..
T Consensus       884 ~----~~~~~~~~~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~  959 (1139)
T 4fhn_B          884 E----FQEIAEKYHHQNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHV  959 (1139)
T ss_dssp             H----HHHHHHTTTSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGH
T ss_pred             c----cccccccccccccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHH
Confidence            0    00111110  011233455556666666666665554443321    111    245666666677777777776


Q ss_pred             HHHHHHHcCCCCcHHHHHHHHHHhc
Q 011249          333 MFLKMRNEGIEPNQVTFIGVLTACS  357 (490)
Q Consensus       333 ~~~~~~~~~~~p~~~~~~~l~~~~~  357 (490)
                      .+-.+.....+  ...+..|+...+
T Consensus       960 aL~~~pd~~~r--~~cLr~LV~~lc  982 (1139)
T 4fhn_B          960 ALMVLSTTPLK--KSCLLDFVNQLT  982 (1139)
T ss_dssp             HHHHHHHSSSC--HHHHHHHHHHHH
T ss_pred             HHHhCCCHHHH--HHHHHHHHHHHH
Confidence            66665543222  234444444433

>3ltm_A Alpha-REP4; protein engineering, heat-like repeat, protein binding; HET: 1PE 12P; 2.15A {Synthetic}

Probab=91.25  E-value=5.2  Score=32.52  Aligned_cols=90  Identities=12%  Similarity=0.212  Sum_probs=45.5

Q ss_pred             HHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHH
Q 011249          136 AQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAA  215 (490)
Q Consensus       136 A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~  215 (490)
                      ...+.+.+..+|...-...+..+.+.|+.+..-.+.+.+..+|...-...+.++...++.+....+.+.+..++...-..
T Consensus        21 ~~~L~~~L~~~~~~vR~~A~~~L~~~~~~~~~~~L~~~l~~~~~~vr~~a~~aL~~~~~~~~~~~L~~~l~~~~~~vr~~  100 (211)
T 3ltm_A           21 VEMYIKNLQDDSYYVRRAAAYALGKIGDERAVEPLIKALKDEDAWVRRAAADALGQIGDERAVEPLIKALKDEDGWVRQS  100 (211)
T ss_dssp             HHHHHHHTTCSSHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSCHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHhCCccHHHHHHHHHcCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHH
Confidence            33344444445555555555666666654444444444444555555555555555555444433444444455555445


Q ss_pred             HHHHHHhcCC
Q 011249          216 MTVCYVQNGY  225 (490)
Q Consensus       216 l~~~~~~~g~  225 (490)
                      .+.++.+.++
T Consensus       101 a~~aL~~~~~  110 (211)
T 3ltm_A          101 AAVALGQIGD  110 (211)
T ss_dssp             HHHHHHHHCC
T ss_pred             HHHHHHHhCc
Confidence            5555555444

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=91.25  E-value=7.1  Score=34.09  Aligned_cols=181  Identities=9%  Similarity=0.088  Sum_probs=104.8

Q ss_pred             HHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHH----HH
Q 011249          158 YANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIE----MY  233 (490)
Q Consensus       158 ~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~----~~  233 (490)
                      -...|++=+|.+.+           .++..-|.+.+++++|++++..           -...+.+.|+...|-+    ++
T Consensus        23 ~I~~G~yYEAhQ~~-----------Rtl~~Ry~~~~~~~eAidlL~~-----------ga~~ll~~~Q~~sa~DLa~llv   80 (312)
T 2wpv_A           23 KIKAGDYYEAHQTL-----------RTIANRYVRSKSYEHAIELISQ-----------GALSFLKAKQGGSGTDLIFYLL   80 (312)
T ss_dssp             HHHHTCHHHHHHHH-----------HHHHHHHHHTTCHHHHHHHHHH-----------HHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HhhccChHHHHHHH-----------HHHHHHHHHhcCHHHHHHHHHH-----------HHHHHHHCCCcchHHHHHHHHH
Confidence            34445555555444           4456777778888888777642           3344566677655444    45


Q ss_pred             HHHHHcCcccChhhHHHHHHHHhccCChH-HHHHHHHHHH----hcC--CCCchhHHHHHHHHHHhcCChHHHHHHHhcc
Q 011249          234 KVMRQENVRISEVAMVGAISACTQLGDVE-MAAILAKHVD----EGC--CDRTNYVSNALIHMHSKCGYLDLAWREFSRI  306 (490)
Q Consensus       234 ~~~~~~~~~p~~~~~~~l~~~~~~~g~~~-~a~~~~~~~~----~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~  306 (490)
                      +-..+.+++++......++..+.....-+ .-.++.+.+.    +.|  ...++.....+...|.+.|++.+|+..|-.-
T Consensus        81 ev~~~~~~~~~~~~~~rl~~l~~~~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~~  160 (312)
T 2wpv_A           81 EVYDLAEVKVDDISVARLVRLIAELDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLG  160 (312)
T ss_dssp             HHHHHTTCCCSHHHHHHHHHHHTTCCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHTS
T ss_pred             HHHHHcCCCCCHHHHHHHHHHHHHCCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHhC
Confidence            55556677888877777777765533211 1223333332    222  2246778888999999999999998877633


Q ss_pred             cCCChhHHHHHHHHHHhc---CChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHH
Q 011249          307 KNKDVISYSSMITAFADH---GKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRV  375 (490)
Q Consensus       307 ~~~~~~~~~~l~~~~~~~---~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~  375 (490)
                      ...++..+..++--+...   |...++-              ...-..++. |.-.|+...|..+++...+.
T Consensus       161 ~~~s~~~~a~~l~~w~~~~~~~~~~e~d--------------lf~~RaVL~-yL~l~n~~~A~~~~~~f~~~  217 (312)
T 2wpv_A          161 THDSMIKYVDLLWDWLCQVDDIEDSTVA--------------EFFSRLVFN-YLFISNISFAHESKDIFLER  217 (312)
T ss_dssp             CHHHHHHHHHHHHHHHHHTTCCCHHHHH--------------HHHHHHHHH-HHHTTBHHHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHHHHHHhcCCCCcchHH--------------HHHHHHHHH-HHHhcCHHHHHHHHHHHHHH
Confidence            322455554444433333   3222211              111222222 44578899999988877654

>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=91.13  E-value=8.7  Score=34.90  Aligned_cols=284  Identities=10%  Similarity=0.002  Sum_probs=144.4

Q ss_pred             HHHHHHHHHhcCChhHHHHHHhhcCC--------CCHHhHHHHHHHHHhcC-ChHHHHHHHHHHHHcCcccChhhH----
Q 011249          182 WVAMIAGYGKCGEVREAKKVFDEISE--------PDASCWAAMTVCYVQNG-YAKAAIEMYKVMRQENVRISEVAM----  248 (490)
Q Consensus       182 ~~~l~~~~~~~~~~~~A~~~~~~~~~--------~~~~~~~~l~~~~~~~g-~~~~A~~~~~~~~~~~~~p~~~~~----  248 (490)
                      ...|+..|.+.|+.++..+++.....        ........++..+.... ..+.-.++..+..+..-. +..+|    
T Consensus        22 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kak~~k~v~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~-~~r~flr~~  100 (394)
T 3txn_A           22 ILQQGELYKQEGKAKELADLIKVTRPFLSSISKAKAAKLVRSLVDMFLDMDAGTGIEVQLCKDCIEWAKQ-EKRTFLRQS  100 (394)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHTTTGGGGSCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHH-TTCHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHH-HHHHHHHHH
Confidence            34555666666666666666655543        12233445555555432 233334444444332111 11222    


Q ss_pred             --HHHHHHHhccCChHHHHHHHHHHHhcCCCCc-----hhHHHHHHHHHHhcCChHHHHHHHhcccC------CChhHHH
Q 011249          249 --VGAISACTQLGDVEMAAILAKHVDEGCCDRT-----NYVSNALIHMHSKCGYLDLAWREFSRIKN------KDVISYS  315 (490)
Q Consensus       249 --~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~-----~~~~~~l~~~~~~~~~~~~A~~~~~~~~~------~~~~~~~  315 (490)
                        ..++..|...|++.+|.+++..+.+.-...|     ..++..-+.+|...+++.++...+.....      +++....
T Consensus       101 l~~kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~~~p~i~a  180 (394)
T 3txn_A          101 LEARLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKVQG  180 (394)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCCCCHHHHH
Confidence              1466777888888888887777765322222     23455567778888998888888866543      2332222


Q ss_pred             ----HHHHHHH-hcCChHHHHHHHHHHHHc-C--CCCc---HHHHHHHHHHhcCCCChHHHHHHHH-HHHHHcCCCCCch
Q 011249          316 ----SMITAFA-DHGKSQEALDMFLKMRNE-G--IEPN---QVTFIGVLTACSHGGLVEDGCKQFE-LMTRVFGIKPLTE  383 (490)
Q Consensus       316 ----~l~~~~~-~~~~~~~a~~~~~~~~~~-~--~~p~---~~~~~~l~~~~~~~g~~~~a~~~~~-~~~~~~~~~~~~~  383 (490)
                          .-...+. ..++|..|...|-+..+. .  ..|.   ...|..+.. ... ++..+...++. .....+ ..|...
T Consensus       181 ~i~~~~Gi~~l~~~rdyk~A~~~F~eaf~~f~~~~~~~~~~~lkYlvL~a-Ll~-~~r~el~~~l~~~~~~~~-~~pei~  257 (394)
T 3txn_A          181 ALDLQSGILHAADERDFKTAFSYFYEAFEGFDSVDSVKALTSLKYMLLCK-IML-GQSDDVNQLVSGKLAITY-SGRDID  257 (394)
T ss_dssp             HHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHH-HHT-TCGGGHHHHHHSHHHHTT-CSHHHH
T ss_pred             HHHHHhhHHHHHhccCHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHH-HHc-CCHHHHHHHhcccccccc-CCccHH
Confidence                1223456 788999998888776531 1  1121   113322222 222 23333323332 222212 344444


Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhc
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASM  461 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  461 (490)
                      .+..++.+| ..+++.+...+++...  ...|+.....+ ..+.+ .-.   ...+.++  ..|-..-.+..++..+.- 
T Consensus       258 ~l~~L~~a~-~~~dl~~f~~iL~~~~~~l~~D~~l~~h~-~~L~~-~Ir---~~~L~~i--~~pYsrIsl~~iA~~l~l-  328 (394)
T 3txn_A          258 AMKSVAEAS-HKRSLADFQAALKEYKKELAEDVIVQAHL-GTLYD-TML---EQNLCRI--IEPYSRVQVAHVAESIQL-  328 (394)
T ss_dssp             HHHHHHHHH-HTTCHHHHHHHHHHSTTTTTTSHHHHHHH-HHHHH-HHH---HHHHHHH--HTTCSEEEHHHHHHHHTC-
T ss_pred             HHHHHHHHH-HhCCHHHHHHHHHHHHHHHhcChHHHHHH-HHHHH-HHH---HHHHHHH--hHhhceeeHHHHHHHHCc-
Confidence            455555554 4567777777776654  22233211111 00000 000   1111111  346666677777766654 


Q ss_pred             CCcchHHHHHHHhhhccc
Q 011249          462 GKWKDSEIVKMMISETEK  479 (490)
Q Consensus       462 g~~~~A~~~~~~~~~~~~  479 (490)
                       ..++++..+-+|...|.
T Consensus       329 -s~~evE~~L~~lI~dg~  345 (394)
T 3txn_A          329 -PMPQVEKKLSQMILDKK  345 (394)
T ss_dssp             -CHHHHHHHHHHHHHTTS
T ss_pred             -CHHHHHHHHHHHHHCCC
Confidence             67889999988887753

>3lpz_A GET4 (YOR164C homolog); protein targeting, tail-anchored protein biogenesis, GET PAT GET5 binding, protein transport; 1.98A {Chaetomium thermophilum}

Probab=90.90  E-value=7.9  Score=34.06  Aligned_cols=167  Identities=11%  Similarity=0.001  Sum_probs=99.6

Q ss_pred             HHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHH----HHHHHcCCCCcHHHHHHHHHHhcC
Q 011249          283 SNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMF----LKMRNEGIEPNQVTFIGVLTACSH  358 (490)
Q Consensus       283 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~----~~~~~~~~~p~~~~~~~l~~~~~~  358 (490)
                      |.++..=|.+.+++++|++++..-           ...+.+.|+...|-++-    +...+.++++|......++..+..
T Consensus        38 ~RTi~~Ry~~~k~y~eAidLL~~G-----------A~~ll~~~Q~~sg~DL~~llvevy~~~~~~~~~~~~~rL~~L~~~  106 (336)
T 3lpz_A           38 TRLVAARYSKQGNWAAAVDILASV-----------SQTLLRSGQGGSGGDLAVLLVDTFRQAGQRVDGASRGKLLGCLRL  106 (336)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHH-----------HHHHHHTTCHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHhhcCHHHHHHHHHHH-----------HHHHHHCCCcchHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHh
Confidence            444556678889999998876542           23455667666554443    555567788888888888877665


Q ss_pred             CCChH-HHHHHHHHHHH---HcC--CCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChHH
Q 011249          359 GGLVE-DGCKQFELMTR---VFG--IKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAEL  432 (490)
Q Consensus       359 ~g~~~-~a~~~~~~~~~---~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  432 (490)
                      ...-+ .=..+++++.+   ++|  ..-++.....+...|.+.+++.+|...|-. ...+.+..+..++.-+...+.   
T Consensus       107 ~~~~~p~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~ig~~~~~e~~~~~Ae~H~il-g~~~s~~~~a~mL~ew~~~~~---  182 (336)
T 3lpz_A          107 FQPGEPVRKRFVKEMIDWSKKFGDYPAGDPELHHVVGTLYVEEGEFEAAEKHLVL-GTKESPEVLARMEYEWYKQDE---  182 (336)
T ss_dssp             SCTTCHHHHHHHHHHHHHHHHHSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHTT-SCTTHHHHHHHHHHHHHHTSC---
T ss_pred             CCCCCcHHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHh-cCCchHHHHHHHHHHHHHhcC---
Confidence            44311 11223333322   123  234567778899999999999999988842 223334566555554444332   


Q ss_pred             HHHHHHHHHhcCCCCCchHH-HHHHHHHhcCCcchHHHHHHHhhh
Q 011249          433 GEIAARHLLELGPEKTGNSA-LLANIYASMGKWKDSEIVKMMISE  476 (490)
Q Consensus       433 a~~~~~~~~~~~p~~~~~~~-~l~~~~~~~g~~~~A~~~~~~~~~  476 (490)
                                  |.....|. ..+--|.-.++...|..+++...+
T Consensus       183 ------------~~e~dlfiaRaVL~yL~l~n~~~A~~~~~~f~~  215 (336)
T 3lpz_A          183 ------------SHTAPLYCARAVLPYLLVANVRAANTAYRIFTS  215 (336)
T ss_dssp             ------------GGGHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             ------------CccHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence                        22233222 233346667788888887666554

>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=90.39  E-value=10  Score=34.45  Aligned_cols=216  Identities=9%  Similarity=0.003  Sum_probs=94.1

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCcccC-----hhhHHHHHHHHhccCChHHHHHHHHHHHhc--CCCCchhHH----
Q 011249          215 AMTVCYVQNGYAKAAIEMYKVMRQENVRIS-----EVAMVGAISACTQLGDVEMAAILAKHVDEG--CCDRTNYVS----  283 (490)
Q Consensus       215 ~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~-----~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~--~~~~~~~~~----  283 (490)
                      -++..|...|++.+|.+++.++.+.--..|     ...+..-+..|...+++..+...+......  .+.+++.+.    
T Consensus       104 kL~~l~~~~~~y~~a~~~i~~l~~~~~~~dd~~~llev~lle~~~~~~~~n~~k~k~~l~~a~~~~~ai~~~p~i~a~i~  183 (394)
T 3txn_A          104 RLIALYFDTALYTEALALGAQLLRELKKLDDKNLLVEVQLLESKTYHALSNLPKARAALTSARTTANAIYCPPKVQGALD  183 (394)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHTTSSCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhccCCCCHHHHHHHH
Confidence            355666666666666666666654211111     123444445556666666666666655332  121222211    


Q ss_pred             HHHHHHHH-hcCChHHHHHHHhcccC-------C---ChhHHHHHHHHHHhcCChHHHHHHHH-HHHHcCCCCcHHHHHH
Q 011249          284 NALIHMHS-KCGYLDLAWREFSRIKN-------K---DVISYSSMITAFADHGKSQEALDMFL-KMRNEGIEPNQVTFIG  351 (490)
Q Consensus       284 ~~l~~~~~-~~~~~~~A~~~~~~~~~-------~---~~~~~~~l~~~~~~~~~~~~a~~~~~-~~~~~~~~p~~~~~~~  351 (490)
                      ..-+..+. ..+++..|...|-+..+       +   +...|..+... .. ++..+.-.++. +....-..|....+..
T Consensus       184 ~~~Gi~~l~~~rdyk~A~~~F~eaf~~f~~~~~~~~~~~lkYlvL~aL-l~-~~r~el~~~l~~~~~~~~~~pei~~l~~  261 (394)
T 3txn_A          184 LQSGILHAADERDFKTAFSYFYEAFEGFDSVDSVKALTSLKYMLLCKI-ML-GQSDDVNQLVSGKLAITYSGRDIDAMKS  261 (394)
T ss_dssp             HHHHHHHHHTTSCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHH-HT-TCGGGHHHHHHSHHHHTTCSHHHHHHHH
T ss_pred             HHhhHHHHHhccCHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHH-Hc-CCHHHHHHHhccccccccCCccHHHHHH
Confidence            11122344 56666666555543321       1   12233222222 22 22222222221 2111112455555666


Q ss_pred             HHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCChH
Q 011249          352 VLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNAE  431 (490)
Q Consensus       352 l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~  431 (490)
                      ++.++. .+++.+...+++....  .+..|+.....+-..+.+  =..   ..+.++..+-...++..+...+.-  ..+
T Consensus       262 L~~a~~-~~dl~~f~~iL~~~~~--~l~~D~~l~~h~~~L~~~--Ir~---~~L~~i~~pYsrIsl~~iA~~l~l--s~~  331 (394)
T 3txn_A          262 VAEASH-KRSLADFQAALKEYKK--ELAEDVIVQAHLGTLYDT--MLE---QNLCRIIEPYSRVQVAHVAESIQL--PMP  331 (394)
T ss_dssp             HHHHHH-TTCHHHHHHHHHHSTT--TTTTSHHHHHHHHHHHHH--HHH---HHHHHHHTTCSEEEHHHHHHHHTC--CHH
T ss_pred             HHHHHH-hCCHHHHHHHHHHHHH--HHhcChHHHHHHHHHHHH--HHH---HHHHHHhHhhceeeHHHHHHHHCc--CHH
Confidence            666653 4677666666665543  333443321111100000  000   111111122234455555555433  567


Q ss_pred             HHHHHHHHHHh
Q 011249          432 LGEIAARHLLE  442 (490)
Q Consensus       432 ~a~~~~~~~~~  442 (490)
                      +++..+-+++.
T Consensus       332 evE~~L~~lI~  342 (394)
T 3txn_A          332 QVEKKLSQMIL  342 (394)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            77777777765

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=90.34  E-value=1.4  Score=46.77  Aligned_cols=94  Identities=10%  Similarity=-0.114  Sum_probs=64.7

Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc-------------------------CCCChhhHHHHHHHHhhhCChHHHHHHHHHH
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK-------------------------DFCDAGTWGALLGACKVHVNAELGEIAARHL  440 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~-------------------------~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~  440 (490)
                      ..++.+|...|++++|.+.|++..                         ......-|..++..+.+.|.++.+.++.+.+
T Consensus       846 yl~g~~~L~~ge~~~A~~~F~kaa~~~~~~~~l~~~~~~~~~~~~~~~~~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lA  925 (1139)
T 4fhn_B          846 YLKALIYLKSKEAVKAVRCFKTTSLVLYSHTSQFAVLREFQEIAEKYHHQNLLSCYYLHLSKKLFEESAYIDALEFSLLA  925 (1139)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHTCCCSCTTCCCSCSSHHHHHHHHHTTTSCCSSHHHHHHHHHHHHHTSCCHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHhhhhcccchhhhhhcccccccccccccccHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            345566666777777777765543                         0111234667777888889999999998888


Q ss_pred             HhcCC-CCC----chHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          441 LELGP-EKT----GNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       441 ~~~~p-~~~----~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ++..+ ++.    ..|..+...+...|++++|...+-.+.....
T Consensus       926 i~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~  969 (1139)
T 4fhn_B          926 DASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPL  969 (1139)
T ss_dssp             HHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSS
T ss_pred             HHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHH
Confidence            87553 332    2577788888899999999888877665443

