Citrus Sinensis ID: 040371

---

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
Protein Sequence
MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccccEEHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEHHHHHHHHHHccccHHHHHHHHHccccccEEEHHHHHHHHHccccHHHHHHHHHHHHHccccccHHHHHHHHHHcccccHHHHHHHHHHHcHHccccccccccHHHHHHHHcccccHHHHHHHHHcccccccHHHHHHHHHHHHHcccHHHHHHHHHHHHccccccHHHHHHHHHHcccccHHHHHHHHHHHccccccccEEEEEEccEEEEEEccccccccHHHHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHcccHHHHHHHHHccccccccEEEEcccccccHHHHHHHHHHHHcccEEEEEccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEHHHHHHHHHHHcccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHcccHHHHHHHHHHcccccccHHHHHHHHHHHHcccHHHHHHHHHHHcccccHHHHHHHHHHHHcccHHHHHHHHHHHHHccccccccEEEEEEccEEEEEEEccccccHHHHHHHHHHHHHHHHHHccccccccEEEccccHHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEccEEcccHHHHHHHHHHHcccEEEEEcccccEEcccccEcccccc
Coil and Loop (DISEMBL)
MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLsskvepdkftFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTAcshcglveeGRKYFDHmrsrysiqpqlEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHqfkagdrshpeAQAIDKILGSLIQrtksegflpatELVLMDVseeekegnlyhhSEKLALAYGIlktspgteirisknlrichDCHSWIKMISRLLRRVIIVRDRIrfhrfegglcscgdyw
Flexible Loop (DISEMBL)
mpdkdvvswnsmiggfvrnARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTfkrlelgevAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKkkgvrksqgksWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRirfhrfegglcscgdyw
Low Complexity Region (SEG)
MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISrllrrviivrdrirFHRFEGGLCSCGDYW
Disordered region (IsUnstruct)
*****VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAG*******QAIDKILGSLIQRTKSEGFLPATELVLMDVS*****GNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDY*
Disordered Region (DISOPRED)
*PDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW
Disordered Region (DISEMBL)
MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW
Disordered Region (DISPRO)
***KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW
Positional Conservation
no confident homologs detected

---

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	410	2.2.26 [Sep-21-2011]
Q9FI49	534	Pentatricopeptide repeat-	yes	no	0.995	0.764	0.650	1e-164
Q9FJY7	620	Pentatricopeptide repeat-	no	no	1.0	0.661	0.449	1e-108
A8MQA3	595	Pentatricopeptide repeat-	no	no	0.997	0.687	0.453	1e-108
Q9LW63	715	Putative pentatricopeptid	no	no	0.992	0.569	0.453	1e-107
Q9FI80	646	Pentatricopeptide repeat-	no	no	0.997	0.633	0.468	1e-107
Q683I9	573	Pentatricopeptide repeat-	no	no	1.0	0.715	0.440	1e-103
Q9SZT8	632	Pentatricopeptide repeat-	no	no	1.0	0.648	0.428	1e-103
Q0WQW5	638	Pentatricopeptide repeat-	no	no	0.997	0.641	0.448	1e-103
P0C899	686	Putative pentatricopeptid	no	no	1.0	0.597	0.454	1e-102
Q9SR82	685	Putative pentatricopeptid	no	no	1.0	0.598	0.443	1e-102

>sp|Q9FI49|PP428_ARATH Pentatricopeptide repeat-containing protein At5g50990 OS=Arabidopsis thaliana GN=PCMP-H59 PE=2 SV=2

 Score =  577 bits (1487), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 266/409 (65%), Positives = 342/409 (83%), Gaps = 1/409 (0%)

Query: 3   DKDVVSWNSMIGGFVRNARFDEALRFFREMLS-SKVEPDKFTFASVIYGCARLGALNHAY 61
           D++V++WN MIGG+VRN +++EAL+  + MLS + ++P+KF+FAS +  CARLG L+HA 
Sbjct: 126 DQNVITWNLMIGGYVRNVQYEEALKALKNMLSFTDIKPNKFSFASSLAACARLGDLHHAK 185

Query: 62  WVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHG 121
           WVH+L+I+  IELN ILS+AL+D+Y+KCG I  ++EVF +V+RNDVS+WNAMI+G A HG
Sbjct: 186 WVHSLMIDSGIELNAILSSALVDVYAKCGDIGTSREVFYSVKRNDVSIWNAMITGFATHG 245

Query: 122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHY 181
           LA +A  +F++ME  +V PDSITFLGLLT CSHCGL+EEG++YF  M  R+SIQP+LEHY
Sbjct: 246 LATEAIRVFSEMEAEHVSPDSITFLGLLTTCSHCGLLEEGKEYFGLMSRRFSIQPKLEHY 305

Query: 182 GAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMG 241
           GAMVDLLGRAG ++EAY LI SM +EPDVV+WR+LLS+ RT+K  ELGE+AI N+S+   
Sbjct: 306 GAMVDLLGRAGRVKEAYELIESMPIEPDVVIWRSLLSSSRTYKNPELGEIAIQNLSKAKS 365

Query: 242 GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQ 301
           GDYVLLSN+Y   K+W++A+ VRE+M K+G+RK++GKSWLE  G+IH+FKAGD SH E +
Sbjct: 366 GDYVLLSNIYSSTKKWESAQKVRELMSKEGIRKAKGKSWLEFGGMIHRFKAGDTSHIETK 425

Query: 302 AIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEI 361
           AI K+L  LIQ+TKS+GF+  T+LVLMDVSEEEKE NL +HSEKLALAY ILK+SPGTEI
Sbjct: 426 AIYKVLEGLIQKTKSQGFVSDTDLVLMDVSEEEKEENLNYHSEKLALAYVILKSSPGTEI 485

Query: 362 RISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           RI KN+R+C DCH+WIK +S+LL RVII+RDRIRFHRFE GLCSC DYW
Sbjct: 486 RIQKNIRMCSDCHNWIKAVSKLLNRVIIMRDRIRFHRFEDGLCSCRDYW 534

Arabidopsis thaliana (taxid: 3702)

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

 Score =  394 bits (1011), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 186/414 (44%), Positives = 270/414 (65%), Gaps = 4/414 (0%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           M +K+ +SW +MI G+V+     EAL+ F EM +S VEPD  + A+ +  CA+LGAL   
Sbjct: 207 MAEKNAISWTTMISGYVQADMNKEALQLFHEMQNSDVEPDNVSLANALSACAQLGALEQG 266

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
            W+H+ + + +I ++ +L   LIDMY+KCG+++ A EVF  +++  V  W A+ISG A H
Sbjct: 267 KWIHSYLNKTRIRMDSVLGCVLIDMYAKCGEMEEALEVFKNIKKKSVQAWTALISGYAYH 326

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           G   +A + F +M+   + P+ ITF  +LTACS+ GLVEEG+  F  M   Y+++P +EH
Sbjct: 327 GHGREAISKFMEMQKMGIKPNVITFTAVLTACSYTGLVEEGKLIFYSMERDYNLKPTIEH 386

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGE---VAIVNIS 237
           YG +VDLLGRAG ++EA   I  M ++P+ V+W ALL ACR  K +ELGE     ++ I 
Sbjct: 387 YGCIVDLLGRAGLLDEAKRFIQEMPLKPNAVIWGALLKACRIHKNIELGEEIGEILIAID 446

Query: 238 RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSH 297
              GG YV  +N++   K+WD A   R +MK++GV K  G S + L G  H+F AGDRSH
Sbjct: 447 PYHGGRYVHKANIHAMDKKWDKAAETRRLMKEQGVAKVPGCSTISLEGTTHEFLAGDRSH 506

Query: 298 PEAQAIDKILGSLIQRTKSEGFLPATELVLMD-VSEEEKEGNLYHHSEKLALAYGILKTS 356
           PE + I      + ++ +  G++P  E +L+D V ++E+E  ++ HSEKLA+ YG++KT 
Sbjct: 507 PEIEKIQSKWRIMRRKLEENGYVPELEEMLLDLVDDDEREAIVHQHSEKLAITYGLIKTK 566

Query: 357 PGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           PGT IRI KNLR+C DCH   K+IS++ +R I++RDR RFH F  G CSCGDYW
Sbjct: 567 PGTIIRIMKNLRVCKDCHKVTKLISKIYKRDIVMRDRTRFHHFRDGKCSCGDYW 620

Arabidopsis thaliana (taxid: 3702)

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

 Score =  391 bits (1004), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 188/415 (45%), Positives = 273/415 (65%), Gaps = 6/415 (1%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           MP+KD+V+WNS+I GF  N + +EAL  + EM S  ++PD FT  S++  CA++GAL   
Sbjct: 182 MPEKDLVAWNSVINGFAENGKPEEALALYTEMNSKGIKPDGFTIVSLLSACAKIGALTLG 241

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFD-TVQRNDVSVWNAMISGVAI 119
             VH  +I+  +  N   S  L+D+Y++CG+++ AK +FD  V +N VS W ++I G+A+
Sbjct: 242 KRVHVYMIKVGLTRNLHSSNVLLDLYARCGRVEEAKTLFDEMVDKNSVS-WTSLIVGLAV 300

Query: 120 HGLAADASAIFTKMEMFN-VLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQL 178
           +G   +A  +F  ME    +LP  ITF+G+L ACSHCG+V+EG +YF  MR  Y I+P++
Sbjct: 301 NGFGKEAIELFKYMESTEGLLPCEITFVGILYACSHCGMVKEGFEYFRRMREEYKIEPRI 360

Query: 179 EHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISR 238
           EH+G MVDLL RAG +++AY  I SM M+P+VV+WR LL AC      +L E A + I +
Sbjct: 361 EHFGCMVDLLARAGQVKKAYEYIKSMPMQPNVVIWRTLLGACTVHGDSDLAEFARIQILQ 420

Query: 239 L---MGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDR 295
           L     GDYVLLSNMY   +RW   + +R+ M + GV+K  G S +E+   +H+F  GD+
Sbjct: 421 LEPNHSGDYVLLSNMYASEQRWSDVQKIRKQMLRDGVKKVPGHSLVEVGNRVHEFLMGDK 480

Query: 296 SHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKT 355
           SHP++ AI   L  +  R +SEG++P    V +DV EEEKE  + +HSEK+A+A+ ++ T
Sbjct: 481 SHPQSDAIYAKLKEMTGRLRSEGYVPQISNVYVDVEEEEKENAVVYHSEKIAIAFMLIST 540

Query: 356 SPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
              + I + KNLR+C DCH  IK++S++  R I+VRDR RFH F+ G CSC DYW
Sbjct: 541 PERSPITVVKNLRVCADCHLAIKLVSKVYNREIVVRDRSRFHHFKNGSCSCQDYW 595

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LW63|PP251_ARATH Putative pentatricopeptide repeat-containing protein At3g23330 OS=Arabidopsis thaliana GN=PCMP-H32 PE=3 SV=1

 Score =  389 bits (999), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 186/410 (45%), Positives = 261/410 (63%), Gaps = 3/410 (0%)

Query: 4   KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWV 63
           +D +SWNS++ G+V+N R++EALR FR+M+++KV+P    F+SVI  CA L  L+    +
Sbjct: 306 RDGISWNSLVAGYVQNGRYNEALRLFRQMVTAKVKPGAVAFSSVIPACAHLATLHLGKQL 365

Query: 64  HNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLA 123
           H  ++      N  +++AL+DMYSKCG I+ A+++FD +   D   W A+I G A+HG  
Sbjct: 366 HGYVLRGGFGSNIFIASALVDMYSKCGNIKAARKIFDRMNVLDEVSWTAIIMGHALHGHG 425

Query: 124 ADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGA 183
            +A ++F +M+   V P+ + F+ +LTACSH GLV+E   YF+ M   Y +  +LEHY A
Sbjct: 426 HEAVSLFEEMKRQGVKPNQVAFVAVLTACSHVGLVDEAWGYFNSMTKVYGLNQELEHYAA 485

Query: 184 MVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVA---IVNISRLM 240
           + DLLGRAG +EEAY  I+ M +EP   VW  LLS+C   K LEL E     I  +    
Sbjct: 486 VADLLGRAGKLEEAYNFISKMCVEPTGSVWSTLLSSCSVHKNLELAEKVAEKIFTVDSEN 545

Query: 241 GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEA 300
            G YVL+ NMY    RW     +R  M+KKG+RK    SW+E+    H F +GDRSHP  
Sbjct: 546 MGAYVLMCNMYASNGRWKEMAKLRLRMRKKGLRKKPACSWIEMKNKTHGFVSGDRSHPSM 605

Query: 301 QAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTE 360
             I++ L +++++ + EG++  T  VL DV EE K   L+ HSE+LA+A+GI+ T PGT 
Sbjct: 606 DKINEFLKAVMEQMEKEGYVADTSGVLHDVDEEHKRELLFGHSERLAVAFGIINTEPGTT 665

Query: 361 IRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           IR++KN+RIC DCH  IK IS++  R IIVRD  RFH F  G CSCGDYW
Sbjct: 666 IRVTKNIRICTDCHVAIKFISKITEREIIVRDNSRFHHFNRGNCSCGDYW 715

Arabidopsis thaliana (taxid: 3702)

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

 Score =  389 bits (998), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 194/414 (46%), Positives = 267/414 (64%), Gaps = 5/414 (1%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           M  + VVSWN+MI G+  N  F +A+  FREM    + P+  T  SV+   +RLG+L   
Sbjct: 234 MRQRSVVSWNTMISGYSLNGFFKDAVEVFREMKKGDIRPNYVTLVSVLPAISRLGSLELG 293

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
            W+H    +  I ++ +L +ALIDMYSKCG I+ A  VF+ + R +V  W+AMI+G AIH
Sbjct: 294 EWLHLYAEDSGIRIDDVLGSALIDMYSKCGIIEKAIHVFERLPRENVITWSAMINGFAIH 353

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           G A DA   F KM    V P  + ++ LLTACSH GLVEEGR+YF  M S   ++P++EH
Sbjct: 354 GQAGDAIDCFCKMRQAGVRPSDVAYINLLTACSHGGLVEEGRRYFSQMVSVDGLEPRIEH 413

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
           YG MVDLLGR+G ++EA   I +M ++PD V+W+ALL ACR    +E+G+  + NI   M
Sbjct: 414 YGCMVDLLGRSGLLDEAEEFILNMPIKPDDVIWKALLGACRMQGNVEMGK-RVANILMDM 472

Query: 241 ----GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRS 296
                G YV LSNMY     W     +R  MK+K +RK  G S +++ GV+H+F   D S
Sbjct: 473 VPHDSGAYVALSNMYASQGNWSEVSEMRLRMKEKDIRKDPGCSLIDIDGVLHEFVVEDDS 532

Query: 297 HPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTS 356
           HP+A+ I+ +L  +  + +  G+ P T  VL+++ EE+KE  L++HSEK+A A+G++ TS
Sbjct: 533 HPKAKEINSMLVEISDKLRLAGYRPITTQVLLNLEEEDKENVLHYHSEKIATAFGLISTS 592

Query: 357 PGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           PG  IRI KNLRIC DCHS IK+IS++ +R I VRDR RFH F+ G CSC DYW
Sbjct: 593 PGKPIRIVKNLRICEDCHSSIKLISKVYKRKITVRDRKRFHHFQDGSCSCMDYW 646

Arabidopsis thaliana (taxid: 3702)

>sp|Q683I9|PP295_ARATH Pentatricopeptide repeat-containing protein At3g62890 OS=Arabidopsis thaliana GN=PCMP-H82 PE=2 SV=1

 Score =  376 bits (965), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 185/420 (44%), Positives = 274/420 (65%), Gaps = 10/420 (2%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSK-----VEPDKFTFASVIYGCARLG 55
           MP+++V+SW+ +I G+V   ++ EAL  FREM   K     V P++FT ++V+  C RLG
Sbjct: 154 MPERNVISWSCLINGYVMCGKYKEALDLFREMQLPKPNEAFVRPNEFTMSTVLSACGRLG 213

Query: 56  ALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTV-QRNDVSVWNAMI 114
           AL    WVH  I +  +E++ +L  ALIDMY+KCG ++ AK VF+ +  + DV  ++AMI
Sbjct: 214 ALEQGKWVHAYIDKYHVEIDIVLGTALIDMYAKCGSLERAKRVFNALGSKKDVKAYSAMI 273

Query: 115 SGVAIHGLAADASAIFTKMEMF-NVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYS 173
             +A++GL  +   +F++M    N+ P+S+TF+G+L AC H GL+ EG+ YF  M   + 
Sbjct: 274 CCLAMYGLTDECFQLFSEMTTSDNINPNSVTFVGILGACVHRGLINEGKSYFKMMIEEFG 333

Query: 174 IQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAI 233
           I P ++HYG MVDL GR+G I+EA   I SM MEPDV++W +LLS  R    ++  E A+
Sbjct: 334 ITPSIQHYGCMVDLYGRSGLIKEAESFIASMPMEPDVLIWGSLLSGSRMLGDIKTCEGAL 393

Query: 234 ---VNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQF 290
              + +  +  G YVLLSN+Y    RW   + +R  M+ KG+ K  G S++E+ GV+H+F
Sbjct: 394 KRLIELDPMNSGAYVLLSNVYAKTGRWMEVKCIRHEMEVKGINKVPGCSYVEVEGVVHEF 453

Query: 291 KAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAY 350
             GD S  E++ I  +L  ++QR +  G++  T+ VL+D++E++KE  L +HSEKLA+A+
Sbjct: 454 VVGDESQQESERIYAMLDEIMQRLREAGYVTDTKEVLLDLNEKDKEIALSYHSEKLAIAF 513

Query: 351 GILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
            ++KT PGT +RI KNLRIC DCH  +KMIS+L  R I+VRD  RFH F  G CSC D+W
Sbjct: 514 CLMKTRPGTPVRIIKNLRICGDCHLVMKMISKLFSREIVVRDCNRFHHFRDGSCSCRDFW 573

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SZT8|PP354_ARATH Pentatricopeptide repeat-containing protein At4g37380, chloroplastic OS=Arabidopsis thaliana GN=PCMP-H48 PE=3 SV=1

 Score =  375 bits (964), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 178/415 (42%), Positives = 270/415 (65%), Gaps = 5/415 (1%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLS-SKVEPDKFTFASVIYGCARLGALNH 59
           M ++D+VSWN MI G+ ++   ++AL  F+++L+  K +PD+ T  + +  C+++GAL  
Sbjct: 218 MCERDIVSWNVMIDGYAQHGFPNDALMLFQKLLAEGKPKPDEITVVAALSACSQIGALET 277

Query: 60  AYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAI 119
             W+H  +   +I LN  +   LIDMYSKCG ++ A  VF+   R D+  WNAMI+G A+
Sbjct: 278 GRWIHVFVKSSRIRLNVKVCTGLIDMYSKCGSLEEAVLVFNDTPRKDIVAWNAMIAGYAM 337

Query: 120 HGLAADASAIFTKMEMFNVL-PDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQL 178
           HG + DA  +F +M+    L P  ITF+G L AC+H GLV EG + F+ M   Y I+P++
Sbjct: 338 HGYSQDALRLFNEMQGITGLQPTDITFIGTLQACAHAGLVNEGIRIFESMGQEYGIKPKI 397

Query: 179 EHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELG-EVA--IVN 235
           EHYG +V LLGRAG ++ AY  I +M M+ D V+W ++L +C+      LG E+A  ++ 
Sbjct: 398 EHYGCLVSLLGRAGQLKRAYETIKNMNMDADSVLWSSVLGSCKLHGDFVLGKEIAEYLIG 457

Query: 236 ISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDR 295
           ++    G YVLLSN+Y  +  ++    VR +MK+KG+ K  G S +E+   +H+F+AGDR
Sbjct: 458 LNIKNSGIYVLLSNIYASVGDYEGVAKVRNLMKEKGIVKEPGISTIEIENKVHEFRAGDR 517

Query: 296 SHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKT 355
            H +++ I  +L  + +R KS G++P T  VL D+ E EKE +L  HSE+LA+AYG++ T
Sbjct: 518 EHSKSKEIYTMLRKISERIKSHGYVPNTNTVLQDLEETEKEQSLQVHSERLAIAYGLIST 577

Query: 356 SPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
            PG+ ++I KNLR+C DCH+  K+IS++  R I++RDR RFH F  G CSCGD+W
Sbjct: 578 KPGSPLKIFKNLRVCSDCHTVTKLISKITGRKIVMRDRNRFHHFTDGSCSCGDFW 632

Arabidopsis thaliana (taxid: 3702)

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

 Score =  374 bits (961), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 192/428 (44%), Positives = 273/428 (63%), Gaps = 19/428 (4%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           MP++ +VSWNSMI   VR   +D AL+ FREM  S  EPD +T  SV+  CA LG+L+  
Sbjct: 212 MPERSLVSWNSMIDALVRFGEYDSALQLFREMQRS-FEPDGYTMQSVLSACAGLGSLSLG 270

Query: 61  YWVHNLIIEK---KIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGV 117
            W H  ++ K    + ++ ++  +LI+MY KCG ++MA++VF  +Q+ D++ WNAMI G 
Sbjct: 271 TWAHAFLLRKCDVDVAMDVLVKNSLIEMYCKCGSLRMAEQVFQGMQKRDLASWNAMILGF 330

Query: 118 AIHGLAADASAIFTKM--EMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQ 175
           A HG A +A   F +M  +  NV P+S+TF+GLL AC+H G V +GR+YFD M   Y I+
Sbjct: 331 ATHGRAEEAMNFFDRMVDKRENVRPNSVTFVGLLIACNHRGFVNKGRQYFDMMVRDYCIE 390

Query: 176 PQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSA-CRTFKRLELGEVAIV 234
           P LEHYG +VDL+ RAG+I EA  ++ SM M+PD V+WR+LL A C+    +EL E    
Sbjct: 391 PALEHYGCIVDLIARAGYITEAIDMVMSMPMKPDAVIWRSLLDACCKKGASVELSEEIAR 450

Query: 235 NI----------SRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELA 284
           NI          +    G YVLLS +Y    RW+    VR++M + G+RK  G S +E+ 
Sbjct: 451 NIIGTKEDNESSNGNCSGAYVLLSRVYASASRWNDVGIVRKLMSEHGIRKEPGCSSIEIN 510

Query: 285 GVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPA-TELVLMDVSEE-EKEGNLYHH 342
           G+ H+F AGD SHP+ + I + L  +  R +S G+LP  ++  L+D + +  KE +L  H
Sbjct: 511 GISHEFFAGDTSHPQTKQIYQQLKVIDDRLRSIGYLPDRSQAPLVDATNDGSKEYSLRLH 570

Query: 343 SEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGG 402
           SE+LA+A+G++   P T IRI KNLR+C+DCH   K+IS++    IIVRDR+RFH F+ G
Sbjct: 571 SERLAIAFGLINLPPQTPIRIFKNLRVCNDCHEVTKLISKVFNTEIIVRDRVRFHHFKDG 630

Query: 403 LCSCGDYW 410
            CSC DYW
Sbjct: 631 SCSCLDYW 638

Arabidopsis thaliana (taxid: 3702)

>sp|P0C899|PP271_ARATH Putative pentatricopeptide repeat-containing protein At3g49142 OS=Arabidopsis thaliana GN=PCMP-H77 PE=3 SV=1

 Score =  373 bits (958), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 190/418 (45%), Positives = 259/418 (61%), Gaps = 8/418 (1%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           M  K +VSWN MIG +++NA   EA+  +  M +   EPD  +  SV+  C    AL+  
Sbjct: 269 MGKKSLVSWNVMIGVYMKNAMPVEAVELYSRMEADGFEPDAVSITSVLPACGDTSALSLG 328

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
             +H  I  KK+  N +L  ALIDMY+KCG ++ A++VF+ ++  DV  W AMIS     
Sbjct: 329 KKIHGYIERKKLIPNLLLENALIDMYAKCGCLEKARDVFENMKSRDVVSWTAMISAYGFS 388

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           G   DA A+F+K++   ++PDSI F+  L ACSH GL+EEGR  F  M   Y I P+LEH
Sbjct: 389 GRGCDAVALFSKLQDSGLVPDSIAFVTTLAACSHAGLLEEGRSCFKLMTDHYKITPRLEH 448

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRL- 239
              MVDLLGRAG ++EAY  I  M+MEP+  VW ALL ACR     ++G +A   + +L 
Sbjct: 449 LACMVDLLGRAGKVKEAYRFIQDMSMEPNERVWGALLGACRVHSDTDIGLLAADKLFQLA 508

Query: 240 --MGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSH 297
               G YVLLSN+Y    RW+   N+R IMK KG++K+ G S +E+  +IH F  GDRSH
Sbjct: 509 PEQSGYYVLLSNIYAKAGRWEEVTNIRNIMKSKGLKKNPGASNVEVNRIIHTFLVGDRSH 568

Query: 298 PEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSP 357
           P++  I + L  L+++ K  G++P +E  L DV EE+KE +L  HSEKLA+ + ++ T  
Sbjct: 569 PQSDEIYRELDVLVKKMKELGYVPDSESALHDVEEEDKETHLAVHSEKLAIVFALMNTKE 628

Query: 358 GTE-----IRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
             E     IRI+KNLRIC DCH   K+IS++  R II+RD  RFH F  G+CSCGDYW
Sbjct: 629 EEEDSNNTIRITKNLRICGDCHVAAKLISQITSREIIIRDTNRFHVFRFGVCSCGDYW 686

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SR82|PP219_ARATH Putative pentatricopeptide repeat-containing protein At3g08820 OS=Arabidopsis thaliana GN=PCMP-H84 PE=3 SV=1

 Score =  373 bits (957), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 183/413 (44%), Positives = 257/413 (62%), Gaps = 3/413 (0%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           M +KD+V+W++MI G+  N+   E +  F +ML   ++PD+F+    +  CA LGAL+  
Sbjct: 273 MVEKDIVTWSTMIQGYASNSFPKEGIELFLQMLQENLKPDQFSIVGFLSSCASLGALDLG 332

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
            W  +LI   +   N  ++ ALIDMY+KCG +    EVF  ++  D+ + NA ISG+A +
Sbjct: 333 EWGISLIDRHEFLTNLFMANALIDMYAKCGAMARGFEVFKEMKEKDIVIMNAAISGLAKN 392

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           G    + A+F + E   + PD  TFLGLL  C H GL+++G ++F+ +   Y+++  +EH
Sbjct: 393 GHVKLSFAVFGQTEKLGISPDGSTFLGLLCGCVHAGLIQDGLRFFNAISCVYALKRTVEH 452

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRL- 239
           YG MVDL GRAG +++AY LI  M M P+ +VW ALLS CR  K  +L E  +  +  L 
Sbjct: 453 YGCMVDLWGRAGMLDDAYRLICDMPMRPNAIVWGALLSGCRLVKDTQLAETVLKELIALE 512

Query: 240 --MGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSH 297
               G+YV LSN+Y    RWD A  VR++M KKG++K  G SW+EL G +H+F A D+SH
Sbjct: 513 PWNAGNYVQLSNIYSVGGRWDEAAEVRDMMNKKGMKKIPGYSWIELEGKVHEFLADDKSH 572

Query: 298 PEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSP 357
           P +  I   L  L    +  GF+P TE V  DV EEEKE  L +HSEKLA+A G++ T  
Sbjct: 573 PLSDKIYAKLEDLGNEMRLMGFVPTTEFVFFDVEEEEKERVLGYHSEKLAVALGLISTDH 632

Query: 358 GTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           G  IR+ KNLR+C DCH  +K+IS++ RR I+VRD  RFH F  G CSC DYW
Sbjct: 633 GQVIRVVKNLRVCGDCHEVMKLISKITRREIVVRDNNRFHCFTNGSCSCNDYW 685

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	410
224122234	511	predicted protein [Populus trichocarpa]	0.958	0.769	0.760	0.0
147860852	562	hypothetical protein VITISV_022557 [Viti	0.946	0.690	0.743	0.0
225456505	523	PREDICTED: pentatricopeptide repeat-cont	0.946	0.741	0.743	0.0
317106614	514	JHL07K02.11 [Jatropha curcas]	0.990	0.789	0.741	0.0
356532565	569	PREDICTED: pentatricopeptide repeat-cont	0.970	0.699	0.702	1e-174
449449673	628	PREDICTED: pentatricopeptide repeat-cont	0.990	0.646	0.643	1e-163
387169524	511	hypothetical protein 11M19.3 [Arabidopsi	0.995	0.798	0.655	1e-163
297792411	534	binding protein [Arabidopsis lyrata subs	0.995	0.764	0.655	1e-162
9758246	511	unnamed protein product [Arabidopsis tha	0.995	0.798	0.650	1e-162
145359106	534	pentatricopeptide repeat-containing prot	0.995	0.764	0.650	1e-162

>gi|224122234|ref|XP_002318784.1| predicted protein [Populus trichocarpa] gi|222859457|gb|EEE97004.1| predicted protein [Populus trichocarpa]

 Score =  665 bits (1715), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 312/410 (76%), Positives = 356/410 (86%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           M  +DVV+WN+MIGG+VR ARF+EALR FR M  S VEPDK+TFASVI GCA+LGAL HA
Sbjct: 102 MRARDVVTWNTMIGGYVRKARFEEALRLFRFMNKSNVEPDKYTFASVINGCAKLGALKHA 161

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
            WVH L+IEK+IELNFILS+ALIDMYSKCGKIQ AKE+FD VQRN+V +WNAMISG+A+H
Sbjct: 162 QWVHELLIEKRIELNFILSSALIDMYSKCGKIQTAKEIFDGVQRNNVCIWNAMISGLAVH 221

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           GLA DA  +FTKME+ NVLPD+ITFLG+LTACSHCGLV+EGRKYFD MRSRYS+QP +EH
Sbjct: 222 GLALDAIKVFTKMEVENVLPDAITFLGILTACSHCGLVKEGRKYFDLMRSRYSVQPHIEH 281

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
           YGAMVDLLGRAG +EEA+ +I SM MEPDVV+WRALL ACRT+K+ ELGE A+ NISRL 
Sbjct: 282 YGAMVDLLGRAGLLEEAFAMIKSMPMEPDVVIWRALLGACRTYKKPELGEAAMANISRLR 341

Query: 241 GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEA 300
            GDYVLLSN+YC  KRWDTA+ V E+MKKKGV K +GKS  E AG +H FKAGDRSHPE 
Sbjct: 342 SGDYVLLSNIYCSQKRWDTAQGVWEMMKKKGVHKVRGKSCFEWAGFLHPFKAGDRSHPET 401

Query: 301 QAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTE 360
           +AI K+L  LIQRTK  G++P T+LV MDVSEEEKEGNLYHHSEKLALAYGILKT+ G E
Sbjct: 402 EAIYKMLEGLIQRTKLAGYVPTTDLVTMDVSEEEKEGNLYHHSEKLALAYGILKTTSGAE 461

Query: 361 IRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           +RISKNLRIC+DCHSWIK++SRLL RVIIVRDRIRFHRFE GLCSCGDYW
Sbjct: 462 VRISKNLRICYDCHSWIKIVSRLLSRVIIVRDRIRFHRFENGLCSCGDYW 511

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860852|emb|CAN83162.1| hypothetical protein VITISV_022557 [Vitis vinifera]

 Score =  650 bits (1676), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 305/410 (74%), Positives = 358/410 (87%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           M  +DVV+WNSMIGG VRN RF+EALRFFREML+S VEPD FTFASVI GCARLG+ +HA
Sbjct: 153 MLRRDVVTWNSMIGGCVRNERFEEALRFFREMLNSNVEPDGFTFASVINGCARLGSSHHA 212

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
             VH L+IEKKI+LNFILS+ALID+YSKCG+I  AK+VF+++Q +DVSVWN+MI+G+AIH
Sbjct: 213 ELVHGLMIEKKIQLNFILSSALIDLYSKCGRINTAKKVFNSIQHDDVSVWNSMINGLAIH 272

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           GLA DA  +F++MEM +V PDSITF+G+LTACSHCGLVE+GR+YFD MR  YSIQPQLEH
Sbjct: 273 GLALDAIGVFSQMEMESVSPDSITFIGILTACSHCGLVEQGRRYFDLMRRHYSIQPQLEH 332

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
           YGAMVDLLGRAG +EEAY +I +M MEPD+V+WRALLSACR FK  ELGEVAI  IS L 
Sbjct: 333 YGAMVDLLGRAGLVEEAYAMIKAMPMEPDIVIWRALLSACRNFKNPELGEVAIAKISHLN 392

Query: 241 GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEA 300
            GDY+LLSNMYC L++WD+AE VRE+MK+ GVRK++G+SW+EL GVIHQFKAGDRSHPE 
Sbjct: 393 SGDYILLSNMYCSLEKWDSAERVREMMKRDGVRKNRGRSWVELGGVIHQFKAGDRSHPET 452

Query: 301 QAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTE 360
            AI K+L  LI+RTK EGF+PAT+LVLMDVS+EE+E NL  HSEKLALAY ILKTSPGTE
Sbjct: 453 GAIYKVLEGLIRRTKLEGFMPATDLVLMDVSDEEREENLNSHSEKLALAYVILKTSPGTE 512

Query: 361 IRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           IR+SKNLR CHDCH W+K++SRLL RVIIVRDRIRFH+FEGGLCSC DYW
Sbjct: 513 IRVSKNLRTCHDCHCWMKILSRLLSRVIIVRDRIRFHQFEGGLCSCRDYW 562

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225456505|ref|XP_002280974.1| PREDICTED: pentatricopeptide repeat-containing protein At5g50990 [Vitis vinifera]

 Score =  649 bits (1675), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 305/410 (74%), Positives = 358/410 (87%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           M  +DVV+WNSMIGG VRN RF+EALRFFREML+S VEPD FTFASVI GCARLG+ +HA
Sbjct: 114 MLRRDVVTWNSMIGGCVRNERFEEALRFFREMLNSNVEPDGFTFASVINGCARLGSSHHA 173

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
             VH L+IEKKI+LNFILS+ALID+YSKCG+I  AK+VF+++Q +DVSVWN+MI+G+AIH
Sbjct: 174 ELVHGLMIEKKIQLNFILSSALIDLYSKCGRINTAKKVFNSIQHDDVSVWNSMINGLAIH 233

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           GLA DA  +F++MEM +V PDSITF+G+LTACSHCGLVE+GR+YFD MR  YSIQPQLEH
Sbjct: 234 GLALDAIGVFSQMEMESVSPDSITFIGILTACSHCGLVEQGRRYFDLMRRHYSIQPQLEH 293

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
           YGAMVDLLGRAG +EEAY +I +M MEPD+V+WRALLSACR FK  ELGEVAI  IS L 
Sbjct: 294 YGAMVDLLGRAGLVEEAYAMIKAMPMEPDIVIWRALLSACRNFKNPELGEVAIAKISHLN 353

Query: 241 GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEA 300
            GDY+LLSNMYC L++WD+AE VRE+MK+ GVRK++G+SW+EL GVIHQFKAGDRSHPE 
Sbjct: 354 SGDYILLSNMYCSLEKWDSAERVREMMKRDGVRKNRGRSWVELGGVIHQFKAGDRSHPET 413

Query: 301 QAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTE 360
            AI K+L  LI+RTK EGF+PAT+LVLMDVS+EE+E NL  HSEKLALAY ILKTSPGTE
Sbjct: 414 GAIYKVLEGLIRRTKLEGFMPATDLVLMDVSDEEREENLNSHSEKLALAYVILKTSPGTE 473

Query: 361 IRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           IR+SKNLR CHDCH W+K++SRLL RVIIVRDRIRFH+FEGGLCSC DYW
Sbjct: 474 IRVSKNLRTCHDCHCWMKILSRLLSRVIIVRDRIRFHQFEGGLCSCRDYW 523

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|317106614|dbj|BAJ53121.1| JHL07K02.11 [Jatropha curcas]

 Score =  639 bits (1648), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 304/410 (74%), Positives = 361/410 (88%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           MPD+DVV+WNSMIGG+VRN +F+EALR F+ MLSS VEPDKFTFASVI  CARLGALNHA
Sbjct: 105 MPDRDVVTWNSMIGGYVRNGKFEEALRSFQAMLSSNVEPDKFTFASVITACARLGALNHA 164

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
            W+H+L+++K+IE+NFILS+ALIDMYSKCG+I+ AKEVF++V+RNDVSVWN++I+G+A+H
Sbjct: 165 QWLHDLMVQKRIEVNFILSSALIDMYSKCGRIETAKEVFESVERNDVSVWNSLINGLAVH 224

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           GLA DA  +F+KME  NVLPDS+TFLG+L ACSHCGLV+EGRKYFD M + YSI+PQLEH
Sbjct: 225 GLALDAMMVFSKMEAENVLPDSLTFLGILKACSHCGLVKEGRKYFDLMENYYSIKPQLEH 284

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
           YGAMVDLLGRAG ++EAY +IT+M MEPDV+VWR LLSACRT +  ELGEVA+ NIS   
Sbjct: 285 YGAMVDLLGRAGLLDEAYAMITAMPMEPDVIVWRILLSACRTHRNTELGEVAVANISGPK 344

Query: 241 GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEA 300
            GDYVLLSN+YC   RWD A+ VRE+MK++GVRK +GKSW E   V+H+F+AGD+SHPE 
Sbjct: 345 SGDYVLLSNIYCSQNRWDNAQEVREMMKEEGVRKRRGKSWFEWEDVVHRFRAGDKSHPET 404

Query: 301 QAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTE 360
           +A+ KIL  LIQRTK EGF+P+TELV+MDVSEEEKE NLYHHSEKLALAYGILKTSPGTE
Sbjct: 405 EALYKILEGLIQRTKLEGFVPSTELVMMDVSEEEKEENLYHHSEKLALAYGILKTSPGTE 464

Query: 361 IRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           IRI KNLRIC+DCH+WIKM+S LL RVII+RDRIRFHRFEGG CSCGDYW
Sbjct: 465 IRIYKNLRICYDCHNWIKMVSGLLSRVIIIRDRIRFHRFEGGSCSCGDYW 514

Source: Jatropha curcas

Species: Jatropha curcas

Genus: Jatropha

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356532565|ref|XP_003534842.1| PREDICTED: pentatricopeptide repeat-containing protein At5g50990-like [Glycine max]

 Score =  618 bits (1594), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 288/410 (70%), Positives = 346/410 (84%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           M  +DVV+WNSMIGG+VRN RF +AL  FR MLS+KVEPD FTFASV+  CARLGAL +A
Sbjct: 160 MSVRDVVTWNSMIGGYVRNLRFFDALSIFRRMLSAKVEPDGFTFASVVTACARLGALGNA 219

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
            WVH L++EK++ELN+ILSAALIDMY+KCG+I ++++VF+ V R+ VSVWNAMISG+AIH
Sbjct: 220 KWVHGLMVEKRVELNYILSAALIDMYAKCGRIDVSRQVFEEVARDHVSVWNAMISGLAIH 279

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           GLA DA+ +F++MEM +VLPDSITF+G+LTACSHCGLVEEGRKYF  M++R+ IQPQLEH
Sbjct: 280 GLAMDATLVFSRMEMEHVLPDSITFIGILTACSHCGLVEEGRKYFGMMQNRFMIQPQLEH 339

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
           YG MVDLLGRAG +EEAY +I  M MEPD+V+WRALLSACR  ++ ELGEVAI NISRL 
Sbjct: 340 YGTMVDLLGRAGLMEEAYAVIKEMRMEPDIVIWRALLSACRIHRKKELGEVAIANISRLE 399

Query: 241 GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEA 300
            GD+VLLSNMYC L  WD AE VR +MK +GVRKS+GKSW+EL   IHQF A  +SHPE 
Sbjct: 400 SGDFVLLSNMYCSLNNWDGAERVRRMMKTRGVRKSRGKSWVELGDGIHQFNAAYQSHPEM 459

Query: 301 QAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTE 360
           ++I ++L  LIQR K EGF P T+LVLMDVSEEEKE NL  HSEKLA+AY +LKTSPGT+
Sbjct: 460 KSIYRVLEGLIQRAKLEGFTPLTDLVLMDVSEEEKEENLMFHSEKLAMAYAVLKTSPGTK 519