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=90.21  E-value=1.5  Score=43.67  Aligned_cols=51  Identities=10%  Similarity=0.008  Sum_probs=35.8

Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCCc-HHHHHHHHHHhcCCCChHHHHHHHHHH
Q 011249          320 AFADHGKSQEALDMFLKMRNEGIEPN-QVTFIGVLTACSHGGLVEDGCKQFELM  372 (490)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~  372 (490)
                      -+...|+++-|+++-++.+..  .|+ -.+|..|..+|...|+++.|+-.+..+
T Consensus       346 FLl~K~~~elAL~~Ak~AV~~--aPseF~tW~~La~vYi~l~d~e~ALLtLNSc  397 (754)
T 4gns_B          346 FLLNRGDYELALGVSNTSTEL--ALDSFESWYNLARCHIKKEEYEKALFAINSM  397 (754)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHS
T ss_pred             HHhccCcHHHHHHHHHHHHhc--CchhhHHHHHHHHHHHHhccHHHHHHHHhcC
Confidence            455667777777777777763  554 347777777777777777777777665

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.40  E-value=14  Score=34.44  Aligned_cols=199  Identities=8%  Similarity=-0.009  Sum_probs=118.2

Q ss_pred             cCChhHHHHHHhhcCC---------CCHHhHHHHHHHHHhcCChHHHHHHHHHHHH-cCcccChhhHHHHHHHH----hc
Q 011249          192 CGEVREAKKVFDEISE---------PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQ-ENVRISEVAMVGAISAC----TQ  257 (490)
Q Consensus       192 ~~~~~~A~~~~~~~~~---------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-~~~~p~~~~~~~l~~~~----~~  257 (490)
                      .|++++|++.+-.+.+         ........++..|...|+++...+.+.-+.+ .|..+.  ....+++.+    ..
T Consensus        29 ~~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~--ai~~~V~~~~~~l~~  106 (445)
T 4b4t_P           29 QNDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKL--SIQYMIQKVMEYLKS  106 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHH--HHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHH--HHHHHHHHHHHHHhc
Confidence            3678888877755432         2455677888999999999998888877664 333222  223444333    22


Q ss_pred             cCChHHHH--HHHHHHHh--cC-CCC---chhHHHHHHHHHHhcCChHHHHHHHhcccC----C-----ChhHHHHHHHH
Q 011249          258 LGDVEMAA--ILAKHVDE--GC-CDR---TNYVSNALIHMHSKCGYLDLAWREFSRIKN----K-----DVISYSSMITA  320 (490)
Q Consensus       258 ~g~~~~a~--~~~~~~~~--~~-~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~----~-----~~~~~~~l~~~  320 (490)
                      ....+...  .+.+.+..  .| +-.   .......|...|...|++.+|..++..+..    .     -...+...+..
T Consensus       107 ~~~~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl  186 (445)
T 4b4t_P          107 SKSLDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMEL  186 (445)
T ss_dssp             HCTTHHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHH
T ss_pred             CCchhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            33333221  12211111  11 111   223446688999999999999999988753    1     13467777888


Q ss_pred             HHhcCChHHHHHHHHHHHH----cCCCCcH--HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh
Q 011249          321 FADHGKSQEALDMFLKMRN----EGIEPNQ--VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR  394 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~----~~~~p~~--~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  394 (490)
                      |...+++.+|..++.++..    ....|+.  ..+...+..+...+++.+|.+.                |..+...+..
T Consensus       187 ~l~~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~----------------y~e~~~~~~~  250 (445)
T 4b4t_P          187 SILKGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQY----------------LQEIYQTDAI  250 (445)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHH----------------HHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHH----------------HHHHHhcccc
Confidence            9999999999999998753    2222222  2344455555566666655433                3445566666


Q ss_pred             cCChHHHHHHHHhc
Q 011249          395 SGQLEKAHSLIMDY  408 (490)
Q Consensus       395 ~g~~~~A~~~~~~~  408 (490)
                      .++.......+..+
T Consensus       251 ~~d~~~~~~~L~~~  264 (445)
T 4b4t_P          251 KSDEAKWKPVLSHI  264 (445)
T ss_dssp             HSCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH
Confidence            67665555544433

>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=89.13  E-value=2.8  Score=29.20  Aligned_cols=63  Identities=14%  Similarity=0.116  Sum_probs=41.6

Q ss_pred             ChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 011249          225 YAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIH  288 (490)
Q Consensus       225 ~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  288 (490)
                      +.-+..+-++.+....+.|++......+.+|.+.+++..|.++++-++... .....+|..+++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~-~~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCchhhHHHHHH
Confidence            344556666666667777777777777788888888888887777775543 222445555543

>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=88.49  E-value=2.3  Score=29.59  Aligned_cols=63  Identities=14%  Similarity=0.181  Sum_probs=45.5

Q ss_pred             ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHH
Q 011249          326 KSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVD  390 (490)
Q Consensus       326 ~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  390 (490)
                      +.-+..+-++.+....+.|++......+++|.+.+++..|.++++-++.+.+  +...+|..+++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~--~~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG--PHKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT--TCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc--CchhhHHHHHH
Confidence            3445666666666667888888888888888888888888888888887533  33455666553

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=88.29  E-value=0.52  Score=39.80  Aligned_cols=56  Identities=21%  Similarity=0.201  Sum_probs=36.7

Q ss_pred             HHhhcCChHHHHHHHHh-ccCCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC
Q 011249          391 LLGRSGQLEKAHSLIMD-YKDFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPE  446 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~-~~~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~  446 (490)
                      .+.+.|++++|++.... ++..| |...-..++..++-.|++++|.+-++.+.+++|.
T Consensus         6 ~ll~~g~L~~al~~~~~~VR~~P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l~p~   63 (273)
T 1zbp_A            6 NALSEGQLQQALELLIEAIKASPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPE   63 (273)
T ss_dssp             HHTTTTCHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGG
T ss_pred             HHHhCCCHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCch
Confidence            45567777777766643 33333 4455556666777777777777777777777776

>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=88.14  E-value=4.1  Score=37.14  Aligned_cols=72  Identities=13%  Similarity=0.103  Sum_probs=52.5

Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHH----HcCCCCCchHHH
Q 011249          314 YSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTR----VFGIKPLTEHLT  386 (490)
Q Consensus       314 ~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~----~~~~~~~~~~~~  386 (490)
                      ...++..+...|+++++...++.+... -+.+...+..+|.++...|+..+|++.|+.+.+    +.|+.|++.+-.
T Consensus       174 ~~~~~~~~l~~g~~~~a~~~l~~~~~~-~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l~~  249 (388)
T 2ff4_A          174 HTAKAEAEIACGRASAVIAELEALTFE-HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLRA  249 (388)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH-STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            344566677788888888888887764 233667888888888888888888888877654    358888776543

>2wpv_A GET4, UPF0363 protein YOR164C; golgi-ER trafficking, tail-anchored protein, protein binding GET4; 1.99A {Saccharomyces cerevisiae} PDB: 3lku_A

Probab=88.08  E-value=13  Score=32.49  Aligned_cols=167  Identities=9%  Similarity=-0.056  Sum_probs=98.4

Q ss_pred             HHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHH----HHHHHHcCCCCcHHHHHHHHHHhcC
Q 011249          283 SNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDM----FLKMRNEGIEPNQVTFIGVLTACSH  358 (490)
Q Consensus       283 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~----~~~~~~~~~~p~~~~~~~l~~~~~~  358 (490)
                      |.++..=|.+.+++++|++++..           -...+.+.|+...|-++    .+...+.+.+++......++..+..
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            44556667788888888887654           22345566776665554    5555567888888888888877655


Q ss_pred             CCChH-HHHHHHHHHHH---HcCC--CCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhh---CC
Q 011249          359 GGLVE-DGCKQFELMTR---VFGI--KPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVH---VN  429 (490)
Q Consensus       359 ~g~~~-~a~~~~~~~~~---~~~~--~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~---g~  429 (490)
                      ...-+ .=.++++++.+   +.|-  .-++.....+...|.+.|++.+|...|-.-. ..++..+..++.-+...   |.
T Consensus       105 ~p~~~~~r~~fi~~ai~WS~~~g~~~~Gdp~LH~~~a~~~~~e~~~~~A~~H~i~~~-~~s~~~~a~~l~~w~~~~~~~~  183 (312)
T 2wpv_A          105 LDPSEPNLKDVITGMNNWSIKFSEYKFGDPYLHNTIGSKLLEGDFVYEAERYFMLGT-HDSMIKYVDLLWDWLCQVDDIE  183 (312)
T ss_dssp             CCTTCTTHHHHHHHHHHHHHHTSSCTTCCHHHHHHHHHHHHHTTCHHHHHHHHHTSC-HHHHHHHHHHHHHHHHHTTCCC
T ss_pred             CCCCCchHHHHHHHHHHHHhhcCCCCCCCHHHHHHHHHHHhhcCCHHHHHHHHHhCC-CccHHHHHHHHHHHHHhcCCCC
Confidence            33211 12234444432   1122  2357778889999999999999998775221 22455555555544443   33


Q ss_pred             hHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhh
Q 011249          430 AELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMIS  475 (490)
Q Consensus       430 ~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  475 (490)
                      ..++--++-              ..+--|.-.|+...|..+++...
T Consensus       184 ~~e~dlf~~--------------RaVL~yL~l~n~~~A~~~~~~f~  215 (312)
T 2wpv_A          184 DSTVAEFFS--------------RLVFNYLFISNISFAHESKDIFL  215 (312)
T ss_dssp             HHHHHHHHH--------------HHHHHHHHTTBHHHHHHHHHHHH
T ss_pred             cchHHHHHH--------------HHHHHHHHhcCHHHHHHHHHHHH
Confidence            332222111              12224456677788877777654

>3ltm_A Alpha-REP4; protein engineering, heat-like repeat, protein binding; HET: 1PE 12P; 2.15A {Synthetic}

Probab=86.79  E-value=11  Score=30.44  Aligned_cols=166  Identities=16%  Similarity=0.109  Sum_probs=78.8

Q ss_pred             hHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCccc
Q 011249          164 MKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRI  243 (490)
Q Consensus       164 ~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p  243 (490)
                      .+....+.+.+..+|...-...+..+.+.++.+....+.+.+..++...-...+.++...+..+ +...+..+..   .+
T Consensus        18 ~~~~~~L~~~L~~~~~~vR~~A~~~L~~~~~~~~~~~L~~~l~~~~~~vr~~a~~aL~~~~~~~-~~~~L~~~l~---~~   93 (211)
T 3ltm_A           18 PEKVEMYIKNLQDDSYYVRRAAAYALGKIGDERAVEPLIKALKDEDAWVRRAAADALGQIGDER-AVEPLIKALK---DE   93 (211)
T ss_dssp             GGGHHHHHHHTTCSSHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSCHHHHHHHHHHHHHHCCGG-GHHHHHHHTT---CS
T ss_pred             HhHHHHHHHHHcCCCHHHHHHHHHHHHHhCCccHHHHHHHHHcCCCHHHHHHHHHHHHhhCCHH-HHHHHHHHHc---CC
Confidence            3333444444445566666666666666666544444555555566665555566666655432 2333333332   23


Q ss_pred             ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHh
Q 011249          244 SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFAD  323 (490)
Q Consensus       244 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~  323 (490)
                      +...-...+.++...|+.+.. ..+..+.+   .++..+-...+.++.+.+..+....+.+.+..++..+-...+.++.+
T Consensus        94 ~~~vr~~a~~aL~~~~~~~~~-~~L~~~l~---d~~~~vr~~a~~aL~~~~~~~~~~~L~~~l~d~~~~vr~~a~~aL~~  169 (211)
T 3ltm_A           94 DGWVRQSAAVALGQIGDERAV-EPLIKALK---DEDWFVRIAAAFALGEIGDERAVEPLIKALKDEDGWVRQSAADALGE  169 (211)
T ss_dssp             SHHHHHHHHHHHHHHCCGGGH-HHHHHHTT---CSSHHHHHHHHHHHHHHCCGGGHHHHHHHTTCSSHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCcHHHH-HHHHHHHh---CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            444555555555555554322 22222221   34444444555555555544333333333333455444455555555


Q ss_pred             cCChHHHHHHHHHHH
Q 011249          324 HGKSQEALDMFLKMR  338 (490)
Q Consensus       324 ~~~~~~a~~~~~~~~  338 (490)
                      .+. ..+...+..+.
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            444 33333344443

>1zbp_A Hypothetical protein VPA1032; alpha-beta protein, structural genomics, PSI, protein struct initiative; 2.40A {Vibrio parahaemolyticus} SCOP: e.61.1.1

Probab=85.29  E-value=13  Score=31.37  Aligned_cols=118  Identities=17%  Similarity=0.129  Sum_probs=71.9

Q ss_pred             HHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCch----HHHHHHHHHhh
Q 011249          320 AFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTE----HLTCMVDLLGR  394 (490)
Q Consensus       320 ~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~----~~~~l~~~~~~  394 (490)
                      ...+.|++++++.....-++.  .| |...=..++..+|-.|++++|.+-++...+.   .|+..    .|..+|.+   
T Consensus         6 ~ll~~g~L~~al~~~~~~VR~--~P~da~~R~~LfqLLcv~G~w~RA~~QL~~~a~l---~p~~~~~a~~yr~lI~a---   77 (273)
T 1zbp_A            6 NALSEGQLQQALELLIEAIKA--SPKDASLRSSFIELLCIDGDFERADEQLMQSIKL---FPEYLPGASQLRHLVKA---   77 (273)
T ss_dssp             HHTTTTCHHHHHHHHHHHHHT--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CGGGHHHHHHHHHHHHH---
T ss_pred             HHHhCCCHHHHHHHHHHHHHh--CCcCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh---CchhhHHHHHHHHHHHH---
Confidence            455678888888888887775  44 5555566777788889999998888888763   44432    33333322   


Q ss_pred             cCChHHHH-HHHHh--cc-CCCChhhH-HHHHHHH--hhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          395 SGQLEKAH-SLIMD--YK-DFCDAGTW-GALLGAC--KVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       395 ~g~~~~A~-~~~~~--~~-~~~~~~~~-~~l~~~~--~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                          +... ++|..  .+ ..-.+..| ..++.+.  ...|+.++|.++-.++.+.-|..+.
T Consensus        78 ----E~~R~~vfaG~~~P~~~g~~~~w~~~ll~Al~~~~~G~~~~A~~lr~~A~e~ap~~~G  135 (273)
T 1zbp_A           78 ----AQARKDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQEKGF  135 (273)
T ss_dssp             ----HHHHHHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCCE
T ss_pred             ----HHHHHHHHcCCCCCCCCCCCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhcCcccCC
Confidence                1121 12221  11 11122223 3344443  4569999999999999888776554

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=84.96  E-value=7.6  Score=26.86  Aligned_cols=59  Identities=14%  Similarity=0.073  Sum_probs=40.4

Q ss_pred             HHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhH
Q 011249          187 AGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAM  248 (490)
Q Consensus       187 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~  248 (490)
                      ..+...|++++|..+.+...-||...|..|.  -.+.|-.+++...+..+...| .|....|
T Consensus        47 sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALc--e~rlGl~s~le~rL~~la~sg-~p~~q~F  105 (115)
T 2uwj_G           47 SSLANQGRYQEALAFAHGNPWPALEPWFALC--EWHLGLGAALDRRLAGLGGSS-DPALADF  105 (115)
T ss_dssp             HHHHHTTCHHHHHGGGTTCCCGGGHHHHHHH--HHHTTCHHHHHHHHHHHHTCS-SHHHHHH
T ss_pred             HHHHcchhHHHHHHhcCCCCCchHHHHHHHH--HHhcccHHHHHHHHHHHHhCC-CHHHHHH
Confidence            3456778888888888877778877776664  446777777777777776665 4444443

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=84.25  E-value=8.3  Score=26.69  Aligned_cols=88  Identities=10%  Similarity=-0.029  Sum_probs=62.7

Q ss_pred             CChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHH
Q 011249          259 GDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMR  338 (490)
Q Consensus       259 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  338 (490)
                      ...++|..+-+.+...+.  ...+-..-+..+.+.|++++|..+.+...-||...|-++..  .+.|-.+++..-+.++.
T Consensus        20 H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la   95 (115)
T 2uwj_G           20 HCHEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGNPWPALEPWFALCE--WHLGLGAALDRRLAGLG   95 (115)
T ss_dssp             TCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHH--HHTTCHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHH
Confidence            356777777777766552  33332233456778999999999999999999999987754  57788888888887877


Q ss_pred             HcCCCCcHHHHHH
Q 011249          339 NEGIEPNQVTFIG  351 (490)
Q Consensus       339 ~~~~~p~~~~~~~  351 (490)
                      ..| .|....|..
T Consensus        96 ~sg-~p~~q~Fa~  107 (115)
T 2uwj_G           96 GSS-DPALADFAA  107 (115)
T ss_dssp             TCS-SHHHHHHHH
T ss_pred             hCC-CHHHHHHHH
Confidence            765 555555544

>2p58_C Putative type III secretion protein YSCG; type III secretion system, structure, needle protein, YSCE, YSCF, transport protein/chaperone complex; 1.80A {Yersinia pestis}

Probab=83.59  E-value=9  Score=26.57  Aligned_cols=88  Identities=13%  Similarity=0.082  Sum_probs=61.7

Q ss_pred             CChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHHHHHHHH
Q 011249          259 GDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALDMFLKMR  338 (490)
Q Consensus       259 g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~  338 (490)
                      ...++|..+-+.+...+.  ...+-..-+..+.+.|++++|..+.+...-||...|-++..  .+.|-.+++..-+.++.
T Consensus        21 H~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la   96 (116)
T 2p58_C           21 HYHEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEPWLALCE--YRLGLGSALESRLNRLA   96 (116)
T ss_dssp             TCHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHH--HHHTCHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHH
Confidence            356777777777766552  33332233456778899999999999999999999987754  46788888888777777


Q ss_pred             HcCCCCcHHHHHH
Q 011249          339 NEGIEPNQVTFIG  351 (490)
Q Consensus       339 ~~~~~p~~~~~~~  351 (490)
                      ..| .|....|..
T Consensus        97 ~sg-~p~~q~Fa~  108 (116)
T 2p58_C           97 RSQ-DPRIQTFVN  108 (116)
T ss_dssp             TCC-CHHHHHHHH
T ss_pred             hCC-CHHHHHHHH
Confidence            665 555555543

>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=83.56  E-value=6.8  Score=28.97  Aligned_cols=61  Identities=13%  Similarity=0.122  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 011249          227 KAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIH  288 (490)
Q Consensus       227 ~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  288 (490)
                      -+..+-++.+....+.|++......+.+|.+.+|+..|.++++-++... .+...+|..+++
T Consensus        70 wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~-~~~~~iY~y~lq  130 (152)
T 2y69_E           70 WELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVIQ  130 (152)
T ss_dssp             HHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHHH
T ss_pred             HHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc-CCchhhHHHHHH
Confidence            3455556666666677777777777777777777777777777765543 233445554443

>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=83.30  E-value=5.1  Score=29.61  Aligned_cols=63  Identities=13%  Similarity=0.141  Sum_probs=47.3

Q ss_pred             ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHH
Q 011249          326 KSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVD  390 (490)
Q Consensus       326 ~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~  390 (490)
                      +.-+..+-++.+....+.|++......+++|.+.+++..|..+|+-++.+.  .+....|..+++
T Consensus        68 D~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~--~~~~~iY~y~lq  130 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA--GPHKEIYPYVIQ  130 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT--TTCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhc--CCchhhHHHHHH
Confidence            344556666666667788999999999999999999999999999888853  344556766653

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.18  E-value=7.5  Score=35.99  Aligned_cols=62  Identities=6%  Similarity=-0.088  Sum_probs=31.1

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHc-CCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVF-GIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                      +...+...|.+.|+++.|.+.+.++.... +...-...+...++.+...+++..+...+.++.
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~  195 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVN  195 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence            34445555555566666666665555431 111113344445555555555555555555443

>3esl_A Checkpoint serine/threonine-protein kinase BUB1; mitotic spindle checkpoint, TPR motif, all-alpha domain, MAD3-like domain; HET: NHE; 1.74A {Saccharomyces cerevisiae}

Probab=81.98  E-value=10  Score=30.46  Aligned_cols=47  Identities=2%  Similarity=-0.245  Sum_probs=25.7

Q ss_pred             hHHHHHHHHhcc----CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC
Q 011249          398 LEKAHSLIMDYK----DFCDAGTWGALLGACKVHVNAELGEIAARHLLELG  444 (490)
Q Consensus       398 ~~~A~~~~~~~~----~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  444 (490)
                      ..++.++|.-|.    ...-...|......+...|++++|.++|+..++..
T Consensus        95 ~~~p~~if~~L~~~~IG~~~AlfYe~wA~~lE~~g~~~~A~~Vy~~GI~~~  145 (202)
T 3esl_A           95 FHESENTFKYMFNKGIGTKLSLFYEEFSKLLENAQFFLEAKVLLELGAENN  145 (202)
T ss_dssp             HHHHHHHHHHHHHHTSSTTBHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT
T ss_pred             cCCHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC
Confidence            445555554443    22334455555555666666666666666666543

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=81.61  E-value=9  Score=35.45  Aligned_cols=93  Identities=11%  Similarity=0.035  Sum_probs=55.9

Q ss_pred             hHHHHHHHHHhcCChhHHHHHHhhcCC------CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHc---CcccChhhHH--
Q 011249          181 TWVAMIAGYGKCGEVREAKKVFDEISE------PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQE---NVRISEVAMV--  249 (490)
Q Consensus       181 ~~~~l~~~~~~~~~~~~A~~~~~~~~~------~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~---~~~p~~~~~~--  249 (490)
                      +...++..|.+.|++++|.+.|.++..      .-...+-..++.+...+++..+...+++....   +..|+.....  
T Consensus       133 ~~~~la~~~~~~Gd~~~A~~~~~~~~~~~~~~~~kid~~l~~irl~l~~~d~~~~~~~~~ka~~~~~~~~d~~~~~~lk~  212 (429)
T 4b4t_R          133 AWINLGEYYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLEAVNSMIEKGGDWERRNRYKT  212 (429)
T ss_dssp             CCHHHHHHHHHHCCCTTHHHHHHHHHHHHTCCCSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTCCCTHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhcCCCHHHHHHHHH
Confidence            556677777777888888777777653      23456677777888888888888877776532   2222221110  


Q ss_pred             HHHHHHhccCChHHHHHHHHHHHh
Q 011249          250 GAISACTQLGDVEMAAILAKHVDE  273 (490)
Q Consensus       250 ~l~~~~~~~g~~~~a~~~~~~~~~  273 (490)
                      .-...+...+++..|...|-+...
T Consensus       213 ~~gl~~l~~r~f~~Aa~~f~e~~~  236 (429)
T 4b4t_R          213 YYGIHCLAVRNFKEAAKLLVDSLA  236 (429)
T ss_dssp             HHHHGGGGTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhChHHHHHHHHHHHhc
Confidence            111123455677777666655543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	490
d1w3ba_	388	a.118.8.1 (A:) O-GlcNAc transferase p110 subunit,	1e-04

>d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]} Length = 388

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]

 Score = 42.0 bits (97), Expect = 1e-04
 Identities = 42/355 (11%), Positives = 105/355 (29%), Gaps = 17/355 (4%)

Query: 127 YTKIGLMDDAQRLFDSMAER---NVISWSAMVAGYANCGNMKAAKEFYDRMTE---KNSV 180
             + G  + A+R    +  +   N      + + +  C  +  +  F     +     + 
Sbjct: 9   EYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPLLAE 68

Query: 181 TWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQEN 240
            +  +   Y + G+++EA + +                       A       +      
Sbjct: 69  AYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSAL 128

Query: 241 VRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVS-NALIHMHSKCGYLDLA 299
               ++  V +           +    A ++          V+ + L  + +  G + LA
Sbjct: 129 QYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLA 188

Query: 300 WREFSR---IKNKDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTAC 356
              F +   +    + +Y ++     +      A+  +L+  +            +    
Sbjct: 189 IHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAV-VHGNLACVY 247

Query: 357 SHGGLVEDGCKQFELMTRVFGIKP-LTEHLTCMVDLLGRSGQLEKAHSLI--MDYKDFCD 413
              GL++     +    R   ++P   +    + + L   G + +A              
Sbjct: 248 YEQGLIDLAIDTYR---RAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTH 304

Query: 414 AGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSE 468
           A +   L    +   N E      R  LE+ PE     + LA++    GK +++ 
Sbjct: 305 ADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEAL 359

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	490
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.95
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.94
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.73
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.73
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.42
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.34
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.33
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.32
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.32
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.31
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	99.24
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.24
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.23
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	99.19
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	99.01
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.98
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.96
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.96
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.88
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.84
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.83
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.83
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.82
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.8
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.79
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.75
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.74
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.67
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.58
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.56
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.54
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	98.52
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	98.52
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.51
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.46
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.45
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.43
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	98.43
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	98.4
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	98.33
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.28
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	98.24
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	98.22
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	98.21
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	98.15
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	98.14
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.13
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	98.12
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.91
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.77
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.75
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.68
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	97.63
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.62
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	97.19
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	96.76
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	96.51
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	96.43
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	96.24
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	96.2
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	95.8
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	88.11
d1qsaa1	450	70 KDa soluble lytic transglycosylase (SLT70), sup	88.09
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	87.7

>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=99.95  E-value=1.4e-24  Score=201.33  Aligned_cols=369  Identities=11%  Similarity=0.064  Sum_probs=296.2

Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhcCCCCCHhhHHHHHHHhcCCCChHHHHHHHHHhcCCHHHHHHHHhhcCC--C-CHhH
Q 011249           74 LIRNHVLHAHFRQSILLYAKMHRLGVLTSGFTFSSVLNACARVPSLLEAVICGYTKIGLMDDAQRLFDSMAE--R-NVIS  150 (490)
Q Consensus        74 l~~~~~~~g~~~~A~~~~~~m~~~g~~p~~~~~~~ll~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~  150 (490)
                      +...+.+.|++++|.+.|+++.+.  .|+.......             +...|.+.|++++|+..|+++.+  | +..+
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~--~p~~~~~~~~-------------la~~~~~~~~~~~A~~~~~~al~~~p~~~~a   69 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQ--EPDNTGVLLL-------------LSSIHFQCRRLDRSAHFSTLAIKQNPLLAEA   69 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHH-------------HHHHHHHTTCHHHHHHHHHHHHHHCTTCHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHH-------------HHHHHHHcCCHHHHHHHHHHHHHhCCCCHHH
Confidence            455677889999999999998876  4543332222             22347888999999999998865  4 5678


Q ss_pred             HHHHHHHHHhCCChHHHHHHHHHhccC---CchhHHHHHHHHHhcCChhHHHHHHhhcC---CCCHHhHHHHHHHHHhcC
Q 011249          151 WSAMVAGYANCGNMKAAKEFYDRMTEK---NSVTWVAMIAGYGKCGEVREAKKVFDEIS---EPDASCWAAMTVCYVQNG  224 (490)
Q Consensus       151 ~~~l~~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~---~~~~~~~~~l~~~~~~~g  224 (490)
                      |..+..++.+.|++++|+..+....+.   +..............+....+........   .................+
T Consensus        70 ~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  149 (388)
T d1w3ba_          70 YSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALG  149 (388)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTS
T ss_pred             HHHHHHHhhhhccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            888999999999999999999888753   33444445555555566555555544432   245556666777778888


Q ss_pred             ChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHh
Q 011249          225 YAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFS  304 (490)
Q Consensus       225 ~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~  304 (490)
                      ....+...+.+..... +-+...+..+...+...|++++|...++...+.. |.+...+..+...+...|++++|...++
T Consensus       150 ~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~  227 (388)
T d1w3ba_         150 RLEEAKACYLKAIETQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRAVAAYL  227 (388)
T ss_dssp             CHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHHHHHHH
T ss_pred             hhhhhHHHHHHhhccC-cchhHHHHhhcccccccCcHHHHHHHHHHHHHhC-cccHHHHHHHhhhhhccccHHHHHHHHH
Confidence            8888888888887654 2256677888888999999999999999988875 5667788889999999999999999998


Q ss_pred             cccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCC
Q 011249          305 RIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKP  380 (490)
Q Consensus       305 ~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~  380 (490)
                      +...   .+...+..+...+.+.|++++|...|+++.+.  .| +...+..+...+...|++++|.+.++....  ..+.
T Consensus       228 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~~~~  303 (388)
T d1w3ba_         228 RALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALR--LCPT  303 (388)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH--HCTT
T ss_pred             HhHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhc--cCCc
Confidence            8765   46677888899999999999999999999884  45 456888889999999999999999999987  4566


Q ss_pred             CchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHH
Q 011249          381 LTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIY  458 (490)
Q Consensus       381 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~  458 (490)
                      +...+..+..++...|++++|++.|++..  .+.+..++..+..++...|++++|++.|+++++++|+++.++..++.+|
T Consensus       304 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~P~~~~a~~~lg~~~  383 (388)
T d1w3ba_         304 HADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTL  383 (388)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCTTCHHHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            77888899999999999999999998876  3345678889999999999999999999999999999999999999999


Q ss_pred             HhcCC
Q 011249          459 ASMGK  463 (490)
Q Consensus       459 ~~~g~  463 (490)
                      .+.|+
T Consensus       384 ~~~~D  388 (388)
T d1w3ba_         384 KEMQD  388 (388)
T ss_dssp             HHTCC
T ss_pred             HHcCC
Confidence            98875

>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=99.94  E-value=1e-23  Score=195.50  Aligned_cols=352  Identities=14%  Similarity=0.082  Sum_probs=296.9

Q ss_pred             HHHHHHhcCCHHHHHHHHhhcCC--C-CHhHHHHHHHHHHhCCChHHHHHHHHHhcc--C-CchhHHHHHHHHHhcCChh
Q 011249          123 VICGYTKIGLMDDAQRLFDSMAE--R-NVISWSAMVAGYANCGNMKAAKEFYDRMTE--K-NSVTWVAMIAGYGKCGEVR  196 (490)
Q Consensus       123 l~~~~~~~g~~~~A~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~--~-~~~~~~~l~~~~~~~~~~~  196 (490)
                      +...+.+.|++++|++.++++.+  | +...+..+..++.+.|++++|+..|+++.+  | +..++..++.+|...|+++
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~l~~~~~~~g~~~   84 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQEPDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQNPLLAEAYSNLGNVYKERGQLQ   84 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHhhhhcccc
Confidence            34457889999999999999875  4 577899999999999999999999999885  4 6678999999999999999


Q ss_pred             HHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHh
Q 011249          197 EAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDE  273 (490)
Q Consensus       197 ~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  273 (490)
                      +|+..+....+   .+...+..........+....+............ ................+....+...+.....
T Consensus        85 ~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (388)
T d1w3ba_          85 EAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNP-DLYCVRSDLGNLLKALGRLEEAKACYLKAIE  163 (388)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCT-TCTHHHHHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccc-ccccccccccccccccchhhhhHHHHHHhhc
Confidence            99999988765   4555566666666677777777776666665443 3445555666677788888888888888877


Q ss_pred             cCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHH
Q 011249          274 GCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFI  350 (490)
Q Consensus       274 ~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~  350 (490)
                      .. +.+...+..+...+...|++++|...+++..+   .+...|..+...+...|++++|...+++....+ ..+...+.
T Consensus       164 ~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  241 (388)
T d1w3ba_         164 TQ-PNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHG  241 (388)
T ss_dssp             HC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             cC-cchhHHHHhhcccccccCcHHHHHHHHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHHHHH
Confidence            65 56677888889999999999999999988765   356788999999999999999999999998853 34566788


Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhC
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHV  428 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g  428 (490)
                      .+...+...|++++|...++++.+  ..+.+...+..+..++...|++++|.+.++...  .+.+...+..+...+...|
T Consensus       242 ~l~~~~~~~~~~~~A~~~~~~al~--~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  319 (388)
T d1w3ba_         242 NLACVYYEQGLIDLAIDTYRRAIE--LQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQG  319 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH--TCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHH--hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCC
Confidence            888899999999999999999987  445567788899999999999999999998776  5567788899999999999


Q ss_pred             ChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          429 NAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       429 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ++++|++.++++++..|+++.++..++.+|.+.|++++|.+.+++..+..+
T Consensus       320 ~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~l~P  370 (388)
T d1w3ba_         320 NIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISP  370 (388)
T ss_dssp             CHHHHHHHHHHHTTSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTTCT
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            999999999999999999999999999999999999999999999887543

>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=99.73  E-value=4.1e-16  Score=140.04  Aligned_cols=251  Identities=11%  Similarity=-0.041  Sum_probs=157.8

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCCh
Q 011249          217 TVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYL  296 (490)
Q Consensus       217 ~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  296 (490)
                      ...+.+.|++++|+..|+++.+..+. +...+..+..++...|++++|...+.++.+.. |.+...+..++.+|...|++
T Consensus        26 g~~~~~~g~~~~A~~~~~~al~~~P~-~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~  103 (323)
T d1fcha_          26 GLRRLQEGDLPNAVLLFEAAVQQDPK-HMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESLQ  103 (323)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHSCTT-CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhCCC-CHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-cccccccccccccccccccc
Confidence            33344444444444444444443211 23344444444444444444444444444433 23334444444444444444


Q ss_pred             HHHHHHHhcccC--C----------------ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcC-CCCcHHHHHHHHHHhc
Q 011249          297 DLAWREFSRIKN--K----------------DVISYSSMITAFADHGKSQEALDMFLKMRNEG-IEPNQVTFIGVLTACS  357 (490)
Q Consensus       297 ~~A~~~~~~~~~--~----------------~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~-~~p~~~~~~~l~~~~~  357 (490)
                      ++|.+.+++...  |                +.......+..+...+.+.++...+.+..+.. -.++...+..+...+.
T Consensus       104 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~~  183 (323)
T d1fcha_         104 RQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFN  183 (323)
T ss_dssp             HHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHH
T ss_pred             cccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHHH
Confidence            444444443321  0                00111112223345566788888888887642 2335667788888899


Q ss_pred             CCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHH
Q 011249          358 HGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEI  435 (490)
Q Consensus       358 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~  435 (490)
                      ..|++++|...+++....  .+.+...+..+..+|...|++++|.+.|++..  .+.+..+|..++.+|...|++++|++
T Consensus       184 ~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~  261 (323)
T d1fcha_         184 LSGEYDKAVDCFTAALSV--RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVE  261 (323)
T ss_dssp             HTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHhhhhccccccccc--ccccccchhhhhhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHHHH
Confidence            999999999999999873  34457788889999999999999999998876  44567789999999999999999999


Q ss_pred             HHHHHHhcCCCCCc-----------hHHHHHHHHHhcCCcchHHHHH
Q 011249          436 AARHLLELGPEKTG-----------NSALLANIYASMGKWKDSEIVK  471 (490)
Q Consensus       436 ~~~~~~~~~p~~~~-----------~~~~l~~~~~~~g~~~~A~~~~  471 (490)
                      .|++++++.|++..           ++..+..++...|+.+.+...-
T Consensus       262 ~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~~~~~  308 (323)
T d1fcha_         262 HFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAAD  308 (323)
T ss_dssp             HHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHH
T ss_pred             HHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            99999998887654           4456777787788877665543

>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=99.73  E-value=1.8e-16  Score=142.37  Aligned_cols=228  Identities=14%  Similarity=0.052  Sum_probs=188.8

Q ss_pred             HHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcC
Q 011249          249 VGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHG  325 (490)
Q Consensus       249 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~  325 (490)
                      ......+.+.|++++|...|+.+.+.. |.+...+..+..+|...|++++|...|++..+   .+...|..++..|...|
T Consensus        23 ~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~  101 (323)
T d1fcha_          23 FEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNES  101 (323)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccccccccccccccccccccc
Confidence            355667889999999999999999886 66788899999999999999999999998765   36778899999999999


Q ss_pred             ChHHHHHHHHHHHHcCCCCcHHH----------------HHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHH
Q 011249          326 KSQEALDMFLKMRNEGIEPNQVT----------------FIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMV  389 (490)
Q Consensus       326 ~~~~a~~~~~~~~~~~~~p~~~~----------------~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  389 (490)
                      ++++|.+.++++...  .|+...                ....+..+...+...+|...+.++.+.....++...+..+.
T Consensus       102 ~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~  179 (323)
T d1fcha_         102 LQRQACEILRDWLRY--TPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLG  179 (323)
T ss_dssp             CHHHHHHHHHHHHHT--STTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHH
T ss_pred             cccccccchhhHHHh--ccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhH
Confidence            999999999998873  332110                01111122334567788888888877533344567788889


Q ss_pred             HHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchH
Q 011249          390 DLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDS  467 (490)
Q Consensus       390 ~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  467 (490)
                      ..+...|++++|+..+++..  .+.+...|..+...+...|++++|++.++++++.+|+++.++..++.+|.+.|++++|
T Consensus       180 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A  259 (323)
T d1fcha_         180 VLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREA  259 (323)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHHHHHHhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHH
Confidence            99999999999999998876  4456788999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhhccc
Q 011249          468 EIVKMMISETEK  479 (490)
Q Consensus       468 ~~~~~~~~~~~~  479 (490)
                      ++.|++..+..+
T Consensus       260 ~~~~~~al~l~p  271 (323)
T d1fcha_         260 VEHFLEALNMQR  271 (323)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCC
Confidence            999999887544

>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=99.42  E-value=3.2e-11  Score=108.89  Aligned_cols=259  Identities=9%  Similarity=-0.037  Sum_probs=124.6

Q ss_pred             HHHHHHhcCChhHHHHHHhhcCC--CC------HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcc-cC----hhhHHHH
Q 011249          185 MIAGYGKCGEVREAKKVFDEISE--PD------ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVR-IS----EVAMVGA  251 (490)
Q Consensus       185 l~~~~~~~~~~~~A~~~~~~~~~--~~------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-p~----~~~~~~l  251 (490)
                      ....+...|++++|++++++..+  |+      ...+..+..++...|++++|+..|++..+.... ++    ...+..+
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            34555666666666666665432  11      234555566666666666666666665542111 11    1234444


Q ss_pred             HHHHhccCChHHHHHHHHHHHhc----CCCCc---hhHHHHHHHHHHhcCChHHHHHHHhcccC--------CChhHHHH
Q 011249          252 ISACTQLGDVEMAAILAKHVDEG----CCDRT---NYVSNALIHMHSKCGYLDLAWREFSRIKN--------KDVISYSS  316 (490)
Q Consensus       252 ~~~~~~~g~~~~a~~~~~~~~~~----~~~~~---~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--------~~~~~~~~  316 (490)
                      ...+...|++..+...+......    ..+..   ...+..+...+...|+++.+...+.....        .....+..
T Consensus        98 ~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~  177 (366)
T d1hz4a_          98 SEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAM  177 (366)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHH
Confidence            55556666666666666554321    11111   12333445555566666666655554432        11223344


Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHc----CCCCc--HHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC---chHHHH
Q 011249          317 MITAFADHGKSQEALDMFLKMRNE----GIEPN--QVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL---TEHLTC  387 (490)
Q Consensus       317 l~~~~~~~~~~~~a~~~~~~~~~~----~~~p~--~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~---~~~~~~  387 (490)
                      ....+...+++..+...+.+....    +..+.  ...+..+...+...|++++|...++..... ....+   ...+..
T Consensus       178 ~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~~~  256 (366)
T d1hz4a_         178 LIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKP-EFANNHFLQGQWRN  256 (366)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCC-CCTTCGGGHHHHHH
T ss_pred             HHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHh-ccccchHHHHHHHH
Confidence            444555556666665555554431    11111  112333344455556666666555555431 11111   122334


Q ss_pred             HHHHHhhcCChHHHHHHHHhcc-------CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcC
Q 011249          388 MVDLLGRSGQLEKAHSLIMDYK-------DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELG  444 (490)
Q Consensus       388 l~~~~~~~g~~~~A~~~~~~~~-------~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~  444 (490)
                      +..++...|++++|...+++..       ..| ....+..+..++...|++++|.+.+++++++.
T Consensus       257 la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~l~  321 (366)
T d1hz4a_         257 IARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALKLA  321 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence            4555556666666665555443       111 12344445555556666666666666655543

>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=99.34  E-value=5.2e-12  Score=113.26  Aligned_cols=232  Identities=8%  Similarity=-0.119  Sum_probs=167.1

Q ss_pred             HHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccC--ChHHHHHHHHHHHhcCCCCchhHH-HHHHHHHHhcCCh
Q 011249          220 YVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLG--DVEMAAILAKHVDEGCCDRTNYVS-NALIHMHSKCGYL  296 (490)
Q Consensus       220 ~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g--~~~~a~~~~~~~~~~~~~~~~~~~-~~l~~~~~~~~~~  296 (490)
                      +...|++++|+..++...+..+. +...+..+..++...+  +++++...+..+.+.. +++...+ ......+...+.+
T Consensus        83 ~~~~~~~~~al~~~~~~l~~~pk-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~  160 (334)
T d1dcea1          83 EESAALVKAELGFLESCLRVNPK-SYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAP  160 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCC-cHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhcccc
Confidence            34455677888888888765422 4555555555555444  5788888888887775 4444443 3455677778889