Query: 361 IRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           IRISKNLRIC DCH+WIK++S++L R IIVRDRIRFH+FEGG+CSC DYW
Sbjct: 520 IRISKNLRICLDCHNWIKIVSKILNRKIIVRDRIRFHQFEGGVCSCKDYW 569

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449449673|ref|XP_004142589.1| PREDICTED: pentatricopeptide repeat-containing protein At5g50990-like [Cucumis sativus]

 Score =  580 bits (1494), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 264/410 (64%), Positives = 332/410 (80%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           MP +DVV+WNS+IGG V+NAR+DEA RFFR+ML+S ++PD FTFAS++  CA+LGA ++ 
Sbjct: 219 MPFRDVVTWNSIIGGCVKNARYDEAFRFFRQMLTSNIQPDGFTFASILNACAQLGAPSNT 278

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
           +WVH  + +KKIELN +L+ ALID YSKCG IQ+AKE+F  +  +D SVWN MI G+AIH
Sbjct: 279 HWVHAQMTQKKIELNSLLTCALIDAYSKCGSIQIAKEIFSNIPHSDTSVWNVMIKGLAIH 338

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           GLA DA ++F +ME  +VLPD+ITFLG+LTAC+H  L++ GR+YF+ M+S YSIQPQLEH
Sbjct: 339 GLAMDALSLFLRMEHESVLPDAITFLGVLTACNHGCLIDHGRRYFELMKSHYSIQPQLEH 398

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
           YG MVDL  RAG +EEAY LI +M +EPDVV WR LLS CR +K  +L EVAI N+S+  
Sbjct: 399 YGVMVDLYSRAGFLEEAYSLIVTMPIEPDVVTWRTLLSGCRIYKNHKLAEVAIANMSQRK 458

Query: 241 GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEA 300
            GDYVLLSN+YC L RW  AE VR++MK   VRK +GKSW+EL G I  FK+GDR HPE+
Sbjct: 459 SGDYVLLSNIYCSLNRWKEAETVRKMMKINRVRKKRGKSWIELGGTIQHFKSGDRLHPES 518

Query: 301 QAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTE 360
            AI+K+L SL++RT++EG++P TELV MD+SEEEKE NL  HSEK+ALAY ILKTSPG +
Sbjct: 519 DAIEKVLCSLMKRTRTEGYMPVTELVFMDISEEEKEENLSFHSEKMALAYAILKTSPGAK 578

Query: 361 IRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           I ISKNLRIC DCH+WIK++SR+L RVI+VRDRIRFH+FEGG+CSCGD W
Sbjct: 579 ISISKNLRICDDCHTWIKLVSRVLCRVIVVRDRIRFHQFEGGMCSCGDRW 628

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|387169524|gb|AFJ66185.1| hypothetical protein 11M19.3 [Arabidopsis halleri]

 Score =  579 bits (1493), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 268/409 (65%), Positives = 343/409 (83%), Gaps = 1/409 (0%)

Query: 3   DKDVVSWNSMIGGFVRNARFDEALRFFREMLS-SKVEPDKFTFASVIYGCARLGALNHAY 61
           D++V++WN MIGG+VRN +++EAL+  + MLS S ++P+KF+FAS +  CARLG L+HA 
Sbjct: 103 DQNVITWNLMIGGYVRNVQYEEALKTLKNMLSFSDIKPNKFSFASSLAACARLGDLHHAK 162

Query: 62  WVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHG 121
           WVH+L+I+  IELN ILS+AL+D+Y+KCG I+ ++EVF +V+RNDVS+WNAMI+G A HG
Sbjct: 163 WVHSLMIDAGIELNAILSSALVDVYAKCGDIETSREVFYSVKRNDVSIWNAMITGFATHG 222

Query: 122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHY 181
           LA +A  +F++ME  +V PDSITFLGLLTACSHCGL+ +G+ YFD M  R+SIQP+LEHY
Sbjct: 223 LATEAIRVFSEMEAEHVSPDSITFLGLLTACSHCGLLGKGKVYFDIMSQRFSIQPKLEHY 282

Query: 182 GAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMG 241
           GAMVDLLGRAG ++EAY LI SM +EPDVV+WR+LLS+ RT+K  ELGE+AI N+S+   
Sbjct: 283 GAMVDLLGRAGRVKEAYELIESMPIEPDVVIWRSLLSSSRTYKNPELGEIAIQNLSKAKS 342

Query: 242 GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQ 301
           GDYVLLSN+Y   K+W++A+ VRE+M K+G+RK++GKSW+E  GVIH+FKAGD SH E +
Sbjct: 343 GDYVLLSNIYSTTKKWESAQKVRELMTKEGIRKAKGKSWVEYGGVIHRFKAGDTSHIEIK 402

Query: 302 AIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEI 361
           AI K+L  LIQ+TKSEGF+  T+LVLMDVSEEEKE NL +HSEKLALAY ILK+SPGTEI
Sbjct: 403 AIYKVLEGLIQKTKSEGFVSDTDLVLMDVSEEEKEENLNYHSEKLALAYVILKSSPGTEI 462

Query: 362 RISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           RI KN+R+C DCH+WIK +S+LL RVII+RDRIRFHRFE GLCSC DYW
Sbjct: 463 RIQKNIRMCSDCHNWIKAVSKLLNRVIIMRDRIRFHRFEDGLCSCKDYW 511

Source: Arabidopsis halleri

Species: Arabidopsis halleri

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297792411|ref|XP_002864090.1| binding protein [Arabidopsis lyrata subsp. lyrata] gi|297309925|gb|EFH40349.1| binding protein [Arabidopsis lyrata subsp. lyrata]

 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 268/409 (65%), Positives = 341/409 (83%), Gaps = 1/409 (0%)

Query: 3   DKDVVSWNSMIGGFVRNARFDEALRFFREMLS-SKVEPDKFTFASVIYGCARLGALNHAY 61
           D++V++WN MIGG+VRN +++EAL+  + MLS S  +P+KF+FAS +  CARLG L+HA 
Sbjct: 126 DQNVITWNLMIGGYVRNVQYEEALKTLKNMLSFSDFKPNKFSFASSLAACARLGDLHHAK 185

Query: 62  WVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHG 121
           WVH+L+I+  IE N ILS+AL+D+Y+KCG I+ ++EVF +V+RNDVS+WNAMI+G A HG
Sbjct: 186 WVHSLMIDGGIEFNAILSSALVDVYAKCGDIETSREVFCSVKRNDVSIWNAMITGFATHG 245

Query: 122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHY 181
           LA +A  +F++ME  +V PDSITFLGLLTACSHCGL+EEG++YF  M  R+SIQP+LEHY
Sbjct: 246 LATEAIRVFSEMEAEHVSPDSITFLGLLTACSHCGLLEEGKEYFGLMSRRFSIQPKLEHY 305

Query: 182 GAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMG 241
           GAMVDLLGRAG ++EAY LI SM +EPDVV+WR+LLS+ RTFK  ELGE+AI N+S+   
Sbjct: 306 GAMVDLLGRAGQVKEAYELIESMPIEPDVVIWRSLLSSSRTFKNPELGEIAIQNLSKAKS 365

Query: 242 GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQ 301
           GDYVLLSN+Y   K+W++A+ VRE+M K+G+RK++GKSW+E  GVIH+FKAGD SH E +
Sbjct: 366 GDYVLLSNIYSSTKKWESAQKVRELMTKEGIRKAKGKSWVEFGGVIHRFKAGDTSHIETK 425

Query: 302 AIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEI 361
           AI K+L  LIQ+TKSEGF+  T+LVLMDVSEEEKE NL +HSEKLALAY ILK+SPGTEI
Sbjct: 426 AIYKVLEGLIQKTKSEGFVSDTDLVLMDVSEEEKEENLNYHSEKLALAYVILKSSPGTEI 485

Query: 362 RISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           RI KN+R+C DCH+WIK +S+LL RVI +RDRIRFHRFE GLCSC DYW
Sbjct: 486 RIQKNIRMCSDCHNWIKAVSKLLNRVITMRDRIRFHRFEDGLCSCKDYW 534

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|9758246|dbj|BAB08745.1| unnamed protein product [Arabidopsis thaliana]

 Score =  577 bits (1487), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 266/409 (65%), Positives = 342/409 (83%), Gaps = 1/409 (0%)

Query: 3   DKDVVSWNSMIGGFVRNARFDEALRFFREMLS-SKVEPDKFTFASVIYGCARLGALNHAY 61
           D++V++WN MIGG+VRN +++EAL+  + MLS + ++P+KF+FAS +  CARLG L+HA 
Sbjct: 103 DQNVITWNLMIGGYVRNVQYEEALKALKNMLSFTDIKPNKFSFASSLAACARLGDLHHAK 162

Query: 62  WVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHG 121
           WVH+L+I+  IELN ILS+AL+D+Y+KCG I  ++EVF +V+RNDVS+WNAMI+G A HG
Sbjct: 163 WVHSLMIDSGIELNAILSSALVDVYAKCGDIGTSREVFYSVKRNDVSIWNAMITGFATHG 222

Query: 122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHY 181
           LA +A  +F++ME  +V PDSITFLGLLT CSHCGL+EEG++YF  M  R+SIQP+LEHY
Sbjct: 223 LATEAIRVFSEMEAEHVSPDSITFLGLLTTCSHCGLLEEGKEYFGLMSRRFSIQPKLEHY 282

Query: 182 GAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMG 241
           GAMVDLLGRAG ++EAY LI SM +EPDVV+WR+LLS+ RT+K  ELGE+AI N+S+   
Sbjct: 283 GAMVDLLGRAGRVKEAYELIESMPIEPDVVIWRSLLSSSRTYKNPELGEIAIQNLSKAKS 342

Query: 242 GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQ 301
           GDYVLLSN+Y   K+W++A+ VRE+M K+G+RK++GKSWLE  G+IH+FKAGD SH E +
Sbjct: 343 GDYVLLSNIYSSTKKWESAQKVRELMSKEGIRKAKGKSWLEFGGMIHRFKAGDTSHIETK 402

Query: 302 AIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEI 361
           AI K+L  LIQ+TKS+GF+  T+LVLMDVSEEEKE NL +HSEKLALAY ILK+SPGTEI
Sbjct: 403 AIYKVLEGLIQKTKSQGFVSDTDLVLMDVSEEEKEENLNYHSEKLALAYVILKSSPGTEI 462

Query: 362 RISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           RI KN+R+C DCH+WIK +S+LL RVII+RDRIRFHRFE GLCSC DYW
Sbjct: 463 RIQKNIRMCSDCHNWIKAVSKLLNRVIIMRDRIRFHRFEDGLCSCRDYW 511

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|145359106|ref|NP_199912.2| pentatricopeptide repeat-containing protein [Arabidopsis thaliana] gi|223635749|sp|Q9FI49.2|PP428_ARATH RecName: Full=Pentatricopeptide repeat-containing protein At5g50990 gi|332008636|gb|AED96019.1| pentatricopeptide repeat-containing protein [Arabidopsis thaliana]

 Score =  577 bits (1487), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 266/409 (65%), Positives = 342/409 (83%), Gaps = 1/409 (0%)

Query: 3   DKDVVSWNSMIGGFVRNARFDEALRFFREMLS-SKVEPDKFTFASVIYGCARLGALNHAY 61
           D++V++WN MIGG+VRN +++EAL+  + MLS + ++P+KF+FAS +  CARLG L+HA 
Sbjct: 126 DQNVITWNLMIGGYVRNVQYEEALKALKNMLSFTDIKPNKFSFASSLAACARLGDLHHAK 185

Query: 62  WVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHG 121
           WVH+L+I+  IELN ILS+AL+D+Y+KCG I  ++EVF +V+RNDVS+WNAMI+G A HG
Sbjct: 186 WVHSLMIDSGIELNAILSSALVDVYAKCGDIGTSREVFYSVKRNDVSIWNAMITGFATHG 245

Query: 122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHY 181
           LA +A  +F++ME  +V PDSITFLGLLT CSHCGL+EEG++YF  M  R+SIQP+LEHY
Sbjct: 246 LATEAIRVFSEMEAEHVSPDSITFLGLLTTCSHCGLLEEGKEYFGLMSRRFSIQPKLEHY 305

Query: 182 GAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMG 241
           GAMVDLLGRAG ++EAY LI SM +EPDVV+WR+LLS+ RT+K  ELGE+AI N+S+   
Sbjct: 306 GAMVDLLGRAGRVKEAYELIESMPIEPDVVIWRSLLSSSRTYKNPELGEIAIQNLSKAKS 365

Query: 242 GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQ 301
           GDYVLLSN+Y   K+W++A+ VRE+M K+G+RK++GKSWLE  G+IH+FKAGD SH E +
Sbjct: 366 GDYVLLSNIYSSTKKWESAQKVRELMSKEGIRKAKGKSWLEFGGMIHRFKAGDTSHIETK 425

Query: 302 AIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEI 361
           AI K+L  LIQ+TKS+GF+  T+LVLMDVSEEEKE NL +HSEKLALAY ILK+SPGTEI
Sbjct: 426 AIYKVLEGLIQKTKSQGFVSDTDLVLMDVSEEEKEENLNYHSEKLALAYVILKSSPGTEI 485

Query: 362 RISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           RI KN+R+C DCH+WIK +S+LL RVII+RDRIRFHRFE GLCSC DYW
Sbjct: 486 RIQKNIRMCSDCHNWIKAVSKLLNRVIIMRDRIRFHRFEDGLCSCRDYW 534

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	410
TAIR|locus:2157368	534	AT5G50990 "AT5G50990" [Arabido	0.995	0.764	0.623	3.4e-141
TAIR|locus:2154855	620	AT5G66520 "AT5G66520" [Arabido	1.0	0.661	0.434	1.2e-95
TAIR|locus:2154389	646	LPA66 "LOW PSII ACCUMULATION 6	0.997	0.633	0.451	1.1e-94
TAIR|locus:4010713895	595	AT4G21065 "AT4G21065" [Arabido	0.997	0.687	0.436	3e-94
TAIR|locus:2205200	741	OTP82 "AT1G08070" [Arabidopsis	0.995	0.550	0.434	1e-91
TAIR|locus:2126352	632	AT4G37380 [Arabidopsis thalian	1.0	0.648	0.414	2.7e-91
TAIR|locus:2081635	573	AT3G62890 [Arabidopsis thalian	1.0	0.715	0.423	5.7e-91
TAIR|locus:2025946	638	CRR28 "CHLORORESPIRATORY REDUC	0.997	0.641	0.432	1.4e-89
TAIR|locus:2077878	685	AT3G08820 "AT3G08820" [Arabido	1.0	0.598	0.426	2.8e-89
TAIR|locus:2056740	603	OTP85 "ORGANELLE TRANSCRIPT PR	0.985	0.669	0.419	1.6e-88

TAIR|locus:2157368 AT5G50990 "AT5G50990" [Arabidopsis thaliana (taxid:3702)]

 Score = 1381 (491.2 bits), Expect = 3.4e-141, P = 3.4e-141
 Identities = 255/409 (62%), Positives = 329/409 (80%)

Query:     3 DKDVVSWNSMIGGFVRNARFDEALRFFREMLS-SKVEPDKFTFASVIYGCARLGALNHAY 61
             D++V++WN MIGG+VRN +++EAL+  + MLS + ++P+KF+FAS +  CARLG L+HA 
Sbjct:   126 DQNVITWNLMIGGYVRNVQYEEALKALKNMLSFTDIKPNKFSFASSLAACARLGDLHHAK 185

Query:    62 WVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHG 121
             WVH+L+I+  IELN ILS+AL+D+Y+KCG I  ++EVF +V+RNDVS+WNAMI+G A HG
Sbjct:   186 WVHSLMIDSGIELNAILSSALVDVYAKCGDIGTSREVFYSVKRNDVSIWNAMITGFATHG 245

Query:   122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHY 181
             LA +A  +F++ME  +V PDSITFLGLLT CSHCGL+EEG++YF  M  R+SIQP+LEHY
Sbjct:   246 LATEAIRVFSEMEAEHVSPDSITFLGLLTTCSHCGLLEEGKEYFGLMSRRFSIQPKLEHY 305

Query:   182 GAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMG 241
             GAMVDLLGRAG ++EAY LI SM +EPDVV+WR+LLS+ RT+K  ELGE+AI N+S+   
Sbjct:   306 GAMVDLLGRAGRVKEAYELIESMPIEPDVVIWRSLLSSSRTYKNPELGEIAIQNLSKAKS 365

Query:   242 GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQ 301
             GDYVLLSN+Y   K+W++A+ VRE+M K+G+RK++GKSWLE  G+IH+FKAGD SH E +
Sbjct:   366 GDYVLLSNIYSSTKKWESAQKVRELMSKEGIRKAKGKSWLEFGGMIHRFKAGDTSHIETK 425

Query:   302 AIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEI 361
             AI K+L  LIQ+TKS+GF+  T+LVLMDVSEEEKE NL +HSEKLALAY ILK+SPGTEI
Sbjct:   426 AIYKVLEGLIQKTKSQGFVSDTDLVLMDVSEEEKEENLNYHSEKLALAYVILKSSPGTEI 485

Query:   362 RISKNLRICHDCHSWIKMISXXXXXXXXXXXXXXFHRFEGGLCSCGDYW 410
             RI KN+R+C DCH+WIK +S              FHRFE GLCSC DYW
Sbjct:   486 RIQKNIRMCSDCHNWIKAVSKLLNRVIIMRDRIRFHRFEDGLCSCRDYW 534

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 951 (339.8 bits), Expect = 1.2e-95, P = 1.2e-95
 Identities = 180/414 (43%), Positives = 259/414 (62%)

Query:     1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
             M +K+ +SW +MI G+V+     EAL+ F EM +S VEPD  + A+ +  CA+LGAL   
Sbjct:   207 MAEKNAISWTTMISGYVQADMNKEALQLFHEMQNSDVEPDNVSLANALSACAQLGALEQG 266

Query:    61 YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
              W+H+ + + +I ++ +L   LIDMY+KCG+++ A EVF  +++  V  W A+ISG A H
Sbjct:   267 KWIHSYLNKTRIRMDSVLGCVLIDMYAKCGEMEEALEVFKNIKKKSVQAWTALISGYAYH 326

Query:   121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
             G   +A + F +M+   + P+ ITF  +LTACS+ GLVEEG+  F  M   Y+++P +EH
Sbjct:   327 GHGREAISKFMEMQKMGIKPNVITFTAVLTACSYTGLVEEGKLIFYSMERDYNLKPTIEH 386

Query:   181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVA---IVNIS 237
             YG +VDLLGRAG ++EA   I  M ++P+ V+W ALL ACR  K +ELGE     ++ I 
Sbjct:   387 YGCIVDLLGRAGLLDEAKRFIQEMPLKPNAVIWGALLKACRIHKNIELGEEIGEILIAID 446

Query:   238 RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSH 297
                GG YV  +N++   K+WD A   R +MK++GV K  G S + L G  H+F AGDRSH
Sbjct:   447 PYHGGRYVHKANIHAMDKKWDKAAETRRLMKEQGVAKVPGCSTISLEGTTHEFLAGDRSH 506

Query:   298 PEAQAIDKILGSLIQRTKSEGFLPATELVLMD-VSEEEKEGNLYHHSEKLALAYGILKTS 356
             PE + I      + ++ +  G++P  E +L+D V ++E+E  ++ HSEKLA+ YG++KT 
Sbjct:   507 PEIEKIQSKWRIMRRKLEENGYVPELEEMLLDLVDDDEREAIVHQHSEKLAITYGLIKTK 566

Query:   357 PGTEIRISKNLRICHDCHSWIKMISXXXXXXXXXXXXXXFHRFEGGLCSCGDYW 410
             PGT IRI KNLR+C DCH   K+IS              FH F  G CSCGDYW
Sbjct:   567 PGTIIRIMKNLRVCKDCHKVTKLISKIYKRDIVMRDRTRFHHFRDGKCSCGDYW 620

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0016556 "mRNA modification" evidence=RCA

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

 Score = 942 (336.7 bits), Expect = 1.1e-94, P = 1.1e-94
 Identities = 187/414 (45%), Positives = 257/414 (62%)

Query:     1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
             M  + VVSWN+MI G+  N  F +A+  FREM    + P+  T  SV+   +RLG+L   
Sbjct:   234 MRQRSVVSWNTMISGYSLNGFFKDAVEVFREMKKGDIRPNYVTLVSVLPAISRLGSLELG 293

Query:    61 YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
              W+H    +  I ++ +L +ALIDMYSKCG I+ A  VF+ + R +V  W+AMI+G AIH
Sbjct:   294 EWLHLYAEDSGIRIDDVLGSALIDMYSKCGIIEKAIHVFERLPRENVITWSAMINGFAIH 353

Query:   121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
             G A DA   F KM    V P  + ++ LLTACSH GLVEEGR+YF  M S   ++P++EH
Sbjct:   354 GQAGDAIDCFCKMRQAGVRPSDVAYINLLTACSHGGLVEEGRRYFSQMVSVDGLEPRIEH 413

Query:   181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
             YG MVDLLGR+G ++EA   I +M ++PD V+W+ALL ACR    +E+G+  + NI   M
Sbjct:   414 YGCMVDLLGRSGLLDEAEEFILNMPIKPDDVIWKALLGACRMQGNVEMGK-RVANILMDM 472

Query:   241 ----GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRS 296
                  G YV LSNMY     W     +R  MK+K +RK  G S +++ GV+H+F   D S
Sbjct:   473 VPHDSGAYVALSNMYASQGNWSEVSEMRLRMKEKDIRKDPGCSLIDIDGVLHEFVVEDDS 532

Query:   297 HPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTS 356
             HP+A+ I+ +L  +  + +  G+ P T  VL+++ EE+KE  L++HSEK+A A+G++ TS
Sbjct:   533 HPKAKEINSMLVEISDKLRLAGYRPITTQVLLNLEEEDKENVLHYHSEKIATAFGLISTS 592

Query:   357 PGTEIRISKNLRICHDCHSWIKMISXXXXXXXXXXXXXXFHRFEGGLCSCGDYW 410
             PG  IRI KNLRIC DCHS IK+IS              FH F+ G CSC DYW
Sbjct:   593 PGKPIRIVKNLRICEDCHSSIKLISKVYKRKITVRDRKRFHHFQDGSCSCMDYW 646

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0009451 "RNA modification" evidence=IMP

GO:0007020 "microtubule nucleation" evidence=RCA

TAIR|locus:4010713895 AT4G21065 "AT4G21065" [Arabidopsis thaliana (taxid:3702)]

 Score = 938 (335.3 bits), Expect = 3.0e-94, P = 3.0e-94
 Identities = 181/415 (43%), Positives = 263/415 (63%)

Query:     1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
             MP+KD+V+WNS+I GF  N + +EAL  + EM S  ++PD FT  S++  CA++GAL   
Sbjct:   182 MPEKDLVAWNSVINGFAENGKPEEALALYTEMNSKGIKPDGFTIVSLLSACAKIGALTLG 241

Query:    61 YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDT-VQRNDVSVWNAMISGVAI 119
               VH  +I+  +  N   S  L+D+Y++CG+++ AK +FD  V +N VS W ++I G+A+
Sbjct:   242 KRVHVYMIKVGLTRNLHSSNVLLDLYARCGRVEEAKTLFDEMVDKNSVS-WTSLIVGLAV 300

Query:   120 HGLAADASAIFTKMEMFN-VLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQL 178
             +G   +A  +F  ME    +LP  ITF+G+L ACSHCG+V+EG +YF  MR  Y I+P++
Sbjct:   301 NGFGKEAIELFKYMESTEGLLPCEITFVGILYACSHCGMVKEGFEYFRRMREEYKIEPRI 360

Query:   179 EHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISR 238
             EH+G MVDLL RAG +++AY  I SM M+P+VV+WR LL AC      +L E A + I +
Sbjct:   361 EHFGCMVDLLARAGQVKKAYEYIKSMPMQPNVVIWRTLLGACTVHGDSDLAEFARIQILQ 420

Query:   239 LM---GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDR 295
             L     GDYVLLSNMY   +RW   + +R+ M + GV+K  G S +E+   +H+F  GD+
Sbjct:   421 LEPNHSGDYVLLSNMYASEQRWSDVQKIRKQMLRDGVKKVPGHSLVEVGNRVHEFLMGDK 480

Query:   296 SHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKT 355
             SHP++ AI   L  +  R +SEG++P    V +DV EEEKE  + +HSEK+A+A+ ++ T
Sbjct:   481 SHPQSDAIYAKLKEMTGRLRSEGYVPQISNVYVDVEEEEKENAVVYHSEKIAIAFMLIST 540

Query:   356 SPGTEIRISKNLRICHDCHSWIKMISXXXXXXXXXXXXXXFHRFEGGLCSCGDYW 410
                + I + KNLR+C DCH  IK++S              FH F+ G CSC DYW
Sbjct:   541 PERSPITVVKNLRVCADCHLAIKLVSKVYNREIVVRDRSRFHHFKNGSCSCQDYW 595

GO:0003674 "molecular_function" evidence=ND

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2205200 OTP82 "AT1G08070" [Arabidopsis thaliana (taxid:3702)]

 Score = 914 (326.8 bits), Expect = 1.0e-91, P = 1.0e-91
 Identities = 181/417 (43%), Positives = 258/417 (61%)

Query:     1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
             +P KDV+SWN++IGG+     + EAL  F+EML S   P+  T  S++  CA LGA++  
Sbjct:   327 LPYKDVISWNTLIGGYTHMNLYKEALLLFQEMLRSGETPNDVTMLSILPACAHLGAIDIG 386

Query:    61 YWVHNLIIEKKIE--LNFI-LSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGV 117
              W+H + I+K+++   N   L  +LIDMY+KCG I+ A +VF+++    +S WNAMI G 
Sbjct:   387 RWIH-VYIDKRLKGVTNASSLRTSLIDMYAKCGDIEAAHQVFNSILHKSLSSWNAMIFGF 445

Query:   118 AIHGLAADASA-IFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP 176
             A+HG  ADAS  +F++M    + PD ITF+GLL+ACSH G+++ GR  F  M   Y + P
Sbjct:   446 AMHG-RADASFDLFSRMRKIGIQPDDITFVGLLSACSHSGMLDLGRHIFRTMTQDYKMTP 504

Query:   177 QLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNI 236
             +LEHYG M+DLLG +G  +EA  +I  M MEPD V+W +LL AC+    +ELGE    N+
Sbjct:   505 KLEHYGCMIDLLGHSGLFKEAEEMINMMEMEPDGVIWCSLLKACKMHGNVELGESFAENL 564

Query:   237 SRLMG---GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAG 293
              ++     G YVLLSN+Y    RW+     R ++  KG++K  G S +E+  V+H+F  G
Sbjct:   565 IKIEPENPGSYVLLSNIYASAGRWNEVAKTRALLNDKGMKKVPGCSSIEIDSVVHEFIIG 624

Query:   294 DRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGIL 353
             D+ HP  + I  +L  +    +  GF+P T  VL ++ EE KEG L HHSEKLA+A+G++
Sbjct:   625 DKFHPRNREIYGMLEEMEVLLEKAGFVPDTSEVLQEMEEEWKEGALRHHSEKLAIAFGLI 684

Query:   354 KTSPGTEIRISKNLRICHDCHSWIKMISXXXXXXXXXXXXXXFHRFEGGLCSCGDYW 410
              T PGT++ I KNLR+C +CH   K+IS              FH F  G+CSC DYW
Sbjct:   685 STKPGTKLTIVKNLRVCRNCHEATKLISKIYKREIIARDRTRFHHFRDGVCSCNDYW 741

GO:0003674 "molecular_function" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0031425 "chloroplast RNA processing" evidence=IMP

TAIR|locus:2126352 AT4G37380 [Arabidopsis thaliana (taxid:3702)]

 Score = 910 (325.4 bits), Expect = 2.7e-91, P = 2.7e-91
 Identities = 172/415 (41%), Positives = 260/415 (62%)

Query:     1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSS-KVEPDKFTFASVIYGCARLGALNH 59
             M ++D+VSWN MI G+ ++   ++AL  F+++L+  K +PD+ T  + +  C+++GAL  
Sbjct:   218 MCERDIVSWNVMIDGYAQHGFPNDALMLFQKLLAEGKPKPDEITVVAALSACSQIGALET 277

Query:    60 AYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAI 119
               W+H  +   +I LN  +   LIDMYSKCG ++ A  VF+   R D+  WNAMI+G A+
Sbjct:   278 GRWIHVFVKSSRIRLNVKVCTGLIDMYSKCGSLEEAVLVFNDTPRKDIVAWNAMIAGYAM 337

Query:   120 HGLAADASAIFTKMEMFNVL-PDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQL 178
             HG + DA  +F +M+    L P  ITF+G L AC+H GLV EG + F+ M   Y I+P++
Sbjct:   338 HGYSQDALRLFNEMQGITGLQPTDITFIGTLQACAHAGLVNEGIRIFESMGQEYGIKPKI 397

Query:   179 EHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELG-EVA--IVN 235
             EHYG +V LLGRAG ++ AY  I +M M+ D V+W ++L +C+      LG E+A  ++ 
Sbjct:   398 EHYGCLVSLLGRAGQLKRAYETIKNMNMDADSVLWSSVLGSCKLHGDFVLGKEIAEYLIG 457

Query:   236 ISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDR 295
             ++    G YVLLSN+Y  +  ++    VR +MK+KG+ K  G S +E+   +H+F+AGDR
Sbjct:   458 LNIKNSGIYVLLSNIYASVGDYEGVAKVRNLMKEKGIVKEPGISTIEIENKVHEFRAGDR 517

Query:   296 SHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKT 355
              H +++ I  +L  + +R KS G++P T  VL D+ E EKE +L  HSE+LA+AYG++ T
Sbjct:   518 EHSKSKEIYTMLRKISERIKSHGYVPNTNTVLQDLEETEKEQSLQVHSERLAIAYGLIST 577

Query:   356 SPGTEIRISKNLRICHDCHSWIKMISXXXXXXXXXXXXXXFHRFEGGLCSCGDYW 410
              PG+ ++I KNLR+C DCH+  K+IS              FH F  G CSCGD+W
Sbjct:   578 KPGSPLKIFKNLRVCSDCHTVTKLISKITGRKIVMRDRNRFHHFTDGSCSCGDFW 632

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0009062 "fatty acid catabolic process" evidence=RCA

TAIR|locus:2081635 AT3G62890 [Arabidopsis thaliana (taxid:3702)]

 Score = 907 (324.3 bits), Expect = 5.7e-91, P = 5.7e-91
 Identities = 178/420 (42%), Positives = 265/420 (63%)

Query:     1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSK-----VEPDKFTFASVIYGCARLG 55
             MP+++V+SW+ +I G+V   ++ EAL  FREM   K     V P++FT ++V+  C RLG
Sbjct:   154 MPERNVISWSCLINGYVMCGKYKEALDLFREMQLPKPNEAFVRPNEFTMSTVLSACGRLG 213

Query:    56 ALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTV-QRNDVSVWNAMI 114
             AL    WVH  I +  +E++ +L  ALIDMY+KCG ++ AK VF+ +  + DV  ++AMI
Sbjct:   214 ALEQGKWVHAYIDKYHVEIDIVLGTALIDMYAKCGSLERAKRVFNALGSKKDVKAYSAMI 273

Query:   115 SGVAIHGLAADASAIFTKMEMF-NVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYS 173
               +A++GL  +   +F++M    N+ P+S+TF+G+L AC H GL+ EG+ YF  M   + 
Sbjct:   274 CCLAMYGLTDECFQLFSEMTTSDNINPNSVTFVGILGACVHRGLINEGKSYFKMMIEEFG 333

Query:   174 IQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAI 233
             I P ++HYG MVDL GR+G I+EA   I SM MEPDV++W +LLS  R    ++  E A+
Sbjct:   334 ITPSIQHYGCMVDLYGRSGLIKEAESFIASMPMEPDVLIWGSLLSGSRMLGDIKTCEGAL 393

Query:   234 ---VNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQF 290
                + +  +  G YVLLSN+Y    RW   + +R  M+ KG+ K  G S++E+ GV+H+F
Sbjct:   394 KRLIELDPMNSGAYVLLSNVYAKTGRWMEVKCIRHEMEVKGINKVPGCSYVEVEGVVHEF 453

Query:   291 KAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAY 350
               GD S  E++ I  +L  ++QR +  G++  T+ VL+D++E++KE  L +HSEKLA+A+
Sbjct:   454 VVGDESQQESERIYAMLDEIMQRLREAGYVTDTKEVLLDLNEKDKEIALSYHSEKLAIAF 513

Query:   351 GILKTSPGTEIRISKNLRICHDCHSWIKMISXXXXXXXXXXXXXXFHRFEGGLCSCGDYW 410
              ++KT PGT +RI KNLRIC DCH  +KMIS              FH F  G CSC D+W
Sbjct:   514 CLMKTRPGTPVRIIKNLRICGDCHLVMKMISKLFSREIVVRDCNRFHHFRDGSCSCRDFW 573

GO:0005739 "mitochondrion" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2025946 CRR28 "CHLORORESPIRATORY REDUCTION28" [Arabidopsis thaliana (taxid:3702)]

 Score = 894 (319.8 bits), Expect = 1.4e-89, P = 1.4e-89
 Identities = 185/428 (43%), Positives = 263/428 (61%)

Query:     1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
             MP++ +VSWNSMI   VR   +D AL+ FREM  S  EPD +T  SV+  CA LG+L+  
Sbjct:   212 MPERSLVSWNSMIDALVRFGEYDSALQLFREMQRS-FEPDGYTMQSVLSACAGLGSLSLG 270

Query:    61 YWVHNLIIEK---KIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGV 117
              W H  ++ K    + ++ ++  +LI+MY KCG ++MA++VF  +Q+ D++ WNAMI G 
Sbjct:   271 TWAHAFLLRKCDVDVAMDVLVKNSLIEMYCKCGSLRMAEQVFQGMQKRDLASWNAMILGF 330

Query:   118 AIHGLAADASAIFTKM--EMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQ 175
             A HG A +A   F +M  +  NV P+S+TF+GLL AC+H G V +GR+YFD M   Y I+
Sbjct:   331 ATHGRAEEAMNFFDRMVDKRENVRPNSVTFVGLLIACNHRGFVNKGRQYFDMMVRDYCIE 390

Query:   176 PQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSAC-RTFKRLELGEVAIV 234
             P LEHYG +VDL+ RAG+I EA  ++ SM M+PD V+WR+LL AC +    +EL E    
Sbjct:   391 PALEHYGCIVDLIARAGYITEAIDMVMSMPMKPDAVIWRSLLDACCKKGASVELSEEIAR 450

Query:   235 NI----------SRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELA 284
             NI          +    G YVLLS +Y    RW+    VR++M + G+RK  G S +E+ 
Sbjct:   451 NIIGTKEDNESSNGNCSGAYVLLSRVYASASRWNDVGIVRKLMSEHGIRKEPGCSSIEIN 510

Query:   285 GVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLP-ATELVLMDVSEE-EKEGNLYHH 342
             G+ H+F AGD SHP+ + I + L  +  R +S G+LP  ++  L+D + +  KE +L  H
Sbjct:   511 GISHEFFAGDTSHPQTKQIYQQLKVIDDRLRSIGYLPDRSQAPLVDATNDGSKEYSLRLH 570

Query:   343 SEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISXXXXXXXXXXXXXXFHRFEGG 402
             SE+LA+A+G++   P T IRI KNLR+C+DCH   K+IS              FH F+ G
Sbjct:   571 SERLAIAFGLINLPPQTPIRIFKNLRVCNDCHEVTKLISKVFNTEIIVRDRVRFHHFKDG 630

Query:   403 LCSCGDYW 410
              CSC DYW
Sbjct:   631 SCSCLDYW 638

GO:0005739 "mitochondrion" evidence=ISM

GO:0004519 "endonuclease activity" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0016556 "mRNA modification" evidence=RCA;IMP

TAIR|locus:2077878 AT3G08820 "AT3G08820" [Arabidopsis thaliana (taxid:3702)]

 Score = 891 (318.7 bits), Expect = 2.8e-89, P = 2.8e-89
 Identities = 176/413 (42%), Positives = 247/413 (59%)

Query:     1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
             M +KD+V+W++MI G+  N+   E +  F +ML   ++PD+F+    +  CA LGAL+  
Sbjct:   273 MVEKDIVTWSTMIQGYASNSFPKEGIELFLQMLQENLKPDQFSIVGFLSSCASLGALDLG 332

Query:    61 YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
              W  +LI   +   N  ++ ALIDMY+KCG +    EVF  ++  D+ + NA ISG+A +
Sbjct:   333 EWGISLIDRHEFLTNLFMANALIDMYAKCGAMARGFEVFKEMKEKDIVIMNAAISGLAKN 392

Query:   121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
             G    + A+F + E   + PD  TFLGLL  C H GL+++G ++F+ +   Y+++  +EH
Sbjct:   393 GHVKLSFAVFGQTEKLGISPDGSTFLGLLCGCVHAGLIQDGLRFFNAISCVYALKRTVEH 452

Query:   181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
             YG MVDL GRAG +++AY LI  M M P+ +VW ALLS CR  K  +L E  +  +  L 
Sbjct:   453 YGCMVDLWGRAGMLDDAYRLICDMPMRPNAIVWGALLSGCRLVKDTQLAETVLKELIALE 512

Query:   241 ---GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSH 297
                 G+YV LSN+Y    RWD A  VR++M KKG++K  G SW+EL G +H+F A D+SH
Sbjct:   513 PWNAGNYVQLSNIYSVGGRWDEAAEVRDMMNKKGMKKIPGYSWIELEGKVHEFLADDKSH 572

Query:   298 PEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSP 357
             P +  I   L  L    +  GF+P TE V  DV EEEKE  L +HSEKLA+A G++ T  
Sbjct:   573 PLSDKIYAKLEDLGNEMRLMGFVPTTEFVFFDVEEEEKERVLGYHSEKLAVALGLISTDH 632

Query:   358 GTEIRISKNLRICHDCHSWIKMISXXXXXXXXXXXXXXFHRFEGGLCSCGDYW 410
             G  IR+ KNLR+C DCH  +K+IS              FH F  G CSC DYW
Sbjct:   633 GQVIRVVKNLRVCGDCHEVMKLISKITRREIVVRDNNRFHCFTNGSCSCNDYW 685

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2056740 OTP85 "ORGANELLE TRANSCRIPT PROCESSING 85" [Arabidopsis thaliana (taxid:3702)]

 Score = 884 (316.2 bits), Expect = 1.6e-88, P = 1.6e-88
 Identities = 172/410 (41%), Positives = 253/410 (61%)

Query:     6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHN 65
             VV +N+MI G+ R  R +EAL  FREM    ++P++ T  SV+  CA LG+L+   W+H 
Sbjct:   195 VVCYNAMITGYARRNRPNEALSLFREMQGKYLKPNEITLLSVLSSCALLGSLDLGKWIHK 254

Query:    66 LIIEKKIELNFI-LSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAA 124
                +K     ++ ++ ALIDM++KCG +  A  +F+ ++  D   W+AMI   A HG A 
Sbjct:   255 YA-KKHSFCKYVKVNTALIDMFAKCGSLDDAVSIFEKMRYKDTQAWSAMIVAYANHGKAE 313

Query:   125 DASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAM 184
              +  +F +M   NV PD ITFLGLL ACSH G VEEGRKYF  M S++ I P ++HYG+M
Sbjct:   314 KSMLMFERMRSENVQPDEITFLGLLNACSHTGRVEEGRKYFSQMVSKFGIVPSIKHYGSM 373

Query:   185 VDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRL---MG 241
             VDLL RAG++E+AY  I  + + P  ++WR LL+AC +   L+L E     I  L    G
Sbjct:   374 VDLLSRAGNLEDAYEFIDKLPISPTPMLWRILLAACSSHNNLDLAEKVSERIFELDDSHG 433