Q ss_pred             HHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHH
Q 011249          297 DLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMT  373 (490)
Q Consensus       297 ~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~  373 (490)
                      +.|+..++.+.+   .+...|+.+..++...|++++|...++...+.  .|+..   .....+...+..+++...+....
T Consensus       161 ~~Al~~~~~~i~~~p~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~---~~~~~~~~l~~~~~a~~~~~~~l  235 (334)
T d1dcea1         161 AEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENV--LLKEL---ELVQNAFFTDPNDQSAWFYHRWL  235 (334)
T ss_dssp             HHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHH--HHHHH---HHHHHHHHHCSSCSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHh--HHHHH---HHHHHHHHhcchhHHHHHHHHHH
Confidence            999998888876   35678888888888888888877666654442  22222   12222344566677888888777


Q ss_pred             HHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchH
Q 011249          374 RVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       374 ~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                      .  ..+++...+..++..+...|+.++|...+.+.. ..| +..++..++.++...|++++|++.++++.+++|.+...|
T Consensus       236 ~--~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ldP~~~~y~  313 (334)
T d1dcea1         236 L--GRAEPLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYL  313 (334)
T ss_dssp             H--SCCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGGHHHH
T ss_pred             H--hCcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCcccHHHH
Confidence            6  455666667778888888999999999998776 223 456788888999999999999999999999999999999


Q ss_pred             HHHHHHHHh
Q 011249          452 ALLANIYAS  460 (490)
Q Consensus       452 ~~l~~~~~~  460 (490)
                      ..|...+.-
T Consensus       314 ~~L~~~~~~  322 (334)
T d1dcea1         314 DDLRSKFLL  322 (334)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhH
Confidence            988777664

>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=99.33  E-value=1.8e-10  Score=103.88  Aligned_cols=260  Identities=14%  Similarity=0.042  Sum_probs=184.1

Q ss_pred             HHHHHHHHHHhCCChHHHHHHHHHhcc--CC------chhHHHHHHHHHhcCChhHHHHHHhhcCC-----CC----HHh
Q 011249          150 SWSAMVAGYANCGNMKAAKEFYDRMTE--KN------SVTWVAMIAGYGKCGEVREAKKVFDEISE-----PD----ASC  212 (490)
Q Consensus       150 ~~~~l~~~~~~~~~~~~a~~~~~~~~~--~~------~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~~----~~~  212 (490)
                      ........+...|++++|++++++..+  |+      ...+..+..++...|++++|+..|++..+     ++    ...
T Consensus        14 ~~~lrA~~~~~~g~~~~A~~~~~~aL~~~~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~   93 (366)
T d1hz4a_          14 FNALRAQVAINDGNPDEAERLAKLALEELPPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWS   93 (366)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCCTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhhCcCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHH
Confidence            344456678889999999999998874  22      23567788889999999999999988754     22    245


Q ss_pred             HHHHHHHHHhcCChHHHHHHHHHHHHc----CcccC---hhhHHHHHHHHhccCChHHHHHHHHHHHhcCCC----Cchh
Q 011249          213 WAAMTVCYVQNGYAKAAIEMYKVMRQE----NVRIS---EVAMVGAISACTQLGDVEMAAILAKHVDEGCCD----RTNY  281 (490)
Q Consensus       213 ~~~l~~~~~~~g~~~~A~~~~~~~~~~----~~~p~---~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~----~~~~  281 (490)
                      +..+...+...|++..+...+.+....    +..+.   ...+..+...+...|+++.+...+.........    ....
T Consensus        94 ~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  173 (366)
T d1hz4a_          94 LIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQ  173 (366)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHH
Confidence            666778888999999999988886542    11111   234556677788899999999998887654322    2234


Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccC-------C---ChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC---cHHH
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKN-------K---DVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP---NQVT  348 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~-------~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p---~~~~  348 (490)
                      .+......+...++...+...+.....       .   ....+..+...+...|++++|...+++..+.....   ....
T Consensus       174 ~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~  253 (366)
T d1hz4a_         174 CLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQ  253 (366)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHH
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHH
Confidence            455566777788888888777665432       1   22345666777888899999999988876532221   2345


Q ss_pred             HHHHHHHhcCCCChHHHHHHHHHHHHH---cCCCCC-chHHHHHHHHHhhcCChHHHHHHHHhcc
Q 011249          349 FIGVLTACSHGGLVEDGCKQFELMTRV---FGIKPL-TEHLTCMVDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       349 ~~~l~~~~~~~g~~~~a~~~~~~~~~~---~~~~~~-~~~~~~l~~~~~~~g~~~~A~~~~~~~~  409 (490)
                      +..+..++...|++++|...++.+...   .+..|+ ...+..+..+|.+.|++++|.+.+++..
T Consensus       254 ~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al  318 (366)
T d1hz4a_         254 WRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDAL  318 (366)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            666778888999999999999887642   133333 4566778889999999999999987654

>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=99.32  E-value=3.4e-11  Score=106.38  Aligned_cols=226  Identities=12%  Similarity=0.023  Sum_probs=179.9

Q ss_pred             hhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcC-ChHHHHHHHhcccC---CChhHHHHHHHHH
Q 011249          246 VAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCG-YLDLAWREFSRIKN---KDVISYSSMITAF  321 (490)
Q Consensus       246 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~~~A~~~~~~~~~---~~~~~~~~l~~~~  321 (490)
                      ..+..+...+.+.+..++|..+++.+++.. |.+...|+....++...| ++++|+..++++.+   .+..+|..+...+
T Consensus        44 ~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~p~~~~a~~~~~~~~  122 (315)
T d2h6fa1          44 DVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQPKNYQVWHHRRVLV  122 (315)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHhhhhHHHHHhHHH
Confidence            466677777888999999999999999987 677788888888888876 58999999998865   4678999999999


Q ss_pred             HhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCC---
Q 011249          322 ADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ---  397 (490)
Q Consensus       322 ~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---  397 (490)
                      .+.|++++|+..++++++.  .| +...|..+...+...|++++|++.++++.+.  .+.+...|+.+..++.+.+.   
T Consensus       123 ~~l~~~~eAl~~~~kal~~--dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~--~p~n~~a~~~r~~~l~~~~~~~~  198 (315)
T d2h6fa1         123 EWLRDPSQELEFIADILNQ--DAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE--DVRNNSVWNQRYFVISNTTGYND  198 (315)
T ss_dssp             HHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCSCS
T ss_pred             HhhccHHHHHHHHhhhhhh--hhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHH--CCccHHHHHHHHHHHHHccccch
Confidence            9999999999999999984  44 5678999999999999999999999999883  34456677777777766665   


Q ss_pred             ---hHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC--CchHHHHHHHHHhc--CCcchHH
Q 011249          398 ---LEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK--TGNSALLANIYASM--GKWKDSE  468 (490)
Q Consensus       398 ---~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~--~~~~~~l~~~~~~~--g~~~~A~  468 (490)
                         +++|++.+.+..  .+.+...|..+...+... ..+++.+.++.+.++.|+.  +..+..++.+|...  ++.+.+.
T Consensus       199 ~~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~~~~~~~~~~~~  277 (315)
T d2h6fa1         199 RAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDR-GLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKE  277 (315)
T ss_dssp             HHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTT-CGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHTTCSSHH
T ss_pred             hhhhHHhHHHHHHHHHhCCCchHHHHHHHHHHHhc-ChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHHHHHhcCHHHHH
Confidence               578888887665  445677777777665544 4688889999999888764  44556677777654  7788888


Q ss_pred             HHHHHhhhc
Q 011249          469 IVKMMISET  477 (490)
Q Consensus       469 ~~~~~~~~~  477 (490)
                      ..+++..+.
T Consensus       278 ~~~~ka~~l  286 (315)
T d2h6fa1         278 DILNKALEL  286 (315)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            888877653

>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=99.32  E-value=1.3e-10  Score=102.47  Aligned_cols=226  Identities=10%  Similarity=-0.003  Sum_probs=170.9

Q ss_pred             HHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccC-ChHHHHHHHHHHHhcCCCCchhHHHHHHH
Q 011249          210 ASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLG-DVEMAAILAKHVDEGCCDRTNYVSNALIH  288 (490)
Q Consensus       210 ~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g-~~~~a~~~~~~~~~~~~~~~~~~~~~l~~  288 (490)
                      ...|+.+..++.+.+.+++|+++++++++..+. +...|.....++...| ++++|...++.+.+.. |-+..+|..+..
T Consensus        43 ~~a~~~~~~~~~~~e~~~~Al~~~~~ai~lnP~-~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~  120 (315)
T d2h6fa1          43 RDVYDYFRAVLQRDERSERAFKLTRDAIELNAA-NYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRV  120 (315)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHCTT-CHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHHHHCCC-ChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhH
Confidence            456778888899999999999999999987422 5667888888888776 5899999999998887 678889999999


Q ss_pred             HHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCC---
Q 011249          289 MHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGL---  361 (490)
Q Consensus       289 ~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~---  361 (490)
                      ++.+.|++++|+..++++.+   .+...|..+...+...|++++|+..++++++.  .| +...|+.+...+.+.+.   
T Consensus       121 ~~~~l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~--~p~n~~a~~~r~~~l~~~~~~~~  198 (315)
T d2h6fa1         121 LVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE--DVRNNSVWNQRYFVISNTTGYND  198 (315)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCSCS
T ss_pred             HHHhhccHHHHHHHHhhhhhhhhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHH--CCccHHHHHHHHHHHHHccccch
Confidence            99999999999999999876   46789999999999999999999999999995  45 45567666655544443   


Q ss_pred             ---hHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc----CCCChhhHHHHHHHHhh--hCChHH
Q 011249          362 ---VEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK----DFCDAGTWGALLGACKV--HVNAEL  432 (490)
Q Consensus       362 ---~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~~~~~~~~~~l~~~~~~--~g~~~~  432 (490)
                         +++|+..+.++.+.  .|.+...|..+...+... ..+++.+.++...    ...+...+..++..+..  .++.+.
T Consensus       199 ~~~~~~ai~~~~~al~~--~P~~~~~~~~l~~ll~~~-~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~~~~~~~~~~  275 (315)
T d2h6fa1         199 RAVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDR-GLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDN  275 (315)
T ss_dssp             HHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTT-CGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHTTCSS
T ss_pred             hhhhHHhHHHHHHHHHh--CCCchHHHHHHHHHHHhc-ChHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHHHHHhcCHHH
Confidence               67899999888873  445677777776666554 4577777776554    22234455555555533  244555


Q ss_pred             HHHHHHHHHh
Q 011249          433 GEIAARHLLE  442 (490)
Q Consensus       433 a~~~~~~~~~  442 (490)
                      +...++++.+
T Consensus       276 ~~~~~~ka~~  285 (315)
T d2h6fa1         276 KEDILNKALE  285 (315)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5555655554

>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=99.31  E-value=2.2e-11  Score=104.72  Aligned_cols=221  Identities=10%  Similarity=-0.085  Sum_probs=137.5

Q ss_pred             ChHHHHHHHHHHHHcCc-cc--ChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHH
Q 011249          225 YAKAAIEMYKVMRQENV-RI--SEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWR  301 (490)
Q Consensus       225 ~~~~A~~~~~~~~~~~~-~p--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~  301 (490)
                      +.+.++.-+++...... .+  ...++..+..++.+.|++++|...|++..+.. |.++.++..+..+|.+.|++++|+.
T Consensus        14 ~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A~~   92 (259)
T d1xnfa_          14 QQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYE   92 (259)
T ss_dssp             HHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHhhh
Confidence            34555556666654321 11  22466667777888888888888888887775 5667778888888888888888888


Q ss_pred             HHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCC
Q 011249          302 EFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGI  378 (490)
Q Consensus       302 ~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  378 (490)
                      .|+++.+   .+..++..+..++...|++++|...|++..+.. +.+......+..++...+..+.+..+......   .
T Consensus        93 ~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~  168 (259)
T d1xnfa_          93 AFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQDD-PNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEK---S  168 (259)
T ss_dssp             HHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH---S
T ss_pred             hhhHHHHHHhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhhc-cccHHHHHHHHHHHHHhhhHHHHHHHHHHhhc---c
Confidence            8887765   345677888888888889999999888888752 22333333333344444544444444444433   2


Q ss_pred             CCCchHHHHHHHHHhhcCC----hHHHHHHHHhcc-CCC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchH
Q 011249          379 KPLTEHLTCMVDLLGRSGQ----LEKAHSLIMDYK-DFC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNS  451 (490)
Q Consensus       379 ~~~~~~~~~l~~~~~~~g~----~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~  451 (490)
                      .+....+. ++..+.....    .+.+...+.... ..| ...+|..+...+...|++++|...|+++++.+|++...|
T Consensus       169 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~  246 (259)
T d1xnfa_         169 DKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNFVEH  246 (259)
T ss_dssp             CCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTTCHHH
T ss_pred             chhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHH
Confidence            22222222 2233322222    222222221111 112 234677788889999999999999999999999876444

>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=99.24  E-value=2.9e-11  Score=104.01  Aligned_cols=215  Identities=10%  Similarity=0.022  Sum_probs=153.0

Q ss_pred             ChHHHHHHHHHHHhcCCCC---chhHHHHHHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHH
Q 011249          260 DVEMAAILAKHVDEGCCDR---TNYVSNALIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDM  333 (490)
Q Consensus       260 ~~~~a~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~  333 (490)
                      +.+.+..-++++.......   ...++..+..+|.+.|++++|+..|++..+   .++.+|..+..++...|++++|+..
T Consensus        14 ~~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~p~~~~a~~~lg~~~~~~g~~~~A~~~   93 (259)
T d1xnfa_          14 QQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEA   93 (259)
T ss_dssp             HHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccCCCCHHHHhhhchHHHHHHHHHHhhhh
Confidence            3455666666665543211   234677788999999999999999999875   4778999999999999999999999


Q ss_pred             HHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CC
Q 011249          334 FLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DF  411 (490)
Q Consensus       334 ~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~  411 (490)
                      |+++.+.  .| +...+..+..++...|++++|...++...+.  .+.+......+...+.+.+..+.+..+..... ..
T Consensus        94 ~~~al~~--~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (259)
T d1xnfa_          94 FDSVLEL--DPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSD  169 (259)
T ss_dssp             HHHHHHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSC
T ss_pred             hhHHHHH--HhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHhh--ccccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccc
Confidence            9999985  45 3557888889999999999999999999884  33344444445555566666555555544433 12


Q ss_pred             CChhhHHHHHHHHh----hhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          412 CDAGTWGALLGACK----VHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       412 ~~~~~~~~l~~~~~----~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +....+. ++..+.    ..+..+.+...+.......|..+.++..++.+|...|++++|.+.+++....++
T Consensus       170 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p  240 (259)
T d1xnfa_         170 KEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNV  240 (259)
T ss_dssp             CCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCC
T ss_pred             hhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHhhhcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCC
Confidence            2222222 222222    223344555555555556677778899999999999999999999999887654

>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=99.24  E-value=1.6e-09  Score=95.44  Aligned_cols=187  Identities=11%  Similarity=0.023  Sum_probs=147.5

Q ss_pred             ChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccC--C-C-hhHHHHHHHHHHhcCChHHHHHHHH
Q 011249          260 DVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKN--K-D-VISYSSMITAFADHGKSQEALDMFL  335 (490)
Q Consensus       260 ~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~--~-~-~~~~~~l~~~~~~~~~~~~a~~~~~  335 (490)
                      ..+++..+|++..+...+.+...+...+..+.+.|+++.|..+|+++.+  | + ...|...+....+.|+.+.|.++|+
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~  158 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFK  158 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            4577888999888766566777888888999999999999999998765  2 3 3468888899999999999999999


Q ss_pred             HHHHcCCCCcHHHHHHHHH-HhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc----C
Q 011249          336 KMRNEGIEPNQVTFIGVLT-ACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK----D  410 (490)
Q Consensus       336 ~~~~~~~~p~~~~~~~l~~-~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~----~  410 (490)
                      ++.+.+.. +...|..... -+...|+.+.|..+|+.+.+.  .+.+...+...+..+.+.|++++|..+|++..    .
T Consensus       159 ~al~~~~~-~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~--~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~  235 (308)
T d2onda1         159 KAREDART-RHHVYVTAALMEYYCSKDKSVAFKIFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSL  235 (308)
T ss_dssp             HHHTSTTC-CTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH--HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSS
T ss_pred             HHHHhCCC-cHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh--hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC
Confidence            99886422 3333333333 244568899999999999984  55667888899999999999999999998865    1


Q ss_pred             CC--ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCc
Q 011249          411 FC--DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTG  449 (490)
Q Consensus       411 ~~--~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~  449 (490)
                      .|  ....|...+..-...|+.+.+..+++++.+..|....
T Consensus       236 ~~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~~~~~~~  276 (308)
T d2onda1         236 PPEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFREEYE  276 (308)
T ss_dssp             CGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTTS
T ss_pred             ChHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCccccc
Confidence            22  2347888888778899999999999999998887654

>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=99.23  E-value=7.9e-10  Score=97.37  Aligned_cols=183  Identities=9%  Similarity=-0.033  Sum_probs=146.8

Q ss_pred             ChHHHHHHHhcccC----CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHH
Q 011249          295 YLDLAWREFSRIKN----KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFE  370 (490)
Q Consensus       295 ~~~~A~~~~~~~~~----~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~  370 (490)
                      ..++|..+|++..+    .+...|...+..+...|+++.|..+|+++.+.........|...+..+.+.|+.+.|.++|+
T Consensus        79 ~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~  158 (308)
T d2onda1          79 FSDEAANIYERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFK  158 (308)
T ss_dssp             HHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHH
Confidence            45778888887654    35567888888999999999999999999975322234578888888889999999999999


Q ss_pred             HHHHHcCCCCCchHHHHHHHH-HhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC
Q 011249          371 LMTRVFGIKPLTEHLTCMVDL-LGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEK  447 (490)
Q Consensus       371 ~~~~~~~~~~~~~~~~~l~~~-~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~  447 (490)
                      ++.+  ..+.+...|...+.. +...|+.+.|..+|+.+.  .+.++..|..++..+...|+++.|..+|+++++..|.+
T Consensus       159 ~al~--~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~  236 (308)
T d2onda1         159 KARE--DARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLP  236 (308)
T ss_dssp             HHHT--STTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSC
T ss_pred             HHHH--hCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCC
Confidence            9987  444455566555543 344689999999998887  45567899999999999999999999999999987765


Q ss_pred             Cc----hHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          448 TG----NSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       448 ~~----~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +.    +|...+......|+.+.+..+++++.+.-.
T Consensus       237 ~~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~~~~~~  272 (308)
T d2onda1         237 PEKSGEIWARFLAFESNIGDLASILKVEKRRFTAFR  272 (308)
T ss_dssp             GGGCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence            53    677888877888999999999998876543

>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=99.19  E-value=3e-11  Score=108.18  Aligned_cols=253  Identities=7%  Similarity=-0.133  Sum_probs=184.6

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCcccChh-hHHH---HHHHH-------hccCChHHHHHHHHHHHhcCCCCchhHHH
Q 011249          216 MTVCYVQNGYAKAAIEMYKVMRQENVRISEV-AMVG---AISAC-------TQLGDVEMAAILAKHVDEGCCDRTNYVSN  284 (490)
Q Consensus       216 l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~-~~~~---l~~~~-------~~~g~~~~a~~~~~~~~~~~~~~~~~~~~  284 (490)
                      +.......+..++|++++++..+.  .|+.. .|+.   ++...       ...|++++|..+++.+.+.. |.+...+.
T Consensus        35 ~~~~~~~~~~~~~al~~~~~~l~~--~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~~~~  111 (334)
T d1dcea1          35 VFQKRQAGELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWH  111 (334)
T ss_dssp             HHHHHHTTCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HHHHHhcccccHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHHHHH
Confidence            333333444458999999998875  45543 3322   22222       23445788999999988876 66777777


Q ss_pred             HHHHHHHhcC--ChHHHHHHHhcccC---CChhHHH-HHHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhc
Q 011249          285 ALIHMHSKCG--YLDLAWREFSRIKN---KDVISYS-SMITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACS  357 (490)
Q Consensus       285 ~l~~~~~~~~--~~~~A~~~~~~~~~---~~~~~~~-~l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~  357 (490)
                      .+..++...+  ++++|...++++.+   ++...+. .....+...+.+++|+..++++++.  .| +...|..+...+.
T Consensus       112 ~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~--~p~~~~a~~~l~~~~~  189 (334)
T d1dcea1         112 HRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITR--NFSNYSSWHYRSCLLP  189 (334)
T ss_dssp             HHHHHHHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTT--TCCCHHHHHHHHHHHH
T ss_pred             HhhHHHHHhccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHc--CCCCHHHHHHHHHHHH
Confidence            7777766655  48899999988765   3455554 4456777889999999999998885  44 5668888888888