Query:   242 GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQ 301
             GDYV+LSN+Y   K+W+  +++R++MK +   K  G S +E+  V+H+F +GD       
Sbjct:   434 GDYVILSNLYARNKKWEYVDSLRKVMKDRKAVKVPGCSSIEVNNVVHEFFSGDGVKSATT 493

Query:   302 AIDKILGSLIQRTKSEGFLPATELVL-MDVSEEEKEGNLYHHSEKLALAYGILKTSPGTE 360
              + + L  +++  K  G++P T +V+  +++++EKE  L +HSEKLA+ +G+L T PGT 
Sbjct:   494 KLHRALDEMVKELKLSGYVPDTSMVVHANMNDQEKEITLRYHSEKLAITFGLLNTPPGTT 553

Query:   361 IRISKNLRICHDCHSWIKMISXXXXXXXXXXXXXXFHRFEGGLCSCGDYW 410
             IR+ KNLR+C DCH+  K+IS              FH FE G CSCGD+W
Sbjct:   554 IRVVKNLRVCRDCHNAAKLISLIFGRKVVLRDVQRFHHFEDGKCSCGDFW 603

GO:0005739 "mitochondrion" evidence=ISM

GO:0009507 "chloroplast" evidence=IDA

GO:0031425 "chloroplast RNA processing" evidence=IMP

GO:0016556 "mRNA modification" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9FI49	PP428_ARATH	No assigned EC number	0.6503	0.9951	0.7640	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	410
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-120
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	1e-115
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	1e-31
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	7e-30
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	8e-30
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	9e-29
pfam14432	116	pfam14432, DYW_deaminase, DYW family of nucleic ac	2e-21
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-15
pfam13041	50	pfam13041, PPR_2, PPR repeat family	6e-14
PLN03077	857	PLN03077, PLN03077, Protein ECB2; Provisional	3e-12
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	1e-11
PLN03081	697	PLN03081, PLN03081, pentatricopeptide (PPR) repeat	3e-11
PLN03218	1060	PLN03218, PLN03218, maturation of RBCL 1; Provisio	2e-09
TIGR00756	35	TIGR00756, PPR, pentatricopeptide repeat domain (P	2e-07
pfam12854	34	pfam12854, PPR_1, PPR repeat	4e-06
pfam01535	31	pfam01535, PPR, PPR repeat	2e-05
pfam13041	50	pfam13041, PPR_2, PPR repeat family	1e-04
pfam13812	34	pfam13812, PPR_3, Pentatricopeptide repeat domain	0.001

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

 Score =  367 bits (944), Expect = e-120
 Identities = 167/411 (40%), Positives = 244/411 (59%), Gaps = 6/411 (1%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           +P+KDV+SW S+I G   N R  EAL FFR+ML   ++P+  T  + +  CAR+GAL   
Sbjct: 450 IPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCG 508

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
             +H  ++   I  +  L  AL+D+Y +CG++  A   F+     DV  WN +++G   H
Sbjct: 509 KEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFN-SHEKDVVSWNILLTGYVAH 567

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           G  + A  +F +M    V PD +TF+ LL ACS  G+V +G +YF  M  +YSI P L+H
Sbjct: 568 GKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKH 627

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
           Y  +VDLLGRAG + EAY  I  M + PD  VW ALL+ACR  + +ELGE+A  +I  L 
Sbjct: 628 YACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELD 687

Query: 241 GGD---YVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSH 297
                 Y+LL N+Y    +WD    VR+ M++ G+    G SW+E+ G +H F   D SH
Sbjct: 688 PNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESH 747

Query: 298 PEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSP 357
           P+ + I+ +L    ++ K+ G    +E   MD  E  K+     HSE+LA+A+G++ T P
Sbjct: 748 PQIKEINTVLEGFYEKMKASGL-AGSESSSMDEIEVSKDDIFCGHSERLAIAFGLINTVP 806

Query: 358 GTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGD 408
           G  I ++KNL +C +CH+ +K IS+++RR I VRD  +FH F+ G CSCGD
Sbjct: 807 GMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFHHFKDGECSCGD 857

Length = 857

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

 Score =  352 bits (904), Expect = e-115
 Identities = 164/416 (39%), Positives = 250/416 (60%), Gaps = 9/416 (2%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           MP+K  V+WNSM+ G+  +   +EAL  + EM  S V  D+FTF+ +I   +RL  L HA
Sbjct: 285 MPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHA 344

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
              H  +I     L+ + + AL+D+YSK G+++ A+ VFD + R ++  WNA+I+G   H
Sbjct: 345 KQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNH 404

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           G    A  +F +M    V P+ +TFL +L+AC + GL E+G + F  M   + I+P+  H
Sbjct: 405 GRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMH 464

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLM 240
           Y  M++LLGR G ++EAY +I     +P V +W ALL+ACR  K LELG +A     +L 
Sbjct: 465 YACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLA---AEKLY 521

Query: 241 G------GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGD 294
           G       +YV+L N+Y    R   A  V E +K+KG+      +W+E+    H F +GD
Sbjct: 522 GMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGD 581

Query: 295 RSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILK 354
           R HP+++ I + L  L++     G++     +L DV E+E++ +  +HSEKLA+A+G++ 
Sbjct: 582 RLHPQSREIYQKLDELMKEISEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLIN 641

Query: 355 TSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFEGGLCSCGDYW 410
           TS  T ++I+++ RIC DCH  IK I+ + +R I+VRD  RFH F+ G CSCGDYW
Sbjct: 642 TSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFHHFKLGKCSCGDYW 697

Length = 697

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

 Score =  127 bits (320), Expect = 1e-31
 Identities = 75/219 (34%), Positives = 116/219 (52%), Gaps = 6/219 (2%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           M  KD VSW +MI G+ +N   D+AL  +  M    V PD+ T ASV+  CA LG L+  
Sbjct: 349 METKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVG 408

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
             +H L   K +    +++ ALI+MYSKC  I  A EVF  +   DV  W ++I+G+ ++
Sbjct: 409 VKLHELAERKGLISYVVVANALIEMYSKCKCIDKALEVFHNIPEKDVISWTSIIAGLRLN 468

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDH-MRSRYSIQPQLE 179
               +A   F +M +  + P+S+T +  L+AC+  G +  G++   H +R+       L 
Sbjct: 469 NRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLP 527

Query: 180 HYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLS 218
           +  A++DL  R G +  A+    S   E DVV W  LL+
Sbjct: 528 N--ALLDLYVRCGRMNYAWNQFNS--HEKDVVSWNILLT 562

Length = 857

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

 Score =  121 bits (306), Expect = 7e-30
 Identities = 88/315 (27%), Positives = 142/315 (45%), Gaps = 49/315 (15%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           MP++D+ SWN ++GG+ +   FDEAL  +  ML + V PD +TF  V+  C  +  L   
Sbjct: 147 MPERDLFSWNVLVGGYAKAGYFDEALCLYHRMLWAGVRPDVYTFPCVLRTCGGIPDLARG 206

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
             VH  ++    EL+  +  ALI MY KCG +  A+ VFD + R D   WNAMISG   +
Sbjct: 207 REVHAHVVRFGFELDVDVVNALITMYVKCGDVVSARLVFDRMPRRDCISWNAMISGYFEN 266

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDH-MRSRYSIQPQLE 179
           G   +   +F  M   +V PD +T   +++AC   G    GR+   + +++ +++   + 
Sbjct: 267 GECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAV--DVS 324

Query: 180 HYGAMVDLLGRAGHIEEAYGLITSM-----------------------------TME--- 207
              +++ +    G   EA  + + M                              ME   
Sbjct: 325 VCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDN 384

Query: 208 --PDVVVWRALLSACRTFKRLELG----EVAIVNISRLMGGDYVLLSN----MYCYLKRW 257
             PD +   ++LSAC     L++G    E+A      L+   YV+++N    MY   K  
Sbjct: 385 VSPDEITIASVLSACACLGDLDVGVKLHELAER--KGLI--SYVVVANALIEMYSKCKCI 440

Query: 258 DTAENVREIMKKKGV 272
           D A  V   + +K V
Sbjct: 441 DKALEVFHNIPEKDV 455

Length = 857

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

 Score =  121 bits (305), Expect = 8e-30
 Identities = 67/236 (28%), Positives = 118/236 (50%), Gaps = 12/236 (5%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           MP++++ SW ++IGG V    + EA   FREM     + +  TF  ++   A LG+    
Sbjct: 184 MPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAG 243

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
             +H  +++  +  +  +S ALIDMYSKCG I+ A+ VFD +       WN+M++G A+H
Sbjct: 244 QQLHCCVLKTGVVGDTFVSCALIDMYSKCGDIEDARCVFDGMPEKTTVAWNSMLAGYALH 303

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           G + +A  ++ +M    V  D  TF  ++   S   L+E  ++    +  R      +  
Sbjct: 304 GYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGL-IRTGFPLDIVA 362

Query: 181 YGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLS----------ACRTFKRL 226
             A+VDL  + G +E+A  +   M  + +++ W AL++          A   F+R+
Sbjct: 363 NTALVDLYSKWGRMEDARNVFDRMPRK-NLISWNALIAGYGNHGRGTKAVEMFERM 417

Length = 697

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

 Score =  118 bits (297), Expect = 9e-29
 Identities = 67/225 (29%), Positives = 108/225 (48%), Gaps = 10/225 (4%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHA 60
           MP +D +SWN+MI G+  N    E L  F  M    V+PD  T  SVI  C  LG     
Sbjct: 248 MPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLG 307

Query: 61  YWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIH 120
             +H  +++    ++  +  +LI MY   G    A++VF  ++  D   W AMISG   +
Sbjct: 308 REMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKN 367

Query: 121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH 180
           GL   A   +  ME  NV PD IT   +L+AC+  G ++ G K         + +  L  
Sbjct: 368 GLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDVGVKL-----HELAERKGLIS 422

Query: 181 Y----GAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACR 221
           Y     A++++  +   I++A  +  ++  E DV+ W ++++  R
Sbjct: 423 YVVVANALIEMYSKCKCIDKALEVFHNIP-EKDVISWTSIIAGLR 466

Length = 857

>gnl|CDD|222749 pfam14432, DYW_deaminase, DYW family of nucleic acid deaminases

 Score = 88.2 bits (219), Expect = 2e-21
 Identities = 46/120 (38%), Positives = 60/120 (50%), Gaps = 17/120 (14%)

Query: 287 IHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEK-----EGNLYH 341
             +  +GD SHP           L QR K EG +P T+ +  DV  EE      +G L  
Sbjct: 8   GKKTLSGDGSHPT------SKEELFQRIKVEGVVPETKEIGHDVDAEEFRDNGIKGKLLA 61

Query: 342 -HSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFHRFE 400
            H+EK ALAYG+L T       I    R+C DCH + + I++   R IIVRD  RFH F+
Sbjct: 62  SHAEKQALAYGLLTTRI-----IKVLKRMCGDCHEFFRYIAKYTGREIIVRDPSRFHHFK 116

A family of nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members of this family are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. The classical DYW family contain an additional C-terminal metal-binding cluster composed of 2 histidines and a CxC motif and are often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems. Length = 116

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

 Score = 78.0 bits (192), Expect = 2e-15
 Identities = 52/240 (21%), Positives = 111/240 (46%), Gaps = 16/240 (6%)

Query: 5   DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVH 64
           D   + ++I    ++ + D     F EM+++ VE +  TF ++I GCAR G +  A+  +
Sbjct: 471 DCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGALIDGCARAGQVAKAFGAY 530

Query: 65  NLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVF-------DTVQRNDVSVWNAMISGV 117
            ++  K ++ + ++  ALI    + G +  A +V          +  + ++V  A++   
Sbjct: 531 GIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITV-GALMKAC 589

Query: 118 AIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ 177
           A  G    A  ++  +  +N+      +   + +CS  G  +     +D M+ +  ++P 
Sbjct: 590 ANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMK-KKGVKPD 648

Query: 178 LEHYGAMVDLLGRAGHIEEAYGLITSMT---MEPDVVVWRALLSACRTF----KRLELGE 230
              + A+VD+ G AG +++A+ ++       ++   V + +L+ AC       K LEL E
Sbjct: 649 EVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYE 708

Length = 1060

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

 Score = 65.5 bits (161), Expect = 6e-14
 Identities = 16/50 (32%), Positives = 33/50 (66%)

Query: 4  KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCAR 53
           DVV++N++I G+ +  + +EAL+ F EM    ++P+ +T++ +I G  +
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|215561 PLN03077, PLN03077, Protein ECB2; Provisional

 Score = 68.0 bits (166), Expect = 3e-12
 Identities = 69/310 (22%), Positives = 112/310 (36%), Gaps = 57/310 (18%)

Query: 10  NSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIE 69
           NS +     + + ++AL+    M   +V  D+  + ++   C    A+     V +  + 
Sbjct: 55  NSQLRALCSHGQLEQALKLLESMQELRVPVDEDAYVALFRLCEWKRAVEEGSRVCSRALS 114

Query: 70  KKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAI 129
               L   L  A++ M+ + G++  A  VF  +   D+  WN ++ G A  G   +A  +
Sbjct: 115 SHPSLGVRLGNAMLSMFVRFGELVHAWYVFGKMPERDLFSWNVLVGGYAKAGYFDEALCL 174

Query: 130 FTKMEMFNVLPDSITFLGLLTACS-----------------------------------H 154
           + +M    V PD  TF  +L  C                                     
Sbjct: 175 YHRMLWAGVRPDVYTFPCVLRTCGGIPDLARGREVHAHVVRFGFELDVDVVNALITMYVK 234

Query: 155 CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAY---GLITSMTM----- 206
           CG V   R  FD M  R  I      + AM+     +G+ E      GL    TM     
Sbjct: 235 CGDVVSARLVFDRMPRRDCIS-----WNAMI-----SGYFENGECLEGLELFFTMRELSV 284

Query: 207 EPDVVVWRALLSACRTFKRLELG-EVAIVNISRLMGGDYVL---LSNMYCYLKRWDTAEN 262
           +PD++   +++SAC       LG E+    +      D  +   L  MY  L  W  AE 
Sbjct: 285 DPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCNSLIQMYLSLGSWGEAEK 344

Query: 263 VREIMKKKGV 272
           V   M+ K  
Sbjct: 345 VFSRMETKDA 354

Length = 857

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

 Score = 66.4 bits (162), Expect = 1e-11
 Identities = 63/273 (23%), Positives = 116/273 (42%), Gaps = 30/273 (10%)

Query: 22  FDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAA 81
            D ALR  R +  + ++ D   + ++I  CA+ G ++  + V + ++   +E N     A
Sbjct: 453 IDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFGA 512

Query: 82  LIDMYSKCGKIQMAKEVFDTVQRNDVS----VWNAMISGVAIHGLAADASAIFTKM--EM 135
           LID  ++ G++  A   +  ++  +V     V+NA+IS     G    A  +  +M  E 
Sbjct: 513 LIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAET 572

Query: 136 FNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIE 195
             + PD IT   L+ AC++ G V+  ++ +  +   Y+I+   E Y   V+   + G  +
Sbjct: 573 HPIDPDHITVGALMKACANAGQVDRAKEVYQMIH-EYNIKGTPEVYTIAVNSCSQKGDWD 631

Query: 196 EAYGLITSMT---MEPDVVVWRALLSACRTFKRLELG------------EVAIVNISRLM 240
            A  +   M    ++PD V + AL+        L+              ++  V+ S LM
Sbjct: 632 FALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLM 691

Query: 241 GGDYVLLSNMYCYLKRWDTAENVREIMKKKGVR 273
           G             K W  A  + E +K   +R
Sbjct: 692 G--------ACSNAKNWKKALELYEDIKSIKLR 716

Length = 1060

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

 Score = 64.9 bits (158), Expect = 3e-11
 Identities = 66/312 (21%), Positives = 115/312 (36%), Gaps = 48/312 (15%)

Query: 4   KDVVSWNSMIGGFVRNARFDEALRFFREM-LSSKVEPDKFTFASVIYGCARLGALNHAYW 62
           K  VS  S I   V   R  EAL  F  +           T+ +++  C  L ++     
Sbjct: 85  KSGVSLCSQIEKLVACGRHREALELFEILEAGCPFTLPASTYDALVEACIALKSIRCVKA 144

Query: 63  VHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGL 122
           V+  +     E +  +   ++ M+ KCG +  A+ +FD +   +++ W  +I G+   G 
Sbjct: 145 VYWHVESSGFEPDQYMMNRVLLMHVKCGMLIDARRLFDEMPERNLASWGTIIGGLVDAGN 204

Query: 123 AADASAIFTKM---------EMFNVLPDSITFLGLL--------------------TAC- 152
             +A A+F +M           F V+  +   LG                       +C 
Sbjct: 205 YREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSCA 264

Query: 153 -----SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMT-- 205
                S CG +E+ R  FD M  + ++      + +M+      G+ EEA  L   M   
Sbjct: 265 LIDMYSKCGDIEDARCVFDGMPEKTTVA-----WNSMLAGYALHGYSEEALCLYYEMRDS 319

Query: 206 -MEPDVVVWRALLSACRTFKRLELGEVAIVN-ISRLMGGDYV---LLSNMYCYLKRWDTA 260
            +  D   +  ++        LE  + A    I      D V    L ++Y    R + A
Sbjct: 320 GVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANTALVDLYSKWGRMEDA 379

Query: 261 ENVREIMKKKGV 272
            NV + M +K +
Sbjct: 380 RNVFDRMPRKNL 391

Length = 697

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

 Score = 59.1 bits (143), Expect = 2e-09
 Identities = 65/258 (25%), Positives = 104/258 (40%), Gaps = 45/258 (17%)

Query: 24  EALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI 83
           EA RF + + +  +     TF  ++  CA    ++ A  V  L+ E  ++ +  L   LI
Sbjct: 424 EAFRFAKLIRNPTLS----TFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLI 479

Query: 84  DMYSKCGKIQMAKEVFDT-----VQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNV 138
              +K GK+    EVF       V+ N V  + A+I G A  G  A A   +  M   NV
Sbjct: 480 STCAKSGKVDAMFEVFHEMVNAGVEAN-VHTFGALIDGCARAGQVAKAFGAYGIMRSKNV 538

Query: 139 LPDSITFLGLLTACSHCGLVEEGRKYFDHMRSR-YSIQPQLEHYGAMVDLLGRAGHIE-- 195
            PD + F  L++AC   G V+        M++  + I P     GA++     AG ++  
Sbjct: 539 KPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACANAGQVDRA 598

Query: 196 -EAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYL 254
            E Y +I    ++    V+   +++C                     GD           
Sbjct: 599 KEVYQMIHEYNIKGTPEVYTIAVNSCS------------------QKGD----------- 629

Query: 255 KRWDTAENVREIMKKKGV 272
             WD A ++ + MKKKGV
Sbjct: 630 --WDFALSIYDDMKKKGV 645

Length = 1060

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

 Score = 46.7 bits (112), Expect = 2e-07
 Identities = 14/34 (41%), Positives = 22/34 (64%)

Query: 7  VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD 40
          V++N++I G  +  R +EAL  F+EM    +EPD
Sbjct: 1  VTYNTLIDGLCKAGRVEEALELFKEMKERGIEPD 34

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

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

 Score = 42.7 bits (102), Expect = 4e-06
 Identities = 13/28 (46%), Positives = 18/28 (64%)

Query: 5  DVVSWNSMIGGFVRNARFDEALRFFREM 32
          DVV++N++I G  R  R DEA+    EM
Sbjct: 6  DVVTYNTLIDGLCRAGRVDEAVELLDEM 33

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

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

 Score = 40.9 bits (97), Expect = 2e-05
 Identities = 12/31 (38%), Positives = 20/31 (64%)

Query: 7  VSWNSMIGGFVRNARFDEALRFFREMLSSKV 37
          V++NS+I G+ +  + +EAL  F+EM    V
Sbjct: 1  VTYNSLISGYCKAGKLEEALELFKEMKEKGV 31

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

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

 Score = 39.3 bits (93), Expect = 1e-04
 Identities = 12/49 (24%), Positives = 22/49 (44%)

Query: 106 DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSH 154
           DV  +N +I G    G   +A  +F +M+   + P+  T+  L+     
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|205985 pfam13812, PPR_3, Pentatricopeptide repeat domain

 Score = 35.6 bits (83), Expect = 0.001
 Identities = 8/34 (23%), Positives = 18/34 (52%)

Query: 6  VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEP 39
          + ++N+++    +    D AL    EM +S ++P
Sbjct: 1  LETYNALLLALAKAGDPDLALAVLEEMKASGLKP 34

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	410
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03077	857	Protein ECB2; Provisional	100.0
PLN03081	697	pentatricopeptide (PPR) repeat-containing protein;	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PLN03218	1060	maturation of RBCL 1; Provisional	100.0
PF14432	116	DYW_deaminase: DYW family of nucleic acid deaminas	99.96
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.86
PRK11788	389	tetratricopeptide repeat protein; Provisional	99.84
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.8
TIGR02917	899	PEP_TPR_lipo putative PEP-CTERM system TPR-repeat	99.79
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.71
PRK15174	656	Vi polysaccharide export protein VexE; Provisional	99.64
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.59
TIGR00990	615	3a0801s09 mitochondrial precursor proteins import	99.58
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.56
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.52
PF13041	50	PPR_2: PPR repeat family	99.52
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.51
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	99.51
KOG4626	966	consensus O-linked N-acetylglucosamine transferase	99.49
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.46
PF13041	50	PPR_2: PPR repeat family	99.45
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.42
PRK11447	1157	cellulose synthase subunit BcsC; Provisional	99.42
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.41
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.39
PF13429	280	TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2	99.38
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.38
PRK09782	987	bacteriophage N4 receptor, outer membrane subunit;	99.35
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.35
KOG1126	638	consensus DNA-binding cell division cycle control	99.35
PRK10049	765	pgaA outer membrane protein PgaA; Provisional	99.34
PRK10747	398	putative protoheme IX biogenesis protein; Provisio	99.31
TIGR02521	234	type_IV_pilW type IV pilus biogenesis/stability pr	99.29
PRK12370	553	invasion protein regulator; Provisional	99.27
KOG4422	625	consensus Uncharacterized conserved protein [Funct	99.24
TIGR00540	409	hemY_coli hemY protein. This is an uncharacterized	99.21
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.14
KOG2003	840	consensus TPR repeat-containing protein [General f	99.13
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	99.13
PRK14574	822	hmsH outer membrane protein; Provisional	99.13
KOG1840	508	consensus Kinesin light chain [Cytoskeleton]	99.12
KOG1126	638	consensus DNA-binding cell division cycle control	99.12
KOG2076	895	consensus RNA polymerase III transcription factor	99.11
PRK12370	553	invasion protein regulator; Provisional	99.09
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.09
PRK14574	822	hmsH outer membrane protein; Provisional	99.09
KOG1155	559	consensus Anaphase-promoting complex (APC), Cdc23	99.08
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	99.06
PRK11189	296	lipoprotein NlpI; Provisional	98.94
KOG1129	478	consensus TPR repeat-containing protein [General f	98.94
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.93
KOG4318	1088	consensus Bicoid mRNA stability factor [RNA proces	98.92
COG3071	400	HemY Uncharacterized enzyme of heme biosynthesis [	98.91
PRK11189	296	lipoprotein NlpI; Provisional	98.86
KOG0495	913	consensus HAT repeat protein [RNA processing and m	98.86
KOG1129	478	consensus TPR repeat-containing protein [General f	98.84
COG2956	389	Predicted N-acetylglucosaminyl transferase [Carboh	98.82
KOG1915	677	consensus Cell cycle control protein (crooked neck	98.82
PF12854	34	PPR_1: PPR repeat	98.81
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.78
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.78
KOG2076	895	consensus RNA polymerase III transcription factor	98.76
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.73
PF12854	34	PPR_1: PPR repeat	98.71
KOG0495	913	consensus HAT repeat protein [RNA processing and m	98.7
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	98.69
COG3063	250	PilF Tfp pilus assembly protein PilF [Cell motilit	98.68
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.67
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.67
KOG2003	840	consensus TPR repeat-containing protein [General f	98.67
KOG1915	677	consensus Cell cycle control protein (crooked neck	98.63
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.63
PF04733	290	Coatomer_E: Coatomer epsilon subunit; InterPro: IP	98.6
KOG2002	1018	consensus TPR-containing nuclear phosphoprotein th	98.6
cd05804	355	StaR_like StaR_like; a well-conserved protein foun	98.59
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.58
KOG0547	606	consensus Translocase of outer mitochondrial membr	98.57
KOG1173	611	consensus Anaphase-promoting complex (APC), Cdc16	98.5
TIGR00756	35	PPR pentatricopeptide repeat domain (PPR motif). T	98.47
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.46
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.46
KOG4340	459	consensus Uncharacterized conserved protein [Funct	98.44
KOG1070	1710	consensus rRNA processing protein Rrp5 [RNA proces	98.42
KOG1125	579	consensus TPR repeat-containing protein [General f	98.41
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	98.36
PF13812	34	PPR_3: Pentatricopeptide repeat domain	98.32
TIGR03302	235	OM_YfiO outer membrane assembly lipoprotein YfiO.	98.27
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	98.26
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.25
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.25
PF12569	517	NARP1: NMDA receptor-regulated protein 1 ; InterPr	98.24
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.23
PLN02789	320	farnesyltranstransferase	98.2
KOG1125	579	consensus TPR repeat-containing protein [General f	98.18
PLN02789	320	farnesyltranstransferase	98.18
PRK10370	198	formate-dependent nitrite reductase complex subuni	98.17
PRK15359	144	type III secretion system chaperone protein SscB;	98.16
COG4783	484	Putative Zn-dependent protease, contains TPR repea	98.13
PF01535	31	PPR: PPR repeat; InterPro: IPR002885 This entry re	98.11
PRK04841	903	transcriptional regulator MalT; Provisional	98.11
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	98.1
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.1
PRK15359	144	type III secretion system chaperone protein SscB;	98.09
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	98.08
COG5010	257	TadD Flp pilus assembly protein TadD, contains TPR	98.08
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	98.07
TIGR02552	135	LcrH_SycD type III secretion low calcium response	98.05
KOG3785	557	consensus Uncharacterized conserved protein [Funct	98.05
KOG3616	1636	consensus Selective LIM binding factor [Transcript	98.01
KOG1128	777	consensus Uncharacterized conserved protein, conta	98.01
KOG2047	835	consensus mRNA splicing factor [RNA processing and	98.01
KOG3616	1636	consensus Selective LIM binding factor [Transcript	97.99
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.96
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.96
KOG1174	564	consensus Anaphase-promoting complex (APC), subuni	97.93
PRK04841	903	transcriptional regulator MalT; Provisional	97.93
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.91
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.91
TIGR02552	135	LcrH_SycD type III secretion low calcium response	97.87
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	97.83
PF09976	145	TPR_21: Tetratricopeptide repeat; InterPro: IPR018	97.82
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	97.81
COG4783	484	Putative Zn-dependent protease, contains TPR repea	97.77
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.77
PRK15179	694	Vi polysaccharide biosynthesis protein TviE; Provi	97.76
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.76
KOG2047	835	consensus mRNA splicing factor [RNA processing and	97.75
PF09295	395	ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); Inter	97.71
KOG0985	1666	consensus Vesicle coat protein clathrin, heavy cha	97.71
KOG1156	700	consensus N-terminal acetyltransferase [Chromatin	97.69
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	97.68
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.67
KOG3081	299	consensus Vesicle coat complex COPI, epsilon subun	97.64
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.6
PF08579	120	RPM2: Mitochondrial ribonuclease P subunit (RPM2);	97.59
PRK14720	906	transcript cleavage factor/unknown domain fusion p	97.58
cd00189	100	TPR Tetratricopeptide repeat domain; typically con	97.54
KOG2376	652	consensus Signal recognition particle, subunit Srp	97.51
PF05843	280	Suf: Suppressor of forked protein (Suf); InterPro:	97.49
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.49
PF12688	120	TPR_5: Tetratrico peptide repeat	97.48
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.47
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.47
KOG0624	504	consensus dsRNA-activated protein kinase inhibitor	97.44
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	97.43
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.42
KOG4340	459	consensus Uncharacterized conserved protein [Funct	97.4
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.4
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.39
KOG2376	652	consensus Signal recognition particle, subunit Srp	97.37
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.35
PF12895	84	Apc3: Anaphase-promoting complex, cyclosome, subun	97.35
PF10037	429	MRP-S27: Mitochondrial 28S ribosomal protein S27;	97.34
KOG3060	289	consensus Uncharacterized conserved protein [Funct	97.32
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.31
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.3
PF06239	228	ECSIT: Evolutionarily conserved signalling interme	97.25
TIGR02795	119	tol_pal_ybgF tol-pal system protein YbgF. Members	97.24
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.24
PRK15363	157	pathogenicity island 2 chaperone protein SscA; Pro	97.21
KOG3617	1416	consensus WD40 and TPR repeat-containing protein [	97.2
KOG3785	557	consensus Uncharacterized conserved protein [Funct	97.19
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	97.14
PLN03088	356	SGT1, suppressor of G2 allele of SKP1; Provisional	97.12
PF12688	120	TPR_5: Tetratrico peptide repeat	97.11
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	97.11
PRK02603	172	photosystem I assembly protein Ycf3; Provisional	97.11
PRK10153	517	DNA-binding transcriptional activator CadC; Provis	97.07
KOG1914	656	consensus mRNA cleavage and polyadenylation factor	97.07
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	97.04
CHL00033	168	ycf3 photosystem I assembly protein Ycf3	97.01
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	96.95
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.94
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.91
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.89
KOG0553	304	consensus TPR repeat-containing protein [General f	96.87
PF14559	68	TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN	96.86
PF04840	319	Vps16_C: Vps16, C-terminal region; InterPro: IPR00	96.84
PF12921	126	ATP13: Mitochondrial ATPase expression; InterPro:	96.8
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.77
KOG2053	932	consensus Mitochondrial inheritance and actin cyto	96.75
PF14938	282	SNAP: Soluble NSF attachment protein, SNAP; PDB: 1	96.71
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	96.68
KOG4162	799	consensus Predicted calmodulin-binding protein [Si	96.66
KOG2796	366	consensus Uncharacterized conserved protein [Funct	96.65
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	96.62
COG4700	251	Uncharacterized protein conserved in bacteria cont	96.6
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.58
KOG1127	1238	consensus TPR repeat-containing protein [RNA proce	96.55
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.5
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	96.49
KOG0553	304	consensus TPR repeat-containing protein [General f	96.42
KOG0548	539	consensus Molecular co-chaperone STI1 [Posttransla	96.38
PF13414	69	TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A	96.37
COG3898	531	Uncharacterized membrane-bound protein [Function u	96.36
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	96.32
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	96.3
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.25
PF13432	65	TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL	96.25
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	96.22
PF03704	146	BTAD: Bacterial transcriptional activator domain;	96.17
PRK10803	263	tol-pal system protein YbgF; Provisional	96.17
PRK10803	263	tol-pal system protein YbgF; Provisional	96.12
KOG3941	406	consensus Intermediate in Toll signal transduction	96.11
KOG2041	1189	consensus WD40 repeat protein [General function pr	96.01
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.91
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	95.9
KOG1538	1081	consensus Uncharacterized conserved protein WDR10,	95.82
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.78
PF13424	78	TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15	95.74
COG4235	287	Cytochrome c biogenesis factor [Posttranslational	95.67
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	95.63
PF13371	73	TPR_9: Tetratricopeptide repeat	95.62
smart00299	140	CLH Clathrin heavy chain repeat homology.	95.59
COG4700	251	Uncharacterized protein conserved in bacteria cont	95.51
PRK15331	165	chaperone protein SicA; Provisional	95.29
KOG3941	406	consensus Intermediate in Toll signal transduction	95.28
KOG0550	486	consensus Molecular chaperone (DnaJ superfamily) [	95.24
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	95.24
PF13371	73	TPR_9: Tetratricopeptide repeat	95.2
COG3898	531	Uncharacterized membrane-bound protein [Function u	95.08
PLN03098	453	LPA1 LOW PSII ACCUMULATION1; Provisional	94.99
PRK15331	165	chaperone protein SicA; Provisional	94.86
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	94.43
PRK10866	243	outer membrane biogenesis protein BamD; Provisiona	94.32
KOG2610	491	consensus Uncharacterized conserved protein [Funct	94.28
COG5107	660	RNA14 Pre-mRNA 3'-end processing (cleavage and pol	94.22
KOG4555	175	consensus TPR repeat-containing protein [Function	94.2
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	94.1
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	94.03
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	93.98
COG3118	304	Thioredoxin domain-containing protein [Posttransla	93.73
PF10300	468	DUF3808: Protein of unknown function (DUF3808); In	93.65
KOG2610	491	consensus Uncharacterized conserved protein [Funct	93.52
PF04053	443	Coatomer_WDAD: Coatomer WD associated region ; Int	93.4
PF09205	161	DUF1955: Domain of unknown function (DUF1955); Int	93.39
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	93.35
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	93.33
PF13281	374	DUF4071: Domain of unknown function (DUF4071)	93.12
PF13431	34	TPR_17: Tetratricopeptide repeat	93.09
PF13512	142	TPR_18: Tetratricopeptide repeat	92.86
PF13170	297	DUF4003: Protein of unknown function (DUF4003)	92.85
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	92.84
COG3629	280	DnrI DNA-binding transcriptional activator of the	92.83
COG0457	291	NrfG FOG: TPR repeat [General function prediction	92.68
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	92.54
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	92.42
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	92.18
COG1729	262	Uncharacterized protein conserved in bacteria [Fun	91.98
COG1747	711	Uncharacterized N-terminal domain of the transcrip	91.77
PF10602	177	RPN7: 26S proteasome subunit RPN7; InterPro: IPR01	91.63
PF13428	44	TPR_14: Tetratricopeptide repeat	91.41
COG4649	221	Uncharacterized protein conserved in bacteria [Fun	91.2
COG4105	254	ComL DNA uptake lipoprotein [General function pred	91.0
PF13176	36	TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_	90.46
KOG1941	518	consensus Acetylcholine receptor-associated protei	90.07
PF08631	278	SPO22: Meiosis protein SPO22/ZIP4 like; InterPro:	89.93
PF13525	203	YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M	89.89
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	89.79
PF13428	44	TPR_14: Tetratricopeptide repeat	89.66
TIGR02508	115	type_III_yscG type III secretion protein, YscG fam	89.61
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	89.44
KOG4555	175	consensus TPR repeat-containing protein [Function	89.37
KOG0543	397	consensus FKBP-type peptidyl-prolyl cis-trans isom	89.32
KOG2114	933	consensus Vacuolar assembly/sorting protein PEP5/V	89.16
PF13431	34	TPR_17: Tetratricopeptide repeat	89.11
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	88.76
TIGR02561	153	HrpB1_HrpK type III secretion protein HrpB1/HrpK.	88.62
KOG2280	829	consensus Vacuolar assembly/sorting protein VPS16	88.59
COG0457	291	NrfG FOG: TPR repeat [General function prediction	88.52
COG3629	280	DnrI DNA-binding transcriptional activator of the	88.43
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	88.33
KOG1585	308	consensus Protein required for fusion of vesicles	88.03
COG3118	304	Thioredoxin domain-containing protein [Posttransla	87.88
KOG1920	1265	consensus IkappaB kinase complex, IKAP component [	87.86
PF11207	203	DUF2989: Protein of unknown function (DUF2989); In	87.78
KOG4570	418	consensus Uncharacterized conserved protein [Funct	87.59
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	87.42
cd00923	103	Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va.	86.72
PF00515	34	TPR_1: Tetratricopeptide repeat; InterPro: IPR0014	86.57
PF02259	352	FAT: FAT domain; InterPro: IPR003151 The FAT domai	86.46
PRK11906	458	transcriptional regulator; Provisional	85.78
PF04184	539	ST7: ST7 protein; InterPro: IPR007311 The ST7 (for	85.64
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	85.12
PRK11906	458	transcriptional regulator; Provisional	85.05
PF13929	292	mRNA_stabil: mRNA stabilisation	84.77
PF09613	160	HrpB1_HrpK: Bacterial type III secretion protein (	84.52
PF00637	143	Clathrin: Region in Clathrin and VPS; InterPro: IP	84.45
PF13374	42	TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT	83.95
PF07719	34	TPR_2: Tetratricopeptide repeat; InterPro: IPR0131	82.82
KOG2297	412	consensus Predicted translation factor, contains W	82.5
PF07035	167	Mic1: Colon cancer-associated protein Mic1-like; I	82.41
COG4785	297	NlpI Lipoprotein NlpI, contains TPR repeats [Gener	82.15
KOG1941	518	consensus Acetylcholine receptor-associated protei	81.35
KOG1130	639	consensus Predicted G-alpha GTPase interaction pro	80.77
PF02284	108	COX5A: Cytochrome c oxidase subunit Va; InterPro:	80.45
PF07079	549	DUF1347: Protein of unknown function (DUF1347); In	80.33
COG4105	254	ComL DNA uptake lipoprotein [General function pred	80.21

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

Probab=100.00  E-value=3.7e-97  Score=751.51  Aligned_cols=410  Identities=40%  Similarity=0.705  Sum_probs=403.8

Q ss_pred             CCCCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHH
Q 040371            1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSA   80 (410)
Q Consensus         1 ~~~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (410)
                      |+.||+++||+||.+|+++|++++|+++|++|.+.|+.||..||++++++|++.|+++.|.++|+.|.+.|++||..++|
T Consensus       285 m~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~pd~~t~~~ll~a~~~~g~~~~a~~i~~~m~~~g~~~d~~~~~  364 (697)
T PLN03081        285 MPEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVSIDQFTFSIMIRIFSRLALLEHAKQAHAGLIRTGFPLDIVANT  364 (697)
T ss_pred             CCCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCCCeeehH
Confidence            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      +||++|+|+|++++|.++|++|.++|+++||+||.+|+++|+.++|+++|++|.+.|+.||.+||++++.+|++.|.+++
T Consensus       365 ~Li~~y~k~G~~~~A~~vf~~m~~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~~~~  444 (697)
T PLN03081        365 ALVDLYSKWGRMEDARNVFDRMPRKNLISWNALIAGYGNHGRGTKAVEMFERMIAEGVAPNHVTFLAVLSACRYSGLSEQ  444 (697)
T ss_pred             HHHHHHHHCCCHHHHHHHHHhCCCCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhcCCcHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhc
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVA---IVNIS  237 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~  237 (410)
                      |.++|+.|.+++|+.|+..+|++||++|+++|++++|.+++++|++.|+..+|++||.+|+.+|+++.|+.+   +.++.
T Consensus       445 a~~~f~~m~~~~g~~p~~~~y~~li~~l~r~G~~~eA~~~~~~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~  524 (697)
T PLN03081        445 GWEIFQSMSENHRIKPRAMHYACMIELLGREGLLDEAYAMIRRAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMG  524 (697)
T ss_pred             HHHHHHHHHHhcCCCCCccchHhHHHHHHhcCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCC
Confidence            999999999878999999999999999999999999999999999999999999999999999999999998   55677