Q ss_pred             CCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHH
Q 011249          358 HGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEI  435 (490)
Q Consensus       358 ~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~  435 (490)
                      ..|++++|...+....+.   .|.   .......+...+..+++...+....  .+++...+..++..+...|+.++|.+
T Consensus       190 ~~~~~~~A~~~~~~~~~~---~~~---~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~a~~  263 (334)
T d1dcea1         190 QLHPQPDSGPQGRLPENV---LLK---ELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELSVEKSTVLQSELESCK  263 (334)
T ss_dssp             HHSCCCCSSSCCSSCHHH---HHH---HHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCCHHHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHhHHh---HHH---HHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHHHHHHHHHhhHHHHHH
Confidence            888888876666655542   111   1223344566677788888776654  34455667777778888999999999


Q ss_pred             HHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          436 AARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       436 ~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .+.++.+.+|.++.++..++.++...|++++|.+.++++.+.++
T Consensus       264 ~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ldP  307 (334)
T d1dcea1         264 ELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDP  307 (334)
T ss_dssp             HHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCG
T ss_pred             HHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCc
Confidence            99999999999999999999999999999999999999987654

>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=99.01  E-value=4e-09  Score=91.82  Aligned_cols=188  Identities=11%  Similarity=-0.045  Sum_probs=94.0

Q ss_pred             HHHHhcCChHHHHHHHhcccC-----CC----hhHHHHHHHHHHhcCChHHHHHHHHHHHHcC---CCC--cHHHHHHHH
Q 011249          288 HMHSKCGYLDLAWREFSRIKN-----KD----VISYSSMITAFADHGKSQEALDMFLKMRNEG---IEP--NQVTFIGVL  353 (490)
Q Consensus       288 ~~~~~~~~~~~A~~~~~~~~~-----~~----~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~---~~p--~~~~~~~l~  353 (490)
                      ..|...+++++|.+.|.+..+     .+    ..+|..+..+|.+.|++++|...+++..+..   -.+  ....+..+.
T Consensus        45 ~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~  124 (290)
T d1qqea_          45 TIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELG  124 (290)
T ss_dssp             HHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHH
Confidence            344444555555555444432     11    2345555666666666666666666554310   011  122444444


Q ss_pred             HHhc-CCCChHHHHHHHHHHHHHcCCCCC----chHHHHHHHHHhhcCChHHHHHHHHhcc-CCCCh--------hhHHH
Q 011249          354 TACS-HGGLVEDGCKQFELMTRVFGIKPL----TEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFCDA--------GTWGA  419 (490)
Q Consensus       354 ~~~~-~~g~~~~a~~~~~~~~~~~~~~~~----~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~~~--------~~~~~  419 (490)
                      ..|. ..|++++|.+.+++..+......+    ..++..++..+...|++++|.+.|+++. ..+..        ..+..
T Consensus       125 ~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~  204 (290)
T d1qqea_         125 EILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLK  204 (290)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHH
T ss_pred             HhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHH
Confidence            4443 356777777777666542111111    2345566677777777777777776654 11110        12233


Q ss_pred             HHHHHhhhCChHHHHHHHHHHHhcCCCCCc-----hHHHHHHHHHh--cCCcchHHHHHHHhh
Q 011249          420 LLGACKVHVNAELGEIAARHLLELGPEKTG-----NSALLANIYAS--MGKWKDSEIVKMMIS  475 (490)
Q Consensus       420 l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~-----~~~~l~~~~~~--~g~~~~A~~~~~~~~  475 (490)
                      .+..+...|+++.|.+.++++.+.+|..+.     .+..++.++..  .+++++|+..|+++.
T Consensus       205 ~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~  267 (290)
T d1qqea_         205 KGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFM  267 (290)
T ss_dssp             HHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSS
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence            444555667777777777777777664332     23444444443  234666666665544

>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=98.98  E-value=1.3e-09  Score=89.45  Aligned_cols=118  Identities=9%  Similarity=-0.182  Sum_probs=76.0

Q ss_pred             CcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-C-CCChhhHHHHH
Q 011249          344 PNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-D-FCDAGTWGALL  421 (490)
Q Consensus       344 p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~-~~~~~~~~~l~  421 (490)
                      |+...+...+..+.+.|++++|+..|+++...  .|.++..|..++.+|.+.|++++|+..|++.. . +.+..+|..++
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~--~p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITR--NPLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHH
Confidence            55666666667777777777777777777662  34456666667777777777777777776665 2 33455666777


Q ss_pred             HHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCC
Q 011249          422 GACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGK  463 (490)
Q Consensus       422 ~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  463 (490)
                      .++...|++++|+..|++++++.|++...+...+..+...++
T Consensus        80 ~~~~~l~~~~~A~~~~~~al~l~p~~~~~~~~~~~~~l~~~~  121 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAYSLAKEQRLNFGDDIPSALRIAK  121 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCCCCSHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHH
Confidence            777777777777777777777666655555444444444333

>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=98.96  E-value=2.8e-09  Score=78.40  Aligned_cols=87  Identities=8%  Similarity=-0.014  Sum_probs=41.3

Q ss_pred             HHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchH
Q 011249          390 DLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDS  467 (490)
Q Consensus       390 ~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  467 (490)
                      ..+.+.|++++|+..|++..  .+.++..|..+..++...|++++|+..++++++.+|+++.+|..++.++...|++++|
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~~~A   90 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEA   90 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccCHHHH
Confidence            33444444444444444433  2333444444444444445555555555555544454444455555455555555555


Q ss_pred             HHHHHHhhh
Q 011249          468 EIVKMMISE  476 (490)
Q Consensus       468 ~~~~~~~~~  476 (490)
                      +..+++..+
T Consensus        91 ~~~~~~a~~   99 (117)
T d1elwa_          91 KRTYEEGLK   99 (117)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHH
Confidence            555444443

>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=98.96  E-value=4.8e-09  Score=77.10  Aligned_cols=107  Identities=10%  Similarity=-0.087  Sum_probs=92.9

Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhC
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHV  428 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g  428 (490)
                      .-...+...|++++|+..|+++.+  -.|.+...|..+..+|...|++++|+..+++..  .+.++..|..+..++...|
T Consensus         8 ~~g~~~~~~g~~~eAi~~~~~al~--~~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~   85 (117)
T d1elwa_           8 EKGNKALSVGNIDDALQCYSEAIK--LDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLN   85 (117)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHh--cCCcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHcc
Confidence            345567888999999999999988  356667788999999999999999999998877  5667889999999999999


Q ss_pred             ChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          429 NAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       429 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      ++++|+..|+++++.+|+++.++..+.++..
T Consensus        86 ~~~~A~~~~~~a~~~~p~~~~~~~~l~~l~~  116 (117)
T d1elwa_          86 RFEEAKRTYEEGLKHEANNPQLKEGLQNMEA  116 (117)
T ss_dssp             CHHHHHHHHHHHHTTCTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCCCHHHHHHHHHHhC
Confidence            9999999999999999999999888876643

>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=98.88  E-value=3.8e-09  Score=76.89  Aligned_cols=90  Identities=14%  Similarity=-0.044  Sum_probs=82.3

Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCC
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGK  463 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  463 (490)
                      ..+...+.+.|++++|+..|++..  .+.++..|..+..++...|++++|+..++++++.+|+++.++..++.+|...|+
T Consensus        20 ~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~~g~   99 (112)
T d1hxia_          20 MEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHN   99 (112)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHhhhcccccccchhhhhhhhhhhhhhhHHHhhcccccccccccccccchHHHHHHHHHCCC
Confidence            456778899999999999999877  445688999999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHHHHhh
Q 011249          464 WKDSEIVKMMIS  475 (490)
Q Consensus       464 ~~~A~~~~~~~~  475 (490)
                      +++|.+.+++..
T Consensus       100 ~~~A~~~l~~~l  111 (112)
T d1hxia_         100 ANAALASLRAWL  111 (112)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999999998753

>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=98.84  E-value=2e-08  Score=78.47  Aligned_cols=119  Identities=5%  Similarity=-0.165  Sum_probs=97.2

Q ss_pred             HHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhh
Q 011249          350 IGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVH  427 (490)
Q Consensus       350 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~  427 (490)
                      ......|.+.|++++|+..|+++.+.  .+.+...|..+..+|...|++++|...|++..  .+.+...|..++.++...
T Consensus        14 ~~~gn~~~~~~~y~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~   91 (159)
T d1a17a_          14 KTQANDYFKAKDYENAIKFYSQAIEL--NPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMAL   91 (159)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCHHHHHHHhhhcccc--chhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHc
Confidence            33455677899999999999999883  45567888889999999999999999998876  455668999999999999


Q ss_pred             CChHHHHHHHHHHHhcCCCCCchHHHHHHHHH--hcCCcchHHHH
Q 011249          428 VNAELGEIAARHLLELGPEKTGNSALLANIYA--SMGKWKDSEIV  470 (490)
Q Consensus       428 g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~--~~g~~~~A~~~  470 (490)
                      |++++|...++++.+.+|+++.++..+..+..  ..+.+++|...
T Consensus        92 g~~~eA~~~~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~~~a~~~  136 (159)
T d1a17a_          92 GKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAG  136 (159)
T ss_dssp             TCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence            99999999999999999999998888776643  34456666544

>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=98.83  E-value=6.2e-09  Score=85.16  Aligned_cols=98  Identities=6%  Similarity=-0.149  Sum_probs=74.1

Q ss_pred             CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHH
Q 011249          309 KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCM  388 (490)
Q Consensus       309 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l  388 (490)
                      |+...+...+..|.+.|++++|+..|+++++.. +-+...|..+..+|.+.|++++|+..|+++.+  -.|-+...|..+
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~--l~p~~~~a~~~l   78 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALE--LDGQSVKAHFFL   78 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTT--SCTTCHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHH--hCCCcHHHHHHH
Confidence            455566677778888888888888888888742 23556788888888888888888888888865  223346677788


Q ss_pred             HHHHhhcCChHHHHHHHHhcc
Q 011249          389 VDLLGRSGQLEKAHSLIMDYK  409 (490)
Q Consensus       389 ~~~~~~~g~~~~A~~~~~~~~  409 (490)
                      +.+|...|++++|...|++..
T Consensus        79 g~~~~~l~~~~~A~~~~~~al   99 (201)
T d2c2la1          79 GQCQLEMESYDEAIANLQRAY   99 (201)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHH
Confidence            888888888888888887665

>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=98.83  E-value=6.7e-08  Score=83.84  Aligned_cols=164  Identities=9%  Similarity=-0.053  Sum_probs=95.5

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHhcccC-----C----ChhHHHHHHHHHH-hcCChHHHHHHHHHHHH----cCCCCc-H
Q 011249          282 VSNALIHMHSKCGYLDLAWREFSRIKN-----K----DVISYSSMITAFA-DHGKSQEALDMFLKMRN----EGIEPN-Q  346 (490)
Q Consensus       282 ~~~~l~~~~~~~~~~~~A~~~~~~~~~-----~----~~~~~~~l~~~~~-~~~~~~~a~~~~~~~~~----~~~~p~-~  346 (490)
                      +|..+..+|.+.|++++|.+.+++..+     .    ...++..+...|. ..|++++|+..+++..+    .+..+. .
T Consensus        79 ~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~  158 (290)
T d1qqea_          79 TYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSN  158 (290)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhh
Confidence            444555555555555555555554432     1    1234455555553 35788888888877654    111221 2


Q ss_pred             HHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCc-----hHHHHHHHHHhhcCChHHHHHHHHhcc-CCC---C---h
Q 011249          347 VTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLT-----EHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC---D---A  414 (490)
Q Consensus       347 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~-----~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~---~---~  414 (490)
                      .++..+...+...|++++|...++++.......+..     ..+...+..+...|+++.|.+.+++.. ..|   +   .
T Consensus       159 ~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~  238 (290)
T d1qqea_         159 KCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLKDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRES  238 (290)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHHHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------H
T ss_pred             hHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHH
Confidence            356777888888888888888888887631111111     123445556777888999988888876 222   1   2


Q ss_pred             hhHHHHHHHHhh--hCChHHHHHHHHHHHhcCC
Q 011249          415 GTWGALLGACKV--HVNAELGEIAARHLLELGP  445 (490)
Q Consensus       415 ~~~~~l~~~~~~--~g~~~~a~~~~~~~~~~~p  445 (490)
                      .....++.++..  .+.+++|+..|+++.+++|
T Consensus       239 ~~l~~l~~a~~~~d~e~~~eai~~y~~~~~lD~  271 (290)
T d1qqea_         239 NFLKSLIDAVNEGDSEQLSEHCKEFDNFMRLDK  271 (290)
T ss_dssp             HHHHHHHHHHHTTCTTTHHHHHHHHTTSSCCCH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCH
Confidence            234555555543  2346777777776665554

>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=98.82  E-value=2.7e-08  Score=80.21  Aligned_cols=124  Identities=12%  Similarity=-0.055  Sum_probs=98.9

Q ss_pred             HHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCC
Q 011249          318 ITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ  397 (490)
Q Consensus       318 ~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~  397 (490)
                      ...+...|++++|++.|.++    .+|+..++..+..++...|++++|+..|++..+.  -+.....|..+..+|.+.|+
T Consensus        12 g~~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~l--dp~~~~a~~~~g~~~~~~g~   85 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINR--DKHLAVAYFQRGMLYYQTEK   85 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHH--hhhhhhhHHHHHHHHHhhcc
Confidence            55677889999999988764    3567778888899999999999999999999873  34557788889999999999


Q ss_pred             hHHHHHHHHhcc--CCCC----------------hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC
Q 011249          398 LEKAHSLIMDYK--DFCD----------------AGTWGALLGACKVHVNAELGEIAARHLLELGPEK  447 (490)
Q Consensus       398 ~~~A~~~~~~~~--~~~~----------------~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~  447 (490)
                      +++|.+.|++..  .+.+                ..++..+..++...|++++|.+.++++.+..|+.
T Consensus        86 ~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~~  153 (192)
T d1hh8a_          86 YDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSEP  153 (192)
T ss_dssp             HHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCSG
T ss_pred             HHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCc
Confidence            999999887764  1111                2345667778889999999999999999988874

>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=98.80  E-value=1.7e-08  Score=78.82  Aligned_cols=94  Identities=12%  Similarity=-0.035  Sum_probs=85.8

Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCC
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGK  463 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~  463 (490)
                      ......|.+.|++++|+..|++..  .+.+...|..+..++...|++++|++.|+++++.+|+++.++..++.++...|+
T Consensus        14 ~~~gn~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~g~   93 (159)
T d1a17a_          14 KTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGK   93 (159)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHcCC
Confidence            345667889999999999999887  566788999999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHHHHhhhccc
Q 011249          464 WKDSEIVKMMISETEK  479 (490)
Q Consensus       464 ~~~A~~~~~~~~~~~~  479 (490)
                      +++|...+++.....+
T Consensus        94 ~~eA~~~~~~a~~~~p  109 (159)
T d1a17a_          94 FRAALRDYETVVKVKP  109 (159)
T ss_dssp             HHHHHHHHHHHHHHST
T ss_pred             HHHHHHHHHHHHHcCC
Confidence            9999999999987654

>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=98.79  E-value=1.5e-07  Score=75.80  Aligned_cols=80  Identities=19%  Similarity=0.126  Sum_probs=37.6

Q ss_pred             HHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCC---CCHHhHHHHHHHHHhcCChHHHHHHHH
Q 011249          158 YANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISE---PDASCWAAMTVCYVQNGYAKAAIEMYK  234 (490)
Q Consensus       158 ~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~g~~~~A~~~~~  234 (490)
                      +...|++++|++.|+++..+++.+|..++.+|...|++++|++.|++..+   .++..|..+..++.+.|++++|++.|+
T Consensus        15 ~~~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ldp~~~~a~~~~g~~~~~~g~~~~A~~~~~   94 (192)
T d1hh8a_          15 AADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRDKHLAVAYFQRGMLYYQTEKYDLAIKDLK   94 (192)
T ss_dssp             HHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhhhhhHHHHHHHHHhhccHHHHHHHHH
Confidence            34444444444444444444444444444444444444444444444432   233444445555555555555555554


Q ss_pred             HHH
Q 011249          235 VMR  237 (490)
Q Consensus       235 ~~~  237 (490)
                      +..
T Consensus        95 kAl   97 (192)
T d1hh8a_          95 EAL   97 (192)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=98.75  E-value=3.5e-06  Score=71.57  Aligned_cols=228  Identities=10%  Similarity=-0.082  Sum_probs=129.7

Q ss_pred             CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhc----cCChHHHHHHHHHHHhcCCCCchhHHH
Q 011249          209 DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQ----LGDVEMAAILAKHVDEGCCDRTNYVSN  284 (490)
Q Consensus       209 ~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~~~~~~~~~~  284 (490)
                      |+..+..|...+.+.+++++|+++|++..+.|   +...+..|...+..    ..+...+..++....+.+         
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---------   68 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---------   68 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---------
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---------
Confidence            34555566666666667777777776666554   33344444444433    334555555555544433         


Q ss_pred             HHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHh----cCChHHHHHHHHHHHHcCCCCcHHHHH-HHHHHhcCC
Q 011249          285 ALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFAD----HGKSQEALDMFLKMRNEGIEPNQVTFI-GVLTACSHG  359 (490)
Q Consensus       285 ~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~a~~~~~~~~~~~~~p~~~~~~-~l~~~~~~~  359 (490)
                                               ++.....+...+..    .++.+.|...++...+.|.......+. .........
T Consensus        69 -------------------------~~~a~~~l~~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~a~~~l~~~~~~~~~~~  123 (265)
T d1ouva_          69 -------------------------YSNGCHLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVT  123 (265)
T ss_dssp             -------------------------CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSC
T ss_pred             -------------------------ccchhhccccccccccccchhhHHHHHHHhhhhhhhhhhHHHhhcccccCCCccc
Confidence                                     22222222222221    345666666676666654322211111 111112234


Q ss_pred             CChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh----cCChHHHHHHHHhccCCCChhhHHHHHHHHhh----hCChH
Q 011249          360 GLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR----SGQLEKAHSLIMDYKDFCDAGTWGALLGACKV----HVNAE  431 (490)
Q Consensus       360 g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~  431 (490)
                      .....+...+.....    ..+...+..+...|..    ..+...+..+++......++.....+...+..    ..+++
T Consensus       124 ~~~~~a~~~~~~~~~----~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~a~~~g~~~A~~~lg~~y~~g~~~~~d~~  199 (265)
T d1ouva_         124 RDFKKAVEYFTKACD----LNDGDGCTILGSLYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFK  199 (265)
T ss_dssp             CCHHHHHHHHHHHHH----TTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHH
T ss_pred             chhHHHHHHhhhhhc----ccccchhhhhhhhhccCCCcccccccchhhhhccccccccccccchhhhcccCcccccchh
Confidence            455566666665544    2344555566666654    44566666666666545566666666665554    56888


Q ss_pred             HHHHHHHHHHhcCCCCCchHHHHHHHHHh----cCCcchHHHHHHHhhhccc
Q 011249          432 LGEIAARHLLELGPEKTGNSALLANIYAS----MGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       432 ~a~~~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~  479 (490)
                      +|+..|+++.+.+  ++..+..|+.+|.+    ..+.++|.+.|++..+.|.
T Consensus       200 ~A~~~~~~aa~~g--~~~a~~~LG~~y~~G~g~~~n~~~A~~~~~kAa~~g~  249 (265)
T d1ouva_         200 EALARYSKACELE--NGGGCFNLGAMQYNGEGVTRNEKQAIENFKKGCKLGA  249 (265)
T ss_dssp             HHHHHHHHHHHTT--CHHHHHHHHHHHHTTSSSSCCSTTHHHHHHHHHHHTC
T ss_pred             hhhhhHhhhhccc--CHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHCcC
Confidence            9999999888864  56778888888875    3478889999988877764

>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=98.74  E-value=6.9e-08  Score=76.07  Aligned_cols=134  Identities=12%  Similarity=0.019  Sum_probs=97.7

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHH
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDL  391 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  391 (490)
                      ..+......+.+.|++++|+..|++.++.  .|..            .+....-......+.        ..+|+.+..+
T Consensus        14 ~~l~~~G~~~~~~~~~~~Ai~~y~~al~~--~~~~------------~~~~~~~~~~~~~~~--------~~~~~nla~~   71 (170)
T d1p5qa1          14 TIVKERGTVYFKEGKYKQALLQYKKIVSW--LEYE------------SSFSNEEAQKAQALR--------LASHLNLAMC   71 (170)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHH--TTTC------------CCCCSHHHHHHHHHH--------HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHH--hhhc------------cccchHHHhhhchhH--------HHHHHHHHHH
Confidence            34555666777888888888888877763  1100            000111111111111        2356778899


Q ss_pred             HhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchH
Q 011249          392 LGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDS  467 (490)
Q Consensus       392 ~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A  467 (490)
                      |.+.|++++|+..++...  .+.++..+..++.++...|++++|+..|+++++++|+++.+...+..+..+.+...+.
T Consensus        72 y~k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~~~~~~~  149 (170)
T d1p5qa1          72 HLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAR  149 (170)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhhhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999998877  5557889999999999999999999999999999999999999999887776655543

>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=98.67  E-value=4.8e-08  Score=71.75  Aligned_cols=108  Identities=15%  Similarity=-0.078  Sum_probs=82.9

Q ss_pred             HHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCC---hHHHHHHHHhcc-CCCCh---hhHHHHHH
Q 011249          350 IGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQ---LEKAHSLIMDYK-DFCDA---GTWGALLG  422 (490)
Q Consensus       350 ~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~---~~~A~~~~~~~~-~~~~~---~~~~~l~~  422 (490)
                      ..++..+...+++++|.+.|++...  .-+.++.++..+..++.+.++   +++|+.+|+++. ..|++   .++..+..
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~--~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~   80 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKA--AGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAV   80 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH--HSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHh--hCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHH
Confidence            3456667777888999999998887  345567788888888876554   456888888876 23333   36778889


Q ss_pred             HHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHH
Q 011249          423 ACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYA  459 (490)
Q Consensus       423 ~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~  459 (490)
                      +|...|++++|++.|+++++++|++..+...+..+..
T Consensus        81 ~y~~~g~~~~A~~~~~~aL~~~P~~~~A~~l~~~I~~  117 (122)
T d1nzna_          81 GNYRLKEYEKALKYVRGLLQTEPQNNQAKELERLIDK  117 (122)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHhhhHHHHHHHHHHHHhCcCCHHHHHHHHHHHH
Confidence            9999999999999999999999999887776655443

>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=98.58  E-value=6.3e-07  Score=70.29  Aligned_cols=93  Identities=9%  Similarity=-0.080  Sum_probs=77.8

Q ss_pred             HHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhc
Q 011249          384 HLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASM  461 (490)
Q Consensus       384 ~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~  461 (490)
                      +|..+..+|.+.|++++|+..++...  .+.+...|..+..++...|++++|+..|+++++++|+++.+...+..+....
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~~~  145 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNPQNKAARLQIFMCQKKA  145 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHH
Confidence            56678889999999999999998877  5667889999999999999999999999999999999999999998887776


Q ss_pred             CCcc-hHHHHHHHhhh
Q 011249          462 GKWK-DSEIVKMMISE  476 (490)
Q Consensus       462 g~~~-~A~~~~~~~~~  476 (490)
                      ++.. ...+.+.+|-+
T Consensus       146 ~~~~e~~kk~~~~~f~  161 (168)
T d1kt1a1         146 KEHNERDRRTYANMFK  161 (168)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             HhHHHHHHHHHHHHHh
Confidence            6544 34455555543

>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=98.56  E-value=3.8e-08  Score=72.34  Aligned_cols=94  Identities=14%  Similarity=0.006  Sum_probs=80.5

Q ss_pred             HHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhh---hCChHHHHHHHHHHHhcCCCC--CchHHHHHHHH
Q 011249          386 TCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKV---HVNAELGEIAARHLLELGPEK--TGNSALLANIY  458 (490)
Q Consensus       386 ~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~---~g~~~~a~~~~~~~~~~~p~~--~~~~~~l~~~~  458 (490)
                      ..++..+...+++++|.+.|++..  .+.++.++..+..++.+   .+++++|+.+++++++.+|.+  +.++..|+.+|
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~y   82 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAGSVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGN   82 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHHH
Confidence            457788889999999999999877  56678899999999876   446668999999999988764  45889999999


Q ss_pred             HhcCCcchHHHHHHHhhhccc
Q 011249          459 ASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       459 ~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .+.|++++|++.++++.+..+
T Consensus        83 ~~~g~~~~A~~~~~~aL~~~P  103 (122)
T d1nzna_          83 YRLKEYEKALKYVRGLLQTEP  103 (122)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCT
T ss_pred             HHHhhhHHHHHHHHHHHHhCc
Confidence            999999999999999987654

>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=98.54  E-value=5.5e-07  Score=69.32  Aligned_cols=128  Identities=9%  Similarity=-0.134  Sum_probs=87.4

Q ss_pred             hHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHH
Q 011249          312 ISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDL  391 (490)
Q Consensus       312 ~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~  391 (490)
                      ..+...+..+.+.|++.+|+..|++++..  .|.           ...............        ....+|..+..+
T Consensus        18 ~~~~~~G~~~f~~~~y~~A~~~Y~~al~~--~~~-----------~~~~~~~~~~~~~~~--------~~~~~~~Nla~~   76 (153)
T d2fbna1          18 FDIKEEGNEFFKKNEINEAIVKYKEALDF--FIH-----------TEEWDDQILLDKKKN--------IEISCNLNLATC   76 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHT--TTT-----------CTTCCCHHHHHHHHH--------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhh--Ccc-----------hhhhhhHHHHHhhhh--------HHHHHHhhHHHH
Confidence            34555666777788888888888777752  110           000000000000111        112466778888


Q ss_pred             HhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHh
Q 011249          392 LGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYAS  460 (490)
Q Consensus       392 ~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~  460 (490)
                      |.+.|++++|++.++...  .+.+..+|..++.++...|++++|+..|+++++++|+++.+...+..+..+
T Consensus        77 ~~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~P~n~~~~~~l~~~~~k  147 (153)
T d2fbna1          77 YNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNPNNLDIRNSYELCVNK  147 (153)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHH
T ss_pred             HHHhcccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            999999999999988766  555778888999999999999999999999999999988887777665443

>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=98.52  E-value=8.2e-05  Score=62.73  Aligned_cols=95  Identities=17%  Similarity=0.035  Sum_probs=71.6

Q ss_pred             CchhHHHHHHHHHhcCChhHHHHHHhhcCC-CCHHhHHHHHHHHHh----cCChHHHHHHHHHHHHcCcccChhhHHHHH
Q 011249          178 NSVTWVAMIAGYGKCGEVREAKKVFDEISE-PDASCWAAMTVCYVQ----NGYAKAAIEMYKVMRQENVRISEVAMVGAI  252 (490)
Q Consensus       178 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~  252 (490)
                      |+..+..|...+...+++++|+++|++..+ .+...+..|...|..    ..++..|...+......+   +......+.
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~a~~~l~   77 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLKENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCHLLG   77 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccchhhccc
Confidence            566788888899999999999999998765 677778788888887    668899999999988766   223333333


Q ss_pred             HHHh----ccCChHHHHHHHHHHHhcC
Q 011249          253 SACT----QLGDVEMAAILAKHVDEGC  275 (490)
Q Consensus       253 ~~~~----~~g~~~~a~~~~~~~~~~~  275 (490)
                      ..+.    ..++.+.|...++...+.|
T Consensus        78 ~~~~~~~~~~~~~~~a~~~~~~a~~~g  104 (265)
T d1ouva_          78 NLYYSGQGVSQNTNKALQYYSKACDLK  104 (265)
T ss_dssp             HHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             cccccccccchhhHHHHHHHhhhhhhh
Confidence            3332    3467788888888887766

>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=98.52  E-value=1.3e-07  Score=74.42  Aligned_cols=113  Identities=6%  Similarity=-0.083  Sum_probs=81.2

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhh
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVH  427 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~  427 (490)
                      .+......+.+.|++++|+..|.+........+....               .-......    ....+|..+..+|.+.
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~~~---------------~~~~~~~~----~~~~~~~nla~~y~k~   75 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSN---------------EEAQKAQA----LRLASHLNLAMCHLKL   75 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCS---------------HHHHHHHH----HHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhccccch---------------HHHhhhch----hHHHHHHHHHHHHHhh
Confidence            3444455666777777777777777663221111100               00000000    1123567788889999


Q ss_pred             CChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          428 VNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       428 g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      |++++|+..++++++++|+++.++..++.+|...|++++|+..|++..+.++
T Consensus        76 ~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~l~P  127 (170)
T d1p5qa1          76 QAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYP  127 (170)
T ss_dssp             TCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCS
T ss_pred             hhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHHhCC
Confidence            9999999999999999999999999999999999999999999999987654

>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=98.51  E-value=2.1e-07  Score=69.24  Aligned_cols=56  Identities=9%  Similarity=0.030  Sum_probs=26.0

Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhc
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDY  408 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~  408 (490)
                      .+...+...|++++|+..|.+..+.  .|.+...+..+..+|.+.|++++|++.++++
T Consensus         9 ~~G~~~~~~~~y~~Ai~~y~~al~~--~p~~~~~~~~~a~~~~~~~~~~~A~~~~~~a   64 (128)
T d1elra_           9 ELGNDAYKKKDFDTALKHYDKAKEL--DPTNMTYITNQAAVYFEKGDYNKCRELCEKA   64 (128)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHh--CcccHHHHHhHHHHHHHcCchHHHHHHHHHH
Confidence            3444444455555555555555442  2223444444444555555555555544443

>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=98.46  E-value=0.00028  Score=60.81  Aligned_cols=127  Identities=15%  Similarity=0.145  Sum_probs=61.5

Q ss_pred             HHHHHHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHH
Q 011249          123 VICGYTKIGLMDDAQRLFDSMAERNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVF  202 (490)
Q Consensus       123 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~  202 (490)
                      +...|.+.|.++.|..++..+.     -|..++..+.+.++++.|.+++.+.  .+..+|..+...+.+.....-|.- .
T Consensus        20 i~~~c~~~~lye~A~~lY~~~~-----d~~rl~~~~v~l~~~~~avd~~~k~--~~~~~~k~~~~~l~~~~e~~la~i-~   91 (336)
T d1b89a_          20 VGDRCYDEKMYDAAKLLYNNVS-----NFGRLASTLVHLGEYQAAVDGARKA--NSTRTWKEVCFACVDGKEFRLAQM-C   91 (336)
T ss_dssp             ---------CTTTHHHHHHHTT-----CHHHHHHHHHTTTCHHHHHHHHHHH--TCHHHHHHHHHHHHHTTCHHHHHH-T
T ss_pred             HHHHHHHCCCHHHHHHHHHhCC-----CHHHHHHHHHhhccHHHHHHHHHHc--CCHHHHHHHHHHHHhCcHHHHHHH-H
Confidence            4444556666666666665442     2444555666666666666665543  345566666666665554433321 1


Q ss_pred             hhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhcc
Q 011249          203 DEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQL  258 (490)
Q Consensus       203 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~  258 (490)
                      ......++.....++..|-..|.+++.+.+++...... .++...++.++..+++.
T Consensus        92 ~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~-~~~~~~~~~L~~lyak~  146 (336)
T d1b89a_          92 GLHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKF  146 (336)
T ss_dssp             TTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTT
T ss_pred             HHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCC-ccchHHHHHHHHHHHHh
Confidence            11111333444456666666666666666666554321 33444555565555554

>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=98.45  E-value=4.7e-07  Score=71.16  Aligned_cols=133  Identities=11%  Similarity=0.017  Sum_probs=92.3

Q ss_pred             HHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHH
Q 011249          313 SYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLL  392 (490)
Q Consensus       313 ~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~  392 (490)
                      .+......+...|++++|+..|+++++.  .+....       .   ......       ..  -.+.....+..+..++
T Consensus        29 ~~~~~~~~~~~~~~y~~Ai~~y~~al~~--~~~~~~-------~---~~~~~~-------~~--~~~~~~~~~~nla~~~   87 (169)
T d1ihga1          29 DLKNIGNTFFKSQNWEMAIKKYTKVLRY--VEGSRA-------A---AEDADG-------AK--LQPVALSCVLNIGACK   87 (169)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--HHHHHH-------H---SCHHHH-------GG--GHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHh--hhhhhh-------h---hhhHHH-------HH--hChhhHHHHHHHHHHH
Confidence            3445566677788888888888776641  110000       0   000000       00  0112345667788899


Q ss_pred             hhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcch
Q 011249          393 GRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKD  466 (490)
Q Consensus       393 ~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~  466 (490)
                      .+.|++++|+..++++.  .+.++..|..+..++...|++++|++.|+++++++|+++.+...+..+..+.....+
T Consensus        88 ~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p~n~~~~~~l~~~~~~l~~~~~  163 (169)
T d1ihga1          88 LKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAPEDKAIQAELLKVKQKIKAQKD  163 (169)
T ss_dssp             HHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHH
Confidence            99999999999998876  455677899999999999999999999999999999999988888877665544443

>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=98.43  E-value=1.9e-08  Score=94.44  Aligned_cols=221  Identities=7%  Similarity=-0.080  Sum_probs=115.9

Q ss_pred             HHHHHHHHHHHcCcccC-hhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCch-hHHHHHHHHHHhcCChHHHHHHHhc
Q 011249          228 AAIEMYKVMRQENVRIS-EVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTN-YVSNALIHMHSKCGYLDLAWREFSR  305 (490)
Q Consensus       228 ~A~~~~~~~~~~~~~p~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~A~~~~~~  305 (490)
                      +|.+.|++..+.  +|+ ...+..+..++...|++.+|   |+++....  |+. ..++.... +.+ ..+..+.+.++.
T Consensus         4 eA~q~~~qA~~l--~p~~a~a~~~la~~~~~~~~l~ea---ye~~i~~d--p~~a~~~~~e~~-Lw~-~~y~~~ie~~r~   74 (497)
T d1ya0a1           4 QSAQYLRQAEVL--KADMTDSKLGPAEVWTSRQALQDL---YQKMLVTD--LEYALDKKVEQD-LWN-HAFKNQITTLQG   74 (497)
T ss_dssp             HHHHHHHHHHHH--HGGGTCSSSCSSSSHHHHHHHHHH---HHHHHHHC--HHHHHHHTHHHH-HHH-HHTHHHHHHHHH
T ss_pred             HHHHHHHHHHHc--CCCCHHHHhhHHHHHHHHchHHHH---HHHHHHcC--hhhHHHHhHHHH-HHH-HHHHHHHHHHHH
Confidence            677888888764  444 34555566666666666654   66665443  221 11111111 111 123445555554


Q ss_pred             ccC----CChhHHHHHHH--HHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCC
Q 011249          306 IKN----KDVISYSSMIT--AFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGI  378 (490)
Q Consensus       306 ~~~----~~~~~~~~l~~--~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~  378 (490)
                      ..+    ++.........  .....+.++.++..++....  +.| +...+..+...+.+.|+.+.|...+......   
T Consensus        75 ~~k~~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~--l~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~---  149 (497)
T d1ya0a1          75 QAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFN--VDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSY---  149 (497)
T ss_dssp             HHSCSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC---------------------------------CCHHHHH---
T ss_pred             hcccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCC---
Confidence            433    22222211111  12233445555555554443  334 3346667777788888888888877766552   


Q ss_pred             CCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHH
Q 011249          379 KPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLAN  456 (490)
Q Consensus       379 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~  456 (490)
                      . ...++..++..+...|++++|...|++..  .+.+...|+.++..+...|+..+|+..|.+++...|+.+.++.+|+.
T Consensus       150 ~-~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~  228 (497)
T d1ya0a1         150 I-CQHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQK  228 (497)
T ss_dssp             H-HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHH
T ss_pred             C-HHHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            1 13466678888888889999998888776  44566788888888888899999999999999888888888888888


Q ss_pred             HHHhcCC
Q 011249          457 IYASMGK  463 (490)
Q Consensus       457 ~~~~~g~  463 (490)
                      ++.+..+
T Consensus       229 ~~~~~~~  235 (497)
T d1ya0a1         229 ALSKALE  235 (497)
T ss_dssp             HHHHHTT
T ss_pred             HHHHhhh
Confidence            7766544

>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=98.43  E-value=3.5e-07  Score=70.47  Aligned_cols=114  Identities=5%  Similarity=-0.096  Sum_probs=81.4

Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhh
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVH  427 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~  427 (490)
                      .+..-+..+.+.|++.+|+..|.++.......+....              ........    .....++..+..+|.+.
T Consensus        19 ~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~--------------~~~~~~~~----~~~~~~~~Nla~~~~~l   80 (153)
T d2fbna1          19 DIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDD--------------QILLDKKK----NIEISCNLNLATCYNKN   80 (153)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCC--------------HHHHHHHH----HHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhh--------------HHHHHhhh----hHHHHHHhhHHHHHHHh
Confidence            3444555667777777777777777652111111000              00000000    11234677888899999


Q ss_pred             CChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          428 VNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       428 g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      |++++|++.++++++.+|.++.+|..++.++...|++++|...|++..+.++
T Consensus        81 ~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l~P  132 (153)
T d2fbna1          81 KDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASLNP  132 (153)
T ss_dssp             TCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHST
T ss_pred             cccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            9999999999999999999999999999999999999999999999887654

>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=98.40  E-value=4.3e-07  Score=71.41  Aligned_cols=67  Identities=9%  Similarity=-0.071  Sum_probs=61.7

Q ss_pred             ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          413 DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       413 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ....+..+..++.+.|++++|+..++++++++|+++.+|..++.+|...|++++|++.|+++.+..+
T Consensus        76 ~~~~~~nla~~~~~~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l~p  142 (169)
T d1ihga1          76 ALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEIAP  142 (169)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCT
T ss_pred             hHHHHHHHHHHHHhhcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHhCC
Confidence            4456777888999999999999999999999999999999999999999999999999999987654

>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=98.33  E-value=9e-07  Score=69.35  Aligned_cols=65  Identities=8%  Similarity=-0.084  Sum_probs=59.6

Q ss_pred             hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          415 GTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       415 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      .+|..+..++...|++++|+..++++++++|+++.+|..++.++...|++++|+..++++.+..+
T Consensus        65 ~~~~Nla~~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l~P  129 (168)
T d1kt1a1          65 AAFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEVNP  129 (168)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCT
T ss_pred             HHHHhHHHHHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCC
Confidence            35667788889999999999999999999999999999999999999999999999999887543

>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=98.28  E-value=2e-06  Score=62.03  Aligned_cols=87  Identities=7%  Similarity=-0.117  Sum_probs=43.7

Q ss_pred             HHHHHHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhc
Q 011249          317 MITAFADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRS  395 (490)
Q Consensus       317 l~~~~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  395 (490)
                      +...+.+.|++++|+..|++.++.  .| +...|..+..++.+.|++++|+..++++.+  ..|.+...+..+..+|...
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~--~~p~~~~a~~~la~~y~~~   97 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQK--EPEREEAWRSLGLTQAENEKDGLAIIALNHARM--LDPKDIAVHAALAVSHTNE   97 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhccc--ccccchhhhhhhhhhhhhhhHHHhhcccccccc--cccccccchHHHHHHHHHC
Confidence            344455555555555555555553  23 334555555555555555555555555554  2233344445555555555


Q ss_pred             CChHHHHHHHHh
Q 011249          396 GQLEKAHSLIMD  407 (490)
Q Consensus       396 g~~~~A~~~~~~  407 (490)
                      |++++|.+.+++
T Consensus        98 g~~~~A~~~l~~  109 (112)
T d1hxia_          98 HNANAALASLRA  109 (112)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH
Confidence            555555555544

>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=98.24  E-value=4.9e-07  Score=84.61  Aligned_cols=259  Identities=5%  Similarity=-0.071  Sum_probs=145.2

Q ss_pred             HHHHHHhhcCC--C-CHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccCh-hhHHHHHHHHhccCChHHHHHHHHHHH
Q 011249          197 EAKKVFDEISE--P-DASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISE-VAMVGAISACTQLGDVEMAAILAKHVD  272 (490)
Q Consensus       197 ~A~~~~~~~~~--~-~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~  272 (490)
                      +|.+.|++..+  | ....+..+..++...|++++|   |+++....  |+. ..+.... .+- ...+..+...++...
T Consensus         4 eA~q~~~qA~~l~p~~a~a~~~la~~~~~~~~l~ea---ye~~i~~d--p~~a~~~~~e~-~Lw-~~~y~~~ie~~r~~~   76 (497)
T d1ya0a1           4 QSAQYLRQAEVLKADMTDSKLGPAEVWTSRQALQDL---YQKMLVTD--LEYALDKKVEQ-DLW-NHAFKNQITTLQGQA   76 (497)
T ss_dssp             HHHHHHHHHHHHHGGGTCSSSCSSSSHHHHHHHHHH---HHHHHHHC--HHHHHHHTHHH-HHH-HHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHhhHHHHHHHHchHHHH---HHHHHHcC--hhhHHHHhHHH-HHH-HHHHHHHHHHHHHhc
Confidence            56677777654  3 345677788888888888876   67776542  221 1111100 000 112445666677666