Q ss_pred             cCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHHHC
Q 040371          238 RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSE  317 (410)
Q Consensus       238 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~  317 (410)
                      |.+..+|..|+++|++.|+|++|.+++++|+++|+++.|++||+++++.+|.|++|+..|++.+++++.++++..+|++.
T Consensus       525 p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g~~k~~g~s~i~~~~~~~~f~~~d~~h~~~~~i~~~l~~l~~~~~~~  604 (697)
T PLN03081        525 PEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEISEY  604 (697)
T ss_pred             CCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHcCCccCCCeeEEEECCeEEEEccCCCCCccHHHHHHHHHHHHHHHHHc
Confidence            88889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcccCCccccccCChHHHhhhhhhhhHHHHHHHHhcCCCCCCcEEEEcccccccchhhHHHHHhhhhCceEEEecCCccc
Q 040371          318 GFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFH  397 (410)
Q Consensus       318 g~~pd~~~~~~~~~~~~~~~~l~~~~e~la~~~~~~~~~~~~~~~~~~n~~~c~~~~~~~~~~~~~~~~~i~~~~~~~~h  397 (410)
                      ||.||+.++++++++++|+..+.+|||+||+||||+++|+++||||+||||+|+|||+++|+||++.+|+|||||.+|||
T Consensus       605 gy~~~~~~~~~~~~~~~~~~~~~~hsekla~a~~l~~~~~~~~i~i~knlr~c~dch~~~k~~s~~~~r~i~~rd~~rfh  684 (697)
T PLN03081        605 GYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSHRICKDCHKVIKFIALVTKREIVVRDASRFH  684 (697)
T ss_pred             CCCCCcchhhccccHHHHHHHHHhccHHHHHHhhCccCCCCCeEEEecCCEECCCchhhHHHHhhhcceEEEEecCCccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCccCCCCCC
Q 040371          398 RFEGGLCSCGDYW  410 (410)
Q Consensus       398 ~~~~g~~sc~~~~  410 (410)
                      ||++|+|||+|||
T Consensus       685 ~f~~g~csc~d~w  697 (697)
T PLN03081        685 HFKLGKCSCGDYW  697 (697)
T ss_pred             cCCCCcccccccC
Confidence            9999999999999

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=9.9e-91  Score=720.11  Aligned_cols=405  Identities=41%  Similarity=0.789  Sum_probs=396.1

Q ss_pred             CCCCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHH
Q 040371            1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSA   80 (410)
Q Consensus         1 ~~~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (410)
                      |++||+++||+||.+|.++|+.++|+++|++|.. +++||..||++++.+|++.|+++.+.++|..+.+.|+.+|..++|
T Consensus       450 m~~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~-~~~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~n  528 (857)
T PLN03077        450 IPEKDVISWTSIIAGLRLNNRCFEALIFFRQMLL-TLKPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPN  528 (857)
T ss_pred             CCCCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHh-CCCCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceech
Confidence            6789999999999999999999999999999986 599999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      +||++|+|+|++++|.++|+++ .+|+++||+||.+|+++|+.++|+++|++|.+.|+.||.+||+++|.+|++.|++++
T Consensus       529 aLi~~y~k~G~~~~A~~~f~~~-~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T~~~ll~a~~~~g~v~e  607 (857)
T PLN03077        529 ALLDLYVRCGRMNYAWNQFNSH-EKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVTFISLLCACSRSGMVTQ  607 (857)
T ss_pred             HHHHHHHHcCCHHHHHHHHHhc-CCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhhcChHHH
Confidence            9999999999999999999999 999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhc
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVA---IVNIS  237 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~  237 (410)
                      |.++|+.|.+++|+.|+..+|++|+++|+++|++++|.+++++|+++||..+|++|+.+|..+|+.+.|+.+   +.+++
T Consensus       608 a~~~f~~M~~~~gi~P~~~~y~~lv~~l~r~G~~~eA~~~~~~m~~~pd~~~~~aLl~ac~~~~~~e~~e~~a~~l~~l~  687 (857)
T PLN03077        608 GLEYFHSMEEKYSITPNLKHYACVVDLLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELGELAAQHIFELD  687 (857)
T ss_pred             HHHHHHHHHHHhCCCCchHHHHHHHHHHHhCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhhC
Confidence            999999999778999999999999999999999999999999999999999999999999999999999888   67889


Q ss_pred             cCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHHHC
Q 040371          238 RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSE  317 (410)
Q Consensus       238 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~  317 (410)
                      |.+...|..|.++|++.|+|++|.++++.|+++|++++||+||+++++.+|.|.+++.+||+.++|++.++++..+|++.
T Consensus       688 p~~~~~y~ll~n~ya~~g~~~~a~~vr~~M~~~g~~k~~g~s~ie~~~~~~~f~~~d~~h~~~~~i~~~l~~l~~~~~~~  767 (857)
T PLN03077        688 PNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKMKAS  767 (857)
T ss_pred             CCCcchHHHHHHHHHHCCChHHHHHHHHHHHHcCCCCCCCccEEEECCEEEEEecCCCCCcchHHHHHHHHHHHHHHHhC
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CcccCCccccccCChHHHhhhhhhhhHHHHHHHHhcCCCCCCcEEEEcccccccchhhHHHHHhhhhCceEEEecCCccc
Q 040371          318 GFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRDRIRFH  397 (410)
Q Consensus       318 g~~pd~~~~~~~~~~~~~~~~l~~~~e~la~~~~~~~~~~~~~~~~~~n~~~c~~~~~~~~~~~~~~~~~i~~~~~~~~h  397 (410)
                      ||.||+..++ ++++++|+..+.+|||+||+||||+++|+++||||+||||+|+|||+++|+||++.+|+|||||.+|||
T Consensus       768 g~~~~~~~~~-~~~~~~k~~~~~~hse~la~a~~l~~~~~~~~i~i~knlr~c~dch~~~k~~s~~~~r~i~~rd~~rfh  846 (857)
T PLN03077        768 GLAGSESSSM-DEIEVSKDDIFCGHSERLAIAFGLINTVPGMPIWVTKNLYMCENCHNTVKFISKIVRREISVRDTEQFH  846 (857)
T ss_pred             CcCCCcchhc-cccHHHHHHHHHhccHHHHHHHhhhcCCCCCeEEEeCCCEeCccHHHHHHHHHHHhCeEEEEecCCcce
Confidence            9999999877 557788999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCccCCCC
Q 040371          398 RFEGGLCSCGD  408 (410)
Q Consensus       398 ~~~~g~~sc~~  408 (410)
                      ||++|+|||+|
T Consensus       847 ~f~~g~csc~d  857 (857)
T PLN03077        847 HFKDGECSCGD  857 (857)
T ss_pred             eCCCCcccCCC
Confidence            99999999998

>PLN03077 Protein ECB2; Provisional

Probab=100.00  E-value=9.6e-54  Score=443.87  Aligned_cols=388  Identities=21%  Similarity=0.327  Sum_probs=330.9

Q ss_pred             CCCCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHH
Q 040371            1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSA   80 (410)
Q Consensus         1 ~~~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (410)
                      |++||+++||+||.+|+++|++++|+++|++|...|+.||..||++++.+|++.|+++.|.++|..|.+.|+.||..+||
T Consensus       248 m~~~d~~s~n~li~~~~~~g~~~eAl~lf~~M~~~g~~Pd~~ty~~ll~a~~~~g~~~~a~~l~~~~~~~g~~~d~~~~n  327 (857)
T PLN03077        248 MPRRDCISWNAMISGYFENGECLEGLELFFTMRELSVDPDLMTITSVISACELLGDERLGREMHGYVVKTGFAVDVSVCN  327 (857)
T ss_pred             CCCCCcchhHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCChhHHHHHHHHHHhcCChHHHHHHHHHHHHhCCccchHHHH
Confidence            68899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      +|+++|+++|++++|.++|++|..||+++||+||.+|++.|++++|+++|++|.+.|+.||..||++++.+|++.|++++
T Consensus       328 ~Li~~y~k~g~~~~A~~vf~~m~~~d~~s~n~li~~~~~~g~~~~A~~lf~~M~~~g~~Pd~~t~~~ll~a~~~~g~~~~  407 (857)
T PLN03077        328 SLIQMYLSLGSWGEAEKVFSRMETKDAVSWTAMISGYEKNGLPDKALETYALMEQDNVSPDEITIASVLSACACLGDLDV  407 (857)
T ss_pred             HHHHHHHhcCCHHHHHHHHhhCCCCCeeeHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCceeHHHHHHHHhccchHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhc---
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNIS---  237 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~---  237 (410)
                      |.++++.|.+. |+.|+..+|++||++|+++|++++|.++|++|. +||..+|+++|.+|.+.|+.++|..++.++.   
T Consensus       408 a~~l~~~~~~~-g~~~~~~~~n~Li~~y~k~g~~~~A~~vf~~m~-~~d~vs~~~mi~~~~~~g~~~eA~~lf~~m~~~~  485 (857)
T PLN03077        408 GVKLHELAERK-GLISYVVVANALIEMYSKCKCIDKALEVFHNIP-EKDVISWTSIIAGLRLNNRCFEALIFFRQMLLTL  485 (857)
T ss_pred             HHHHHHHHHHh-CCCcchHHHHHHHHHHHHcCCHHHHHHHHHhCC-CCCeeeHHHHHHHHHHCCCHHHHHHHHHHHHhCC
Confidence            99999999975 999999999999999999999999999999995 5788999999999999999999988854443   


Q ss_pred             cCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCc-----------------------------eeEEEECCEEE
Q 040371          238 RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQG-----------------------------KSWLELAGVIH  288 (410)
Q Consensus       238 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~-----------------------------~s~~~~~~~~~  288 (410)
                      ++|..+|..++.+|++.|.++.+.+++..|.+.|+.++..                             .+|.       
T Consensus       486 ~pd~~t~~~lL~a~~~~g~l~~~~~i~~~~~~~g~~~~~~~~naLi~~y~k~G~~~~A~~~f~~~~~d~~s~n-------  558 (857)
T PLN03077        486 KPNSVTLIAALSACARIGALMCGKEIHAHVLRTGIGFDGFLPNALLDLYVRCGRMNYAWNQFNSHEKDVVSWN-------  558 (857)
T ss_pred             CCCHhHHHHHHHHHhhhchHHHhHHHHHHHHHhCCCccceechHHHHHHHHcCCHHHHHHHHHhcCCChhhHH-------
Confidence            4555666666655555555555555555555555543321                             2342       


Q ss_pred             EEEeCCCCCccHHHHHHHHHHHHHHHHHCCcccCCccccccCChHHHhhhh---hhhhHHHHHHHHhcCCCCCCcEEEEc
Q 040371          289 QFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNL---YHHSEKLALAYGILKTSPGTEIRISK  365 (410)
Q Consensus       289 ~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~~~~~~~~~~~~l---~~~~e~la~~~~~~~~~~~~~~~~~~  365 (410)
                      .++.++..+|+.++|.++|+    +|.+.|+.||..++...+..+.+.+.+   ...++.+...+|+.++..... ++++
T Consensus       559 ~lI~~~~~~G~~~~A~~lf~----~M~~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~-~lv~  633 (857)
T PLN03077        559 ILLTGYVAHGKGSMAVELFN----RMVESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYA-CVVD  633 (857)
T ss_pred             HHHHHHHHcCCHHHHHHHHH----HHHHcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHH-HHHH
Confidence            26788889999999999988    889999999999998888888766654   334556655677766655544 5788


Q ss_pred             ccccccchhhHHHHHhhhhCc------eEEEecCCccccccCC
Q 040371          366 NLRICHDCHSWIKMISRLLRR------VIIVRDRIRFHRFEGG  402 (410)
Q Consensus       366 n~~~c~~~~~~~~~~~~~~~~------~i~~~~~~~~h~~~~g  402 (410)
                      .+.++|+.++|.++|.+|+.+      ..++..|+.+.+.+.|
T Consensus       634 ~l~r~G~~~eA~~~~~~m~~~pd~~~~~aLl~ac~~~~~~e~~  676 (857)
T PLN03077        634 LLGRAGKLTEAYNFINKMPITPDPAVWGALLNACRIHRHVELG  676 (857)
T ss_pred             HHHhCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHcCChHHH
Confidence            899999999999999999643      2334445444444433

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

Probab=100.00  E-value=6.9e-52  Score=420.61  Aligned_cols=386  Identities=20%  Similarity=0.304  Sum_probs=333.8

Q ss_pred             CCCCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHH
Q 040371            1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSA   80 (410)
Q Consensus         1 ~~~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (410)
                      |++||+++||+||.+|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|+++.+.++|..+.+.|+.||..++|
T Consensus       184 m~~~~~~t~n~li~~~~~~g~~~~A~~lf~~M~~~g~~p~~~t~~~ll~a~~~~~~~~~~~~l~~~~~~~g~~~d~~~~n  263 (697)
T PLN03081        184 MPERNLASWGTIIGGLVDAGNYREAFALFREMWEDGSDAEPRTFVVMLRASAGLGSARAGQQLHCCVLKTGVVGDTFVSC  263 (697)
T ss_pred             CCCCCeeeHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCChhhHHHHHHHHhcCCcHHHHHHHHHHHHHhCCCccceeHH
Confidence            68899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      +||++|+++|++++|.++|++|+.+|+++||+||.+|++.|+.++|+++|++|.+.|+.||..||++++.+|++.|.+++
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            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhc---
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNIS---  237 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~---  237 (410)
                      |.+++..|.+. |+.||..+|++||++|+++|++++|.++|++|. +||..+|++||.+|+++|+.++|.+++.++.   
T Consensus       344 a~~i~~~m~~~-g~~~d~~~~~~Li~~y~k~G~~~~A~~vf~~m~-~~d~~t~n~lI~~y~~~G~~~~A~~lf~~M~~~g  421 (697)
T PLN03081        344 AKQAHAGLIRT-GFPLDIVANTALVDLYSKWGRMEDARNVFDRMP-RKNLISWNALIAGYGNHGRGTKAVEMFERMIAEG  421 (697)
T ss_pred             HHHHHHHHHHh-CCCCCeeehHHHHHHHHHCCCHHHHHHHHHhCC-CCCeeeHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            99999999975 999999999999999999999999999999995 6899999999999999999999999966543   


Q ss_pred             -cCCCchHHHHHHHHHhcCChhHHHHHHHHHHh-CCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHH
Q 040371          238 -RLMGGDYVLLSNMYCYLKRWDTAENVREIMKK-KGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTK  315 (410)
Q Consensus       238 -~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~-~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~  315 (410)
                       .+|..+|..++.+|++.|++++|.++|+.|.+ .|+.|+....        ..++.++...|+.++|+++++       
T Consensus       422 ~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y--------~~li~~l~r~G~~~eA~~~~~-------  486 (697)
T PLN03081        422 VAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHY--------ACMIELLGREGLLDEAYAMIR-------  486 (697)
T ss_pred             CCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccch--------HhHHHHHHhcCCHHHHHHHHH-------
Confidence             56778999999999999999999999999976 5888765322        225677888999999998876       


Q ss_pred             HCCcccCCccccccCChHHHhhhhhhhhHHHHHHHHhcCCCCCCcEEEEcccccccchhhHHHHHhhhhCceEEEec---
Q 040371          316 SEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIRISKNLRICHDCHSWIKMISRLLRRVIIVRD---  392 (410)
Q Consensus       316 ~~g~~pd~~~~~~~~~~~~~~~~l~~~~e~la~~~~~~~~~~~~~~~~~~n~~~c~~~~~~~~~~~~~~~~~i~~~~---  392 (410)
                      +.++.||..++...+..+.+.+.+..-.+-....+++.+.....-+.+++-+..+|+..+|.+++.+|..+.+-...   
T Consensus       487 ~~~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~~~p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g~~k~~g~s  566 (697)
T PLN03081        487 RAPFKPTVNMWAALLTACRIHKNLELGRLAAEKLYGMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACT  566 (697)
T ss_pred             HCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhCCCCCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHcCCccCCCee
Confidence            35788998877666666655554322111111223443333333345666789999999999999999888653221   


Q ss_pred             ----CCccccccCCc
Q 040371          393 ----RIRFHRFEGGL  403 (410)
Q Consensus       393 ----~~~~h~~~~g~  403 (410)
                          .+..|.|-.|-
T Consensus       567 ~i~~~~~~~~f~~~d  581 (697)
T PLN03081        567 WIEVKKQDHSFFSGD  581 (697)
T ss_pred             EEEECCeEEEEccCC
Confidence                23456665553

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=7.4e-49  Score=402.79  Aligned_cols=324  Identities=20%  Similarity=0.310  Sum_probs=297.2

Q ss_pred             CCCCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHH
Q 040371            1 MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSA   80 (410)
Q Consensus         1 ~~~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (410)
                      |+.||..+||.+|.+|++.|++++|.++|++|.+.|+.||..+|++++.+|++.|+++.|.++|+.|.+.|+.||..+|+
T Consensus       432 M~~pd~~Tyn~LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~~tynsLI~~y~k~G~vd~A~~vf~eM~~~Gv~PdvvTyn  511 (1060)
T PLN03218        432 IRNPTLSTFNMLMSVCASSQDIDGALRVLRLVQEAGLKADCKLYTTLISTCAKSGKVDAMFEVFHEMVNAGVEANVHTFG  511 (1060)
T ss_pred             cCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCcCHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            56799999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcc----cCChhhHHHHHHHHHHcCChHHHHHHHHHHHH--CCCCCCHHHHHHHHHHHHc
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQ----RNDVSVWNAMISGVAIHGLAADASAIFTKMEM--FNVLPDSITFLGLLTACSH  154 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~--~g~~p~~~t~~~ll~a~~~  154 (410)
                      +||++|++.|++++|.++|++|.    .||..+||+||.+|++.|++++|.++|++|..  .|+.||.+||++++.+|++
T Consensus       512 aLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTynaLI~ay~k  591 (1060)
T PLN03218        512 ALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVGALMKACAN  591 (1060)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHH
Confidence            99999999999999999999996    47999999999999999999999999999986  5789999999999999999


Q ss_pred             cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC---CCCCCHHHHHHHHHHHHhcCchhHHHH
Q 040371          155 CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM---TMEPDVVVWRALLSACRTFKRLELGEV  231 (410)
Q Consensus       155 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m---~~~p~~~~~~~li~~~~~~g~~~~a~~  231 (410)
                      .|++++|.++|+.|.+. |+.|+..+|+.+|.+|++.|++++|.++|++|   ++.||..+|+++|.+|++.|++++|.+
T Consensus       592 ~G~ldeA~elf~~M~e~-gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G~~eeA~~  670 (1060)
T PLN03218        592 AGQVDRAKEVYQMIHEY-NIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAGDLDKAFE  670 (1060)
T ss_pred             CCCHHHHHHHHHHHHHc-CCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHH
Confidence            99999999999999975 99999999999999999999999999999999   688999999999999999999999999


Q ss_pred             HHHhhc----cCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHH
Q 040371          232 AIVNIS----RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKIL  307 (410)
Q Consensus       232 ~~~~~~----~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l  307 (410)
                      ++.++.    +++..+|+.|+.+|++.|++++|.++|++|.+.|+.|+. .+|.       .++.++...|+.++|.++|
T Consensus       671 l~~eM~k~G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~Pdv-vtyN-------~LI~gy~k~G~~eeAlelf  742 (1060)
T PLN03218        671 ILQDARKQGIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTV-STMN-------ALITALCEGNQLPKALEVL  742 (1060)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCH-HHHH-------HHHHHHHHCCCHHHHHHHH
Confidence            955443    466789999999999999999999999999999998875 3342       2678889999999999998


Q ss_pred             HHHHHHHHHCCcccCCccccccCChHHHhh
Q 040371          308 GSLIQRTKSEGFLPATELVLMDVSEEEKEG  337 (410)
Q Consensus       308 ~~l~~~m~~~g~~pd~~~~~~~~~~~~~~~  337 (410)
                      +    +|++.|+.||..++...+..+.+.+
T Consensus       743 ~----eM~~~Gi~Pd~~Ty~sLL~a~~k~G  768 (1060)
T PLN03218        743 S----EMKRLGLCPNTITYSILLVASERKD  768 (1060)
T ss_pred             H----HHHHcCCCCCHHHHHHHHHHHHHCC
Confidence            8    7888999999988766666555443

>PLN03218 maturation of RBCL 1; Provisional

Probab=100.00  E-value=7.7e-49  Score=402.67  Aligned_cols=378  Identities=18%  Similarity=0.235  Sum_probs=305.8

Q ss_pred             CCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHH--cCCCccHHHHH
Q 040371            3 DKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIE--KKIELNFILSA   80 (410)
Q Consensus         3 ~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~--~g~~~~~~~~~   80 (410)
                      .||+++||+||.+|++.|++++|+++|++|.+.|+.||..||+.++.+|++.|++++|.++|+.|.+  .|+.||..+|+
T Consensus       504 ~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~~Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~~~~~gi~PD~vTyn  583 (1060)
T PLN03218        504 EANVHTFGALIDGCARAGQVAKAFGAYGIMRSKNVKPDRVVFNALISACGQSGAVDRAFDVLAEMKAETHPIDPDHITVG  583 (1060)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCcHHHHH
Confidence            5889999999999999999999999999999999999999999999999999999999999999976  57889999999


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhccc----CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQR----NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCG  156 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g  156 (410)
                      +||++|+++|++++|.++|++|.+    |+..+||++|.+|++.|++++|+++|++|.+.|+.||..||++++.+|++.|
T Consensus       584 aLI~ay~k~G~ldeA~elf~~M~e~gi~p~~~tynsLI~ay~k~G~~deAl~lf~eM~~~Gv~PD~~TynsLI~a~~k~G  663 (1060)
T PLN03218        584 ALMKACANAGQVDRAKEVYQMIHEYNIKGTPEVYTIAVNSCSQKGDWDFALSIYDDMKKKGVKPDEVFFSALVDVAGHAG  663 (1060)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCC
Confidence            999999999999999999999975    4668999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC---CCCCCHHHHHHHHHHHHhcCchhHHHHHH
Q 040371          157 LVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM---TMEPDVVVWRALLSACRTFKRLELGEVAI  233 (410)
Q Consensus       157 ~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m---~~~p~~~~~~~li~~~~~~g~~~~a~~~~  233 (410)
                      ++++|.++|+.|.+. |+.|+..+|++||++|+++|++++|.++|++|   ++.||..+|++||.+|++.|++++|.+++
T Consensus       664 ~~eeA~~l~~eM~k~-G~~pd~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~PdvvtyN~LI~gy~k~G~~eeAlelf  742 (1060)
T PLN03218        664 DLDKAFEILQDARKQ-GIKLGTVSYSSLMGACSNAKNWKKALELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVL  742 (1060)
T ss_pred             CHHHHHHHHHHHHHc-CCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            999999999999965 99999999999999999999999999999998   67899999999999999999999999996


Q ss_pred             Hhhc----cCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECC-------------EEEEEEeCC--
Q 040371          234 VNIS----RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAG-------------VIHQFKAGD--  294 (410)
Q Consensus       234 ~~~~----~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~-------------~~~~~~~~~--  294 (410)
                      .++.    .++..+|..|+.+|++.|++++|.++|++|.+.|+.|+..+....++-             .+-.|-.+.  
T Consensus       743 ~eM~~~Gi~Pd~~Ty~sLL~a~~k~G~le~A~~l~~~M~k~Gi~pd~~tynsLIglc~~~y~ka~~l~~~v~~f~~g~~~  822 (1060)
T PLN03218        743 SEMKRLGLCPNTITYSILLVASERKDDADVGLDLLSQAKEDGIKPNLVMCRCITGLCLRRFEKACALGEPVVSFDSGRPQ  822 (1060)
T ss_pred             HHHHHcCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhhhhhhhhhhhccccc
Confidence            6543    456788999999999999999999999999999998886433221110             000011111  


Q ss_pred             CCCccHHHHHHHHHHHHHHHHHCCcccCCccccccCChHHHhhhhhhhhHHHHHHHHhcCCCCCCcE--EEEcccccccc
Q 040371          295 RSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEI--RISKNLRICHD  372 (410)
Q Consensus       295 ~~~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~~~~~~~~~~~~l~~~~e~la~~~~~~~~~~~~~~--~~~~n~~~c~~  372 (410)
                      ......++|+.+|+    +|.+.|+.||..++...+ .|.....-...+..+-..+++.+.+++...  .+++++   +.
T Consensus       823 ~~n~w~~~Al~lf~----eM~~~Gi~Pd~~T~~~vL-~cl~~~~~~~~~~~m~~~m~~~~~~~~~~~y~~Li~g~---~~  894 (1060)
T PLN03218        823 IENKWTSWALMVYR----ETISAGTLPTMEVLSQVL-GCLQLPHDATLRNRLIENLGISADSQKQSNLSTLVDGF---GE  894 (1060)
T ss_pred             cccchHHHHHHHHH----HHHHCCCCCCHHHHHHHH-HHhcccccHHHHHHHHHHhccCCCCcchhhhHHHHHhh---cc
Confidence            11234566777776    999999999998887666 343222223345566666777776665332  244443   22


Q ss_pred             -hhhHHHHHhhhhCceEE
Q 040371          373 -CHSWIKMISRLLRRVII  389 (410)
Q Consensus       373 -~~~~~~~~~~~~~~~i~  389 (410)
                       -.+|..++.+|..+.|+
T Consensus       895 ~~~~A~~l~~em~~~Gi~  912 (1060)
T PLN03218        895 YDPRAFSLLEEAASLGVV  912 (1060)
T ss_pred             ChHHHHHHHHHHHHcCCC
Confidence             25799999998877544

>PF14432 DYW_deaminase: DYW family of nucleic acid deaminases

Probab=99.96  E-value=3.4e-29  Score=191.38  Aligned_cols=106  Identities=58%  Similarity=0.995  Sum_probs=94.4

Q ss_pred             ceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHHHCCcccCCccccccCChHHH--------hhhhhhhhHHHHH
Q 040371          277 GKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEEK--------EGNLYHHSEKLAL  348 (410)
Q Consensus       277 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~~~~~~~~~--------~~~l~~~~e~la~  348 (410)
                      +++|.++    |.|++|+.+||+.        ++..++...|+.|+...+.++++++++        ...+.+|||+||+
T Consensus         2 ~~~w~~~----h~F~sgd~shp~~--------~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~d~~~~~~~~~~HSEKlAi   69 (116)
T PF14432_consen    2 GCSWIEV----HSFVSGDRSHPQS--------ELINKMKEEGYVPDTKEVGHDVDEEEKHDYDEEEKEESLCYHSEKLAI   69 (116)
T ss_pred             CCCccce----EEEEeCCCcCccH--------HHHHHHHHcCCcchhhhhCCCchhhhhhhcccccchhhhhccHHHHHH
Confidence            5789765    8999999999998        333467789999999998888777655        5688999999999


Q ss_pred             HHHhcCCCCCCcEEEEccc-ccccchhhHHHHHhhhhCceEEEecCCcccccc
Q 040371          349 AYGILKTSPGTEIRISKNL-RICHDCHSWIKMISRLLRRVIIVRDRIRFHRFE  400 (410)
Q Consensus       349 ~~~~~~~~~~~~~~~~~n~-~~c~~~~~~~~~~~~~~~~~i~~~~~~~~h~~~  400 (410)
                      |||++++      +++||+ |+|+|||+++|+||++++|+|+|||.+|||||+
T Consensus        70 afgli~~------~vvkn~~RvC~DCH~~~K~iS~~~~ReIiVRD~~rfHhFk  116 (116)
T PF14432_consen   70 AFGLINT------RVVKNLKRVCGDCHSFIKFISKITGREIIVRDSNRFHHFK  116 (116)
T ss_pred             Hhcccce------eEEecCCccchHHHHHHHHHHHHHCeEEEEeCCCeeeeCC
Confidence            9999998      889999 999999999999999999999999999999996

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.86  E-value=5.6e-19  Score=168.25  Aligned_cols=297  Identities=13%  Similarity=0.059  Sum_probs=234.2

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc---HHHHHHHHHHHHh
Q 040371           12 MIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN---FILSAALIDMYSK   88 (410)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~---~~~~~~li~~y~~   88 (410)
                      ....+...|++++|+..|+++.+.+ +.+..++..+...+...|+++.|..+++.+++.+..++   ..++..+...|.+
T Consensus        41 ~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~  119 (389)
T PRK11788         41 KGLNFLLNEQPDKAIDLFIEMLKVD-PETVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLK  119 (389)
T ss_pred             HHHHHHhcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            3445678899999999999999863 34566899999999999999999999999988643222   3578899999999


Q ss_pred             cCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHccCCHHHH
Q 040371           89 CGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS----ITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~----~t~~~ll~a~~~~g~~~~a  161 (410)
                      .|++++|..+|+++.+   .+..+++.++..|.+.|++++|++.|+++...+..++.    ..+..+...+.+.|++++|
T Consensus       120 ~g~~~~A~~~~~~~l~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A  199 (389)
T PRK11788        120 AGLLDRAEELFLQLVDEGDFAEGALQQLLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAA  199 (389)
T ss_pred             CCCHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHH
Confidence            9999999999999975   46779999999999999999999999999886543322    2345677788899999999


Q ss_pred             HHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC--HHHHHHHHHHHHhcCchhHHHHHHH---h
Q 040371          162 RKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD--VVVWRALLSACRTFKRLELGEVAIV---N  235 (410)
Q Consensus       162 ~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~---~  235 (410)
                      ..+|+++.+.  .+.+...+..+...|.+.|++++|.++|+++ ...|+  ..++..+..++...|++++|...+.   +
T Consensus       200 ~~~~~~al~~--~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~  277 (389)
T PRK11788        200 RALLKKALAA--DPQCVRASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVLPKLMECYQALGDEAEGLEFLRRALE  277 (389)
T ss_pred             HHHHHHHHhH--CcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            9999999853  2334667888999999999999999999998 33454  3568889999999999999999943   3


Q ss_pred             hccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeC---CCCCccHHHHHHHHHHHHH
Q 040371          236 ISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAG---DRSHPEAQAIDKILGSLIQ  312 (410)
Q Consensus       236 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~---~~~~~~~~~~~~~l~~l~~  312 (410)
                      ..|.. ..+..++..|.+.|++++|..+++++.+..  |+.. .+..       ++..   ...+|+..+++..++    
T Consensus       278 ~~p~~-~~~~~la~~~~~~g~~~~A~~~l~~~l~~~--P~~~-~~~~-------l~~~~~~~~~~g~~~~a~~~~~----  342 (389)
T PRK11788        278 EYPGA-DLLLALAQLLEEQEGPEAAQALLREQLRRH--PSLR-GFHR-------LLDYHLAEAEEGRAKESLLLLR----  342 (389)
T ss_pred             hCCCc-hHHHHHHHHHHHhCCHHHHHHHHHHHHHhC--cCHH-HHHH-------HHHHhhhccCCccchhHHHHHH----
Confidence            44543 456889999999999999999999887652  3321 1110       1111   123678889998888    


Q ss_pred             HHHHCCcccCCccc
Q 040371          313 RTKSEGFLPATELV  326 (410)
Q Consensus       313 ~m~~~g~~pd~~~~  326 (410)
                      +|.+.++.||..++
T Consensus       343 ~~~~~~~~~~p~~~  356 (389)
T PRK11788        343 DLVGEQLKRKPRYR  356 (389)
T ss_pred             HHHHHHHhCCCCEE
Confidence            67777888888764

>PRK11788 tetratricopeptide repeat protein; Provisional

Probab=99.84  E-value=2.4e-18  Score=163.96  Aligned_cols=269  Identities=12%  Similarity=0.067  Sum_probs=220.6

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD---KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAA   81 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd---~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~   81 (410)
                      +..+|..+...|.+.|++++|+.+++.+...+..++   ..++..+...+...|+++.|..++..+.+.. +.+..+++.
T Consensus        68 ~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~~~~~~~~~~~La~~~~~~g~~~~A~~~~~~~l~~~-~~~~~~~~~  146 (389)
T PRK11788         68 TVELHLALGNLFRRRGEVDRAIRIHQNLLSRPDLTREQRLLALQELGQDYLKAGLLDRAEELFLQLVDEG-DFAEGALQQ  146 (389)
T ss_pred             cHHHHHHHHHHHHHcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCC-cchHHHHHH
Confidence            456899999999999999999999999987542222   2567888999999999999999999998863 457889999


Q ss_pred             HHHHHHhcCCHHHHHHHHHhcccCC--------hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040371           82 LIDMYSKCGKIQMAKEVFDTVQRND--------VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACS  153 (410)
Q Consensus        82 li~~y~~~g~~~~A~~~f~~m~~~~--------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~  153 (410)
                      ++.+|.+.|++++|.+.|+.+.+.+        ...|..+...+.+.|++++|...|+++.+.. +.+...+..+...+.
T Consensus       147 la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~  225 (389)
T PRK11788        147 LLEIYQQEKDWQKAIDVAERLEKLGGDSLRVEIAHFYCELAQQALARGDLDAARALLKKALAAD-PQCVRASILLGDLAL  225 (389)
T ss_pred             HHHHHHHhchHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhHC-cCCHHHHHHHHHHHH
Confidence            9999999999999999999986432        1245667788899999999999999998753 224557778889999


Q ss_pred             ccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHH
Q 040371          154 HCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      +.|++++|.++|+.+.+. +-.....+++.++.+|.+.|++++|...++++ ...|+...+..+...+...|++++|..+
T Consensus       226 ~~g~~~~A~~~~~~~~~~-~p~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~la~~~~~~g~~~~A~~~  304 (389)
T PRK11788        226 AQGDYAAAIEALERVEEQ-DPEYLSEVLPKLMECYQALGDEAEGLEFLRRALEEYPGADLLLALAQLLEEQEGPEAAQAL  304 (389)
T ss_pred             HCCCHHHHHHHHHHHHHH-ChhhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHhCCHHHHHHH
Confidence            999999999999999854 21222467889999999999999999999998 5568877778899999999999999999


Q ss_pred             HH---hhccCCCchHHHHHHHHHh---cCChhHHHHHHHHHHhCCCcCCCc
Q 040371          233 IV---NISRLMGGDYVLLSNMYCY---LKRWDTAENVREIMKKKGVRKSQG  277 (410)
Q Consensus       233 ~~---~~~~~~~~~~~~l~~~~~~---~g~~~~a~~~~~~m~~~g~~~~~~  277 (410)
                      +.   +..|.+ ..+..++..+..   .|+.+++..++++|.+++++++|.
T Consensus       305 l~~~l~~~P~~-~~~~~l~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~~p~  354 (389)
T PRK11788        305 LREQLRRHPSL-RGFHRLLDYHLAEAEEGRAKESLLLLRDLVGEQLKRKPR  354 (389)
T ss_pred             HHHHHHhCcCH-HHHHHHHHHhhhccCCccchhHHHHHHHHHHHHHhCCCC
Confidence            43   334444 356666666654   568999999999999999999885

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

Probab=99.80  E-value=6.9e-17  Score=169.74  Aligned_cols=289  Identities=12%  Similarity=0.039  Sum_probs=178.4

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      ...|..+...|.+.|++++|+..|+++.+.. +.+...+..+..++...|++++|..+++.+.+.. +.+...+..+...
T Consensus       601 ~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~  678 (899)
T TIGR02917       601 PEAWLMLGRAQLAAGDLNKAVSSFKKLLALQ-PDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLAQL  678 (899)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            4455555555555555555555555555432 2234445555555555555555555555555442 3345555555555


Q ss_pred             HHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040371           86 YSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGR  162 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  162 (410)
                      +.+.|++++|.++++.+.+   .+...|..+...|.+.|++++|++.|+++...  .|+..++..+..++.+.|+.++|.
T Consensus       679 ~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~l~~~~~~~g~~~~A~  756 (899)
T TIGR02917       679 LLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKR--APSSQNAIKLHRALLASGNTAEAV  756 (899)
T ss_pred             HHHcCCHHHHHHHHHHHHhhCcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHCCCHHHHH
Confidence            5556666666655555542   23445566666666666677777776666654  344455566666777777777777


Q ss_pred             HHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhc
Q 040371          163 KYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNIS  237 (410)
Q Consensus       163 ~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~  237 (410)
                      +.++.+.+.  .+.+...+..+...|.+.|++++|...|+++ ...| +...+..+...+...|+ ++|...   .....
T Consensus       757 ~~~~~~l~~--~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~-~~A~~~~~~~~~~~  833 (899)
T TIGR02917       757 KTLEAWLKT--HPNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKAPDNAVVLNNLAWLYLELKD-PRALEYAEKALKLA  833 (899)
T ss_pred             HHHHHHHHh--CCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCc-HHHHHHHHHHHhhC
Confidence            777776642  3345667777777777788888888777776 2333 56677777777777777 667776   34456


Q ss_pred             cCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHH
Q 040371          238 RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSL  310 (410)
Q Consensus       238 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l  310 (410)
                      |.++..+..+..+|...|++++|.+.++++.+.+.. ++.+...        +...+...|+.++|.+.++++
T Consensus       834 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~-~~~~~~~--------l~~~~~~~g~~~~A~~~~~~~  897 (899)
T TIGR02917       834 PNIPAILDTLGWLLVEKGEADRALPLLRKAVNIAPE-AAAIRYH--------LALALLATGRKAEARKELDKL  897 (899)
T ss_pred             CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCC-ChHHHHH--------HHHHHHHcCCHHHHHHHHHHH
Confidence            777777777888888888888888888888876532 2211111        223345567788888877743

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

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

Probab=99.79  E-value=7.1e-17  Score=169.66  Aligned_cols=262  Identities=13%  Similarity=0.031  Sum_probs=173.3

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +..+|+.+...|.+.|++++|...|+++...+ +.+...+..+...+...|+++.|.++++.+.+.. +.+..+|..+..
T Consensus       532 ~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~  609 (899)
T TIGR02917       532 NLRAILALAGLYLRTGNEEEAVAWLEKAAELN-PQEIEPALALAQYYLGKGQLKKALAILNEAADAA-PDSPEAWLMLGR  609 (899)
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchhHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHH
Confidence            34455556666666666666666666655432 3344455566666666666666666666665543 445666667777


Q ss_pred             HHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a  161 (410)
                      .|.+.|++++|...|+++.+   .+...|..+...|.+.|++++|...|+++.... +.+..++..+...+...|++++|
T Consensus       610 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A  688 (899)
T TIGR02917       610 AQLAAGDLNKAVSSFKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELK-PDNTEAQIGLAQLLLAAKRTESA  688 (899)
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHcCCHHHH
Confidence            77777777777777766542   244566666677777777777777777666532 22456666667777777777777


Q ss_pred             HHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhc
Q 040371          162 RKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVA---IVNIS  237 (410)
Q Consensus       162 ~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~  237 (410)
                      .++++.+.+.  .+++...+..+...|.+.|++++|.+.|+++ ...|+..++..+...+...|++++|...   ..+..
T Consensus       689 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~~  766 (899)
T TIGR02917       689 KKIAKSLQKQ--HPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNAIKLHRALLASGNTAEAVKTLEAWLKTH  766 (899)
T ss_pred             HHHHHHHHhh--CcCChHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCchHHHHHHHHHHHCCCHHHHHHHHHHHHHhC
Confidence            7777777643  2345566777777777778888887777776 4456666777777777888888888777   44456


Q ss_pred             cCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          238 RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       238 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      |.+...+..+...|.+.|++++|.+.|+++.+..
T Consensus       767 ~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~  800 (899)
T TIGR02917       767 PNDAVLRTALAELYLAQKDYDKAIKHYRTVVKKA  800 (899)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHhC
Confidence            6677777778888888888888888888877654

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.

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.71  E-value=1.9e-14  Score=144.86  Aligned_cols=259  Identities=8%  Similarity=-0.090  Sum_probs=194.4

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      ..+..++.+....|++++|++.|+++.... +.+...+..+..++...|+++.|...++.+++.. +.+...+..+...|
T Consensus        77 ~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~-P~~~~a~~~la~~l~~~g~~~~Ai~~l~~Al~l~-P~~~~a~~~la~~l  154 (656)
T PRK15174         77 DLLRRWVISPLASSQPDAVLQVVNKLLAVN-VCQPEDVLLVASVLLKSKQYATVADLAEQAWLAF-SGNSQIFALHLRTL  154 (656)
T ss_pred             hHHHHHhhhHhhcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            345556677777899999999999888752 3355677778888888899999999998888763 44677888888889


Q ss_pred             HhcCCHHHHHHHHHhcc--cC-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQ--RN-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRK  163 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~--~~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~  163 (410)
                      ...|++++|...++.+.  .| +...+..+ ..+.+.|++++|...++++......++......+..++...|++++|..
T Consensus       155 ~~~g~~~eA~~~~~~~~~~~P~~~~a~~~~-~~l~~~g~~~eA~~~~~~~l~~~~~~~~~~~~~l~~~l~~~g~~~eA~~  233 (656)
T PRK15174        155 VLMDKELQAISLARTQAQEVPPRGDMIATC-LSFLNKSRLPEDHDLARALLPFFALERQESAGLAVDTLCAVGKYQEAIQ  233 (656)
T ss_pred             HHCCChHHHHHHHHHHHHhCCCCHHHHHHH-HHHHHcCCHHHHHHHHHHHHhcCCCcchhHHHHHHHHHHHCCCHHHHHH
Confidence            99999999988888764  23 33334333 3477788999999988888765433444555555677788888999998


Q ss_pred             HHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHH----HHHHHHhC-CCCCC-HHHHHHHHHHHHhcCchhHHHHH---HH
Q 040371          164 YFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEE----AYGLITSM-TMEPD-VVVWRALLSACRTFKRLELGEVA---IV  234 (410)
Q Consensus       164 ~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~----A~~~~~~m-~~~p~-~~~~~~li~~~~~~g~~~~a~~~---~~  234 (410)
                      .|+.+.+.  -+.+...+..+...|.+.|++++    |...|++. ...|+ ...+..+...+...|++++|...   ..
T Consensus       234 ~~~~al~~--~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al  311 (656)
T PRK15174        234 TGESALAR--GLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFNSDNVRIVTLYADALIRTGQNEKAIPLLQQSL  311 (656)
T ss_pred             HHHHHHhc--CCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            88888753  23346677788888888888885    67788776 45564 56777888888888888888887   55


Q ss_pred             hhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          235 NISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       235 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      ...|.++..+..+..+|.+.|++++|...++.+.+.
T Consensus       312 ~l~P~~~~a~~~La~~l~~~G~~~eA~~~l~~al~~  347 (656)
T PRK15174        312 ATHPDLPYVRAMYARALRQVGQYTAASDEFVQLARE  347 (656)
T ss_pred             HhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            667777777788888888888888888888887764

>PRK15174 Vi polysaccharide export protein VexE; Provisional

Probab=99.64  E-value=1.9e-13  Score=137.63  Aligned_cols=256  Identities=9%  Similarity=-0.036  Sum_probs=206.5

Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhc
Q 040371           10 NSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKC   89 (410)
Q Consensus        10 n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~   89 (410)
                      -.++..+.+.|++++|+.+++..+..... +...+..++.+....|+++.|.+.++.+.+.. +.+...+..+...+.+.
T Consensus        46 ~~~~~~~~~~g~~~~A~~l~~~~l~~~p~-~~~~l~~l~~~~l~~g~~~~A~~~l~~~l~~~-P~~~~a~~~la~~l~~~  123 (656)
T PRK15174         46 ILFAIACLRKDETDVGLTLLSDRVLTAKN-GRDLLRRWVISPLASSQPDAVLQVVNKLLAVN-VCQPEDVLLVASVLLKS  123 (656)
T ss_pred             HHHHHHHHhcCCcchhHHHhHHHHHhCCC-chhHHHHHhhhHhhcCCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHc
Confidence            34677888999999999999999876433 44556666677778999999999999999874 45678889999999999


Q ss_pred             CCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Q 040371           90 GKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFD  166 (410)
Q Consensus        90 g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~  166 (410)
                      |++++|...|++...  | +...|..+...+...|+.++|...++++......+ ...+.. +..+...|++++|...++
T Consensus       124 g~~~~Ai~~l~~Al~l~P~~~~a~~~la~~l~~~g~~~eA~~~~~~~~~~~P~~-~~a~~~-~~~l~~~g~~~eA~~~~~  201 (656)
T PRK15174        124 KQYATVADLAEQAWLAFSGNSQIFALHLRTLVLMDKELQAISLARTQAQEVPPR-GDMIAT-CLSFLNKSRLPEDHDLAR  201 (656)
T ss_pred             CCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHCCChHHHHHHHHHHHHhCCCC-HHHHHH-HHHHHHcCCHHHHHHHHH
Confidence            999999999998864  3 56789999999999999999999999887653222 223323 345788999999999999


Q ss_pred             HhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhH----HHHH---HHhhc
Q 040371          167 HMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLEL----GEVA---IVNIS  237 (410)
Q Consensus       167 ~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~----a~~~---~~~~~  237 (410)
                      .+.+. .-.++...+..+...+.+.|++++|...+++. ...| +...+..+-..+...|++++    |...   ..+..
T Consensus       202 ~~l~~-~~~~~~~~~~~l~~~l~~~g~~~eA~~~~~~al~~~p~~~~~~~~Lg~~l~~~G~~~eA~~~A~~~~~~Al~l~  280 (656)
T PRK15174        202 ALLPF-FALERQESAGLAVDTLCAVGKYQEAIQTGESALARGLDGAALRRSLGLAYYQSGRSREAKLQAAEHWRHALQFN  280 (656)
T ss_pred             HHHhc-CCCcchhHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhhHHHHHHHHHHHHhhC
Confidence            98753 22233445566678899999999999999987 4455 46778888888999999986    5555   56677


Q ss_pred             cCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          238 RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       238 ~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      |.+...+..+..++.+.|++++|...+++..+.
T Consensus       281 P~~~~a~~~lg~~l~~~g~~~eA~~~l~~al~l  313 (656)
T PRK15174        281 SDNVRIVTLYADALIRTGQNEKAIPLLQQSLAT  313 (656)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            888889999999999999999999999998875

>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=99.59  E-value=5.1e-12  Score=127.35  Aligned_cols=255  Identities=13%  Similarity=0.076  Sum_probs=177.9

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK   88 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~   88 (410)
                      +...-..|.+.|++++|+..|++.+.  +.|+...|..+..++.+.|+++.|.+.+...++.. +.+...+..+..+|..
T Consensus       130 ~k~~G~~~~~~~~~~~Ai~~y~~al~--~~p~~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~a~a~~~  206 (615)
T TIGR00990       130 LKEKGNKAYRNKDFNKAIKLYSKAIE--CKPDPVYYSNRAACHNALGDWEKVVEDTTAALELD-PDYSKALNRRANAYDG  206 (615)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHh--cCCchHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHH
Confidence            34455566666666666666666654  34566666666666666666666666666666543 2344555555556666


Q ss_pred             cCCHHHHH------------------------------------------------------------------------
Q 040371           89 CGKIQMAK------------------------------------------------------------------------   96 (410)
Q Consensus        89 ~g~~~~A~------------------------------------------------------------------------   96 (410)
                      .|++++|.                                                                        
T Consensus       207 lg~~~eA~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  286 (615)
T TIGR00990       207 LGKYADALLDLTASCIIDGFRNEQSAQAVERLLKKFAESKAKEILETKPENLPSVTFVGNYLQSFRPKPRPAGLEDSNEL  286 (615)
T ss_pred             cCCHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHccCCcchhhhhccccc
Confidence            66655554                                                                        


Q ss_pred             ----------------------------HHHHhccc-----C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC-
Q 040371           97 ----------------------------EVFDTVQR-----N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD-  141 (410)
Q Consensus        97 ----------------------------~~f~~m~~-----~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-  141 (410)
                                                  +.|++..+     | +...|+.+...+...|++++|+..|++..+.  .|+ 
T Consensus       287 ~~~~~~~~~~l~~~~~e~~~~~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l--~P~~  364 (615)
T TIGR00990       287 DEETGNGQLQLGLKSPESKADESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIEL--DPRV  364 (615)
T ss_pred             ccccccchHHHHHHHHHhhhhhhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCc
Confidence                                        33333221     1 2234566666667778888888888887763  454 


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHHHHH
Q 040371          142 SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRALLSA  219 (410)
Q Consensus       142 ~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~li~~  219 (410)
                      ...|..+...+...|++++|...|+.+.+.  -+.+...|..+...|...|++++|...|++. ...|+ ...|..+...
T Consensus       365 ~~~~~~la~~~~~~g~~~eA~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l~P~~~~~~~~la~~  442 (615)
T TIGR00990       365 TQSYIKRASMNLELGDPDKAEEDFDKALKL--NSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDLDPDFIFSHIQLGVT  442 (615)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCccCHHHHHHHHHH
Confidence            456777777788888899999888887743  2334678888888899999999999888887 55564 5667777778


Q ss_pred             HHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          220 CRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       220 ~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      +...|++++|...   ..+..|.++..+..+..+|...|++++|.+.|++..+.
T Consensus       443 ~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l  496 (615)
T TIGR00990       443 QYKEGSIASSMATFRRCKKNFPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIEL  496 (615)
T ss_pred             HHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhc
Confidence            8899999999988   44567888888899999999999999999999887664

>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=99.58  E-value=3.2e-12  Score=128.82  Aligned_cols=246  Identities=15%  Similarity=0.056  Sum_probs=199.0

Q ss_pred             CCHhHHHHHHHHHHHCC-CCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           20 ARFDEALRFFREMLSSK-VEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        20 g~~~~a~~l~~~m~~~g-~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      +++++|++.|++....+ ..| +...|..+...+...|++++|...++..++.. +.+...|..+...|...|++++|..
T Consensus       308 ~~y~~A~~~~~~al~~~~~~~~~a~a~~~lg~~~~~~g~~~eA~~~~~kal~l~-P~~~~~~~~la~~~~~~g~~~eA~~  386 (615)
T TIGR00990       308 ESYEEAARAFEKALDLGKLGEKEAIALNLRGTFKCLKGKHLEALADLSKSIELD-PRVTQSYIKRASMNLELGDPDKAEE  386 (615)
T ss_pred             hhHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHCCCHHHHHH
Confidence            67899999999998764 334 44577888888889999999999999998864 3346788899999999999999999


Q ss_pred             HHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcC
Q 040371           98 VFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYS  173 (410)
Q Consensus        98 ~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~  173 (410)
                      .|++..+   .+...|..+...|...|++++|+..|++....  .| +...+..+...+.+.|++++|...|+...+.  
T Consensus       387 ~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~kal~l--~P~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~--  462 (615)
T TIGR00990       387 DFDKALKLNSEDPDIYYHRAQLHFIKGEFAQAGKDYQKSIDL--DPDFIFSHIQLGVTQYKEGSIASSMATFRRCKKN--  462 (615)
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--
Confidence            9998753   35778999999999999999999999999875  44 4566777888999999999999999998853  


Q ss_pred             CCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCH-H-------HHHHHHHHHHhcCchhHHHHH---HHhhccCCC
Q 040371          174 IQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDV-V-------VWRALLSACRTFKRLELGEVA---IVNISRLMG  241 (410)
Q Consensus       174 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~-~-------~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~  241 (410)
                      .+.+...|+.+...|...|++++|.+.|++. ...|+. .       .++..+..+...|++++|..+   ..+..|.+.
T Consensus       463 ~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p~~~  542 (615)
T TIGR00990       463 FPEAPDVYNYYGELLLDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIIDPECD  542 (615)
T ss_pred             CCCChHHHHHHHHHHHHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcH
Confidence            3335778999999999999999999999985 444421 1       122222233446999999998   345677777


Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          242 GDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       242 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      ..+..+..+|.+.|++++|.+.|++..+.
T Consensus       543 ~a~~~la~~~~~~g~~~eAi~~~e~A~~l  571 (615)
T TIGR00990       543 IAVATMAQLLLQQGDVDEALKLFERAAEL  571 (615)
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHH
Confidence            77889999999999999999999987654

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

Probab=99.56  E-value=1.8e-13  Score=127.88  Aligned_cols=253  Identities=12%  Similarity=0.149  Sum_probs=165.8

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHH-HHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFI-LSAALID   84 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~-~~~~li~   84 (410)
                      .+|..+...+-..|++++|+.+++.|.+.  +| ....|..+..++...|+.+.|.+.|...++.  .|+.. +.+.+..
T Consensus       117 e~ysn~aN~~kerg~~~~al~~y~~aiel--~p~fida~inla~al~~~~~~~~a~~~~~~alql--nP~l~ca~s~lgn  192 (966)
T KOG4626|consen  117 EAYSNLANILKERGQLQDALALYRAAIEL--KPKFIDAYINLAAALVTQGDLELAVQCFFEALQL--NPDLYCARSDLGN  192 (966)
T ss_pred             HHHHHHHHHHHHhchHHHHHHHHHHHHhc--CchhhHHHhhHHHHHHhcCCCcccHHHHHHHHhc--CcchhhhhcchhH
Confidence            47888999999999999999999999985  55 5668999999999999999999999988885  45443 3445555


Q ss_pred             HHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCCH--
Q 040371           85 MYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD-SITFLGLLTACSHCGLV--  158 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~--  158 (410)
                      .....|++++|...+.+..+  | -.+.|+.|...+-..|+..+|++.|++...  +.|+ ...|..|...|...+.+  
T Consensus       193 Llka~Grl~ea~~cYlkAi~~qp~fAiawsnLg~~f~~~Gei~~aiq~y~eAvk--ldP~f~dAYiNLGnV~ke~~~~d~  270 (966)
T KOG4626|consen  193 LLKAEGRLEEAKACYLKAIETQPCFAIAWSNLGCVFNAQGEIWLAIQHYEEAVK--LDPNFLDAYINLGNVYKEARIFDR  270 (966)
T ss_pred             HHHhhcccchhHHHHHHHHhhCCceeeeehhcchHHhhcchHHHHHHHHHHhhc--CCCcchHHHhhHHHHHHHHhcchH
Confidence            66668888888888876653  3 246888888888888888888888888765  4454 34455555555554444  


Q ss_pred             --------------------------------HHHHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC-
Q 040371          159 --------------------------------EEGRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM-  204 (410)
Q Consensus       159 --------------------------------~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m-  204 (410)
                                                      |.|+..+++..+   +.|+ ...|+.|..++-..|++.+|.+.+.+. 
T Consensus       271 Avs~Y~rAl~lrpn~A~a~gNla~iYyeqG~ldlAI~~Ykral~---~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL  347 (966)
T KOG4626|consen  271 AVSCYLRALNLRPNHAVAHGNLACIYYEQGLLDLAIDTYKRALE---LQPNFPDAYNNLANALKDKGSVTEAVDCYNKAL  347 (966)
T ss_pred             HHHHHHHHHhcCCcchhhccceEEEEeccccHHHHHHHHHHHHh---cCCCchHHHhHHHHHHHhccchHHHHHHHHHHH
Confidence                                            444444444442   2333 345555555555555555555555544 


Q ss_pred             CCCCC-HHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          205 TMEPD-VVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       205 ~~~p~-~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                      ...|+ ....+.|-..+...|.+++|.++   ..+..|.-...++.|...|-+.|++++|...+++..
T Consensus       348 ~l~p~hadam~NLgni~~E~~~~e~A~~ly~~al~v~p~~aaa~nNLa~i~kqqgnl~~Ai~~Ykeal  415 (966)
T KOG4626|consen  348 RLCPNHADAMNNLGNIYREQGKIEEATRLYLKALEVFPEFAAAHNNLASIYKQQGNLDDAIMCYKEAL  415 (966)
T ss_pred             HhCCccHHHHHHHHHHHHHhccchHHHHHHHHHHhhChhhhhhhhhHHHHHHhcccHHHHHHHHHHHH
Confidence            23332 33445555555555555555555   233344444455555555666666666655555543

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

Probab=99.52  E-value=3.1e-14  Score=129.13  Aligned_cols=253  Identities=15%  Similarity=0.112  Sum_probs=107.3

Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhc
Q 040371           11 SMIGGFVRNARFDEALRFFREMLSSKVEPDKF-TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKC   89 (410)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~-t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~   89 (410)
                      .+...+.+.|++++|++++++-.....+|+.. -|..+...+...++.+.|.+.++++.+.+.. ++..+..++.. ...
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            45677889999999999996654443245444 4444555667789999999999999987633 67778888888 789


Q ss_pred             CCHHHHHHHHHhcc--cCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHccCCHHHHHHHHH
Q 040371           90 GKIQMAKEVFDTVQ--RNDVSVWNAMISGVAIHGLAADASAIFTKMEMFN-VLPDSITFLGLLTACSHCGLVEEGRKYFD  166 (410)
Q Consensus        90 g~~~~A~~~f~~m~--~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~t~~~ll~a~~~~g~~~~a~~~~~  166 (410)
                      +++++|.++++..-  .++...+..++..+.+.++++++.+++++..... .+++...|..+...+.+.|+.++|.+.++
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            99999999988764  3466778889999999999999999999987543 34567778888889999999999999999


Q ss_pred             HhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhccCC
Q 040371          167 HMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSMT--MEPDVVVWRALLSACRTFKRLELGEVA---IVNISRLM  240 (410)
Q Consensus       167 ~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~  240 (410)
                      ...+.   .| +....+.++..+...|+.+++.++++...  ...|...|..+..++...|+.++|...   ..+..|.|
T Consensus       171 ~al~~---~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p~d  247 (280)
T PF13429_consen  171 KALEL---DPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNPDD  247 (280)
T ss_dssp             HHHHH----TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHSTT-
T ss_pred             HHHHc---CCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhccccccccccccccccccccccc
Confidence            99864   55 47788999999999999999888777661  234566788999999999999999999   55667888


Q ss_pred             CchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          241 GGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       241 ~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                      +.....+.+++...|+.++|.+++++..
T Consensus       248 ~~~~~~~a~~l~~~g~~~~A~~~~~~~~  275 (280)
T PF13429_consen  248 PLWLLAYADALEQAGRKDEALRLRRQAL  275 (280)
T ss_dssp             HHHHHHHHHHHT----------------
T ss_pred             cccccccccccccccccccccccccccc
Confidence            8899999999999999999999987654

>PF13041 PPR_2: PPR repeat family

Probab=99.52  E-value=3.4e-14  Score=92.24  Aligned_cols=50  Identities=36%  Similarity=0.833  Sum_probs=48.5

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCAR   53 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~   53 (410)
                      ||+++||++|.+|++.|++++|+++|++|.+.|++||..||++++++|++
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            89999999999999999999999999999999999999999999999874

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.51  E-value=1.6e-11  Score=131.87  Aligned_cols=226  Identities=12%  Similarity=0.062  Sum_probs=145.6

Q ss_pred             HHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHH-------------
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFL-------------  146 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~-------------  146 (410)
                      ..+...|++++|++.|++..+  | +...+..+...|.+.|++++|...|++..+.  .| +...+.             
T Consensus       469 ~~~~~~g~~~eA~~~~~~Al~~~P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~--~P~~~~~~~a~al~l~~~~~~~  546 (1157)
T PRK11447        469 EALENQGKWAQAAELQRQRLALDPGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQ--KPNDPEQVYAYGLYLSGSDRDR  546 (1157)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHhCCCHH
Confidence            344456677777777766543  2 3345556666666677777777777666543  22 222221             


Q ss_pred             -------------------------------HHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHH
Q 040371          147 -------------------------------GLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIE  195 (410)
Q Consensus       147 -------------------------------~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~  195 (410)
                                                     .+...+...|+.++|..+++.      .+++...+..+...|.+.|+++
T Consensus       547 ~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~------~p~~~~~~~~La~~~~~~g~~~  620 (1157)
T PRK11447        547 AALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQ------QPPSTRIDLTLADWAQQRGDYA  620 (1157)
T ss_pred             HHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHh------CCCCchHHHHHHHHHHHcCCHH
Confidence                                           223344455555666555541      1334566778888999999999


Q ss_pred             HHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHHH---HhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          196 EAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVAI---VNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       196 ~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~~---~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      +|++.|++. ...| +...+..+...+...|++++|+..+   .+..|.++..+..+..++...|++++|.++++.+...
T Consensus       621 ~A~~~y~~al~~~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~~eA~~~~~~al~~  700 (1157)
T PRK11447        621 AARAAYQRVLTREPGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQRRVALAWAALGDTAAAQRTFNRLIPQ  700 (1157)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence            999999987 4556 5778889999999999999999983   4445666677778889999999999999999998765


Q ss_pred             CCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHHHCCcccCC
Q 040371          271 GVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPAT  323 (410)
Q Consensus       271 g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~pd~  323 (410)
                      .-...+......+-   ......+...|+.++|...+++.   |...|+.|+.
T Consensus       701 ~~~~~~~~~~a~~~---~~~a~~~~~~G~~~~A~~~y~~A---l~~~~~~~~~  747 (1157)
T PRK11447        701 AKSQPPSMESALVL---RDAARFEAQTGQPQQALETYKDA---MVASGITPTR  747 (1157)
T ss_pred             CccCCcchhhHHHH---HHHHHHHHHcCCHHHHHHHHHHH---HhhcCCCCCC
Confidence            32211111010000   00112235678999999998864   4455776643

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

Probab=99.51  E-value=4.8e-13  Score=129.59  Aligned_cols=270  Identities=15%  Similarity=0.130  Sum_probs=200.0

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCC
Q 040371           27 RFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRND  106 (410)
Q Consensus        27 ~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~  106 (410)
                      .++-.|...|+.||.+||.+++.-|+..|+.+.|- +|..|.-..++.+..++++++......++.+.+.       +|.
T Consensus        11 nfla~~e~~gi~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk-------ep~   82 (1088)
T KOG4318|consen   11 NFLALHEISGILPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK-------EPL   82 (1088)
T ss_pred             hHHHHHHHhcCCCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC-------CCc
Confidence            45677888999999999999999999999999998 9999998888999999999999999999988875       788


Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHH
Q 040371          107 VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVD  186 (410)
Q Consensus       107 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~  186 (410)
                      ..+|+.+..+|.++|+...    |+...+        -.-.+...++..|.-..-..++..+.-..+.-||.   ...+.
T Consensus        83 aDtyt~Ll~ayr~hGDli~----fe~veq--------dLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda---~n~il  147 (1088)
T KOG4318|consen   83 ADTYTNLLKAYRIHGDLIL----FEVVEQ--------DLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDA---ENAIL  147 (1088)
T ss_pred             hhHHHHHHHHHHhccchHH----HHHHHH--------HHHHHHhhhhhhccCcHHHHHHhhcccCcccchhH---HHHHH
Confidence            8899999999999999865    333332        22334556666776666666665543223444554   34566


Q ss_pred             HHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCc-hhHHHHHHHhhc-cCCCchHHHHHHHHHhcCChhHHHHHH
Q 040371          187 LLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKR-LELGEVAIVNIS-RLMGGDYVLLSNMYCYLKRWDTAENVR  264 (410)
Q Consensus       187 ~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~-~~~a~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~a~~~~  264 (410)
                      ...-.|.++.++++...+|...-..++..+|.-+..... +++-......+. ..++.+|..++..-..+|+.+.|..++
T Consensus       148 llv~eglwaqllkll~~~Pvsa~~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll  227 (1088)
T KOG4318|consen  148 LLVLEGLWAQLLKLLAKVPVSAWNAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLL  227 (1088)
T ss_pred             HHHHHHHHHHHHHHHhhCCcccccchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHH
Confidence            677788899999999888644322233234655554433 333333322222 467789999999999999999999999


Q ss_pred             HHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHHHCCcccCCccccccCChHH
Q 040371          265 EIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPATELVLMDVSEEE  334 (410)
Q Consensus       265 ~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~pd~~~~~~~~~~~~  334 (410)
                      .+|+++|++-.+...|.++        .|       .++...++.+.+-|++.|+.|+..+...-+.++-
T Consensus       228 ~emke~gfpir~HyFwpLl--------~g-------~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l  282 (1088)
T KOG4318|consen  228 YEMKEKGFPIRAHYFWPLL--------LG-------INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQL  282 (1088)
T ss_pred             HHHHHcCCCcccccchhhh--------hc-------CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhh
Confidence            9999999999998888753        33       2233455666679999999999988755444443

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

Probab=99.49  E-value=2.3e-12  Score=120.65  Aligned_cols=256  Identities=11%  Similarity=0.170  Sum_probs=209.4

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD-KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      .+.|+.|-..+-.+|+...|+.-|++...  +.|+ ...|..+.+.+...+.++.|...+.+..... +....++..|..
T Consensus       218 AiawsnLg~~f~~~Gei~~aiq~y~eAvk--ldP~f~dAYiNLGnV~ke~~~~d~Avs~Y~rAl~lr-pn~A~a~gNla~  294 (966)
T KOG4626|consen  218 AIAWSNLGCVFNAQGEIWLAIQHYEEAVK--LDPNFLDAYINLGNVYKEARIFDRAVSCYLRALNLR-PNHAVAHGNLAC  294 (966)
T ss_pred             eeeehhcchHHhhcchHHHHHHHHHHhhc--CCCcchHHHhhHHHHHHHHhcchHHHHHHHHHHhcC-CcchhhccceEE
Confidence            35789999999999999999999998876  4555 3578889999999999999998888887653 335677888888


Q ss_pred             HHHhcCCHHHHHHHHHhccc--CC-hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCCHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQR--ND-VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD-SITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~--~~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~  160 (410)
                      .|-..|.+|.|+..+++..+  |+ ..+||.|..++-..|+..+|.+.|.+.+..  .|+ ....+.|...+...|.+++
T Consensus       295 iYyeqG~ldlAI~~Ykral~~~P~F~~Ay~NlanALkd~G~V~ea~~cYnkaL~l--~p~hadam~NLgni~~E~~~~e~  372 (966)
T KOG4626|consen  295 IYYEQGLLDLAIDTYKRALELQPNFPDAYNNLANALKDKGSVTEAVDCYNKALRL--CPNHADAMNNLGNIYREQGKIEE  372 (966)
T ss_pred             EEeccccHHHHHHHHHHHHhcCCCchHHHhHHHHHHHhccchHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHhccchH
Confidence            89999999999999988764  33 468999999999999999999999888774  444 4668888999999999999


Q ss_pred             HHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCchhHHHHH---HH
Q 040371          161 GRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRALLSACRTFKRLELGEVA---IV  234 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~li~~~~~~g~~~~a~~~---~~  234 (410)
                      |..+|....+   +.|. ....+.|...|-+.|++++|...+++. .++|+ ...++.+-..|...|+.+.|.+.   ..
T Consensus       373 A~~ly~~al~---v~p~~aaa~nNLa~i~kqqgnl~~Ai~~YkealrI~P~fAda~~NmGnt~ke~g~v~~A~q~y~rAI  449 (966)
T KOG4626|consen  373 ATRLYLKALE---VFPEFAAAHNNLASIYKQQGNLDDAIMCYKEALRIKPTFADALSNMGNTYKEMGDVSAAIQCYTRAI  449 (966)
T ss_pred             HHHHHHHHHh---hChhhhhhhhhHHHHHHhcccHHHHHHHHHHHHhcCchHHHHHHhcchHHHHhhhHHHHHHHHHHHH
Confidence            9999988763   3454 567888999999999999999988886 78887 46788888889999999999888   44


Q ss_pred             hhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040371          235 NISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       235 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                      ...|.-...+..|...|-.+|++.+|.+-+++..+
T Consensus       450 ~~nPt~AeAhsNLasi~kDsGni~~AI~sY~~aLk  484 (966)
T KOG4626|consen  450 QINPTFAEAHSNLASIYKDSGNIPEAIQSYRTALK  484 (966)
T ss_pred             hcCcHHHHHHhhHHHHhhccCCcHHHHHHHHHHHc
Confidence            55566667788899999999999999998887654

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.46  E-value=1e-10  Score=121.21  Aligned_cols=258  Identities=12%  Similarity=0.045  Sum_probs=204.8

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +...|..+..++.. +++++|+..|.+....  .|+......+..++...|++++|...++.+...  +|+...+..+..
T Consensus       476 ~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~--~Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~--~p~~~a~~~la~  550 (987)
T PRK09782        476 DAAAWNRLAKCYRD-TLPGVALYAWLQAEQR--QPDAWQHRAVAYQAYQVEDYATALAAWQKISLH--DMSNEDLLAAAN  550 (987)
T ss_pred             CHHHHHHHHHHHHh-CCcHHHHHHHHHHHHh--CCchHHHHHHHHHHHHCCCHHHHHHHHHHHhcc--CCCcHHHHHHHH
Confidence            56678888888876 8999999988887764  466655555556667899999999999998664  444455677788


Q ss_pred             HHHhcCCHHHHHHHHHhcccCChhhHHHHH---HHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQRNDVSVWNAMI---SGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~~~~~~~~~li---~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a  161 (410)
                      .+.+.|+.++|...|++..+.+...++...   ....+.|++++|+..|++..+  ..|+...+..+..++.+.|+.++|
T Consensus       551 all~~Gd~~eA~~~l~qAL~l~P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~--l~P~~~a~~~LA~~l~~lG~~deA  628 (987)
T PRK09782        551 TAQAAGNGAARDRWLQQAEQRGLGDNALYWWLHAQRYIPGQPELALNDLTRSLN--IAPSANAYVARATIYRQRHNVPAA  628 (987)
T ss_pred             HHHHCCCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHH--hCCCHHHHHHHHHHHHHCCCHHHH
Confidence            899999999999999988765443333333   333345999999999999987  457788889999999999999999


Q ss_pred             HHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHh
Q 040371          162 RKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVN  235 (410)
Q Consensus       162 ~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~  235 (410)
                      ...|+.....   .| +...++.+...+...|++++|+..+++. ...| +...+..+-.++...|++++|+..   ..+
T Consensus       629 ~~~l~~AL~l---~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~  705 (987)
T PRK09782        629 VSDLRAALEL---EPNNSNYQAALGYALWDSGDIAQSREMLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLVID  705 (987)
T ss_pred             HHHHHHHHHh---CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence            9999998853   44 4678888888999999999999999987 5566 567888999999999999999998   556


Q ss_pred             hccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 040371          236 ISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       236 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  272 (410)
                      ..|.+..+.........+..+++.|.+-+++-...+.
T Consensus       706 l~P~~a~i~~~~g~~~~~~~~~~~a~~~~~r~~~~~~  742 (987)
T PRK09782        706 DIDNQALITPLTPEQNQQRFNFRRLHEEVGRRWTFSF  742 (987)
T ss_pred             cCCCCchhhhhhhHHHHHHHHHHHHHHHHHHHhhcCc
Confidence            7787777777788888888888888887776655544

>PF13041 PPR_2: PPR repeat family

Probab=99.45  E-value=2.8e-13  Score=87.91  Aligned_cols=50  Identities=30%  Similarity=0.440  Sum_probs=46.7

Q ss_pred             CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040371          105 NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSH  154 (410)
Q Consensus       105 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~  154 (410)
                      ||+++||++|.+|++.|++++|+++|++|++.|+.||..||+.++++|++
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            68899999999999999999999999999999999999999999999875

>TIGR00540 hemY_coli hemY protein

Probab=99.42  E-value=1e-10  Score=111.85  Aligned_cols=295  Identities=9%  Similarity=-0.059  Sum_probs=200.6

Q ss_pred             HHHHHHHH--HcCCHhHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371           10 NSMIGGFV--RNARFDEALRFFREMLSSKVEPDK-FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus        10 n~li~~~~--~~g~~~~a~~l~~~m~~~g~~pd~-~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      ..+..|..  ..|+++.|.+.+.+..+.  .|+. ..+.....+....|+.+.+.+.+....+..-.++..+.-.....+
T Consensus        86 ~~~~~glla~~~g~~~~A~~~l~~~~~~--~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~p~~~l~~~~~~a~l~  163 (409)
T TIGR00540        86 KQTEEALLKLAEGDYAKAEKLIAKNADH--AAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELAGNDNILVEIARTRIL  163 (409)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHHHHhhc--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCcCchHHHHHHHHHH
Confidence            33444443  479999999999887664  4553 445556677888999999999999998764333344555668889


Q ss_pred             HhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHH---HccCCHHH
Q 040371           87 SKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTAC---SHCGLVEE  160 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~---~~~g~~~~  160 (410)
                      ...|+++.|...++.+.+  | +...+..+...|.+.|++++|.+++..+.+.++.++......-..++   ...+..++
T Consensus       164 l~~~~~~~Al~~l~~l~~~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~  243 (409)
T TIGR00540       164 LAQNELHAARHGVDKLLEMAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADE  243 (409)
T ss_pred             HHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999874  3 56688899999999999999999999999987543332211111222   22233333


Q ss_pred             HHHHHHHhhhhc--CCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHH-HHHHHHH--HhcCchhHHHHH--
Q 040371          161 GRKYFDHMRSRY--SIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVW-RALLSAC--RTFKRLELGEVA--  232 (410)
Q Consensus       161 a~~~~~~m~~~~--~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~-~~li~~~--~~~g~~~~a~~~--  232 (410)
                      +.+.+..+.+..  ....+...+..+...+...|+.++|.+++++. ...||.... ..++..+  ...++.+.+.+.  
T Consensus       244 ~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~g~~~~A~~~l~~~l~~~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e  323 (409)
T TIGR00540       244 GIDGLLNWWKNQPRHRRHNIALKIALAEHLIDCDDHDSAQEIIFDGLKKLGDDRAISLPLCLPIPRLKPEDNEKLEKLIE  323 (409)
T ss_pred             CHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHCCChHHHHHHHHHHHhhCCCcccchhHHHHHhhhcCCCChHHHHHHHH
Confidence            334555444321  11237888999999999999999999999987 555665421 0122322  334666666666  


Q ss_pred             -HHhhccCCC--chHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHH
Q 040371          233 -IVNISRLMG--GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGS  309 (410)
Q Consensus       233 -~~~~~~~~~--~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  309 (410)
                       ..+..|.++  ....++...|.+.|+|++|.+.|+........|++.... .       +..-+...|+.++|.+.+++
T Consensus       324 ~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~~~-~-------La~ll~~~g~~~~A~~~~~~  395 (409)
T TIGR00540       324 KQAKNVDDKPKCCINRALGQLLMKHGEFIEAADAFKNVAACKEQLDANDLA-M-------AADAFDQAGDKAEAAAMRQD  395 (409)
T ss_pred             HHHHhCCCChhHHHHHHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHHHH-H-------HHHHHHHcCCHHHHHHHHHH
Confidence             566778888  777899999999999999999999544433344442211 0       22224456777888777775


Q ss_pred             HHHHH
Q 040371          310 LIQRT  314 (410)
Q Consensus       310 l~~~m  314 (410)
                      -...+
T Consensus       396 ~l~~~  400 (409)
T TIGR00540       396 SLGLM  400 (409)
T ss_pred             HHHHH
Confidence            44433

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.

>PRK11447 cellulose synthase subunit BcsC; Provisional

Probab=99.42  E-value=4.6e-10  Score=120.81  Aligned_cols=257  Identities=11%  Similarity=0.042  Sum_probs=200.2

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK   88 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~   88 (410)
                      |..+...+...|++++|++.|++.++.. +-+...+..+...+.+.|++++|...++.+++.. +.+...+..+...+.+
T Consensus       464 ~~~~a~~~~~~g~~~eA~~~~~~Al~~~-P~~~~~~~~LA~~~~~~G~~~~A~~~l~~al~~~-P~~~~~~~a~al~l~~  541 (1157)
T PRK11447        464 LAQQAEALENQGKWAQAAELQRQRLALD-PGSVWLTYRLAQDLRQAGQRSQADALMRRLAQQK-PNDPEQVYAYGLYLSG  541 (1157)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHh
Confidence            4556677889999999999999998753 2255677888899999999999999999998764 3456666666667788


Q ss_pred             cCCHHHHHHHHHhcccCC----h---------hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc
Q 040371           89 CGKIQMAKEVFDTVQRND----V---------SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHC  155 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~~~----~---------~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~  155 (410)
                      .|+.++|...++.++...    .         ..+..+...+...|+.++|.++++.     .+++...+..+...+.+.
T Consensus       542 ~~~~~~Al~~l~~l~~~~~~~~~~~l~~~l~~~~~l~~a~~l~~~G~~~eA~~~l~~-----~p~~~~~~~~La~~~~~~  616 (1157)
T PRK11447        542 SDRDRAALAHLNTLPRAQWNSNIQELAQRLQSDQVLETANRLRDSGKEAEAEALLRQ-----QPPSTRIDLTLADWAQQR  616 (1157)
T ss_pred             CCCHHHHHHHHHhCCchhcChhHHHHHHHHhhhHHHHHHHHHHHCCCHHHHHHHHHh-----CCCCchHHHHHHHHHHHc
Confidence            999999999999886421    1         1123456678889999999999872     344556677788899999


Q ss_pred             CCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHHH
Q 040371          156 GLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVAI  233 (410)
Q Consensus       156 g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~~  233 (410)
                      |+.++|...|+...+.  -+.+...+..+...|...|++++|++.++.. ...| +..++..+..++...|++++|.+++
T Consensus       617 g~~~~A~~~y~~al~~--~P~~~~a~~~la~~~~~~g~~~eA~~~l~~ll~~~p~~~~~~~~la~~~~~~g~~~eA~~~~  694 (1157)
T PRK11447        617 GDYAAARAAYQRVLTR--EPGNADARLGLIEVDIAQGDLAAARAQLAKLPATANDSLNTQRRVALAWAALGDTAAAQRTF  694 (1157)
T ss_pred             CCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCChHHHHHHHHHHHhCCCHHHHHHHH
Confidence            9999999999999853  2335788999999999999999999999987 3455 4566777778888999999999994


Q ss_pred             Hhh---ccCCC------chHHHHHHHHHhcCChhHHHHHHHHHH-hCCCcC
Q 040371          234 VNI---SRLMG------GDYVLLSNMYCYLKRWDTAENVREIMK-KKGVRK  274 (410)
Q Consensus       234 ~~~---~~~~~------~~~~~l~~~~~~~g~~~~a~~~~~~m~-~~g~~~  274 (410)
                      .+.   .|.++      ..+..+...+...|++++|...++... ..|+.|
T Consensus       695 ~~al~~~~~~~~~~~~a~~~~~~a~~~~~~G~~~~A~~~y~~Al~~~~~~~  745 (1157)
T PRK11447        695 NRLIPQAKSQPPSMESALVLRDAARFEAQTGQPQQALETYKDAMVASGITP  745 (1157)
T ss_pred             HHHhhhCccCCcchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcCCCC
Confidence            433   33332      244556888999999999999998774 345543

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.41  E-value=3e-10  Score=102.35  Aligned_cols=225  Identities=18%  Similarity=0.216  Sum_probs=176.8

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      ++..||.+||.|.++--..+.|.+++++-.....+.+..+||.++.+-+-    ..++.+...|....+.||..++|+++
T Consensus       205 KT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~----~~~K~Lv~EMisqkm~Pnl~TfNalL  280 (625)
T KOG4422|consen  205 KTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSY----SVGKKLVAEMISQKMTPNLFTFNALL  280 (625)
T ss_pred             CCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHh----hccHHHHHHHHHhhcCCchHhHHHHH
Confidence            35579999999999999999999999999988889999999999987653    44588999999999999999999999


Q ss_pred             HHHHhcCCHHHHHHHH----Hhcc----cCChhhHHHHHHHHHHcCChHH-HHHHHHHHHHC----CCC---C-CHHHHH
Q 040371           84 DMYSKCGKIQMAKEVF----DTVQ----RNDVSVWNAMISGVAIHGLAAD-ASAIFTKMEMF----NVL---P-DSITFL  146 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f----~~m~----~~~~~~~~~li~~~~~~g~~~~-A~~l~~~m~~~----g~~---p-~~~t~~  146 (410)
                      .+.++.|+++.|++.+    .+|+    +|...+|.-+|..+.+.+++.+ |..+..+.+..    .++   | |...|.
T Consensus       281 ~c~akfg~F~~ar~aalqil~EmKeiGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fkp~~p~d~~FF~  360 (625)
T KOG4422|consen  281 SCAAKFGKFEDARKAALQILGEMKEIGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFKPITPTDNKFFQ  360 (625)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCcccCCCCchhHHHH
Confidence            9999999998877655    4554    5788899999999999988754 45555565543    233   3 456688