Q ss_pred             hcCCCCchhHHHH--HHHHHHhcCChHHHHHHHhcccC---CChhHHHHHHHHHHhcCChHHHHHHHHHHHHcCCCCcHH
Q 011249          273 EGCCDRTNYVSNA--LIHMHSKCGYLDLAWREFSRIKN---KDVISYSSMITAFADHGKSQEALDMFLKMRNEGIEPNQV  347 (490)
Q Consensus       273 ~~~~~~~~~~~~~--l~~~~~~~~~~~~A~~~~~~~~~---~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~  347 (490)
                      +....++..-...  ....+...+.++.|+..+....+   ++...+..+...+.+.|+.+.|...++.....  .| ..
T Consensus        77 k~~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~~l~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~~-~~  153 (497)
T d1ya0a1          77 KNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNVDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSY--IC-QH  153 (497)
T ss_dssp             SCSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC-------------------------------CCHHHHH--HH-HH
T ss_pred             ccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCC--CH-HH
Confidence            5543343322221  22233445677788877776654   45667888888899999999999988877652  22 34


Q ss_pred             HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHh
Q 011249          348 TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACK  425 (490)
Q Consensus       348 ~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~  425 (490)
                      .+..+...+...|++++|...|+++.+  -.|.+...|+.++..+...|+..+|...|.+..  .+|-+.++..|...+.
T Consensus       154 ~~~~LG~l~~~~~~~~~A~~~y~~A~~--l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~~~~  231 (497)
T d1ya0a1         154 CLVHLGDIARYRNQTSQAESYYRHAAQ--LVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALS  231 (497)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHH--HCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHH--HCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence            777888899999999999999999998  355667899999999999999999999998766  5677888888887765


Q ss_pred             hhCChHHHHHHHHHHHhcCCCC---CchHHHHHHHHHhcCCcchHHHHHHHh
Q 011249          426 VHVNAELGEIAARHLLELGPEK---TGNSALLANIYASMGKWKDSEIVKMMI  474 (490)
Q Consensus       426 ~~g~~~~a~~~~~~~~~~~p~~---~~~~~~l~~~~~~~g~~~~A~~~~~~~  474 (490)
                      +..+..++       .+..+..   ...+..+...+...+..++..++.+++
T Consensus       232 ~~~~~~~~-------~~~~~~~~~~~~~f~~~~~~l~~~~~~~~~~~~~~~~  276 (497)
T d1ya0a1         232 KALESRDE-------VKTKWGVSDFIKAFIKFHGHVYLSKSLEKLSPLREKL  276 (497)
T ss_dssp             HHTTSCCC-------CCSSCCHHHHHHHHHHHHHHHHHTCCGGGHHHHHHHH
T ss_pred             Hhhhhhhh-------hccccccchHHHHHHHHHHHHHhCCchhhHHHHHHHH
Confidence            44322110       0111111   223444555566777777777766554

>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=98.22  E-value=0.001  Score=57.15  Aligned_cols=176  Identities=12%  Similarity=0.040  Sum_probs=98.9

Q ss_pred             CCHhHHHHHHHHHHhCCChHHHHHHHHHhccCCchhHHHHHHHHHhcCChhHHHHHHhhcCCCCHHhHHHHHHHHHhcCC
Q 011249          146 RNVISWSAMVAGYANCGNMKAAKEFYDRMTEKNSVTWVAMIAGYGKCGEVREAKKVFDEISEPDASCWAAMTVCYVQNGY  225 (490)
Q Consensus       146 ~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~g~  225 (490)
                      +|..--..++.-|.+.|.++.|..+|..+.     -|..++..+.+.++++.|.+++.+..  +..+|..+...+.+...
T Consensus        12 ~n~~d~~~i~~~c~~~~lye~A~~lY~~~~-----d~~rl~~~~v~l~~~~~avd~~~k~~--~~~~~k~~~~~l~~~~e   84 (336)
T d1b89a_          12 PNNAHIQQVGDRCYDEKMYDAAKLLYNNVS-----NFGRLASTLVHLGEYQAAVDGARKAN--STRTWKEVCFACVDGKE   84 (336)
T ss_dssp             C----------------CTTTHHHHHHHTT-----CHHHHHHHHHTTTCHHHHHHHHHHHT--CHHHHHHHHHHHHHTTC
T ss_pred             CCcCCHHHHHHHHHHCCCHHHHHHHHHhCC-----CHHHHHHHHHhhccHHHHHHHHHHcC--CHHHHHHHHHHHHhCcH
Confidence            455455556777778888888888887553     45666777777888888777776543  55677777777777666


Q ss_pred             hHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhc
Q 011249          226 AKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSR  305 (490)
Q Consensus       226 ~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~  305 (490)
                      ..-+     ++.......++.....++..|...|.+++...+++...... +.+...++.++..|++.+ .++..+.+..
T Consensus        85 ~~la-----~i~~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~~-~~~~~~~~~L~~lyak~~-~~kl~e~l~~  157 (336)
T d1b89a_          85 FRLA-----QMCGLHIVVHADELEELINYYQDRGYFEELITMLEAALGLE-RAHMGMFTELAILYSKFK-PQKMREHLEL  157 (336)
T ss_dssp             HHHH-----HHTTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTST-TCCHHHHHHHHHHHHTTC-HHHHHHHHHH
T ss_pred             HHHH-----HHHHHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcCC-ccchHHHHHHHHHHHHhC-hHHHHHHHHh
Confidence            5443     22223333455556677777778888888888887765443 456667777777777654 3343333333


Q ss_pred             ccCCChhHHHHHHHHHHhcCChHHHHHHHHHH
Q 011249          306 IKNKDVISYSSMITAFADHGKSQEALDMFLKM  337 (490)
Q Consensus       306 ~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~  337 (490)
                      ..  +......++..|.+.+-+.++.-++.++
T Consensus       158 ~s--~~y~~~k~~~~c~~~~l~~elv~Ly~~~  187 (336)
T d1b89a_         158 FW--SRVNIPKVLRAAEQAHLWAELVFLYDKY  187 (336)
T ss_dssp             HS--TTSCHHHHHHHHHTTTCHHHHHHHHHHT
T ss_pred             cc--ccCCHHHHHHHHHHcCChHHHHHHHHhc
Confidence            21  2222334455666666666666655543

>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=98.21  E-value=2.9e-06  Score=58.92  Aligned_cols=76  Identities=13%  Similarity=0.046  Sum_probs=60.9

Q ss_pred             hHHHHHHHHHhhcCChHHHHHHHHhcc----C----CC-ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHH
Q 011249          383 EHLTCMVDLLGRSGQLEKAHSLIMDYK----D----FC-DAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSAL  453 (490)
Q Consensus       383 ~~~~~l~~~~~~~g~~~~A~~~~~~~~----~----~~-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~  453 (490)
                      ..+..+...+.+.|++++|+..|++..    .    .+ ...++..+..++.+.|++++|+..++++++++|+++.++..
T Consensus         6 ddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P~~~~a~~N   85 (95)
T d1tjca_           6 EDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPEHQRANGN   85 (95)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCcCCHHHHHH
Confidence            344567778888888888888887654    1    11 24578889999999999999999999999999999999988


Q ss_pred             HHHHH
Q 011249          454 LANIY  458 (490)
Q Consensus       454 l~~~~  458 (490)
                      +....
T Consensus        86 l~~~~   90 (95)
T d1tjca_          86 LKYFE   90 (95)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            86543

>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=98.15  E-value=3.4e-06  Score=66.38  Aligned_cols=121  Identities=12%  Similarity=-0.087  Sum_probs=84.2

Q ss_pred             HHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCChhhHHHHHHHHhhhCCh
Q 011249          351 GVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCDAGTWGALLGACKVHVNA  430 (490)
Q Consensus       351 ~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~  430 (490)
                      .........|++++|...|.....-+   +....-     . ...+.+  +...-..+. ......+..++.++...|++
T Consensus        16 ~~g~~~~~~g~~e~A~~~~~~AL~l~---rG~~l~-----~-~~~~~w--~~~~r~~l~-~~~~~a~~~la~~~~~~g~~   83 (179)
T d2ff4a2          16 TAGVHAAAAGRFEQASRHLSAALREW---RGPVLD-----D-LRDFQF--VEPFATALV-EDKVLAHTAKAEAEIACGRA   83 (179)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTTC---CSSTTG-----G-GTTSTT--HHHHHHHHH-HHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhhC---cccccc-----c-CcchHH--HHHHHHHHH-HHHHHHHHHHHHHHHHCCCc
Confidence            33445778899999999999887631   211100     0 000111  111111111 12235677788889999999


Q ss_pred             HHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhh-----cccccCC
Q 011249          431 ELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISE-----TEKKKSP  483 (490)
Q Consensus       431 ~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~-----~~~~~~~  483 (490)
                      ++|+..++++++.+|.+...|..++.+|.+.|++++|++.|+++.+     .|+.+.+
T Consensus        84 ~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~  141 (179)
T d2ff4a2          84 SAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGP  141 (179)
T ss_dssp             HHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCH
T ss_pred             hHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCH
Confidence            9999999999999999999999999999999999999999998743     4776654

>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=98.14  E-value=1.1e-06  Score=66.81  Aligned_cols=75  Identities=11%  Similarity=0.004  Sum_probs=48.8

Q ss_pred             hHHHHHHHHhcc--CCCChhhHHHHHHHHhhhC-----------ChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCc
Q 011249          398 LEKAHSLIMDYK--DFCDAGTWGALLGACKVHV-----------NAELGEIAARHLLELGPEKTGNSALLANIYASMGKW  464 (490)
Q Consensus       398 ~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~~g-----------~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~  464 (490)
                      +++|+..|++..  .+.+..+|..+..+|...|           ++++|.+.|+++++++|++...+..|...       
T Consensus        57 ~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~l~P~~~~~~~~L~~~-------  129 (145)
T d1zu2a1          57 IQEAITKFEEALLIDPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVDEQPDNTHYLKSLEMT-------  129 (145)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH-------
T ss_pred             HHHHHHHHHHHHHhcchhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccccCCCHHHHHHHHHHH-------
Confidence            345555555444  3334455555555554433           46889999999999999998877777755       


Q ss_pred             chHHHHHHHhhhccc
Q 011249          465 KDSEIVKMMISETEK  479 (490)
Q Consensus       465 ~~A~~~~~~~~~~~~  479 (490)
                      .+|.+++.++.++|+
T Consensus       130 ~ka~~~~~e~~k~~~  144 (145)
T d1zu2a1         130 AKAPQLHAEAYKQGL  144 (145)
T ss_dssp             HTHHHHHHHHHHSSS
T ss_pred             HHHHHHHHHHHHHhc
Confidence            455666666665553

>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=98.13  E-value=8.1e-06  Score=60.33  Aligned_cols=58  Identities=10%  Similarity=-0.019  Sum_probs=26.9

Q ss_pred             HHHHHHHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHH
Q 011249          316 SMITAFADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTR  374 (490)
Q Consensus       316 ~l~~~~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~  374 (490)
                      .+...+.+.|++++|+..|++.++.+ +.+...+..+..+|...|++++|+..++++.+
T Consensus         9 ~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~   66 (128)
T d1elra_           9 ELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIE   66 (128)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHH
Confidence            34444445555555555555544431 11233444444445555555555555554443

>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=98.12  E-value=1.4e-06  Score=66.21  Aligned_cols=87  Identities=13%  Similarity=0.016  Sum_probs=64.0

Q ss_pred             hhcCChHHHHHHHHhcc--CCCChhhHHHHHHHHhh----------hCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHh
Q 011249          393 GRSGQLEKAHSLIMDYK--DFCDAGTWGALLGACKV----------HVNAELGEIAARHLLELGPEKTGNSALLANIYAS  460 (490)
Q Consensus       393 ~~~g~~~~A~~~~~~~~--~~~~~~~~~~l~~~~~~----------~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~  460 (490)
                      .+.+.+++|.+.|+...  .+.++.++..+..++..          .+.+++|+..|+++++++|+++.+|..++.+|..
T Consensus         8 ~r~~~fe~A~~~~e~al~~~P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~P~~~~a~~~lG~~y~~   87 (145)
T d1zu2a1           8 DRILLFEQIRQDAENTYKSNPLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLIDPKKDEAVWCIGNAYTS   87 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHccHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhcchhhHHHhhHHHHHHH
Confidence            34455666666666554  44455556555555543          3456899999999999999999999999999988


Q ss_pred             cCC-----------cchHHHHHHHhhhccc
Q 011249          461 MGK-----------WKDSEIVKMMISETEK  479 (490)
Q Consensus       461 ~g~-----------~~~A~~~~~~~~~~~~  479 (490)
                      .|+           +++|.+.|++..+..+
T Consensus        88 ~g~~~~~~~~~~~~~~~A~~~~~kal~l~P  117 (145)
T d1zu2a1          88 FAFLTPDETEAKHNFDLATQFFQQAVDEQP  117 (145)
T ss_dssp             HHHHCCCHHHHHHHHHHHHHHHHHHHHHCT
T ss_pred             cccchhhHHHHHHhHHHhhhhhhcccccCC
Confidence            764           6889999998876554

>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=97.91  E-value=1.7e-05  Score=60.88  Aligned_cols=88  Identities=13%  Similarity=-0.091  Sum_probs=60.3

Q ss_pred             HHhhcCChHHHHHHHHhcc----CCC----------ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCC----------
Q 011249          391 LLGRSGQLEKAHSLIMDYK----DFC----------DAGTWGALLGACKVHVNAELGEIAARHLLELGPE----------  446 (490)
Q Consensus       391 ~~~~~g~~~~A~~~~~~~~----~~~----------~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~----------  446 (490)
                      .+...|++++|+..|++..    ..|          ....|+.+..++...|++++|.+.++++++..|.          
T Consensus        18 ~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~   97 (156)
T d2hr2a1          18 RQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGK   97 (156)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccc
Confidence            3445566666666555443    111          1245677778888888888888888888765432          


Q ss_pred             -CCchHHHHHHHHHhcCCcchHHHHHHHhhhcc
Q 011249          447 -KTGNSALLANIYASMGKWKDSEIVKMMISETE  478 (490)
Q Consensus       447 -~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~  478 (490)
                       ...++..++.+|...|++++|.+.|++..+..
T Consensus        98 ~~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l~  130 (156)
T d2hr2a1          98 LWISAVYSRALALDGLGRGAEAMPEFKKVVEMI  130 (156)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             hhHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhh
Confidence             12367788999999999999999999877653

>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=97.77  E-value=2.2e-05  Score=65.81  Aligned_cols=127  Identities=14%  Similarity=0.038  Sum_probs=86.4

Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCC-chHHHHHHHHHhhcCCh
Q 011249          321 FADHGKSQEALDMFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPL-TEHLTCMVDLLGRSGQL  398 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~g~~  398 (490)
                      ..+.|++++|+..+++.++.  .| |...+..+...++..|++++|.+.++...+.   .|+ ...+..+...+...+..
T Consensus         6 aL~~G~l~eAl~~l~~al~~--~P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l---~P~~~~~~~~l~~ll~a~~~~   80 (264)
T d1zbpa1           6 ALSEGQLQQALELLIEAIKA--SPKDASLRSSFIELLCIDGDFERADEQLMQSIKL---FPEYLPGASQLRHLVKAAQAR   80 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHHT--CTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---CGGGHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCcHHHHHHHHHHHHhcccc
Confidence            34578899999999988885  45 5568888888888999999999999988773   343 44444455555544544


Q ss_pred             HHHHHHHHhcc--CCCC-hhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHH
Q 011249          399 EKAHSLIMDYK--DFCD-AGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSA  452 (490)
Q Consensus       399 ~~A~~~~~~~~--~~~~-~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~  452 (490)
                      +++..-.....  ..|+ ...+...+..+...|+.++|.+.++++.+..|..+..++
T Consensus        81 ~~a~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~p~~~~~~~  137 (264)
T d1zbpa1          81 KDFAQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQEKGFLAN  137 (264)
T ss_dssp             HHHTTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCCCCEEET
T ss_pred             HHHHHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCcccc
Confidence            44433322211  2222 233344456677889999999999999999988776544

>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=97.75  E-value=1.3e-05  Score=67.17  Aligned_cols=122  Identities=13%  Similarity=0.043  Sum_probs=88.4

Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhcc-CCC-ChhhHHHHHHHHhhhCChHHH
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYK-DFC-DAGTWGALLGACKVHVNAELG  433 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~-~~~-~~~~~~~l~~~~~~~g~~~~a  433 (490)
                      ..+.|++++|+..+++..+  ..|.+...+..++..|+..|++++|.+.++... ..| +...+..+...+...+..+++
T Consensus         6 aL~~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           6 ALSEGQLQQALELLIEAIK--ASPKDASLRSSFIELLCIDGDFERADEQLMQSIKLFPEYLPGASQLRHLVKAAQARKDF   83 (264)
T ss_dssp             HTTTTCHHHHHHHHHHHHH--TCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhccccHHH
Confidence            4567999999999999998  567778999999999999999999999998887 334 445555555555444444433


Q ss_pred             HHHHHHHHh-cCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          434 EIAARHLLE-LGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       434 ~~~~~~~~~-~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      ..-...... ..|+....+...+..+...|++++|.+.++++.+...
T Consensus        84 ~~~~~~~~~~~~p~~~~~~l~~a~~~~~~gd~~~A~~~~~~a~e~~p  130 (264)
T d1zbpa1          84 AQGAATAKVLGENEELTKSLVSFNLSMVSQDYEQVSELALQIEELRQ  130 (264)
T ss_dssp             TTSCCCEECCCSCHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCC
T ss_pred             HHHhhhhhcccCchHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCC
Confidence            322222111 2244445556667889999999999999999877643

>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=97.68  E-value=3.6e-05  Score=59.01  Aligned_cols=92  Identities=8%  Similarity=-0.117  Sum_probs=56.4

Q ss_pred             hcCCCChHHHHHHHHHHHHHcCCCCC----------chHHHHHHHHHhhcCChHHHHHHHHhcc--------CCC-----
Q 011249          356 CSHGGLVEDGCKQFELMTRVFGIKPL----------TEHLTCMVDLLGRSGQLEKAHSLIMDYK--------DFC-----  412 (490)
Q Consensus       356 ~~~~g~~~~a~~~~~~~~~~~~~~~~----------~~~~~~l~~~~~~~g~~~~A~~~~~~~~--------~~~-----  412 (490)
                      +...|++++|+..|++..+.....|+          ...|+.+..+|...|++++|.+.+++..        ..+     
T Consensus        19 ~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al~~~~~~~~~~~~~~~~   98 (156)
T d2hr2a1          19 QLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALHYFNRRGELNQDEGKL   98 (156)
T ss_dssp             HHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHCCTTSTHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhhhcccccccccccccch
Confidence            33445555555555555443222121          2345566667777777777776665543        111     


Q ss_pred             ChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC
Q 011249          413 DAGTWGALLGACKVHVNAELGEIAARHLLELGPEK  447 (490)
Q Consensus       413 ~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~  447 (490)
                      ....+..+..++...|++++|++.|++++++.|..
T Consensus        99 ~~~a~~~~g~~~~~lg~~eeA~~~~~~Al~l~~~~  133 (156)
T d2hr2a1          99 WISAVYSRALALDGLGRGAEAMPEFKKVVEMIEER  133 (156)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHC
T ss_pred             hHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhHHh
Confidence            12256677888999999999999999999876543

>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=97.63  E-value=4.6e-05  Score=52.57  Aligned_cols=66  Identities=11%  Similarity=-0.029  Sum_probs=55.8

Q ss_pred             hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCC-------CchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          415 GTWGALLGACKVHVNAELGEIAARHLLELGPEK-------TGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       415 ~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~-------~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                      ..+-.+...+.+.|++++|+..|++++++.|.+       ..++..|+.++.+.|++++|+..++++.+.++.
T Consensus         6 ddc~~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~P~   78 (95)
T d1tjca_           6 EDSFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELDPE   78 (95)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhCcC
Confidence            334567888999999999999999999876543       357899999999999999999999999887543

>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=97.62  E-value=0.00069  Score=52.72  Aligned_cols=121  Identities=12%  Similarity=0.082  Sum_probs=77.7