Q ss_pred             HHHHHHHccCCHHHHHHHHHHhhhhcC---CCCC---hhHHHHHHHHHHhcCCHHHHHHHHHhC-C--CCCCHHHHHHHH
Q 040371          147 GLLTACSHCGLVEEGRKYFDHMRSRYS---IQPQ---LEHYGAMVDLLGRAGHIEEAYGLITSM-T--MEPDVVVWRALL  217 (410)
Q Consensus       147 ~ll~a~~~~g~~~~a~~~~~~m~~~~~---~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m-~--~~p~~~~~~~li  217 (410)
                      ..+..|.+..+.+.|.++..-....-+   +.|+   ..-|..+.++.++....+.-+++++.| |  .-|+..+...++
T Consensus       361 ~AM~Ic~~l~d~~LA~~v~~ll~tg~N~~~ig~~~~~~fYyr~~~~licq~es~~~~~~~Y~~lVP~~y~p~~~~m~~~l  440 (625)
T KOG4422|consen  361 SAMSICSSLRDLELAYQVHGLLKTGDNWKFIGPDQHRNFYYRKFFDLICQMESIDVTLKWYEDLVPSAYFPHSQTMIHLL  440 (625)
T ss_pred             HHHHHHHHhhhHHHHHHHHHHHHcCCchhhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceecCCchhHHHHH
Confidence            999999999999999999887764211   2233   234667888888888899999999988 2  447777777777


Q ss_pred             HHHHhcCchhHHHHH
Q 040371          218 SACRTFKRLELGEVA  232 (410)
Q Consensus       218 ~~~~~~g~~~~a~~~  232 (410)
                      .+....+.++..-++
T Consensus       441 rA~~v~~~~e~ipRi  455 (625)
T KOG4422|consen  441 RALDVANRLEVIPRI  455 (625)
T ss_pred             HHHhhcCcchhHHHH
Confidence            777766665544443

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.39  E-value=5.8e-10  Score=106.12  Aligned_cols=274  Identities=11%  Similarity=0.034  Sum_probs=199.6

Q ss_pred             cCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHH--HHHHHHHHHHhcCCHHHHH
Q 040371           19 NARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFI--LSAALIDMYSKCGKIQMAK   96 (410)
Q Consensus        19 ~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~--~~~~li~~y~~~g~~~~A~   96 (410)
                      .|++++|.+.+....+..-.| ...|.....+..+.|+++.+.+.+.++.+.  .|+..  ..-.....+...|+++.|.
T Consensus        97 eGd~~~A~k~l~~~~~~~~~p-~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al  173 (398)
T PRK10747         97 EGDYQQVEKLMTRNADHAEQP-VVNYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAAR  173 (398)
T ss_pred             CCCHHHHHHHHHHHHhcccch-HHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHH
Confidence            599999998887755432112 334555556668999999999999999875  44443  3334477899999999999


Q ss_pred             HHHHhcccC---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH-------HHHHHHHHHHHccCCHHHHHHHHH
Q 040371           97 EVFDTVQRN---DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS-------ITFLGLLTACSHCGLVEEGRKYFD  166 (410)
Q Consensus        97 ~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~-------~t~~~ll~a~~~~g~~~~a~~~~~  166 (410)
                      ..++++.+.   +......+...|.+.|++++|.+++..+.+.+..++.       .+|..++..-....+.+...++++
T Consensus       174 ~~l~~~~~~~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~  253 (398)
T PRK10747        174 HGVDKLLEVAPRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWK  253 (398)
T ss_pred             HHHHHHHhcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHH
Confidence            999988743   5678888999999999999999999999988765433       234444444445556677777777


Q ss_pred             HhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCc
Q 040371          167 HMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVA---IVNISRLMGG  242 (410)
Q Consensus       167 ~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~  242 (410)
                      ...+.  .+.++....++...+...|+.++|.+++++. ...||....  ++.+....++.+.+.+.   ..+..|+++.
T Consensus       254 ~lp~~--~~~~~~~~~~~A~~l~~~g~~~~A~~~L~~~l~~~~~~~l~--~l~~~l~~~~~~~al~~~e~~lk~~P~~~~  329 (398)
T PRK10747        254 NQSRK--TRHQVALQVAMAEHLIECDDHDTAQQIILDGLKRQYDERLV--LLIPRLKTNNPEQLEKVLRQQIKQHGDTPL  329 (398)
T ss_pred             hCCHH--HhCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHH--HHHhhccCCChHHHHHHHHHHHhhCCCCHH
Confidence            77643  3457888999999999999999999999887 444555322  23333455888888888   6677888988


Q ss_pred             hHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHH
Q 040371          243 DYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGS  309 (410)
Q Consensus       243 ~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  309 (410)
                      .+..+...+.+.|+|++|.+.|+...+..  |++.. +..       +...+...|+.+++...+++
T Consensus       330 l~l~lgrl~~~~~~~~~A~~~le~al~~~--P~~~~-~~~-------La~~~~~~g~~~~A~~~~~~  386 (398)
T PRK10747        330 LWSTLGQLLMKHGEWQEASLAFRAALKQR--PDAYD-YAW-------LADALDRLHKPEEAAAMRRD  386 (398)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhcC--CCHHH-HHH-------HHHHHHHcCCHHHHHHHHHH
Confidence            89999999999999999999999988753  33211 111       22334456777777666653

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

Probab=99.38  E-value=4.1e-13  Score=121.82  Aligned_cols=258  Identities=14%  Similarity=0.091  Sum_probs=102.4

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHHHHcC-CCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCC---hhhHHHHHHHHHHcC
Q 040371           46 SVIYGCARLGALNHAYWVHNLIIEKK-IELNFILSAALIDMYSKCGKIQMAKEVFDTVQRND---VSVWNAMISGVAIHG  121 (410)
Q Consensus        46 ~ll~a~~~~~~~~~a~~~~~~~~~~g-~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~---~~~~~~li~~~~~~g  121 (410)
                      .+...+.+.|+++.|.+++....... .+.|...|..+.......|+.+.|++.++++...+   ...+..++.. ...+
T Consensus        13 ~~A~~~~~~~~~~~Al~~L~~~~~~~~~~~~~~~~~~~a~La~~~~~~~~A~~ay~~l~~~~~~~~~~~~~l~~l-~~~~   91 (280)
T PF13429_consen   13 RLARLLYQRGDYEKALEVLKKAAQKIAPPDDPEYWRLLADLAWSLGDYDEAIEAYEKLLASDKANPQDYERLIQL-LQDG   91 (280)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc-cccc
Confidence            55778889999999999996655443 35577788888888899999999999999998543   4466667766 6899


Q ss_pred             ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHH
Q 040371          122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLI  201 (410)
Q Consensus       122 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~  201 (410)
                      ++++|.+++.+..+.  .++...+...+..+...++++++..+++.+......+++...|..+...+.+.|+.++|++.+
T Consensus        92 ~~~~A~~~~~~~~~~--~~~~~~l~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~  169 (280)
T PF13429_consen   92 DPEEALKLAEKAYER--DGDPRYLLSALQLYYRLGDYDEAEELLEKLEELPAAPDSARFWLALAEIYEQLGDPDKALRDY  169 (280)
T ss_dssp             ----------------------------H-HHHTT-HHHHHHHHHHHHH-T---T-HHHHHHHHHHHHHCCHHHHHHHHH
T ss_pred             ccccccccccccccc--ccccchhhHHHHHHHHHhHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            999999999877654  356667778888999999999999999998754345667888999999999999999999999


Q ss_pred             HhC-CCCCC-HHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCC
Q 040371          202 TSM-TMEPD-VVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQ  276 (410)
Q Consensus       202 ~~m-~~~p~-~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~  276 (410)
                      ++. ...|+ ......++..+...|+.+++..+   +.+..|.++..+..+..+|...|+.++|...+++.....- .+|
T Consensus       170 ~~al~~~P~~~~~~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~~~~~~~la~~~~~lg~~~~Al~~~~~~~~~~p-~d~  248 (280)
T PF13429_consen  170 RKALELDPDDPDARNALAWLLIDMGDYDEAREALKRLLKAAPDDPDLWDALAAAYLQLGRYEEALEYLEKALKLNP-DDP  248 (280)
T ss_dssp             HHHHHH-TT-HHHHHHHHHHHCTTCHHHHHHHHHHHHHHH-HTSCCHCHHHHHHHHHHT-HHHHHHHHHHHHHHST-T-H
T ss_pred             HHHHHcCCCCHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCcCHHHHHHHHHHHhccccccccccccccccccccc-ccc
Confidence            987 56674 67888999999999999997777   4555578888899999999999999999999999876431 122


Q ss_pred             ceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHH
Q 040371          277 GKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTK  315 (410)
Q Consensus       277 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~  315 (410)
                        .|..      .+...+...|+.++|..+.+++.+.++
T Consensus       249 --~~~~------~~a~~l~~~g~~~~A~~~~~~~~~~l~  279 (280)
T PF13429_consen  249 --LWLL------AYADALEQAGRKDEALRLRRQALRLLR  279 (280)
T ss_dssp             --HHHH------HHHHHHT--------------------
T ss_pred             --cccc------ccccccccccccccccccccccccccC
Confidence              2211      022334567888888888877666554

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.38  E-value=1.7e-09  Score=111.40  Aligned_cols=293  Identities=10%  Similarity=0.016  Sum_probs=177.4

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      ...+..+...+...|++++|+..+++..+. -+.+.. +..+..++...|+.+.|...++++++.. +.+..++..+...
T Consensus        83 ~~a~~~la~~l~~~g~~~eA~~~l~~~l~~-~P~~~~-~~~la~~l~~~g~~~~Al~~l~~al~~~-P~~~~~~~~la~~  159 (765)
T PRK10049         83 DDYQRGLILTLADAGQYDEALVKAKQLVSG-APDKAN-LLALAYVYKRAGRHWDELRAMTQALPRA-PQTQQYPTEYVQA  159 (765)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHH-HHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            344556666666667777777766666654 122344 6666666666677777777777666653 2344444555555


Q ss_pred             HHhcCCHHHHHHHHHhccc---------------------------------------------------CChh-hH---
Q 040371           86 YSKCGKIQMAKEVFDTVQR---------------------------------------------------NDVS-VW---  110 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~---------------------------------------------------~~~~-~~---  110 (410)
                      +.+.|..++|.+.++....                                                   |+.. .+   
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            5555555544443332111                                                   0000 00   


Q ss_pred             -HHHHHHHHHcCChHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCC--ChhHHHHHHH
Q 040371          111 -NAMISGVAIHGLAADASAIFTKMEMFNVL-PDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP--QLEHYGAMVD  186 (410)
Q Consensus       111 -~~li~~~~~~g~~~~A~~l~~~m~~~g~~-p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~--~~~~~~~li~  186 (410)
                       ...+..+...|+.++|+..|+++.+.+.. |+. .-..+..++...|++++|...|+.+.......+  .......+..
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             00122345667888888888888776532 332 222246678888888888888888764311110  1234566666


Q ss_pred             HHHhcCCHHHHHHHHHhC-CCCC-------------C---HHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHH
Q 040371          187 LLGRAGHIEEAYGLITSM-TMEP-------------D---VVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVL  246 (410)
Q Consensus       187 ~~~~~g~~~~A~~~~~~m-~~~p-------------~---~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~  246 (410)
                      ++.+.|++++|..+++++ ...|             +   ...+..+...+...|++++|+.+   +....|.++..+..
T Consensus       319 a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~  398 (765)
T PRK10049        319 SLLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRID  398 (765)
T ss_pred             HHHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            788889999998888877 2222             2   12345566677888999999988   44566888888888


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHH
Q 040371          247 LSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLI  311 (410)
Q Consensus       247 l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~  311 (410)
                      +..++...|+.++|++.+++.....  |+....++.       ........++.++|...++++.
T Consensus       399 lA~l~~~~g~~~~A~~~l~~al~l~--Pd~~~l~~~-------~a~~al~~~~~~~A~~~~~~ll  454 (765)
T PRK10049        399 YASVLQARGWPRAAENELKKAEVLE--PRNINLEVE-------QAWTALDLQEWRQMDVLTDDVV  454 (765)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHhhC--CCChHHHHH-------HHHHHHHhCCHHHHHHHHHHHH
Confidence            9999999999999999998877643  332111110       1111234567888888877543

>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional

Probab=99.35  E-value=1e-09  Score=113.91  Aligned_cols=224  Identities=10%  Similarity=-0.025  Sum_probs=180.1

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--CChhhHHHHHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--NDVSVWNAMISGV  117 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~~~~~~~li~~~  117 (410)
                      +...|..+..++.. ++.++|...+.......  |+......+...+.+.|++++|...|+++..  ++...+..+...+
T Consensus       476 ~~~a~~~LG~~l~~-~~~~eAi~a~~~Al~~~--Pd~~~~L~lA~al~~~Gr~eeAi~~~rka~~~~p~~~a~~~la~al  552 (987)
T PRK09782        476 DAAAWNRLAKCYRD-TLPGVALYAWLQAEQRQ--PDAWQHRAVAYQAYQVEDYATALAAWQKISLHDMSNEDLLAAANTA  552 (987)
T ss_pred             CHHHHHHHHHHHHh-CCcHHHHHHHHHHHHhC--CchHHHHHHHHHHHHCCCHHHHHHHHHHHhccCCCcHHHHHHHHHH
Confidence            56677777777766 88888999888777653  5544444455556789999999999998763  4455677778888


Q ss_pred             HHcCChHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHH
Q 040371          118 AIHGLAADASAIFTKMEMFNVLPDS-ITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEE  196 (410)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~  196 (410)
                      .+.|+.++|...|++.....  |+. ..+..+.......|++++|...++...+   +.|+...|..+...+.+.|++++
T Consensus       553 l~~Gd~~eA~~~l~qAL~l~--P~~~~l~~~La~~l~~~Gr~~eAl~~~~~AL~---l~P~~~a~~~LA~~l~~lG~~de  627 (987)
T PRK09782        553 QAAGNGAARDRWLQQAEQRG--LGDNALYWWLHAQRYIPGQPELALNDLTRSLN---IAPSANAYVARATIYRQRHNVPA  627 (987)
T ss_pred             HHCCCHHHHHHHHHHHHhcC--CccHHHHHHHHHHHHhCCCHHHHHHHHHHHHH---hCCCHHHHHHHHHHHHHCCCHHH
Confidence            99999999999999998754  433 3343444455567999999999999884   36778899999999999999999


Q ss_pred             HHHHHHhC-CCCCC-HHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          197 AYGLITSM-TMEPD-VVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       197 A~~~~~~m-~~~p~-~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      |...+++. ...|+ ...+..+-.++...|+.++|...   ..+..|.++..+..+..+|...|++++|...+++..+..
T Consensus       628 A~~~l~~AL~l~Pd~~~a~~nLG~aL~~~G~~eeAi~~l~~AL~l~P~~~~a~~nLA~al~~lGd~~eA~~~l~~Al~l~  707 (987)
T PRK09782        628 AVSDLRAALELEPNNSNYQAALGYALWDSGDIAQSREMLERAHKGLPDDPALIRQLAYVNQRLDDMAATQHYARLVIDDI  707 (987)
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC
Confidence            99999987 56675 55677777789999999999998   567789999999999999999999999999999887643

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.35  E-value=1e-09  Score=96.10  Aligned_cols=192  Identities=13%  Similarity=0.094  Sum_probs=102.4

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      ..|..+...|...|++++|.+.|++..+.. +.+...+..+...+...|+++.|.+.++...+.. +.+...+..+...|
T Consensus        32 ~~~~~la~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~  109 (234)
T TIGR02521        32 KIRVQLALGYLEQGDLEVAKENLDKALEHD-PDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTFL  109 (234)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHH
Confidence            345555666666666666666666655432 2234455555556666666666666666665543 23444555555566


Q ss_pred             HhcCCHHHHHHHHHhcccC-----ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQRN-----DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~~-----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a  161 (410)
                      ...|++++|.+.|++....     ....|..+...|...|++++|...|.+..... +.+...+..+...+...|++++|
T Consensus       110 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A  188 (234)
T TIGR02521       110 CQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQID-PQRPESLLELAELYYLRGQYKDA  188 (234)
T ss_pred             HHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCChHHHHHHHHHHHHcCCHHHH
Confidence            6666666666666554321     22344445555555666666666665555432 11233445555555556666666


Q ss_pred             HHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371          162 RKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITS  203 (410)
Q Consensus       162 ~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  203 (410)
                      ...++...+.  .+.+...+..+...+...|+.++|..+.+.
T Consensus       189 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~  228 (234)
T TIGR02521       189 RAYLERYQQT--YNQTAESLWLGIRIARALGDVAAAQRYGAQ  228 (234)
T ss_pred             HHHHHHHHHh--CCCCHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            6666555532  122334444555555555555555555444

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.

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

Probab=99.35  E-value=1.5e-10  Score=109.81  Aligned_cols=242  Identities=13%  Similarity=0.064  Sum_probs=186.0

Q ss_pred             CHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC--CCccHHHHHHHHHHHHhcCCHHHHHHH
Q 040371           21 RFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKK--IELNFILSAALIDMYSKCGKIQMAKEV   98 (410)
Q Consensus        21 ~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g--~~~~~~~~~~li~~y~~~g~~~~A~~~   98 (410)
                      +.++|+.+|.+.... +.-.......+..+|...+++++++.+|+.+.+..  .--+..+|.+.+-..-+.=.+.---+-
T Consensus       334 ~~~~A~~~~~klp~h-~~nt~wvl~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~v~Ls~Laq~  412 (638)
T KOG1126|consen  334 NCREALNLFEKLPSH-HYNTGWVLSQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDEVALSYLAQD  412 (638)
T ss_pred             HHHHHHHHHHhhHHh-cCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhhHHHHHHHHH
Confidence            568899999985443 34345677788899999999999999999998763  123567787776554433222221111


Q ss_pred             HHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC
Q 040371           99 FDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ  177 (410)
Q Consensus        99 f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~  177 (410)
                      +-.+......+|-++.+.|..+++.+.|++.|++..+  +.| ..++|+.+..-+.....+|.|...|+....     .+
T Consensus       413 Li~~~~~sPesWca~GNcfSLQkdh~~Aik~f~RAiQ--ldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~-----~~  485 (638)
T KOG1126|consen  413 LIDTDPNSPESWCALGNCFSLQKDHDTAIKCFKRAIQ--LDPRFAYAYTLLGHESIATEEFDKAMKSFRKALG-----VD  485 (638)
T ss_pred             HHhhCCCCcHHHHHhcchhhhhhHHHHHHHHHHHhhc--cCCccchhhhhcCChhhhhHHHHhHHHHHHhhhc-----CC
Confidence            2222233568999999999999999999999999876  456 678888888888888899999999987663     36


Q ss_pred             hhHHHHH---HHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHH
Q 040371          178 LEHYGAM---VDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSN  249 (410)
Q Consensus       178 ~~~~~~l---i~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~  249 (410)
                      +.+|+++   .-.|.+.++++.|+-.|++. .+.| +.+....+-..+-+.|+.|+|+++   ...++|.++..-.--+.
T Consensus       486 ~rhYnAwYGlG~vy~Kqek~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~  565 (638)
T KOG1126|consen  486 PRHYNAWYGLGTVYLKQEKLEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRAS  565 (638)
T ss_pred             chhhHHHHhhhhheeccchhhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHH
Confidence            6677654   45688999999999999887 7777 566667777778899999999999   56678888888888888


Q ss_pred             HHHhcCChhHHHHHHHHHHhC
Q 040371          250 MYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       250 ~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      .+...++.++|.+.++++++-
T Consensus       566 il~~~~~~~eal~~LEeLk~~  586 (638)
T KOG1126|consen  566 ILFSLGRYVEALQELEELKEL  586 (638)
T ss_pred             HHHhhcchHHHHHHHHHHHHh
Confidence            899999999999999999874

>PRK10049 pgaA outer membrane protein PgaA; Provisional

Probab=99.34  E-value=3.4e-09  Score=109.25  Aligned_cols=263  Identities=9%  Similarity=-0.018  Sum_probs=189.7

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhhCCHHH------------------------
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEP-DKFTFASVIYGCARLGALNH------------------------   59 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~~~~~~~~------------------------   59 (410)
                      +.. |..+...+...|++++|+..+++..+.  .| +...+..+..++...+..+.                        
T Consensus       116 ~~~-~~~la~~l~~~g~~~~Al~~l~~al~~--~P~~~~~~~~la~~l~~~~~~e~Al~~l~~~~~~p~~~~~l~~~~~~  192 (765)
T PRK10049        116 KAN-LLALAYVYKRAGRHWDELRAMTQALPR--APQTQQYPTEYVQALRNNRLSAPALGAIDDANLTPAEKRDLEADAAA  192 (765)
T ss_pred             CHH-HHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHCCChHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            344 888889999999999999999999875  44 44455555555555555443                        


Q ss_pred             ----------------------HHHHHHHHHHc-CCCccHH--HHHH---HHHHHHhcCCHHHHHHHHHhcccCC--hh-
Q 040371           60 ----------------------AYWVHNLIIEK-KIELNFI--LSAA---LIDMYSKCGKIQMAKEVFDTVQRND--VS-  108 (410)
Q Consensus        60 ----------------------a~~~~~~~~~~-g~~~~~~--~~~~---li~~y~~~g~~~~A~~~f~~m~~~~--~~-  108 (410)
                                            |.+.++.+++. ...|+..  ...+   .+..+...|++++|+..|+++.+.+  .. 
T Consensus       193 ~~~r~~~~~~~~~~~r~~~ad~Al~~~~~ll~~~~~~p~~~~~~~~a~~d~l~~Ll~~g~~~eA~~~~~~ll~~~~~~P~  272 (765)
T PRK10049        193 ELVRLSFMPTRSEKERYAIADRALAQYDALEALWHDNPDATADYQRARIDRLGALLARDRYKDVISEYQRLKAEGQIIPP  272 (765)
T ss_pred             HHHHhhcccccChhHHHHHHHHHHHHHHHHHhhcccCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhccCCCCCH
Confidence                                  33344444432 1122211  1111   1234457799999999999988542  11 


Q ss_pred             -hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC---CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcC----------C
Q 040371          109 -VWNAMISGVAIHGLAADASAIFTKMEMFNVLP---DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYS----------I  174 (410)
Q Consensus       109 -~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p---~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~----------~  174 (410)
                       .--.+...|...|++++|+..|+++.......   .......+..++...|++++|.++++.+.+...          -
T Consensus       273 ~a~~~la~~yl~~g~~e~A~~~l~~~l~~~p~~~~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~  352 (765)
T PRK10049        273 WAQRWVASAYLKLHQPEKAQSILTELFYHPETIADLSDEELADLFYSLLESENYPGALTVTAHTINNSPPFLRLYGSPTS  352 (765)
T ss_pred             HHHHHHHHHHHhcCCcHHHHHHHHHHhhcCCCCCCCChHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCceEeecCCCCC
Confidence             11224678999999999999999987643111   123456677788999999999999999885311          1


Q ss_pred             CCC---hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHH
Q 040371          175 QPQ---LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVL  246 (410)
Q Consensus       175 ~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~  246 (410)
                      .|+   ...+..+...+...|++++|+++++++ ...| +...+..+...+...|++++|+..   .....|.+...+..
T Consensus       353 ~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~al~~~P~n~~l~~~lA~l~~~~g~~~~A~~~l~~al~l~Pd~~~l~~~  432 (765)
T PRK10049        353 IPNDDWLQGQSLLSQVAKYSNDLPQAEMRARELAYNAPGNQGLRIDYASVLQARGWPRAAENELKKAEVLEPRNINLEVE  432 (765)
T ss_pred             CCCchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhhCCCChHHHHH
Confidence            122   234566778899999999999999997 4445 567888999999999999999999   66778888888999


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhC
Q 040371          247 LSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       247 l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      ++..+.+.|++++|+.+++++.+.
T Consensus       433 ~a~~al~~~~~~~A~~~~~~ll~~  456 (765)
T PRK10049        433 QAWTALDLQEWRQMDVLTDDVVAR  456 (765)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHh
Confidence            999999999999999999998764

>PRK10747 putative protoheme IX biogenesis protein; Provisional

Probab=99.31  E-value=4e-09  Score=100.38  Aligned_cols=252  Identities=9%  Similarity=0.021  Sum_probs=189.3

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHH--HHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFA--SVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~--~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      .|-....+..+.|+++.|.+.|.++.+.  .|+.....  .....+...|+++.|.+.++.+.+.. +.++.+...+...
T Consensus       120 ~~llaA~aA~~~g~~~~A~~~l~~A~~~--~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~-P~~~~al~ll~~~  196 (398)
T PRK10747        120 NYLLAAEAAQQRGDEARANQHLERAAEL--ADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVA-PRHPEVLRLAEQA  196 (398)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhc--CCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            3433344447899999999999999763  66654433  33567788999999999999999886 5578999999999


Q ss_pred             HHhcCCHHHHHHHHHhcccCCh-----------hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040371           86 YSKCGKIQMAKEVFDTVQRNDV-----------SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSH  154 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~~~~-----------~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~  154 (410)
                      |.+.|++++|.+++..+.+...           .+|..++.......+.+...++++..-.. .+.+......+..++..
T Consensus       197 ~~~~gdw~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~l~~~w~~lp~~-~~~~~~~~~~~A~~l~~  275 (398)
T PRK10747        197 YIRTGAWSSLLDILPSMAKAHVGDEEHRAMLEQQAWIGLMDQAMADQGSEGLKRWWKNQSRK-TRHQVALQVAMAEHLIE  275 (398)
T ss_pred             HHHHHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHhCCHH-HhCCHHHHHHHHHHHHH
Confidence            9999999999999999875422           13444444444555566667777766443 34567788889999999


Q ss_pred             cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCchhHHHHH
Q 040371          155 CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       155 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      .|+.++|..+++...+.   .|+...  .++.+....++.+++++..++. ...|+ ......+-..|...+++++|.+.
T Consensus       276 ~g~~~~A~~~L~~~l~~---~~~~~l--~~l~~~l~~~~~~~al~~~e~~lk~~P~~~~l~l~lgrl~~~~~~~~~A~~~  350 (398)
T PRK10747        276 CDDHDTAQQIILDGLKR---QYDERL--VLLIPRLKTNNPEQLEKVLRQQIKQHGDTPLLWSTLGQLLMKHGEWQEASLA  350 (398)
T ss_pred             CCCHHHHHHHHHHHHhc---CCCHHH--HHHHhhccCCChHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            99999999999988753   444422  2333344569999999999887 55665 45677888889999999999999


Q ss_pred             HHhhc--cCCCchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          233 IVNIS--RLMGGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       233 ~~~~~--~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                      +.+.-  .++...+..|..++.+.|+.++|.+++++-.
T Consensus       351 le~al~~~P~~~~~~~La~~~~~~g~~~~A~~~~~~~l  388 (398)
T PRK10747        351 FRAALKQRPDAYDYAWLADALDRLHKPEEAAAMRRDGL  388 (398)
T ss_pred             HHHHHhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            54432  2333567789999999999999999998653

>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW

Probab=99.29  E-value=1.8e-09  Score=94.47  Aligned_cols=193  Identities=14%  Similarity=0.049  Sum_probs=108.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040371           76 FILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTAC  152 (410)
Q Consensus        76 ~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~  152 (410)
                      ...+..+...|.+.|++++|...|++..+   .+...|..+...|...|++++|.+.|++..+.. +.+...+..+...+
T Consensus        31 ~~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~~~~~  109 (234)
T TIGR02521        31 AKIRVQLALGYLEQGDLEVAKENLDKALEHDPDDYLAYLALALYYQQLGELEKAEDSFRRALTLN-PNNGDVLNNYGTFL  109 (234)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHH
Confidence            44455555666666666666666655432   134455555566666666666666666655532 22334455555566


Q ss_pred             HccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHH
Q 040371          153 SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGE  230 (410)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~  230 (410)
                      ...|++++|...++...+..........+..+...|...|++++|...+++. ...| +...+..+...+...|++++|.
T Consensus       110 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~  189 (234)
T TIGR02521       110 CQQGKYEQAMQQFEQAIEDPLYPQPARSLENAGLCALKAGDFDKAEKYLTRALQIDPQRPESLLELAELYYLRGQYKDAR  189 (234)
T ss_pred             HHcccHHHHHHHHHHHHhccccccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCChHHHHHHHHHHHHcCCHHHHH
Confidence            6666666666666665532111122344555556666666666666666654 2233 3445555666666666666666


Q ss_pred             HH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040371          231 VA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       231 ~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                      ..   .....|.++..+..+...+...|+.++|..+.+.+..
T Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  231 (234)
T TIGR02521       190 AYLERYQQTYNQTAESLWLGIRIARALGDVAAAQRYGAQLQK  231 (234)
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            65   2223344445555666777777777777777666544

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.

>PRK12370 invasion protein regulator; Provisional

Probab=99.27  E-value=9.4e-09  Score=102.09  Aligned_cols=257  Identities=12%  Similarity=0.010  Sum_probs=181.4

Q ss_pred             ChhHHHHHHHHHHH-----cCCHhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHh---------hCCHHHHHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVR-----NARFDEALRFFREMLSSKVEPD-KFTFASVIYGCAR---------LGALNHAYWVHNLIIE   69 (410)
Q Consensus         5 ~~~~~n~li~~~~~-----~g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~a~~~---------~~~~~~a~~~~~~~~~   69 (410)
                      +..+|...+.+-..     .+..++|+.+|++..+.  .|+ ...|..+..++..         .+++++|...++++++
T Consensus       255 ~~da~~~~lrg~~~~~~~~~~~~~~A~~~~~~Al~l--dP~~a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~  332 (553)
T PRK12370        255 SIDSTMVYLRGKHELNQYTPYSLQQALKLLTQCVNM--SPNSIAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATE  332 (553)
T ss_pred             ChHHHHHHHHhHHHHHccCHHHHHHHHHHHHHHHhc--CCccHHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHh
Confidence            44566666666422     13467999999999874  454 4456555554432         2347899999999998


Q ss_pred             cCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH-HHH
Q 040371           70 KKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS-ITF  145 (410)
Q Consensus        70 ~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~-~t~  145 (410)
                      .. +.+...+..+...+...|++++|...|++..+  | +...|..+...+...|++++|+..|++..+.  .|+. ..+
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            75 45788888999999999999999999998764  4 4568888899999999999999999999885  4442 233


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHH-HHHHHHHHHHh
Q 040371          146 LGLLTACSHCGLVEEGRKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVV-VWRALLSACRT  222 (410)
Q Consensus       146 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~-~~~~li~~~~~  222 (410)
                      ..++..+...|++++|...++...+. . .| +...+..+...|...|++++|...++++ +..|+.. .++.+...+..
T Consensus       410 ~~~~~~~~~~g~~eeA~~~~~~~l~~-~-~p~~~~~~~~la~~l~~~G~~~eA~~~~~~~~~~~~~~~~~~~~l~~~~~~  487 (553)
T PRK12370        410 ITKLWITYYHTGIDDAIRLGDELRSQ-H-LQDNPILLSMQVMFLSLKGKHELARKLTKEISTQEITGLIAVNLLYAEYCQ  487 (553)
T ss_pred             HHHHHHHHhccCHHHHHHHHHHHHHh-c-cccCHHHHHHHHHHHHhCCCHHHHHHHHHHhhhccchhHHHHHHHHHHHhc
Confidence            33444566789999999999998753 2 34 3556777888899999999999999987 4455544 44555556677


Q ss_pred             cCchhHHHHHH---HhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          223 FKRLELGEVAI---VNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       223 ~g~~~~a~~~~---~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      .|+  .+...+   .+.....+..+..+...|+-.|+-+.+..+ +++.+.|
T Consensus       488 ~g~--~a~~~l~~ll~~~~~~~~~~~~~~~~~~~~g~~~~~~~~-~~~~~~~  536 (553)
T PRK12370        488 NSE--RALPTIREFLESEQRIDNNPGLLPLVLVAHGEAIAEKMW-NKFKNED  536 (553)
T ss_pred             cHH--HHHHHHHHHHHHhhHhhcCchHHHHHHHHHhhhHHHHHH-HHhhccc
Confidence            774  555542   222222222233366667778887877777 7777665

>KOG4422 consensus Uncharacterized conserved protein [Function unknown]

Probab=99.24  E-value=4.8e-09  Score=94.78  Aligned_cols=221  Identities=15%  Similarity=0.247  Sum_probs=163.9

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHH--hhCCHHHHH-HHHHHHHH-------------
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCA--RLGALNHAY-WVHNLIIE-------------   69 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~--~~~~~~~a~-~~~~~~~~-------------   69 (410)
                      +++=|.|+.. ..+|..+++.-+|+.|.+.|+......-..++..-+  ...++--+. +-|-.|.+             
T Consensus       116 V~~E~nL~km-IS~~EvKDs~ilY~~m~~e~~~vS~kvq~~L~~LV~~~Ns~~~~~~E~~~Fv~~~~~~E~S~~sWK~G~  194 (625)
T KOG4422|consen  116 VETENNLLKM-ISSREVKDSCILYERMRSENVDVSEKVQLELFRLVTYYNSSNVPFAEWEEFVGMRNFGEDSTSSWKSGA  194 (625)
T ss_pred             hcchhHHHHH-HhhcccchhHHHHHHHHhcCCCCCHHHHHHHHHHHHhhcCCCCcchhHHHHhhcccccccccccccccc
Confidence            3455666654 357889999999999999998877766555554332  222221111 11111111             


Q ss_pred             ------cCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccC----ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCC
Q 040371           70 ------KKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRN----DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVL  139 (410)
Q Consensus        70 ------~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  139 (410)
                            .-.+.+..++.++|.+.+|--..+.|++++.+-...    +..++|.+|.+-.-..    ..++..+|....++
T Consensus       195 vAdL~~E~~PKT~et~s~mI~Gl~K~~~~ERA~~L~kE~~~~k~kv~~~aFN~lI~~~S~~~----~K~Lv~EMisqkm~  270 (625)
T KOG4422|consen  195 VADLLFETLPKTDETVSIMIAGLCKFSSLERARELYKEHRAAKGKVYREAFNGLIGASSYSV----GKKLVAEMISQKMT  270 (625)
T ss_pred             HHHHHHhhcCCCchhHHHHHHHHHHHHhHHHHHHHHHHHHHhhheeeHHhhhhhhhHHHhhc----cHHHHHHHHHhhcC
Confidence                  123556789999999999999999999999987643    6778999987654332    27899999999999


Q ss_pred             CCHHHHHHHHHHHHccCCHHH----HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHH-HHHHHHhC----------
Q 040371          140 PDSITFLGLLTACSHCGLVEE----GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEE-AYGLITSM----------  204 (410)
Q Consensus       140 p~~~t~~~ll~a~~~~g~~~~----a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~-A~~~~~~m----------  204 (410)
                      ||..|||++++..++.|+++.    |.+++.+|++ .|++|...+|..+|..+.+-++..+ |..++.++          
T Consensus       271 Pnl~TfNalL~c~akfg~F~~ar~aalqil~EmKe-iGVePsLsSyh~iik~f~re~dp~k~as~~i~dI~N~ltGK~fk  349 (625)
T KOG4422|consen  271 PNLFTFNALLSCAAKFGKFEDARKAALQILGEMKE-IGVEPSLSSYHLIIKNFKRESDPQKVASSWINDIQNSLTGKTFK  349 (625)
T ss_pred             CchHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHH-hCCCcchhhHHHHHHHhcccCCchhhhHHHHHHHHHhhccCccc
Confidence            999999999999999998765    5567788885 5999999999999999999887754 44444433          


Q ss_pred             CCCC-CHHHHHHHHHHHHhcCchhHHHHH
Q 040371          205 TMEP-DVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       205 ~~~p-~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      ++.| |..-|.+.++.|....+.+.|.++
T Consensus       350 p~~p~d~~FF~~AM~Ic~~l~d~~LA~~v  378 (625)
T KOG4422|consen  350 PITPTDNKFFQSAMSICSSLRDLELAYQV  378 (625)
T ss_pred             CCCCchhHHHHHHHHHHHHhhhHHHHHHH
Confidence            3445 456788889999999999999998

>TIGR00540 hemY_coli hemY protein

Probab=99.21  E-value=2.9e-08  Score=94.96  Aligned_cols=255  Identities=11%  Similarity=-0.005  Sum_probs=182.3

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCH--HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDK--FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~--~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      .+=....++.+.|++++|.+.|.+..+.  .|+.  ..-..........|+++.|.+.++.+.+.. +.+..+...+...
T Consensus       120 ~~llaA~aa~~~g~~~~A~~~l~~a~~~--~p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~-P~~~~~l~ll~~~  196 (409)
T TIGR00540       120 NLIKAAEAAQQRGDEARANQHLEEAAEL--AGNDNILVEIARTRILLAQNELHAARHGVDKLLEMA-PRHKEVLKLAEEA  196 (409)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            3444556677889999999999998764  3444  234445777888999999999999999986 5578899999999


Q ss_pred             HHhcCCHHHHHHHHHhcccC---ChhhHHH----HHHHHHHcCChHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHcc
Q 040371           86 YSKCGKIQMAKEVFDTVQRN---DVSVWNA----MISGVAIHGLAADASAIFTKMEMFNV---LPDSITFLGLLTACSHC  155 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~~---~~~~~~~----li~~~~~~g~~~~A~~l~~~m~~~g~---~p~~~t~~~ll~a~~~~  155 (410)
                      |.+.|++++|.+.++.+.+.   +...+..    ...++...+..+++.+.+..+.....   +.+...+..+...+...
T Consensus       197 ~~~~~d~~~a~~~l~~l~k~~~~~~~~~~~l~~~a~~~~l~~~~~~~~~~~L~~~~~~~p~~~~~~~~l~~~~a~~l~~~  276 (409)
T TIGR00540       197 YIRSGAWQALDDIIDNMAKAGLFDDEEFADLEQKAEIGLLDEAMADEGIDGLLNWWKNQPRHRRHNIALKIALAEHLIDC  276 (409)
T ss_pred             HHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHCCHHHhCCHHHHHHHHHHHHHC
Confidence            99999999999999988854   2222211    11122333333444445555554321   13677888888999999


Q ss_pred             CCHHHHHHHHHHhhhhcCCCCChhH-HHHHHHHH--HhcCCHHHHHHHHHhC-CCCCCH---HHHHHHHHHHHhcCchhH
Q 040371          156 GLVEEGRKYFDHMRSRYSIQPQLEH-YGAMVDLL--GRAGHIEEAYGLITSM-TMEPDV---VVWRALLSACRTFKRLEL  228 (410)
Q Consensus       156 g~~~~a~~~~~~m~~~~~~~~~~~~-~~~li~~~--~~~g~~~~A~~~~~~m-~~~p~~---~~~~~li~~~~~~g~~~~  228 (410)
                      |+.++|.++++...++   .|+... ...++..+  ...++.+.+.+.+++. ...|+.   ....++-..+.+.|++++
T Consensus       277 g~~~~A~~~l~~~l~~---~pd~~~~~~~~l~~~~~l~~~~~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~~~~~~~  353 (409)
T TIGR00540       277 DDHDSAQEIIFDGLKK---LGDDRAISLPLCLPIPRLKPEDNEKLEKLIEKQAKNVDDKPKCCINRALGQLLMKHGEFIE  353 (409)
T ss_pred             CChHHHHHHHHHHHhh---CCCcccchhHHHHHhhhcCCCChHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHcccHHH
Confidence            9999999999999864   344331 11133333  3357778888888776 444543   455677888999999999


Q ss_pred             HHHHHHh--h--ccCCCchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          229 GEVAIVN--I--SRLMGGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       229 a~~~~~~--~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                      |.+.+..  .  ..+++..+..+...+.+.|+.++|.+++++-.
T Consensus       354 A~~~le~a~a~~~~p~~~~~~~La~ll~~~g~~~~A~~~~~~~l  397 (409)
T TIGR00540       354 AADAFKNVAACKEQLDANDLAMAADAFDQAGDKAEAAAMRQDSL  397 (409)
T ss_pred             HHHHHHHhHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            9999662  3  23455567899999999999999999998743

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.

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.14  E-value=1.6e-08  Score=96.64  Aligned_cols=228  Identities=17%  Similarity=0.141  Sum_probs=168.5

Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHHc-----CC-CccHH-HHHHHHHHHHhcCCHHHHHHHHHhccc-------C-
Q 040371           41 KFTFASVIYGCARLGALNHAYWVHNLIIEK-----KI-ELNFI-LSAALIDMYSKCGKIQMAKEVFDTVQR-------N-  105 (410)
Q Consensus        41 ~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~-----g~-~~~~~-~~~~li~~y~~~g~~~~A~~~f~~m~~-------~-  105 (410)
                      ..|...+...|...|+++.|..++++.++.     |. .|.+. ..+.+...|...+++++|..+|+++..       + 
T Consensus       199 ~~~~~~La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~~G~~  278 (508)
T KOG1840|consen  199 LRTLRNLAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEVFGED  278 (508)
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhcCCC
Confidence            346677889999999999999999888765     21 22222 334577789999999999999987752       1 


Q ss_pred             ---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHC-----CCC-CCH-HHHHHHHHHHHccCCHHHHHHHHHHhhhhcC--
Q 040371          106 ---DVSVWNAMISGVAIHGLAADASAIFTKMEMF-----NVL-PDS-ITFLGLLTACSHCGLVEEGRKYFDHMRSRYS--  173 (410)
Q Consensus       106 ---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g~~-p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~--  173 (410)
                         -..+++.|...|.+.|++++|...+++..+-     |.. |.. .-++.+...|...+.+++|..+++...+.+-  
T Consensus       279 h~~va~~l~nLa~ly~~~GKf~EA~~~~e~Al~I~~~~~~~~~~~v~~~l~~~~~~~~~~~~~Eea~~l~q~al~i~~~~  358 (508)
T KOG1840|consen  279 HPAVAATLNNLAVLYYKQGKFAEAEEYCERALEIYEKLLGASHPEVAAQLSELAAILQSMNEYEEAKKLLQKALKIYLDA  358 (508)
T ss_pred             CHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHHHHHhhccChHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhh
Confidence               2357888888999999999888888766431     222 222 2366777888999999999999988765432  


Q ss_pred             CCCC----hhHHHHHHHHHHhcCCHHHHHHHHHhC---------CCCCC-HHHHHHHHHHHHhcCchhHHHHH-------
Q 040371          174 IQPQ----LEHYGAMVDLLGRAGHIEEAYGLITSM---------TMEPD-VVVWRALLSACRTFKRLELGEVA-------  232 (410)
Q Consensus       174 ~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~m---------~~~p~-~~~~~~li~~~~~~g~~~~a~~~-------  232 (410)
                      ..++    ..+++.|...|-..|++++|.+++++.         +..+. ....+.|-.+|.+.+++++|.++       
T Consensus       359 ~g~~~~~~a~~~~nl~~l~~~~gk~~ea~~~~k~ai~~~~~~~~~~~~~~~~~l~~la~~~~~~k~~~~a~~l~~~~~~i  438 (508)
T KOG1840|consen  359 PGEDNVNLAKIYANLAELYLKMGKYKEAEELYKKAIQILRELLGKKDYGVGKPLNQLAEAYEELKKYEEAEQLFEEAKDI  438 (508)
T ss_pred             ccccchHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHhcccCcChhhhHHHHHHHHHHHHhcccchHHHHHHHHHHH
Confidence            1222    467999999999999999999999887         11222 45667788889999999988887       


Q ss_pred             HHhhccCC---CchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          233 IVNISRLM---GGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       233 ~~~~~~~~---~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                      .....|..   ..+|..|..+|.+.|++++|.++.+...
T Consensus       439 ~~~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~~~~~~  477 (508)
T KOG1840|consen  439 MKLCGPDHPDVTYTYLNLAALYRAQGNYEAAEELEEKVL  477 (508)
T ss_pred             HHHhCCCCCchHHHHHHHHHHHHHcccHHHHHHHHHHHH
Confidence            22223333   3468889999999999999999988765

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

Probab=99.13  E-value=6.1e-08  Score=88.31  Aligned_cols=198  Identities=13%  Similarity=0.069  Sum_probs=153.3

Q ss_pred             hCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc---cCChhhHHHHHHHHHHcCChHHHHHHH
Q 040371           54 LGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ---RNDVSVWNAMISGVAIHGLAADASAIF  130 (410)
Q Consensus        54 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~---~~~~~~~~~li~~~~~~g~~~~A~~l~  130 (410)
                      .|+++.|.+.+...+...-.-....||. .-.+-+.|++++|+..|-++.   ..++...-.+.+.|-...++..|++++
T Consensus       503 ngd~dka~~~ykeal~ndasc~ealfni-glt~e~~~~ldeald~f~klh~il~nn~evl~qianiye~led~aqaie~~  581 (840)
T KOG2003|consen  503 NGDLDKAAEFYKEALNNDASCTEALFNI-GLTAEALGNLDEALDCFLKLHAILLNNAEVLVQIANIYELLEDPAQAIELL  581 (840)
T ss_pred             cCcHHHHHHHHHHHHcCchHHHHHHHHh-cccHHHhcCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhCHHHHHHHH
Confidence            4678888888888877643333334433 234667889999999887664   456667777788888888999999988


Q ss_pred             HHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC
Q 040371          131 TKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP  208 (410)
Q Consensus       131 ~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p  208 (410)
                      .+...  +.| |......|...|-+.|+-.+|.+.+-.--+  -++.+..+...|..-|....-+++|...|++. -++|
T Consensus       582 ~q~~s--lip~dp~ilskl~dlydqegdksqafq~~ydsyr--yfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp  657 (840)
T KOG2003|consen  582 MQANS--LIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYR--YFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQP  657 (840)
T ss_pred             HHhcc--cCCCCHHHHHHHHHHhhcccchhhhhhhhhhccc--ccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCc
Confidence            66543  444 677788888999999999999988766442  34567888888888899999999999999988 5789


Q ss_pred             CHHHHHHHHHHH-HhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCC
Q 040371          209 DVVVWRALLSAC-RTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKR  256 (410)
Q Consensus       209 ~~~~~~~li~~~-~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~  256 (410)
                      +..-|..+|..| ++.|++..|..+   ..+..|.+....-.|+..+...|.
T Consensus       658 ~~~kwqlmiasc~rrsgnyqka~d~yk~~hrkfpedldclkflvri~~dlgl  709 (840)
T KOG2003|consen  658 NQSKWQLMIASCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFLVRIAGDLGL  709 (840)
T ss_pred             cHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCccchHHHHHHHHHhccccc
Confidence            999999999876 678999999999   455668888888888888887775

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

Probab=99.13  E-value=1.1e-07  Score=83.17  Aligned_cols=246  Identities=11%  Similarity=0.101  Sum_probs=181.7

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCc---cHHHHHHHHHHHHhcCCHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIEL---NFILSAALIDMYSKCGKIQM   94 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~---~~~~~~~li~~y~~~g~~~~   94 (410)
                      -+.++++|.++|.+|.+.. +-+..+-.++.+.+-+.|..|.|+.+|+-+.++.--+   .....-.|..=|.+.|-+|.
T Consensus        47 Ls~Q~dKAvdlF~e~l~~d-~~t~e~~ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DR  125 (389)
T COG2956          47 LSNQPDKAVDLFLEMLQED-PETFEAHLTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDR  125 (389)
T ss_pred             hhcCcchHHHHHHHHHhcC-chhhHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhH
Confidence            4678999999999999842 3344567788899999999999999999998863211   23445677888999999999


Q ss_pred             HHHHHHhcccCCh---hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHH----HHHHHHHHHHccCCHHHHHHHHHH
Q 040371           95 AKEVFDTVQRNDV---SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSI----TFLGLLTACSHCGLVEEGRKYFDH  167 (410)
Q Consensus        95 A~~~f~~m~~~~~---~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~----t~~~ll~a~~~~g~~~~a~~~~~~  167 (410)
                      |+.+|..+.+.+.   .+..-++..|-+..+|++|++.-+++...+-.+..+    .|.-+........+++.|...+..
T Consensus       126 AE~~f~~L~de~efa~~AlqqLl~IYQ~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~k  205 (389)
T COG2956         126 AEDIFNQLVDEGEFAEGALQQLLNIYQATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKK  205 (389)
T ss_pred             HHHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence            9999999887433   466678999999999999999999998876555432    355566666678899999999998


Q ss_pred             hhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCH--HHHHHHHHHHHhcCchhHHHHHHHhhccCCC--
Q 040371          168 MRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDV--VVWRALLSACRTFKRLELGEVAIVNISRLMG--  241 (410)
Q Consensus       168 m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~--~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~--  241 (410)
                      ..+.   .|+ +..--.+.+.+...|+++.|.+.++.. ...|+.  .+...|..+|.+.|+.+++...+.+....+.  
T Consensus       206 Alqa---~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQn~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g~  282 (389)
T COG2956         206 ALQA---DKKCVRASIILGRVELAKGDYQKAVEALERVLEQNPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTGA  282 (389)
T ss_pred             HHhh---CccceehhhhhhHHHHhccchHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCc
Confidence            8753   333 444556678899999999999999988 445653  4677889999999999999998555433322  


Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHH
Q 040371          242 GDYVLLSNMYCYLKRWDTAENVREIM  267 (410)
Q Consensus       242 ~~~~~l~~~~~~~g~~~~a~~~~~~m  267 (410)
                      ..-..|...-....-.+.|...+.+-
T Consensus       283 ~~~l~l~~lie~~~G~~~Aq~~l~~Q  308 (389)
T COG2956         283 DAELMLADLIELQEGIDAAQAYLTRQ  308 (389)
T ss_pred             cHHHHHHHHHHHhhChHHHHHHHHHH
Confidence            23333334334444455555554433

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.13  E-value=1.4e-07  Score=96.30  Aligned_cols=255  Identities=12%  Similarity=0.076  Sum_probs=174.3

Q ss_pred             HHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCH
Q 040371           13 IGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKI   92 (410)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~   92 (410)
                      ...|...|++++|+++|+++.+.. +-|...+..++..+...++.++|.+.++.+.+.  .|+...+-.++..+...++.
T Consensus       109 A~ly~~~gdyd~Aiely~kaL~~d-P~n~~~l~gLa~~y~~~~q~~eAl~~l~~l~~~--dp~~~~~l~layL~~~~~~~  185 (822)
T PRK14574        109 ARAYRNEKRWDQALALWQSSLKKD-PTNPDLISGMIMTQADAGRGGVVLKQATELAER--DPTVQNYMTLSYLNRATDRN  185 (822)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhhcCCHHHHHHHHHHhccc--CcchHHHHHHHHHHHhcchH
Confidence            446666788888888888877653 234555666667777777777777777777664  34444444444444445555


Q ss_pred             HHHHHHHHhccc--C------------------------------Ch---------------------------------
Q 040371           93 QMAKEVFDTVQR--N------------------------------DV---------------------------------  107 (410)
Q Consensus        93 ~~A~~~f~~m~~--~------------------------------~~---------------------------------  107 (410)
                      .+|.+.++++.+  |                              +.                                 
T Consensus       186 ~~AL~~~ekll~~~P~n~e~~~~~~~~l~~~~~~~~a~~l~~~~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~  265 (822)
T PRK14574        186 YDALQASSEAVRLAPTSEEVLKNHLEILQRNRIVEPALRLAKENPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERFD  265 (822)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCcHHHHHHHHhCccccCHHHHHHHHHHHHHHHHhhcccccccchhhHH
Confidence            456666655431  1                              00                                 


Q ss_pred             -----------------------hhH----HHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371          108 -----------------------SVW----NAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus       108 -----------------------~~~----~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                                             ..|    --.+-++...|+..++++.|+.|...|.+....+-..+..+|...+..++
T Consensus       266 ~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~k  345 (822)
T PRK14574        266 IADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQTADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEK  345 (822)
T ss_pred             HHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHH
Confidence                                   000    01234566678888899999998888866555677888899999999999


Q ss_pred             HHHHHHHhhhhcC----CCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCC--------------C--CCHH-HHHHHHHH
Q 040371          161 GRKYFDHMRSRYS----IQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTM--------------E--PDVV-VWRALLSA  219 (410)
Q Consensus       161 a~~~~~~m~~~~~----~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~--------------~--p~~~-~~~~li~~  219 (410)
                      |..++..+....+    ..++......|.-+|..++++++|..+++++.-              .  ||-. ....++..
T Consensus       346 A~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~~l~~~~~~~p~~~~~~~~~~~~pn~d~~~~~~l~a~~  425 (822)
T PRK14574        346 AAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQFAVNYSEQTPYQVGVYGLPGKEPNDDWIEGQTLLVQS  425 (822)
T ss_pred             HHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHHHHHHHHhcCCcEEeccCCCCCCCCccHHHHHHHHHHH
Confidence            9999998865322    123344457788889999999999999888711              1  2322 33445666


Q ss_pred             HHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          220 CRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       220 ~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      +.-.|++.+|++.   +....|.|+.....+.+++...|...+|++.++.....
T Consensus       426 ~~~~gdl~~Ae~~le~l~~~aP~n~~l~~~~A~v~~~Rg~p~~A~~~~k~a~~l  479 (822)
T PRK14574        426 LVALNDLPTAQKKLEDLSSTAPANQNLRIALASIYLARDLPRKAEQELKAVESL  479 (822)
T ss_pred             HHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHhhh
Confidence            7888999999998   45556888888889999999999999999999766543

>KOG1840 consensus Kinesin light chain [Cytoskeleton]

Probab=99.12  E-value=1.4e-08  Score=96.97  Aligned_cols=225  Identities=13%  Similarity=0.094  Sum_probs=171.0

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHC-----C-CCCCHHH-HHHHHHHHHhhCCHHHHHHHHHHHHHc-----CC--C
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSS-----K-VEPDKFT-FASVIYGCARLGALNHAYWVHNLIIEK-----KI--E   73 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~-----g-~~pd~~t-~~~ll~a~~~~~~~~~a~~~~~~~~~~-----g~--~   73 (410)
                      +...+...|...|++++|..+++..++.     | ..|...+ .+.+...|...+.+++|..+|+.++..     |-  +
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            4445999999999999999999988753     2 1344443 334677888999999999999998754     21  2


Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHhccc----------CCh-hhHHHHHHHHHHcCChHHHHHHHHHHHHC---CCC
Q 040371           74 LNFILSAALIDMYSKCGKIQMAKEVFDTVQR----------NDV-SVWNAMISGVAIHGLAADASAIFTKMEMF---NVL  139 (410)
Q Consensus        74 ~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~----------~~~-~~~~~li~~~~~~g~~~~A~~l~~~m~~~---g~~  139 (410)
                      .-..+++.|...|.+.|++++|...+++..+          +.+ ...+.++..+...+++++|..+++...+.   -..
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            2245667777889999999999888775431          222 24677788888999999999999876542   233


Q ss_pred             CCH----HHHHHHHHHHHccCCHHHHHHHHHHhhhhc----C-CCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC-----
Q 040371          140 PDS----ITFLGLLTACSHCGLVEEGRKYFDHMRSRY----S-IQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM-----  204 (410)
Q Consensus       140 p~~----~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~----~-~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m-----  204 (410)
                      ++.    .+++.+...|.+.|++++|.++|..+....    + ..+. ...++.|...|.+.+++.+|.++|.+.     
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            333    578899999999999999999999987542    1 1222 456788888999999999998888775     


Q ss_pred             ---CCCCC-HHHHHHHHHHHHhcCchhHHHHH
Q 040371          205 ---TMEPD-VVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       205 ---~~~p~-~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                         +-.|+ ..+|..|...|...|+++.|.++
T Consensus       441 ~~g~~~~~~~~~~~nL~~~Y~~~g~~e~a~~~  472 (508)
T KOG1840|consen  441 LCGPDHPDVTYTYLNLAALYRAQGNYEAAEEL  472 (508)
T ss_pred             HhCCCCCchHHHHHHHHHHHHHcccHHHHHHH
Confidence               23455 46899999999999999999998

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

Probab=99.12  E-value=1.3e-08  Score=96.94  Aligned_cols=251  Identities=14%  Similarity=0.036  Sum_probs=192.3

Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHHHCC-C-CCCHHHHHHHHHHHHhhCCHHHHHHHHHH-HHHcCCCccHHHHHHHHHHH
Q 040371           10 NSMIGGFVRNARFDEALRFFREMLSSK-V-EPDKFTFASVIYGCARLGALNHAYWVHNL-IIEKKIELNFILSAALIDMY   86 (410)
Q Consensus        10 n~li~~~~~~g~~~~a~~l~~~m~~~g-~-~pd~~t~~~ll~a~~~~~~~~~a~~~~~~-~~~~g~~~~~~~~~~li~~y   86 (410)
                      .-+-.+|...+++++|.++|+...+.. . .-+...|+++|--+-+.    .+...+.+ +++. -+..+.+|.++.++|
T Consensus       357 ~q~GrayFEl~~Y~~a~~~F~~~r~~~p~rv~~meiyST~LWHLq~~----v~Ls~Laq~Li~~-~~~sPesWca~GNcf  431 (638)
T KOG1126|consen  357 SQLGRAYFELIEYDQAERIFSLVRRIEPYRVKGMEIYSTTLWHLQDE----VALSYLAQDLIDT-DPNSPESWCALGNCF  431 (638)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhHHHHHHHHHHhh----HHHHHHHHHHHhh-CCCCcHHHHHhcchh
Confidence            346678889999999999999998642 1 12567888887655321    12222222 2222 245689999999999


Q ss_pred             HhcCCHHHHHHHHHhcccC---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCCHHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQRN---DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD-SITFLGLLTACSHCGLVEEGR  162 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~  162 (410)
                      +-.++.+.|++.|++..+-   ...+|+.+-.-+.....++.|...|+..+.  +.|. -..|-.+.-.|.+.++++.|+
T Consensus       432 SLQkdh~~Aik~f~RAiQldp~faYayTLlGhE~~~~ee~d~a~~~fr~Al~--~~~rhYnAwYGlG~vy~Kqek~e~Ae  509 (638)
T KOG1126|consen  432 SLQKDHDTAIKCFKRAIQLDPRFAYAYTLLGHESIATEEFDKAMKSFRKALG--VDPRHYNAWYGLGTVYLKQEKLEFAE  509 (638)
T ss_pred             hhhhHHHHHHHHHHHhhccCCccchhhhhcCChhhhhHHHHhHHHHHHhhhc--CCchhhHHHHhhhhheeccchhhHHH
Confidence            9999999999999998754   456888888888889999999999998754  3443 345667788899999999999


Q ss_pred             HHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhh
Q 040371          163 KYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNI  236 (410)
Q Consensus       163 ~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~  236 (410)
                      -.|+.+.   .+.|. .+....+...+-+.|+.++|++++++. ...| |...--.-...+...++.++|...   +.+.
T Consensus       510 ~~fqkA~---~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~ld~kn~l~~~~~~~il~~~~~~~eal~~LEeLk~~  586 (638)
T KOG1126|consen  510 FHFQKAV---EINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIHLDPKNPLCKYHRASILFSLGRYVEALQELEELKEL  586 (638)
T ss_pred             HHHHhhh---cCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHhcCCCCchhHHHHHHHHHhhcchHHHHHHHHHHHHh
Confidence            9999987   45554 556667778899999999999999998 4444 444444455566778899999988   5555


Q ss_pred             ccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          237 SRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       237 ~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      -|.+..+|..+...|-+.|+.+.|..-|..+.+-
T Consensus       587 vP~es~v~~llgki~k~~~~~~~Al~~f~~A~~l  620 (638)
T KOG1126|consen  587 VPQESSVFALLGKIYKRLGNTDLALLHFSWALDL  620 (638)
T ss_pred             CcchHHHHHHHHHHHHHHccchHHHHhhHHHhcC
Confidence            6888899999999999999999999888777654

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

Probab=99.11  E-value=1.1e-07  Score=93.61  Aligned_cols=272  Identities=16%  Similarity=0.203  Sum_probs=174.6

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      +...|-+|-..|-+.|+.++++..+-..  ..+.| |..-|..+..-..++|.+++|+-.|.++++.. +++....---.
T Consensus       172 ~~~ay~tL~~IyEqrGd~eK~l~~~llA--AHL~p~d~e~W~~ladls~~~~~i~qA~~cy~rAI~~~-p~n~~~~~ers  248 (895)
T KOG2076|consen  172 NPIAYYTLGEIYEQRGDIEKALNFWLLA--AHLNPKDYELWKRLADLSEQLGNINQARYCYSRAIQAN-PSNWELIYERS  248 (895)
T ss_pred             chhhHHHHHHHHHHcccHHHHHHHHHHH--HhcCCCChHHHHHHHHHHHhcccHHHHHHHHHHHHhcC-CcchHHHHHHH
Confidence            4566777888888888887777766333  22333 55677777777777888888888888887775 45555555566


Q ss_pred             HHHHhcCCHHHHHHHHHhcccCCh--------------------------------------------hhHHHHHHHHHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQRNDV--------------------------------------------SVWNAMISGVAI  119 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~~~~--------------------------------------------~~~~~li~~~~~  119 (410)
                      .+|-+.|+...|...|.++.+.+.                                            ..+|.++..|.+
T Consensus       249 ~L~~~~G~~~~Am~~f~~l~~~~p~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~s~~~~~~~~ed~ni~ael~l~  328 (895)
T KOG2076|consen  249 SLYQKTGDLKRAMETFLQLLQLDPPVDIERIEDLIRRVAHYFITHNERERAAKALEGALSKEKDEASLEDLNILAELFLK  328 (895)
T ss_pred             HHHHHhChHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhhccccccccHHHHHHHHHHH
Confidence            777888888877777766543211                                            123333334444


Q ss_pred             cCChHHHHHHHHHHHHCCCCCCH----------------------HHHH----HHHHHHHccCCHHHHHHHHHHhhhhcC
Q 040371          120 HGLAADASAIFTKMEMFNVLPDS----------------------ITFL----GLLTACSHCGLVEEGRKYFDHMRSRYS  173 (410)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~----------------------~t~~----~ll~a~~~~g~~~~a~~~~~~m~~~~~  173 (410)
                      ...++.|......+......+|.                      ..|.    -+.-+..+....+....+.....++ .
T Consensus       329 ~~q~d~~~~~i~~~~~r~~e~d~~e~~~~~~~~~~~~~~~~~~~~~s~~l~v~rl~icL~~L~~~e~~e~ll~~l~~~-n  407 (895)
T KOG2076|consen  329 NKQSDKALMKIVDDRNRESEKDDSEWDTDERRREEPNALCEVGKELSYDLRVIRLMICLVHLKERELLEALLHFLVED-N  407 (895)
T ss_pred             hHHHHHhhHHHHHHhccccCCChhhhhhhhhccccccccccCCCCCCccchhHhHhhhhhcccccchHHHHHHHHHHh-c
Confidence            44444444444444331111111                      0000    1111122222233333333333322 3


Q ss_pred             --CCCChhHHHHHHHHHHhcCCHHHHHHHHHhCC---CCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHH
Q 040371          174 --IQPQLEHYGAMVDLLGRAGHIEEAYGLITSMT---MEPDVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYV  245 (410)
Q Consensus       174 --~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~---~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~  245 (410)
                        ..-++..|.-+.++|...|++.+|+++|..+-   ..-+...|-.+...|...|..+.|.+.   .....|.+..+-.
T Consensus       408 ~~~~d~~dL~~d~a~al~~~~~~~~Al~~l~~i~~~~~~~~~~vw~~~a~c~~~l~e~e~A~e~y~kvl~~~p~~~D~Ri  487 (895)
T KOG2076|consen  408 VWVSDDVDLYLDLADALTNIGKYKEALRLLSPITNREGYQNAFVWYKLARCYMELGEYEEAIEFYEKVLILAPDNLDARI  487 (895)
T ss_pred             CChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHhcCccccchhhhHHHHHHHHHHhhHHHHHHHHHHHHhcCCCchhhhh
Confidence              22346678889999999999999999999982   223678999999999999999999999   6778899989999


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeE
Q 040371          246 LLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSW  280 (410)
Q Consensus       246 ~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~  280 (410)
                      .|...|.+.|+.++|.+++..|..-+-..-++..|
T Consensus       488 ~Lasl~~~~g~~EkalEtL~~~~~~D~~~~e~~a~  522 (895)
T KOG2076|consen  488 TLASLYQQLGNHEKALETLEQIINPDGRNAEACAW  522 (895)
T ss_pred             hHHHHHHhcCCHHHHHHHHhcccCCCccchhhccc
Confidence            99999999999999999998876333222244555

>PRK12370 invasion protein regulator; Provisional

Probab=99.09  E-value=5e-08  Score=96.94  Aligned_cols=217  Identities=9%  Similarity=-0.047  Sum_probs=156.3

Q ss_pred             hhHHHHHHHHHHH---------cCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccH
Q 040371            6 VVSWNSMIGGFVR---------NARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNF   76 (410)
Q Consensus         6 ~~~~n~li~~~~~---------~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~   76 (410)
                      ...|..+..+|..         .+++++|...+++..+.. +-+...+..+..++...|++++|...++++++.+ +.+.
T Consensus       295 a~a~~~La~~~~~~~~~g~~~~~~~~~~A~~~~~~Al~ld-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~Al~l~-P~~~  372 (553)
T PRK12370        295 IAPYCALAECYLSMAQMGIFDKQNAMIKAKEHAIKATELD-HNNPQALGLLGLINTIHSEYIVGSLLFKQANLLS-PISA  372 (553)
T ss_pred             HHHHHHHHHHHHHHHHcCCcccchHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCH
Confidence            3456655555442         345899999999998753 3367788888888899999999999999999986 5567


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhccc--CC-hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHH
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQR--ND-VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD-SITFLGLLTAC  152 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~  152 (410)
                      ..+..+...|...|++++|...|++..+  |+ ...+..++..+...|++++|+..+++..... .|+ ...+..+..++
T Consensus       373 ~a~~~lg~~l~~~G~~~eAi~~~~~Al~l~P~~~~~~~~~~~~~~~~g~~eeA~~~~~~~l~~~-~p~~~~~~~~la~~l  451 (553)
T PRK12370        373 DIKYYYGWNLFMAGQLEEALQTINECLKLDPTRAAAGITKLWITYYHTGIDDAIRLGDELRSQH-LQDNPILLSMQVMFL  451 (553)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHhccCHHHHHHHHHHHHHhc-cccCHHHHHHHHHHH
Confidence            7889999999999999999999999864  33 2233444555777899999999999987653 343 44466677788


Q ss_pred             HccCCHHHHHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC----CCCCCHHHHHHHHHHHHhcCchh
Q 040371          153 SHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM----TMEPDVVVWRALLSACRTFKRLE  227 (410)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~p~~~~~~~li~~~~~~g~~~  227 (410)
                      ...|+.++|...+..+...   .|+ ....+.+...|...|  ++|...++.+    ...|....+..++  ++-+|+.+
T Consensus       452 ~~~G~~~eA~~~~~~~~~~---~~~~~~~~~~l~~~~~~~g--~~a~~~l~~ll~~~~~~~~~~~~~~~~--~~~~g~~~  524 (553)
T PRK12370        452 SLKGKHELARKLTKEISTQ---EITGLIAVNLLYAEYCQNS--ERALPTIREFLESEQRIDNNPGLLPLV--LVAHGEAI  524 (553)
T ss_pred             HhCCCHHHHHHHHHHhhhc---cchhHHHHHHHHHHHhccH--HHHHHHHHHHHHHhhHhhcCchHHHHH--HHHHhhhH
Confidence            8999999999999987643   333 444556666677777  4666666555    3344444444444  45566666


Q ss_pred             HHHHH
Q 040371          228 LGEVA  232 (410)
Q Consensus       228 ~a~~~  232 (410)
                      .+..+
T Consensus       525 ~~~~~  529 (553)
T PRK12370        525 AEKMW  529 (553)
T ss_pred             HHHHH
Confidence            66655

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

Probab=99.09  E-value=9.4e-08  Score=87.40  Aligned_cols=252  Identities=12%  Similarity=0.081  Sum_probs=169.9

Q ss_pred             HHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCC--CccHHHHHHHHHHHHhcCC
Q 040371           14 GGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKI--ELNFILSAALIDMYSKCGK   91 (410)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~--~~~~~~~~~li~~y~~~g~   91 (410)
                      .+|....+.++++.=.+.....|.+-+...-+-...+.-...++++|+.+|+.+.+...  --|..+|+.++-.-..+.+
T Consensus       235 ~a~~el~q~~e~~~k~e~l~~~gf~~~~~i~~~~A~~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~sk  314 (559)
T KOG1155|consen  235 KAYQELHQHEEALQKKERLSSVGFPNSMYIKTQIAAASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSK  314 (559)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhccCCccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHH
Confidence            34444456666666666666666544443333333444556677777777777777621  1145566555432222222


Q ss_pred             HH-HHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhh
Q 040371           92 IQ-MAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRS  170 (410)
Q Consensus        92 ~~-~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~  170 (410)
                      +. -|..+++ +.+--..|--++.+-|+-.++.++|...|++.++.+ +-....++.+..-|....+...|.+-++...+
T Consensus       315 Ls~LA~~v~~-idKyR~ETCCiIaNYYSlr~eHEKAv~YFkRALkLN-p~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvd  392 (559)
T KOG1155|consen  315 LSYLAQNVSN-IDKYRPETCCIIANYYSLRSEHEKAVMYFKRALKLN-PKYLSAWTLMGHEYVEMKNTHAAIESYRRAVD  392 (559)
T ss_pred             HHHHHHHHHH-hccCCccceeeehhHHHHHHhHHHHHHHHHHHHhcC-cchhHHHHHhhHHHHHhcccHHHHHHHHHHHh
Confidence            21 1222221 122223445556667777888999999999888753 22345677777888888999999999988884


Q ss_pred             hcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHHH---HhhccCCCchHH
Q 040371          171 RYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVAI---VNISRLMGGDYV  245 (410)
Q Consensus       171 ~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~~---~~~~~~~~~~~~  245 (410)
                        -.+.|-..|-.|..+|.-.+...-|+-.|++. ..+| |...|.+|-..|.+.++.++|++.+   ......+...+.
T Consensus       393 --i~p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~~~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~  470 (559)
T KOG1155|consen  393 --INPRDYRAWYGLGQAYEIMKMHFYALYYFQKALELKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALV  470 (559)
T ss_pred             --cCchhHHHHhhhhHHHHHhcchHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHH
Confidence              23446678889999999999999999888887 6677 6788999999999999999999983   333344557888


Q ss_pred             HHHHHHHhcCChhHHHHHHHHHHh
Q 040371          246 LLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       246 ~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                      .|.+.|.+.++.++|.+.++.-.+
T Consensus       471 ~LakLye~l~d~~eAa~~yek~v~  494 (559)
T KOG1155|consen  471 RLAKLYEELKDLNEAAQYYEKYVE  494 (559)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHH
Confidence            999999999999999998887655

>PRK14574 hmsH outer membrane protein; Provisional

Probab=99.09  E-value=4.3e-07  Score=92.87  Aligned_cols=256  Identities=14%  Similarity=0.015  Sum_probs=174.9

Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC
Q 040371           11 SMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG   90 (410)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g   90 (410)
                      .++..+...|+.++|+..+++.... -+........+...+...|+++.|.++++.+++.. +.+..++..++..|.+.+
T Consensus        73 dll~l~~~~G~~~~A~~~~eka~~p-~n~~~~~llalA~ly~~~gdyd~Aiely~kaL~~d-P~n~~~l~gLa~~y~~~~  150 (822)
T PRK14574         73 DWLQIAGWAGRDQEVIDVYERYQSS-MNISSRGLASAARAYRNEKRWDQALALWQSSLKKD-PTNPDLISGMIMTQADAG  150 (822)
T ss_pred             HHHHHHHHcCCcHHHHHHHHHhccC-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHhhcC
Confidence            7788888889999998888887621 12223333444567788899999999999998875 445777778888999999


Q ss_pred             CHHHHHHHHHhcccCChhhHHHHHHHHHH--cCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHH----
Q 040371           91 KIQMAKEVFDTVQRNDVSVWNAMISGVAI--HGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRK----  163 (410)
Q Consensus        91 ~~~~A~~~f~~m~~~~~~~~~~li~~~~~--~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~----  163 (410)
                      +.++|++.++++...+......+..+|..  .++..+|++.++++.+.  .| +...+..+..+..+.|....|.+    
T Consensus       151 q~~eAl~~l~~l~~~dp~~~~~l~layL~~~~~~~~~AL~~~ekll~~--~P~n~e~~~~~~~~l~~~~~~~~a~~l~~~  228 (822)
T PRK14574        151 RGGVVLKQATELAERDPTVQNYMTLSYLNRATDRNYDALQASSEAVRL--APTSEEVLKNHLEILQRNRIVEPALRLAKE  228 (822)
T ss_pred             CHHHHHHHHHHhcccCcchHHHHHHHHHHHhcchHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCcHHHHHHHHh
Confidence            99999999998875443322224445544  45665699999999885  35 44455555566655444333333    


Q ss_pred             --------------------------------------------HHHHhhhhcCCCCCh-hH----HHHHHHHHHhcCCH
Q 040371          164 --------------------------------------------YFDHMRSRYSIQPQL-EH----YGAMVDLLGRAGHI  194 (410)
Q Consensus       164 --------------------------------------------~~~~m~~~~~~~~~~-~~----~~~li~~~~~~g~~  194 (410)
                                                                  -++.+....+-.|.. ..    ..-.+-++...|++
T Consensus       229 ~p~~f~~~~~~~l~~~~~a~~vr~a~~~~~~~~~r~~~~d~ala~~~~l~~~~~~~p~~~~~~~~~~~Drl~aL~~r~r~  308 (822)
T PRK14574        229 NPNLVSAEHYRQLERDAAAEQVRMAVLPTRSETERFDIADKALADYQNLLTRWGKDPEAQADYQRARIDRLGALLVRHQT  308 (822)
T ss_pred             CccccCHHHHHHHHHHHHHHHHhhcccccccchhhHHHHHHHHHHHHHHHhhccCCCccchHHHHHHHHHHHHHHHhhhH
Confidence                                                        333333222222321 11    12334467788999


Q ss_pred             HHHHHHHHhCCCCC---CHHHHHHHHHHHHhcCchhHHHHHHHhhccC---------CCchHHHHHHHHHhcCChhHHHH
Q 040371          195 EEAYGLITSMTMEP---DVVVWRALLSACRTFKRLELGEVAIVNISRL---------MGGDYVLLSNMYCYLKRWDTAEN  262 (410)
Q Consensus       195 ~~A~~~~~~m~~~p---~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~---------~~~~~~~l~~~~~~~g~~~~a~~  262 (410)
                      .++.+.++.++..+   -..+-.++.++|...+.+++|+.++......         +......|..+|...+++++|..
T Consensus       309 ~~vi~~y~~l~~~~~~~P~y~~~a~adayl~~~~P~kA~~l~~~~~~~~~~~~~~~~~~~~~~~L~yA~ld~e~~~~A~~  388 (822)
T PRK14574        309 ADLIKEYEAMEAEGYKMPDYARRWAASAYIDRRLPEKAAPILSSLYYSDGKTFRNSDDLLDADDLYYSLNESEQLDKAYQ  388 (822)
T ss_pred             HHHHHHHHHhhhcCCCCCHHHHHHHHHHHHhcCCcHHHHHHHHHHhhccccccCCCcchHHHHHHHHHHHhcccHHHHHH
Confidence            99999999994222   3457778999999999999999995544221         11224678999999999999999


Q ss_pred             HHHHHHhC
Q 040371          263 VREIMKKK  270 (410)
Q Consensus       263 ~~~~m~~~  270 (410)
                      +++.+.+.
T Consensus       389 ~l~~~~~~  396 (822)
T PRK14574        389 FAVNYSEQ  396 (822)
T ss_pred             HHHHHHhc
Confidence            99999873

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

Probab=99.08  E-value=1.3e-07  Score=86.50  Aligned_cols=268  Identities=15%  Similarity=0.114  Sum_probs=197.5

Q ss_pred             HHHHcCCHhHHHHHHHHHHHCC-CC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCH
Q 040371           15 GFVRNARFDEALRFFREMLSSK-VE-PDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKI   92 (410)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~~g-~~-pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~   92 (410)
                      ++-.+.++++|+.+|+++.+.. .+ -|..||+.++-+-.....+.---+....+-    +-.+.|...+.+-|+-.++-
T Consensus       271 ~~y~~rDfD~a~s~Feei~knDPYRl~dmdlySN~LYv~~~~skLs~LA~~v~~id----KyR~ETCCiIaNYYSlr~eH  346 (559)
T KOG1155|consen  271 ASYNQRDFDQAESVFEEIRKNDPYRLDDMDLYSNVLYVKNDKSKLSYLAQNVSNID----KYRPETCCIIANYYSLRSEH  346 (559)
T ss_pred             HHhhhhhHHHHHHHHHHHHhcCCCcchhHHHHhHHHHHHhhhHHHHHHHHHHHHhc----cCCccceeeehhHHHHHHhH
Confidence            3445689999999999998762 11 166789888865433222221111111111    22356777888899999999


Q ss_pred             HHHHHHHHhcccC---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371           93 QMAKEVFDTVQRN---DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus        93 ~~A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      ++|...|++..+-   -...|+.|..-|....+...|++-++...+-. +.|-..|-.|.++|.-.+...-|+-+|+...
T Consensus       347 EKAv~YFkRALkLNp~~~~aWTLmGHEyvEmKNt~AAi~sYRrAvdi~-p~DyRAWYGLGQaYeim~Mh~YaLyYfqkA~  425 (559)
T KOG1155|consen  347 EKAVMYFKRALKLNPKYLSAWTLMGHEYVEMKNTHAAIESYRRAVDIN-PRDYRAWYGLGQAYEIMKMHFYALYYFQKAL  425 (559)
T ss_pred             HHHHHHHHHHHhcCcchhHHHHHhhHHHHHhcccHHHHHHHHHHHhcC-chhHHHHhhhhHHHHHhcchHHHHHHHHHHH
Confidence            9999999987753   45689999999999999999999999998742 3478889999999999999999999999987


Q ss_pred             hhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCchhHHHHHHHh----h--c-cCC
Q 040371          170 SRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM--TMEPDVVVWRALLSACRTFKRLELGEVAIVN----I--S-RLM  240 (410)
Q Consensus       170 ~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m--~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~----~--~-~~~  240 (410)
                      .  -.+-|...|.+|.+.|.+.+++++|.+-|++.  .-..+...+..|...+-+.++.++|...+.+    .  . ..+
T Consensus       426 ~--~kPnDsRlw~aLG~CY~kl~~~~eAiKCykrai~~~dte~~~l~~LakLye~l~d~~eAa~~yek~v~~~~~eg~~~  503 (559)
T KOG1155|consen  426 E--LKPNDSRLWVALGECYEKLNRLEEAIKCYKRAILLGDTEGSALVRLAKLYEELKDLNEAAQYYEKYVEVSELEGEID  503 (559)
T ss_pred             h--cCCCchHHHHHHHHHHHHhccHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcccc
Confidence            3  33446899999999999999999999999987  2223557889999999999999999888221    1  1 111


Q ss_pred             C---chHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHH
Q 040371          241 G---GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTK  315 (410)
Q Consensus       241 ~---~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~  315 (410)
                      +   .+-.-|..-+.+.+++++|.........                       |   ....+++-.+++++.+.|.
T Consensus       504 ~~t~ka~~fLA~~f~k~~~~~~As~Ya~~~~~-----------------------~---~~e~eeak~LlReir~~~~  555 (559)
T KOG1155|consen  504 DETIKARLFLAEYFKKMKDFDEASYYATLVLK-----------------------G---ETECEEAKALLREIRKIQA  555 (559)
T ss_pred             hHHHHHHHHHHHHHHhhcchHHHHHHHHHHhc-----------------------C---CchHHHHHHHHHHHHHhcC
Confidence            2   2233467778899999999876543321                       1   3467888888887765543

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

Probab=99.06  E-value=4.4e-07  Score=81.78  Aligned_cols=255  Identities=16%  Similarity=0.095  Sum_probs=201.8

Q ss_pred             HHHHHHH--cCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhc
Q 040371           12 MIGGFVR--NARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKC   89 (410)
Q Consensus        12 li~~~~~--~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~   89 (410)
                      +..+..+  .|+|.+|..+..+-.+.+-.| ...|.....+.-..|+.+.+-..+.++.+..-.++..+.-+........
T Consensus        88 ~~egl~~l~eG~~~qAEkl~~rnae~~e~p-~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~  166 (400)
T COG3071          88 LNEGLLKLFEGDFQQAEKLLRRNAEHGEQP-VLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNR  166 (400)
T ss_pred             HHHHHHHHhcCcHHHHHHHHHHhhhcCcch-HHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhC
Confidence            4444443  599999999999877665443 4567777788889999999999999999885577888888999999999