Q ss_pred             HHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHhcCChHHHHH
Q 011249          253 SACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFADHGKSQEALD  332 (490)
Q Consensus       253 ~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~  332 (490)
                      ......|++++|...|.........+ ..         ......+.+...-..+.......+..++..+...|++++|+.
T Consensus        19 ~~~~~~g~~e~A~~~~~~AL~l~rG~-~l---------~~~~~~~w~~~~r~~l~~~~~~a~~~la~~~~~~g~~~~Al~   88 (179)
T d2ff4a2          19 VHAAAAGRFEQASRHLSAALREWRGP-VL---------DDLRDFQFVEPFATALVEDKVLAHTAKAEAEIACGRASAVIA   88 (179)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTCCSS-TT---------GGGTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHhhCccc-cc---------ccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCchHHHH
Confidence            44566777777777777776542100 00         000000011111111112234567778888899999999999


Q ss_pred             HHHHHHHcCCCC-cHHHHHHHHHHhcCCCChHHHHHHHHHHHH----HcCCCCCchHH
Q 011249          333 MFLKMRNEGIEP-NQVTFIGVLTACSHGGLVEDGCKQFELMTR----VFGIKPLTEHL  385 (490)
Q Consensus       333 ~~~~~~~~~~~p-~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~----~~~~~~~~~~~  385 (490)
                      .++++++.  .| +...|..++.++...|+.++|++.|+++.+    ..|+.|+..+-
T Consensus        89 ~~~~al~~--~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l~  144 (179)
T d2ff4a2          89 ELEALTFE--HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTLR  144 (179)
T ss_dssp             HHHHHHHH--STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHHH
T ss_pred             HHHHHHHh--CCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHHH
Confidence            99999884  44 667889999999999999999999988744    35888887653

>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=97.19  E-value=0.074  Score=47.82  Aligned_cols=316  Identities=9%  Similarity=-0.036  Sum_probs=164.8

Q ss_pred             HHhcCCHHHHHHHHhhcCCCCHhHHHHHHHHHH--hCCChHHHHHHHHHhccC--CchhHHHHHHHHHhcCChhHHHHHH
Q 011249          127 YTKIGLMDDAQRLFDSMAERNVISWSAMVAGYA--NCGNMKAAKEFYDRMTEK--NSVTWVAMIAGYGKCGEVREAKKVF  202 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~~~~~~~~~~~~~l~~~~~--~~~~~~~a~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~A~~~~  202 (490)
                      ..+.|+.+.+.++...+..--...|-..-..-.  .....+++..++++-...  ....-...+..+.+.++++..+..+
T Consensus        16 a~~~~~~~~~~~~~~~L~dypL~pYl~~~~l~~~~~~~~~~~i~~Fl~~~p~~P~~~~lr~~~l~~L~~~~~w~~~~~~~   95 (450)
T d1qsaa1          16 AWDNRQMDVVEQMMPGLKDYPLYPYLEYRQITDDLMNQPAVTVTNFVRANPTLPPARTLQSRFVNELARREDWRGLLAFS   95 (450)
T ss_dssp             HHHTTCHHHHHHHSGGGTTSTTHHHHHHHHHHHTGGGCCHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHTTCHHHHHHHC
T ss_pred             HHHCCCHHHHHHHHhhhcCCCCHHHHHHHHHHhccccCCHHHHHHHHHHCCCChhHHHHHHHHHHHHHhccCHHHHHHhc
Confidence            467899999999888885411333333322222  234555666555553221  1112234456778888988877766


Q ss_pred             hhcCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHH--HHHHHHHHhcC-----
Q 011249          203 DEISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMA--AILAKHVDEGC-----  275 (490)
Q Consensus       203 ~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a--~~~~~~~~~~~-----  275 (490)
                      ..-+ .+...-.....+....|+.+.|.+.+..+-..|. ..+..+..+...+...|.+...  ..-+..+...+     
T Consensus        96 ~~~p-~~~~~~c~~~~A~~~~g~~~~a~~~~~~lW~~~~-~~p~~c~~l~~~~~~~~~lt~~~~~~R~~~~l~~~~~~~a  173 (450)
T d1qsaa1          96 PEKP-GTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTGK-SQPNACDKLFSVWRASGKQDPLAYLERIRLAMKAGNTGLV  173 (450)
T ss_dssp             CSCC-SSHHHHHHHHHHHHHTTCHHHHHHHHHHHHSCSS-CCCTHHHHHHHHHHHTTCSCHHHHHHHHHHHHHTTCHHHH
T ss_pred             cCCC-CCHHHHHHHHHHHHHcCChHHHHHHHHHHHhcCC-CCchHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCChhhH
Confidence            5422 3555555677888889999998888877765542 1223333444433333332211  11111111111     


Q ss_pred             ------CCCc-hhHHHHHHHHHHhcCChHHHHHHHhcccCCChhHHHHHHHHHHh--cCChHHHHHHHHHHHHcC-CCCc
Q 011249          276 ------CDRT-NYVSNALIHMHSKCGYLDLAWREFSRIKNKDVISYSSMITAFAD--HGKSQEALDMFLKMRNEG-IEPN  345 (490)
Q Consensus       276 ------~~~~-~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~a~~~~~~~~~~~-~~p~  345 (490)
                            ++++ .......+.....   ...+........ .+......+..++.+  ..+.+.+..++....... ..++
T Consensus       174 ~~l~~~l~~~~~~~~~a~~~l~~~---p~~~~~~~~~~~-~~~~~~~~~~~~l~rla~~d~~~a~~~l~~~~~~~~~~~~  249 (450)
T d1qsaa1         174 TVLAGQMPADYQTIASAIISLANN---PNTVLTFARTTG-ATDFTRQMAAVAFASVARQDAENARLMIPSLAQAQQLNED  249 (450)
T ss_dssp             HHHHHTCCGGGHHHHHHHHHHHHC---GGGHHHHHHHSC-CCHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHTTCCHH
T ss_pred             HHHHhhCChhHHHHHHHHHHHHhC---hHhHHHHHhcCC-CChhhhHHHHHHHHHHhccChhHHHHHHHhhhhcccccHH
Confidence                  1111 1122222222221   122222211111 222222222333322  346778888887776542 2222


Q ss_pred             HH--HHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHHHHHHHHhccCCCC--hhhHHHHH
Q 011249          346 QV--TFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEKAHSLIMDYKDFCD--AGTWGALL  421 (490)
Q Consensus       346 ~~--~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~--~~~~~~l~  421 (490)
                      ..  ....+.......+..+.+...+......   ..+.......+....+.+++..+...+..+...+.  ..-.--+.
T Consensus       250 ~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~---~~~~~~~~w~~~~al~~~~~~~~~~~~~~l~~~~~~~~r~~YW~g  326 (450)
T d1qsaa1         250 QIQELRDIVAWRLMGNDVTDEQAKWRDDAIMR---SQSTSLIERRVRMALGTGDRRGLNTWLARLPMEAKEKDEWRYWQA  326 (450)
T ss_dssp             HHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHT---CCCHHHHHHHHHHHHHHTCHHHHHHHHHHSCTTGGGSHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCchHHHHHHHHhhccc---ccchHHHHHHHHHHHHcCChHHHHHHHHhcCcccccHHHHHHHHH
Confidence            21  1222333445566677777777766552   23344444455556677888888888888873322  22334456


Q ss_pred             HHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHH
Q 011249          422 GACKVHVNAELGEIAARHLLELGPEKTGNSALLA  455 (490)
Q Consensus       422 ~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~  455 (490)
                      .++...|+.+.|...|..+.. .   +++|-.|+
T Consensus       327 Ra~~~~G~~~~A~~~~~~~a~-~---~~fYG~LA  356 (450)
T d1qsaa1         327 DLLLERGREAEAKEILHQLMQ-Q---RGFYPMVA  356 (450)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHT-S---CSHHHHHH
T ss_pred             HHHHHcCChhhHHHHHHHHhc-C---CChHHHHH
Confidence            778888999999988888765 2   23555554

>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=96.76  E-value=0.035  Score=38.54  Aligned_cols=141  Identities=11%  Similarity=0.088  Sum_probs=92.3

Q ss_pred             HHhcCChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhhcCChHH
Q 011249          321 FADHGKSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGRSGQLEK  400 (490)
Q Consensus       321 ~~~~~~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~  400 (490)
                      +.-.|..++..+++.+....   .+...|+.++.-....-+-+-..+.++.+-+-+.+.|-. ....++.++...+    
T Consensus        12 ~ildG~ve~Gveii~k~~~s---s~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls~C~-Nlk~vv~C~~~~n----   83 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKS---STKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLDKCQ-NLKSVVECGVINN----   83 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHH---SCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGGGCS-CTHHHHHHHHHTT----
T ss_pred             HHHhhhHHhHHHHHHHHccc---CCccccceeeeecccccchHHHHHHHHHHhhhcCchhhh-cHHHHHHHHHHhc----
Confidence            34567888888888887763   344556666655555555566666666665532222211 1223344444333    


Q ss_pred             HHHHHHhccCCCChhhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHHHHHHHHhcCCcchHHHHHHHhhhcccc
Q 011249          401 AHSLIMDYKDFCDAGTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSALLANIYASMGKWKDSEIVKMMISETEKK  480 (490)
Q Consensus       401 A~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~  480 (490)
                                 .+...++..+......|.-+.-.+++..+.+.+..+|.+...++.+|.+.|...++-+++.+.-+.|.+
T Consensus        84 -----------~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          84 -----------TLNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             -----------CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             -----------chHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence                       244455556667778888888888888888877667888888999999999999999999888888764

>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=96.51  E-value=0.042  Score=38.17  Aligned_cols=138  Identities=12%  Similarity=0.110  Sum_probs=86.0

Q ss_pred             HHhcCCHHHHHHHHhhcCC-CCHhHHHHHHHHHHhCCChHHHHHHHHHhccC-CchhHHHHHHHHHhcCChhHHHHHHhh
Q 011249          127 YTKIGLMDDAQRLFDSMAE-RNVISWSAMVAGYANCGNMKAAKEFYDRMTEK-NSVTWVAMIAGYGKCGEVREAKKVFDE  204 (490)
Q Consensus       127 ~~~~g~~~~A~~~~~~~~~-~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~A~~~~~~  204 (490)
                      +.-.|.+++..+++.+... .+..-||-++--....-+-+...++++.+-+- |.          ..+++.......+-.
T Consensus        12 ~ildG~ve~Gveii~k~~~ss~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDl----------s~C~Nlk~vv~C~~~   81 (161)
T d1wy6a1          12 FLLDGYIDEGVKIVLEITKSSTKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDL----------DKCQNLKSVVECGVI   81 (161)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSCHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCG----------GGCSCTHHHHHHHHH
T ss_pred             HHHhhhHHhHHHHHHHHcccCCccccceeeeecccccchHHHHHHHHHHhhhcCc----------hhhhcHHHHHHHHHH
Confidence            4556777777777776665 35555666666666666666666666665432 21          112222222222222


Q ss_pred             cCCCCHHhHHHHHHHHHhcCChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCC
Q 011249          205 ISEPDASCWAAMTVCYVQNGYAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCC  276 (490)
Q Consensus       205 ~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~  276 (490)
                      +.. +....+.-++...++|+-++-.++++.+.+.+ +|++.....+..+|.+.|+..++..++.++-+.|.
T Consensus        82 ~n~-~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~-~i~~~~llkia~A~kkig~~re~nell~~ACe~G~  151 (161)
T d1wy6a1          82 NNT-LNEHVNKALDILVIQGKRDKLEEIGREILKNN-EVSASILVAIANALRRVGDERDATTLLIEACKKGE  151 (161)
T ss_dssp             TTC-CCHHHHHHHHHHHHTTCHHHHHHHHHHHC--C-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTC
T ss_pred             hcc-hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhH
Confidence            221 22344556677778888888888888876644 67777788888888888888888888888877764

>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=96.43  E-value=0.013  Score=42.63  Aligned_cols=48  Identities=6%  Similarity=-0.103  Sum_probs=25.6

Q ss_pred             ChHHHHHHHHHHHhcCCCCCchHHHHHHHHHh----cCCcchHHHHHHHhhhcc
Q 011249          429 NAELGEIAARHLLELGPEKTGNSALLANIYAS----MGKWKDSEIVKMMISETE  478 (490)
Q Consensus       429 ~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~----~g~~~~A~~~~~~~~~~~  478 (490)
                      |.++|.+.|+++.+.+  ++.....|+.+|..    ..+.++|.+++++..+.|
T Consensus        74 d~~~A~~~~~~aa~~g--~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          74 DLRKAAQYYSKACGLN--DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             CHHHHHHHHHHHHHTT--CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHhhhhccC--cchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            4555666666555532  34455555555544    234556666666555544

>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=96.24  E-value=0.0033  Score=44.39  Aligned_cols=74  Identities=12%  Similarity=-0.049  Sum_probs=50.3

Q ss_pred             CCchHHHHHHHHHhhcC---ChHHHHHHHHhcc-CCC-Ch-hhHHHHHHHHhhhCChHHHHHHHHHHHhcCCCCCchHHH
Q 011249          380 PLTEHLTCMVDLLGRSG---QLEKAHSLIMDYK-DFC-DA-GTWGALLGACKVHVNAELGEIAARHLLELGPEKTGNSAL  453 (490)
Q Consensus       380 ~~~~~~~~l~~~~~~~g---~~~~A~~~~~~~~-~~~-~~-~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~p~~~~~~~~  453 (490)
                      ++..+--..+.++.+..   +.++++.+++.+. ..| +. ..+..+..+|.+.|++++|.+.++++++++|++..+...
T Consensus        33 ~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ieP~n~qA~~L  112 (124)
T d2pqrb1          33 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHERNNKQVGAL  112 (124)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             CCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccCCCcHHHHHH
Confidence            44445555666666543   4567888887765 223 32 466667778888888888888888888888887765443

>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=96.20  E-value=0.064  Score=38.65  Aligned_cols=111  Identities=10%  Similarity=-0.019  Sum_probs=74.6

Q ss_pred             ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHHHHHhh----cCChHHH
Q 011249          326 KSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMVDLLGR----SGQLEKA  401 (490)
Q Consensus       326 ~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~A  401 (490)
                      ++++|..+|++..+.|... .  ...+.  .....+.++|.+.+++..+. +   ++.....|...|..    ..+.++|
T Consensus         8 d~~~A~~~~~kaa~~g~~~-a--~~~l~--~~~~~~~~~a~~~~~~aa~~-g---~~~a~~~Lg~~y~~g~~~~~d~~~A   78 (133)
T d1klxa_           8 DLKKAIQYYVKACELNEMF-G--CLSLV--SNSQINKQKLFQYLSKACEL-N---SGNGCRFLGDFYENGKYVKKDLRKA   78 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCTT-H--HHHHH--TCTTSCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             CHHHHHHHHHHHHHCCChh-h--hhhhc--cccccCHHHHHHHHhhhhcc-c---chhhhhhHHHhhhhccccchhhHHH
Confidence            5778888888887766322 1  22222  23456788888888888763 3   34445556666653    4578888


Q ss_pred             HHHHHhccCCCChhhHHHHHHHHhh----hCChHHHHHHHHHHHhcCC
Q 011249          402 HSLIMDYKDFCDAGTWGALLGACKV----HVNAELGEIAARHLLELGP  445 (490)
Q Consensus       402 ~~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~~~~~~p  445 (490)
                      .++|++.....++.....|...|..    ..|.++|.+.|+++.+.+.
T Consensus        79 ~~~~~~aa~~g~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G~  126 (133)
T d1klxa_          79 AQYYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLGS  126 (133)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTC
T ss_pred             HHHHhhhhccCcchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCCC
Confidence            9988887755566666667666654    4588899999999887663

>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=95.80  E-value=0.066  Score=37.53  Aligned_cols=68  Identities=9%  Similarity=-0.023  Sum_probs=46.9

Q ss_pred             CChhhHHHHHHHHhhh---CChHHHHHHHHHHHhcCCCCC-chHHHHHHHHHhcCCcchHHHHHHHhhhccc
Q 011249          412 CDAGTWGALLGACKVH---VNAELGEIAARHLLELGPEKT-GNSALLANIYASMGKWKDSEIVKMMISETEK  479 (490)
Q Consensus       412 ~~~~~~~~l~~~~~~~---g~~~~a~~~~~~~~~~~p~~~-~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~  479 (490)
                      +...+--.+++++.+.   .+.++++.+++++.+.+|.+. ..+..|+-+|.+.|++++|.+.++++.+..+
T Consensus        33 ~s~qt~F~YAw~Lv~S~~~~d~~~gI~lLe~~~~~~p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L~ieP  104 (124)
T d2pqrb1          33 ATIQSRFNYAWGLIKSTDVNDERLGVKILTDIYKEAESRRRECLYYLTIGCYKLGEYSMAKRYVDTLFEHER  104 (124)
T ss_dssp             SCHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCT
T ss_pred             CCcchHHHHHHHHHcCCcHHHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHhhHHHHHHHHHHHHccCC
Confidence            4444555566666543   455678888888887777654 5777778888888888888888887776543

>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=88.11  E-value=1.7  Score=28.32  Aligned_cols=62  Identities=15%  Similarity=0.112  Sum_probs=41.5

Q ss_pred             ChHHHHHHHHHHHHcCcccChhhHHHHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHH
Q 011249          225 YAKAAIEMYKVMRQENVRISEVAMVGAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALI  287 (490)
Q Consensus       225 ~~~~A~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~  287 (490)
                      +.-+..+-++.+......|++....+.+.+|.+.+++..|.++++-++... .++...|..++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~-~~~k~~y~yil   82 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKA-GPHKEIYPYVI   82 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TTCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHh-cCcHHHHHHHH
Confidence            344556666666667777888888888888888888888888887776543 22344555444

>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=88.09  E-value=7.8  Score=33.84  Aligned_cols=113  Identities=11%  Similarity=-0.038  Sum_probs=57.8

Q ss_pred             CChHHHHHHHHHHHHcCcccChhhHH----HHHHHHhccCChHHHHHHHHHHHhcCCCCchhHHHHHHHHHHhcCChHHH
Q 011249          224 GYAKAAIEMYKVMRQENVRISEVAMV----GAISACTQLGDVEMAAILAKHVDEGCCDRTNYVSNALIHMHSKCGYLDLA  299 (490)
Q Consensus       224 g~~~~A~~~~~~~~~~~~~p~~~~~~----~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A  299 (490)
                      .+.+.+..++......... +.....    .+.......+..+.+..++......+  .+.......+......+++..+
T Consensus       228 ~d~~~a~~~l~~~~~~~~~-~~~~~~~~~~~~a~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~w~~~~al~~~~~~~~  304 (450)
T d1qsaa1         228 QDAENARLMIPSLAQAQQL-NEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRS--QSTSLIERRVRMALGTGDRRGL  304 (450)
T ss_dssp             HCHHHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHTSCSTTCCHHHHHHHHHHHHTC--CCHHHHHHHHHHHHHHTCHHHH
T ss_pred             cChhHHHHHHHhhhhcccc-cHHHHHHHHHHHHHHHHHcCchHHHHHHHHhhcccc--cchHHHHHHHHHHHHcCChHHH
Confidence            4566677777666543211 111111    12222234455566666666554443  2333333344445556677777


Q ss_pred             HHHHhcccCC---ChhHHHHHHHHHHhcCChHHHHHHHHHHHH
Q 011249          300 WREFSRIKNK---DVISYSSMITAFADHGKSQEALDMFLKMRN  339 (490)
Q Consensus       300 ~~~~~~~~~~---~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~  339 (490)
                      ...+..+...   ...-.-=+..++...|+.+.|...|..+..
T Consensus       305 ~~~~~~l~~~~~~~~r~~YW~gRa~~~~G~~~~A~~~~~~~a~  347 (450)
T d1qsaa1         305 NTWLARLPMEAKEKDEWRYWQADLLLERGREAEAKEILHQLMQ  347 (450)
T ss_dssp             HHHHHHSCTTGGGSHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHhcCcccccHHHHHHHHHHHHHHcCChhhHHHHHHHHhc
Confidence            7777666541   122223345566667777777777776653

>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=87.70  E-value=1.3  Score=28.86  Aligned_cols=62  Identities=15%  Similarity=0.179  Sum_probs=44.9

Q ss_pred             ChHHHHHHHHHHHHcCCCCcHHHHHHHHHHhcCCCChHHHHHHHHHHHHHcCCCCCchHHHHHH
Q 011249          326 KSQEALDMFLKMRNEGIEPNQVTFIGVLTACSHGGLVEDGCKQFELMTRVFGIKPLTEHLTCMV  389 (490)
Q Consensus       326 ~~~~a~~~~~~~~~~~~~p~~~~~~~l~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~l~  389 (490)
                      +.-++.+-+..+....+.|++......+++|.+.+++..|.++++.++.+.+  ++...|..++
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~--~~k~~y~yil   82 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG--PHKEIYPYVI   82 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT--TCTTHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc--CcHHHHHHHH
Confidence            3445566666666667788888888888888888888888888888887533  3455665554