Q ss_pred             CCHHHHHHHHHhcc---cCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH-------HHHHHHHHHHHccCCHH
Q 040371           90 GKIQMAKEVFDTVQ---RNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS-------ITFLGLLTACSHCGLVE  159 (410)
Q Consensus        90 g~~~~A~~~f~~m~---~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~-------~t~~~ll~a~~~~g~~~  159 (410)
                      |+++.|+.-.+++.   .++.........+|.+.|++.+...+..+|.+.|+--|+       .++..++.-+...+..+
T Consensus       167 ~d~~aA~~~v~~ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~  246 (400)
T COG3071         167 RDYPAARENVDQLLEMTPRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSE  246 (400)
T ss_pred             CCchhHHHHHHHHHHhCcCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccch
Confidence            99999998877654   467889999999999999999999999999999876664       47788888888877777


Q ss_pred             HHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHH---HHh
Q 040371          160 EGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVA---IVN  235 (410)
Q Consensus       160 ~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~  235 (410)
                      .-...++....  ...-++..-.+++.-+.++|..++|.++.++. +..-|.. ...++ .+.+.++.+.-++.   ..+
T Consensus       247 gL~~~W~~~pr--~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~-L~~~~-~~l~~~d~~~l~k~~e~~l~  322 (400)
T COG3071         247 GLKTWWKNQPR--KLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR-LCRLI-PRLRPGDPEPLIKAAEKWLK  322 (400)
T ss_pred             HHHHHHHhccH--HhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh-HHHHH-hhcCCCCchHHHHHHHHHHH
Confidence            77778887775  44556777788999999999999999988776 3233333 22222 34556666555555   556


Q ss_pred             hccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          236 ISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       236 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      ..|.++..+.+|...|.+.+.|.+|...|+...+.+
T Consensus       323 ~h~~~p~L~~tLG~L~~k~~~w~kA~~~leaAl~~~  358 (400)
T COG3071         323 QHPEDPLLLSTLGRLALKNKLWGKASEALEAALKLR  358 (400)
T ss_pred             hCCCChhHHHHHHHHHHHhhHHHHHHHHHHHHHhcC
Confidence            678899999999999999999999999999665544

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.94  E-value=4.1e-07  Score=82.98  Aligned_cols=209  Identities=13%  Similarity=0.095  Sum_probs=128.1

Q ss_pred             CHHHHHHHHHHHHHcC-CCc--cHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHH
Q 040371           56 ALNHAYWVHNLIIEKK-IEL--NFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAI  129 (410)
Q Consensus        56 ~~~~a~~~~~~~~~~g-~~~--~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l  129 (410)
                      ..+.+..-+.+++... ..|  ....|..+...|.+.|+.++|...|++..+   .+...|+.+...|...|++++|.+.
T Consensus        41 ~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~~g~~~~A~~~  120 (296)
T PRK11189         41 QQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALRPDMADAYNYLGIYLTQAGNFDAAYEA  120 (296)
T ss_pred             HHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            4455555555555432 122  234566677777778888888877776653   2456777777778888888888888


Q ss_pred             HHHHHHCCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC--CC
Q 040371          130 FTKMEMFNVLPD-SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM--TM  206 (410)
Q Consensus       130 ~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m--~~  206 (410)
                      |++..+.  .|+ ..++..+..++...|++++|.+.|+...+.   .|+..........+...+++++|...|.+.  ..
T Consensus       121 ~~~Al~l--~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~---~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~~~~  195 (296)
T PRK11189        121 FDSVLEL--DPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD---DPNDPYRALWLYLAESKLDPKQAKENLKQRYEKL  195 (296)
T ss_pred             HHHHHHh--CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHccCCHHHHHHHHHHHHhhC
Confidence            8777763  443 456666777777778888888888777643   343322222222334456778887777553  22


Q ss_pred             CCCHHHHHHHHHHHHhcCchhHHHHH--HH-------hhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 040371          207 EPDVVVWRALLSACRTFKRLELGEVA--IV-------NISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       207 ~p~~~~~~~li~~~~~~g~~~~a~~~--~~-------~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  272 (410)
                      .|+...| .+  .....|+...+..+  +.       +..|.....|..+...|.+.|++++|...|++..+.+.
T Consensus       196 ~~~~~~~-~~--~~~~lg~~~~~~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~~Al~~~~  267 (296)
T PRK11189        196 DKEQWGW-NI--VEFYLGKISEETLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFKLALANNV  267 (296)
T ss_pred             CccccHH-HH--HHHHccCCCHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCC
Confidence            2332222 11  11224444333211  22       23344456789999999999999999999998876653

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.94  E-value=1.1e-07  Score=83.26  Aligned_cols=219  Identities=13%  Similarity=0.005  Sum_probs=108.9

Q ss_pred             HHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCCh
Q 040371           47 VIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLA  123 (410)
Q Consensus        47 ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~  123 (410)
                      +..+|.++|.+..|...++..++.  .|-+.+|--|-..|.+..+...|+.+|.+-.+  | |+.-..-+...+-..++.
T Consensus       229 ~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~fP~~VT~l~g~ARi~eam~~~  306 (478)
T KOG1129|consen  229 MGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDSFPFDVTYLLGQARIHEAMEQQ  306 (478)
T ss_pred             HHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhcCCchhhhhhhhHHHHHHHHhH
Confidence            344444444444444444444443  22333344444444444444444444444332  2 222222233334444444


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371          124 ADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITS  203 (410)
Q Consensus       124 ~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  203 (410)
                      ++|.++|++..+.. ..+.....++...|.-.++.+-|+.++.++.. .|+. +...|+.+.-++...+++|-++--|.+
T Consensus       307 ~~a~~lYk~vlk~~-~~nvEaiAcia~~yfY~~~PE~AlryYRRiLq-mG~~-speLf~NigLCC~yaqQ~D~~L~sf~R  383 (478)
T KOG1129|consen  307 EDALQLYKLVLKLH-PINVEAIACIAVGYFYDNNPEMALRYYRRILQ-MGAQ-SPELFCNIGLCCLYAQQIDLVLPSFQR  383 (478)
T ss_pred             HHHHHHHHHHHhcC-CccceeeeeeeeccccCCChHHHHHHHHHHHH-hcCC-ChHHHhhHHHHHHhhcchhhhHHHHHH
Confidence            55555554444321 12333333444444444455555555554443 2332 334444444444444445444444443


Q ss_pred             C---CCCCC--HHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          204 M---TMEPD--VVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       204 m---~~~p~--~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      .   -..|+  ...|-.+-......|++..|.+.   ....++++...++.|.-.-.+.|++++|..++......
T Consensus       384 Alstat~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Arsll~~A~s~  458 (478)
T KOG1129|consen  384 ALSTATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGARSLLNAAKSV  458 (478)
T ss_pred             HHhhccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHHHHHHHhhhh
Confidence            3   11122  23455555555666777777766   33445666778888888888999999999998877654

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

Probab=98.93  E-value=7.2e-07  Score=83.69  Aligned_cols=257  Identities=16%  Similarity=0.073  Sum_probs=198.5

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      +..--.-..-+...+++++.+++++...+. .+++...+..=|.++...|+-..-..+=..+++. .|....+|-++.--
T Consensus       244 ~dll~~~ad~~y~~c~f~~c~kit~~lle~-dpfh~~~~~~~ia~l~el~~~n~Lf~lsh~LV~~-yP~~a~sW~aVg~Y  321 (611)
T KOG1173|consen  244 LDLLAEKADRLYYGCRFKECLKITEELLEK-DPFHLPCLPLHIACLYELGKSNKLFLLSHKLVDL-YPSKALSWFAVGCY  321 (611)
T ss_pred             HHHHHHHHHHHHHcChHHHHHHHhHHHHhh-CCCCcchHHHHHHHHHHhcccchHHHHHHHHHHh-CCCCCcchhhHHHH
Confidence            333344455667789999999999998875 3666666666677888888876666555566665 46678899999999


Q ss_pred             HHhcCCHHHHHHHHHhcccCC---hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040371           86 YSKCGKIQMAKEVFDTVQRND---VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGR  162 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~~~---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  162 (410)
                      |.-.|+.++|++.|.+...-|   ...|-.....|+-.|..++|+..+...-+. ++-..--+.-+.--|.+.+++..|.
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 YLMIGKYSEARRYFSKATTLDPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARL-MPGCHLPSLYLGMEYMRTNNLKLAE  400 (611)
T ss_pred             HHHhcCcHHHHHHHHHHhhcCccccHHHHHHhHHhhhcchHHHHHHHHHHHHHh-ccCCcchHHHHHHHHHHhccHHHHH
Confidence            999999999999998766443   468999999999999999999988776553 1111222333455678899999999


Q ss_pred             HHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhCC--------CCC-CHHHHHHHHHHHHhcCchhHHHHH
Q 040371          163 KYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSMT--------MEP-DVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       163 ~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~--------~~p-~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      ++|.+..   ++.| |+...+-+.-..-..+.+.+|..+|+..-        ..+ -..+++.|-.+|++.+.+++|+..
T Consensus       401 ~Ff~~A~---ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rkl~~~~eAI~~  477 (611)
T KOG1173|consen  401 KFFKQAL---AIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRKLNKYEEAIDY  477 (611)
T ss_pred             HHHHHHH---hcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHHHhhHHHHHHH
Confidence            9999987   5555 46667777666777888999999888761        111 345677788899999999999998


Q ss_pred             ---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          233 ---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       233 ---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                         ...+.|.+..+|.++.-.|...|+++.|.+.|.+-.
T Consensus       478 ~q~aL~l~~k~~~~~asig~iy~llgnld~Aid~fhKaL  516 (611)
T KOG1173|consen  478 YQKALLLSPKDASTHASIGYIYHLLGNLDKAIDHFHKAL  516 (611)
T ss_pred             HHHHHHcCCCchhHHHHHHHHHHHhcChHHHHHHHHHHH
Confidence               667889999999999999999999999999997643

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

Probab=98.92  E-value=1.1e-08  Score=99.95  Aligned_cols=208  Identities=11%  Similarity=0.147  Sum_probs=118.4

Q ss_pred             CCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 040371            3 DKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAAL   82 (410)
Q Consensus         3 ~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l   82 (410)
                      .||-+||.++|.-|+..|+.+.|- +|.-|.-...+.+...|+.++......++.+.+.           .|-..+|+.|
T Consensus        22 ~PnRvtyqsLiarYc~~gdieaat-if~fm~~ksLpv~e~vf~~lv~sh~~And~Enpk-----------ep~aDtyt~L   89 (1088)
T KOG4318|consen   22 LPNRVTYQSLIARYCTKGDIEAAT-IFPFMEIKSLPVREGVFRGLVASHKEANDAENPK-----------EPLADTYTNL   89 (1088)
T ss_pred             CCchhhHHHHHHHHcccCCCcccc-chhhhhcccccccchhHHHHHhcccccccccCCC-----------CCchhHHHHH
Confidence            478899999999999999999988 8888876555555555555555555555554443           4455555555


Q ss_pred             HHHHHhcCCHHH---HHHHHHhccc-------------------------CChh----------hHHHHHHHH-------
Q 040371           83 IDMYSKCGKIQM---AKEVFDTVQR-------------------------NDVS----------VWNAMISGV-------  117 (410)
Q Consensus        83 i~~y~~~g~~~~---A~~~f~~m~~-------------------------~~~~----------~~~~li~~~-------  117 (410)
                      ...|...|++..   .++-++.+..                         ||..          .|..++...       
T Consensus        90 l~ayr~hGDli~fe~veqdLe~i~~sfs~~Gvgs~e~~fl~k~~c~p~~lpda~n~illlv~eglwaqllkll~~~Pvsa  169 (1088)
T KOG4318|consen   90 LKAYRIHGDLILFEVVEQDLESINQSFSDHGVGSPERWFLMKIHCCPHSLPDAENAILLLVLEGLWAQLLKLLAKVPVSA  169 (1088)
T ss_pred             HHHHHhccchHHHHHHHHHHHHHHhhhhhhccCcHHHHHHhhcccCcccchhHHHHHHHHHHHHHHHHHHHHHhhCCccc
Confidence            555555555332   2221111100                         0110          122222211       


Q ss_pred             --------HHcC--ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHH
Q 040371          118 --------AIHG--LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDL  187 (410)
Q Consensus       118 --------~~~g--~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~  187 (410)
                              .++.  ......++....+...-.|+..+|..++.+-..+|+++.|..++..|.++ |++.+..-+-.|+-+
T Consensus       170 ~~~p~~vfLrqnv~~ntpvekLl~~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~ll~emke~-gfpir~HyFwpLl~g  248 (1088)
T KOG4318|consen  170 WNAPFQVFLRQNVVDNTPVEKLLNMCKSLVEAPTSETLHAVLKRALAAGDVDGAKNLLYEMKEK-GFPIRAHYFWPLLLG  248 (1088)
T ss_pred             ccchHHHHHHHhccCCchHHHHHHHHHHhhcCCChHHHHHHHHHHHhcCchhhHHHHHHHHHHc-CCCcccccchhhhhc
Confidence                    1110  11111122211111111477778888888777888888888888888765 777776655555544


Q ss_pred             HHhcCCHHHHHHHHHhC---CCCCCHHHHHHHHHHHHhcCch
Q 040371          188 LGRAGHIEEAYGLITSM---TMEPDVVVWRALLSACRTFKRL  226 (410)
Q Consensus       188 ~~~~g~~~~A~~~~~~m---~~~p~~~~~~~li~~~~~~g~~  226 (410)
                         .+...-+..+++.|   ++.|+..|+.-.+-.+..+|..
T Consensus       249 ---~~~~q~~e~vlrgmqe~gv~p~seT~adyvip~l~N~~t  287 (1088)
T KOG4318|consen  249 ---INAAQVFEFVLRGMQEKGVQPGSETQADYVIPQLSNGQT  287 (1088)
T ss_pred             ---CccchHHHHHHHHHHHhcCCCCcchhHHHHHhhhcchhh
Confidence               45544444455444   7777777777666666665543

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

Probab=98.91  E-value=2.8e-06  Score=76.71  Aligned_cols=253  Identities=13%  Similarity=0.086  Sum_probs=189.6

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      +..|-.-..+--+.|+.+.+-..+.+.-+..-.++...+.+........|+++.|+.-...+.+.+ +.++.+.......
T Consensus       118 ~l~~l~aA~AA~qrgd~~~an~yL~eaae~~~~~~l~v~ltrarlll~~~d~~aA~~~v~~ll~~~-pr~~~vlrLa~r~  196 (400)
T COG3071         118 VLAYLLAAEAAQQRGDEDRANRYLAEAAELAGDDTLAVELTRARLLLNRRDYPAARENVDQLLEMT-PRHPEVLRLALRA  196 (400)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHhccCCCchHHHHHHHHHHHHhCCCchhHHHHHHHHHHhC-cCChHHHHHHHHH
Confidence            456666677777889999999999988764335555666777778889999999999999998876 5678899999999


Q ss_pred             HHhcCCHHHHHHHHHhcccCCh-----------hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040371           86 YSKCGKIQMAKEVFDTVQRNDV-----------SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSH  154 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~~~~-----------~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~  154 (410)
                      |.+.|++.....+...|.+..+           .+|+.++.-....+..+.-...|+..-.. .+-+...-.+++.-+..
T Consensus       197 y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~-lr~~p~l~~~~a~~li~  275 (400)
T COG3071         197 YIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRK-LRNDPELVVAYAERLIR  275 (400)
T ss_pred             HHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHH-hhcChhHHHHHHHHHHH
Confidence            9999999999999999986532           47888877666555555555555554433 45556667778888899


Q ss_pred             cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHH--HHhcCCHHHHHHH----HHhCCCCCCHHHHHHHHHHHHhcCchhH
Q 040371          155 CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDL--LGRAGHIEEAYGL----ITSMTMEPDVVVWRALLSACRTFKRLEL  228 (410)
Q Consensus       155 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~--~~~~g~~~~A~~~----~~~m~~~p~~~~~~~li~~~~~~g~~~~  228 (410)
                      +|+.++|.++..+..++ +..|+      |...  ..+-++.+.-++.    ...-|..|  ..+.+|-..|.+++.+.+
T Consensus       276 l~~~~~A~~~i~~~Lk~-~~D~~------L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p--~L~~tLG~L~~k~~~w~k  346 (400)
T COG3071         276 LGDHDEAQEIIEDALKR-QWDPR------LCRLIPRLRPGDPEPLIKAAEKWLKQHPEDP--LLLSTLGRLALKNKLWGK  346 (400)
T ss_pred             cCChHHHHHHHHHHHHh-ccChh------HHHHHhhcCCCCchHHHHHHHHHHHhCCCCh--hHHHHHHHHHHHhhHHHH
Confidence            99999999999998865 66555      2222  2334444443333    33334444  778888889999999999


Q ss_pred             HHHHHHhh--ccCCCchHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040371          229 GEVAIVNI--SRLMGGDYVLLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       229 a~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                      |...+..-  ..++...|..+..+|.+.|+.++|.+++++-..
T Consensus       347 A~~~leaAl~~~~s~~~~~~la~~~~~~g~~~~A~~~r~e~L~  389 (400)
T COG3071         347 ASEALEAALKLRPSASDYAELADALDQLGEPEEAEQVRREALL  389 (400)
T ss_pred             HHHHHHHHHhcCCChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Confidence            99995433  234557899999999999999999999987653

>PRK11189 lipoprotein NlpI; Provisional

Probab=98.86  E-value=2.3e-06  Score=78.08  Aligned_cols=211  Identities=11%  Similarity=-0.033  Sum_probs=144.1

Q ss_pred             HHHcCCHhHHHHHHHHHHHCC-CCCC--HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCH
Q 040371           16 FVRNARFDEALRFFREMLSSK-VEPD--KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKI   92 (410)
Q Consensus        16 ~~~~g~~~~a~~l~~~m~~~g-~~pd--~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~   92 (410)
                      ...++..+.++.-+.+++... ..|+  ...|......+...|+.+.|...|.+.++.. +.+...|+.+...|...|++
T Consensus        36 ~~~~~~~e~~i~~~~~~l~~~~~~~~~~a~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~-P~~~~a~~~lg~~~~~~g~~  114 (296)
T PRK11189         36 LQPTLQQEVILARLNQILASRDLTDEERAQLHYERGVLYDSLGLRALARNDFSQALALR-PDMADAYNYLGIYLTQAGNF  114 (296)
T ss_pred             cCCchHHHHHHHHHHHHHccccCCcHhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHCCCH
Confidence            334567788888888888542 2332  3457777778889999999999999988875 45688899999999999999


Q ss_pred             HHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371           93 QMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus        93 ~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      ++|...|++..+  | +..+|..+...+...|++++|++.|++..+.  .|+..........+...++.++|...|....
T Consensus       115 ~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~~al~~--~P~~~~~~~~~~l~~~~~~~~~A~~~l~~~~  192 (296)
T PRK11189        115 DAAYEAFDSVLELDPTYNYAYLNRGIALYYGGRYELAQDDLLAFYQD--DPNDPYRALWLYLAESKLDPKQAKENLKQRY  192 (296)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHccCCHHHHHHHHHHHH
Confidence            999999998754  3 4567888888888899999999999988874  4543322222223445678999999997755


Q ss_pred             hhcCCCCChhHHHHHHHHHHhcCCHHHH--HHHHHhC-CC----CC-CHHHHHHHHHHHHhcCchhHHHHHHH
Q 040371          170 SRYSIQPQLEHYGAMVDLLGRAGHIEEA--YGLITSM-TM----EP-DVVVWRALLSACRTFKRLELGEVAIV  234 (410)
Q Consensus       170 ~~~~~~~~~~~~~~li~~~~~~g~~~~A--~~~~~~m-~~----~p-~~~~~~~li~~~~~~g~~~~a~~~~~  234 (410)
                      .  ...|+...+ .++.  ...|++.++  .+.+.+- ..    .| ....|..+-..+...|++++|...+.
T Consensus       193 ~--~~~~~~~~~-~~~~--~~lg~~~~~~~~~~~~~~~~~~~~l~~~~~ea~~~Lg~~~~~~g~~~~A~~~~~  260 (296)
T PRK11189        193 E--KLDKEQWGW-NIVE--FYLGKISEETLMERLKAGATDNTELAERLCETYFYLAKYYLSLGDLDEAAALFK  260 (296)
T ss_pred             h--hCCccccHH-HHHH--HHccCCCHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            3  223333222 2333  334554433  3222211 11    12 23578888888899999999999844

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

Probab=98.86  E-value=6e-06  Score=78.92  Aligned_cols=288  Identities=16%  Similarity=0.130  Sum_probs=209.7

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHH----HHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc--HHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFRE----MLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN--FILSA   80 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~----m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~--~~~~~   80 (410)
                      ..|-+-..-=-++|+.+....+..+    +...|+..|...|..=..+|-..|..-.+..+....+..|+...  -.+|+
T Consensus       441 ~IWitaa~LEE~ngn~~mv~kii~rgl~~L~~ngv~i~rdqWl~eAe~~e~agsv~TcQAIi~avigigvEeed~~~tw~  520 (913)
T KOG0495|consen  441 EIWITAAKLEEANGNVDMVEKIIDRGLSELQANGVEINRDQWLKEAEACEDAGSVITCQAIIRAVIGIGVEEEDRKSTWL  520 (913)
T ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcceeecHHHHHHHHHHHhhcCChhhHHHHHHHHHhhccccchhHhHHh
Confidence            4455444444556666666655543    23456677777777777777777777777777777776665432  45677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGL  157 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~  157 (410)
                      .-.+.+.+.+.++-|+.+|....+   .+...|...+..--.+|..++-..+|++.... ++-....+.......-..|+
T Consensus       521 ~da~~~~k~~~~~carAVya~alqvfp~k~slWlra~~~ek~hgt~Esl~Allqkav~~-~pkae~lwlM~ake~w~agd  599 (913)
T KOG0495|consen  521 DDAQSCEKRPAIECARAVYAHALQVFPCKKSLWLRAAMFEKSHGTRESLEALLQKAVEQ-CPKAEILWLMYAKEKWKAGD  599 (913)
T ss_pred             hhHHHHHhcchHHHHHHHHHHHHhhccchhHHHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCcchhHHHHHHHHHHhcCC
Confidence            777788888888888888877664   35677888777777789999999999998875 33355666666777778899


Q ss_pred             HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHH---H
Q 040371          158 VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVA---I  233 (410)
Q Consensus       158 ~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~---~  233 (410)
                      +..|+.++.+..+.  .+-+...|-+-+.....+.++++|..+|.+. ...|+...|.--+..-...++.++|.++   .
T Consensus       600 v~~ar~il~~af~~--~pnseeiwlaavKle~en~e~eraR~llakar~~sgTeRv~mKs~~~er~ld~~eeA~rllEe~  677 (913)
T KOG0495|consen  600 VPAARVILDQAFEA--NPNSEEIWLAAVKLEFENDELERARDLLAKARSISGTERVWMKSANLERYLDNVEEALRLLEEA  677 (913)
T ss_pred             cHHHHHHHHHHHHh--CCCcHHHHHHHHHHhhccccHHHHHHHHHHHhccCCcchhhHHHhHHHHHhhhHHHHHHHHHHH
Confidence            99999999998853  2336788999999999999999999999988 5678899998888888889999999999   4


Q ss_pred             HhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCcee--EEEECCEEEEEEeCCCCCccHHHHHHHHH
Q 040371          234 VNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKS--WLELAGVIHQFKAGDRSHPEAQAIDKILG  308 (410)
Q Consensus       234 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  308 (410)
                      .+..|.-...|..+...|.+.++++.|.+.+.    .|.+.-|.+.  |+++.       .-....|+.-.|...|+
T Consensus       678 lk~fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~----~G~k~cP~~ipLWllLa-------kleEk~~~~~rAR~ild  743 (913)
T KOG0495|consen  678 LKSFPDFHKLWLMLGQIEEQMENIEMAREAYL----QGTKKCPNSIPLWLLLA-------KLEEKDGQLVRARSILD  743 (913)
T ss_pred             HHhCCchHHHHHHHhHHHHHHHHHHHHHHHHH----hccccCCCCchHHHHHH-------HHHHHhcchhhHHHHHH
Confidence            45567777788899999999999999998884    5666555433  54321       11222345555666655

>KOG1129 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.84  E-value=2.1e-07  Score=81.61  Aligned_cols=221  Identities=11%  Similarity=0.047  Sum_probs=169.7

Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhc
Q 040371           10 NSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKC   89 (410)
Q Consensus        10 n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~   89 (410)
                      +-|-.+|.+.|-+.+|...|+.-+..  .|-+.||..+-.+|.+..+.+.|..++..-++. ++-|+.........+-..
T Consensus       227 ~Q~gkCylrLgm~r~AekqlqssL~q--~~~~dTfllLskvY~ridQP~~AL~~~~~gld~-fP~~VT~l~g~ARi~eam  303 (478)
T KOG1129|consen  227 QQMGKCYLRLGMPRRAEKQLQSSLTQ--FPHPDTFLLLSKVYQRIDQPERALLVIGEGLDS-FPFDVTYLLGQARIHEAM  303 (478)
T ss_pred             HHHHHHHHHhcChhhhHHHHHHHhhc--CCchhHHHHHHHHHHHhccHHHHHHHHhhhhhc-CCchhhhhhhhHHHHHHH
Confidence            56778888899999998888887764  566778888888999999999998888887765 455666666777778888


Q ss_pred             CCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Q 040371           90 GKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFD  166 (410)
Q Consensus        90 g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~  166 (410)
                      ++.++|.+++....+   .++.+..++..+|.-.++++-|+..|++++..|+. +...|+.+.-.|.-.+++|-+..-|+
T Consensus       304 ~~~~~a~~lYk~vlk~~~~nvEaiAcia~~yfY~~~PE~AlryYRRiLqmG~~-speLf~NigLCC~yaqQ~D~~L~sf~  382 (478)
T KOG1129|consen  304 EQQEDALQLYKLVLKLHPINVEAIACIAVGYFYDNNPEMALRYYRRILQMGAQ-SPELFCNIGLCCLYAQQIDLVLPSFQ  382 (478)
T ss_pred             HhHHHHHHHHHHHHhcCCccceeeeeeeeccccCCChHHHHHHHHHHHHhcCC-ChHHHhhHHHHHHhhcchhhhHHHHH
Confidence            888999988887654   36667777788888889999999999999888865 66778888888888888998888888


Q ss_pred             HhhhhcCCCCC--hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHHHHh
Q 040371          167 HMRSRYSIQPQ--LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVAIVN  235 (410)
Q Consensus       167 ~m~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~  235 (410)
                      +...- --.|+  ..+|-.+-......|++.-|.+-|+-. .-.| +...++.|.-.-.+.|+++.|..++..
T Consensus       383 RAlst-at~~~~aaDvWYNlg~vaV~iGD~nlA~rcfrlaL~~d~~h~ealnNLavL~~r~G~i~~Arsll~~  454 (478)
T KOG1129|consen  383 RALST-ATQPGQAADVWYNLGFVAVTIGDFNLAKRCFRLALTSDAQHGEALNNLAVLAARSGDILGARSLLNA  454 (478)
T ss_pred             HHHhh-ccCcchhhhhhhccceeEEeccchHHHHHHHHHHhccCcchHHHHHhHHHHHhhcCchHHHHHHHHH
Confidence            87642 22233  356777777777788888888888765 2233 456777777777888899888888443

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

Probab=98.82  E-value=6.1e-06  Score=72.57  Aligned_cols=267  Identities=10%  Similarity=0.067  Sum_probs=187.7

Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHHHCC-CCCC--HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371           10 NSMIGGFVRNARFDEALRFFREMLSSK-VEPD--KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus        10 n~li~~~~~~g~~~~a~~l~~~m~~~g-~~pd--~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      -+|-+-|.+.|..+.|+.+-+.+.++. .+-+  ....-.+..-|...|-+|.|+.+|..+...| .--.....-|+..|
T Consensus        73 ltLGnLfRsRGEvDRAIRiHQ~L~~spdlT~~qr~lAl~qL~~Dym~aGl~DRAE~~f~~L~de~-efa~~AlqqLl~IY  151 (389)
T COG2956          73 LTLGNLFRSRGEVDRAIRIHQTLLESPDLTFEQRLLALQQLGRDYMAAGLLDRAEDIFNQLVDEG-EFAEGALQQLLNIY  151 (389)
T ss_pred             HHHHHHHHhcchHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHhcch-hhhHHHHHHHHHHH
Confidence            357788889999999999999887642 1111  1234446677788999999999999998755 22355677889999


Q ss_pred             HhcCCHHHHHHHHHhcccCChhhHHH--------HHHHHHHcCChHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHccCC
Q 040371           87 SKCGKIQMAKEVFDTVQRNDVSVWNA--------MISGVAIHGLAADASAIFTKMEMFNVLPDS-ITFLGLLTACSHCGL  157 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~~~~~~~~~--------li~~~~~~g~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~a~~~~g~  157 (410)
                      -+..+|++|+.+-+++.+-+...|+.        +...+....+.+.|..++.+..+..  |+. ..-..+.......|+
T Consensus       152 Q~treW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq~~~~~~~~d~A~~~l~kAlqa~--~~cvRAsi~lG~v~~~~g~  229 (389)
T COG2956         152 QATREWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQQALASSDVDRARELLKKALQAD--KKCVRASIILGRVELAKGD  229 (389)
T ss_pred             HHhhHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhC--ccceehhhhhhHHHHhccc
Confidence            99999999999999877554444443        4445555788999999999988764  332 223345667788999


Q ss_pred             HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHHHHhh
Q 040371          158 VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVAIVNI  236 (410)
Q Consensus       158 ~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~  236 (410)
                      ++.|.+.++.+.+. +..--..+...|..+|.+.|+.++...++.++ ...+....-..+-.--....-.+.|...+.+.
T Consensus       230 y~~AV~~~e~v~eQ-n~~yl~evl~~L~~~Y~~lg~~~~~~~fL~~~~~~~~g~~~~l~l~~lie~~~G~~~Aq~~l~~Q  308 (389)
T COG2956         230 YQKAVEALERVLEQ-NPEYLSEVLEMLYECYAQLGKPAEGLNFLRRAMETNTGADAELMLADLIELQEGIDAAQAYLTRQ  308 (389)
T ss_pred             hHHHHHHHHHHHHh-ChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCccHHHHHHHHHHHhhChHHHHHHHHHH
Confidence            99999999999865 44444677888999999999999999988877 44444444444444444444556666663322


Q ss_pred             c--cCCCchHHHHHHHH---HhcCChhHHHHHHHHHHhCCCcCCCceeE
Q 040371          237 S--RLMGGDYVLLSNMY---CYLKRWDTAENVREIMKKKGVRKSQGKSW  280 (410)
Q Consensus       237 ~--~~~~~~~~~l~~~~---~~~g~~~~a~~~~~~m~~~g~~~~~~~s~  280 (410)
                      -  .|+...+..|+..-   +.-|++.+...+++.|....++..|....
T Consensus       309 l~r~Pt~~gf~rl~~~~l~daeeg~~k~sL~~lr~mvge~l~~~~~YRC  357 (389)
T COG2956         309 LRRKPTMRGFHRLMDYHLADAEEGRAKESLDLLRDMVGEQLRRKPRYRC  357 (389)
T ss_pred             HhhCCcHHHHHHHHHhhhccccccchhhhHHHHHHHHHHHHhhcCCcee
Confidence            2  22334455566543   34466888888899998777766664443

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

Probab=98.82  E-value=6.7e-06  Score=75.81  Aligned_cols=299  Identities=14%  Similarity=0.131  Sum_probs=209.1

Q ss_pred             CCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc-CC-CccHHHHH
Q 040371            3 DKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK-KI-ELNFILSA   80 (410)
Q Consensus         3 ~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~-g~-~~~~~~~~   80 (410)
                      .|+...|++.|.-=.+-...+.|..+|++..-  +.|+..+|.-....=.+.|....++++|+.+++. |- ..+..+++
T Consensus       171 ~P~eqaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~d~~~e~lfv  248 (677)
T KOG1915|consen  171 EPDEQAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYARFEEKHGNVALARSVYERAIEFLGDDEEAEILFV  248 (677)
T ss_pred             CCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence            58888999999998888999999999988875  5688888888888888888888888888887764 21 11233445


Q ss_pred             HHHHHHHhcCCHHHHHHHHHh----cccC-------------------------------------------ChhhHHHH
Q 040371           81 ALIDMYSKCGKIQMAKEVFDT----VQRN-------------------------------------------DVSVWNAM  113 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~----m~~~-------------------------------------------~~~~~~~l  113 (410)
                      +....=.++..++.|+-+|.-    +++.                                           |-.+|--.
T Consensus       249 aFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~np~nYDsWfdy  328 (677)
T KOG1915|consen  249 AFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKNPYNYDSWFDY  328 (677)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhCCCCchHHHHH
Confidence            555544556666666666532    2211                                           23356666


Q ss_pred             HHHHHHcCChHHHHHHHHHHHHCCCCCCH-------HHHHHHHHHH---HccCCHHHHHHHHHHhhhhcCCCCChhHHHH
Q 040371          114 ISGVAIHGLAADASAIFTKMEMFNVLPDS-------ITFLGLLTAC---SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGA  183 (410)
Q Consensus       114 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~-------~t~~~ll~a~---~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~  183 (410)
                      +..-...|+.+...++|++.... ++|-.       ..|.-+=-+|   ....+++.+.++++...+  -++...+|+.-
T Consensus       329 lrL~e~~g~~~~Ire~yErAIan-vpp~~ekr~W~RYIYLWinYalyeEle~ed~ertr~vyq~~l~--lIPHkkFtFaK  405 (677)
T KOG1915|consen  329 LRLEESVGDKDRIRETYERAIAN-VPPASEKRYWRRYIYLWINYALYEELEAEDVERTRQVYQACLD--LIPHKKFTFAK  405 (677)
T ss_pred             HHHHHhcCCHHHHHHHHHHHHcc-CCchhHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh--hcCcccchHHH
Confidence            66666778999999999988765 56632       1222221222   246788888888888874  45555667766


Q ss_pred             HHHHHH----hcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcC
Q 040371          184 MVDLLG----RAGHIEEAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLK  255 (410)
Q Consensus       184 li~~~~----~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g  255 (410)
                      +=-+|+    ++.++..|.+++... |.-|-..+|...|..=.+.++++....+   +.+..|.+..++.-....-...|
T Consensus       406 iWlmyA~feIRq~~l~~ARkiLG~AIG~cPK~KlFk~YIelElqL~efDRcRkLYEkfle~~Pe~c~~W~kyaElE~~Lg  485 (677)
T KOG1915|consen  406 IWLMYAQFEIRQLNLTGARKILGNAIGKCPKDKLFKGYIELELQLREFDRCRKLYEKFLEFSPENCYAWSKYAELETSLG  485 (677)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHhccCCchhHHHHHHHHHHHHhhHHHHHHHHHHHHhcChHhhHHHHHHHHHHHHhh
Confidence            665655    567888888888765 7788888898888888888899998888   77778888888888777788889


Q ss_pred             ChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHH
Q 040371          256 RWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQR  313 (410)
Q Consensus       256 ~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  313 (410)
                      +++.|..+|+...+....--|-.-|   ..    .+.-....++.+.+.+++++++++
T Consensus       486 dtdRaRaifelAi~qp~ldmpellw---ka----YIdFEi~~~E~ekaR~LYerlL~r  536 (677)
T KOG1915|consen  486 DTDRARAIFELAISQPALDMPELLW---KA----YIDFEIEEGEFEKARALYERLLDR  536 (677)
T ss_pred             hHHHHHHHHHHHhcCcccccHHHHH---HH----hhhhhhhcchHHHHHHHHHHHHHh
Confidence            9999999998877664322232333   11    223334567778888887766554

>PF12854 PPR_1: PPR repeat

Probab=98.81  E-value=8e-09  Score=60.34  Aligned_cols=33  Identities=33%  Similarity=0.535  Sum_probs=26.7

Q ss_pred             CCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           71 KIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        71 g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      |+.||..+||+||++|++.|++++|.++|++|+
T Consensus         2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M~   34 (34)
T PF12854_consen    2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEMK   34 (34)
T ss_pred             CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence            677888888888888888888888888888774

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=98.78  E-value=1.5e-05  Score=77.45  Aligned_cols=300  Identities=15%  Similarity=0.098  Sum_probs=191.6

Q ss_pred             HHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC---
Q 040371           14 GGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG---   90 (410)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g---   90 (410)
                      ..+...|++++|++.+..-... +......+......+.++|+.++|..++..+++.+ +.|..-|..|..+..-..   
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 SILEEAGDYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRN-PDNYDYYRGLEEALGLQLQLS   89 (517)
T ss_pred             HHHHHCCCHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHhhhcccc
Confidence            3457889999999999775432 44344566667788899999999999999999986 446666667766663322   


Q ss_pred             --CHHHHHHHHHhcccC----------------------------------Ch-hhHHHHHHHHHHcCChHHHHHHHHHH
Q 040371           91 --KIQMAKEVFDTVQRN----------------------------------DV-SVWNAMISGVAIHGLAADASAIFTKM  133 (410)
Q Consensus        91 --~~~~A~~~f~~m~~~----------------------------------~~-~~~~~li~~~~~~g~~~~A~~l~~~m  133 (410)
                        +.+...++|+++...                                  ++ .+++.+-..|....+..-..+++...
T Consensus        90 ~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~~~  169 (517)
T PF12569_consen   90 DEDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVEEY  169 (517)
T ss_pred             cccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHHHH
Confidence              456667777765321                                  22 34555555555445555555666655


Q ss_pred             HHC----C----------CCCCH--HHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHH
Q 040371          134 EMF----N----------VLPDS--ITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEE  196 (410)
Q Consensus       134 ~~~----g----------~~p~~--~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~  196 (410)
                      ...    +          -.|..  .++..+...|...|++++|..+.+...+.   .|+ +..|..-...|-+.|++.+
T Consensus       170 ~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~h---tPt~~ely~~KarilKh~G~~~~  246 (517)
T PF12569_consen  170 VNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEH---TPTLVELYMTKARILKHAGDLKE  246 (517)
T ss_pred             HHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhc---CCCcHHHHHHHHHHHHHCCCHHH
Confidence            432    1          12333  24455677788999999999999998853   566 6788889999999999999


Q ss_pred             HHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHHHHhhccCC--Cc--------hH--HHHHHHHHhcCChhHHHH
Q 040371          197 AYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVAIVNISRLM--GG--------DY--VLLSNMYCYLKRWDTAEN  262 (410)
Q Consensus       197 A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~--~~--------~~--~~l~~~~~~~g~~~~a~~  262 (410)
                      |.+.++.. ...+ |-..=+-....+.+.|++++|.+.+......+  +.        .|  .....+|.+.|++..|.+
T Consensus       247 Aa~~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~a~a~~r~~~~~~ALk  326 (517)
T PF12569_consen  247 AAEAMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETECAEAYLRQGDYGLALK  326 (517)
T ss_pred             HHHHHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence            99988877 3333 55666667777889999999999933332222  11        12  235778999999999887


Q ss_pred             HHHHHHhC--CCcCCC--ceeEEEECCEEE------EEEeCCCCCccHHHHHHHHHHHHHHHHHCC
Q 040371          263 VREIMKKK--GVRKSQ--GKSWLELAGVIH------QFKAGDRSHPEAQAIDKILGSLIQRTKSEG  318 (410)
Q Consensus       263 ~~~~m~~~--g~~~~~--~~s~~~~~~~~~------~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g  318 (410)
                      .|..+.+.  .+.-+.  -.+|..-...+.      .+.....+|+..-+|....-++.-++-+..
T Consensus       327 ~~~~v~k~f~~~~~DQfDFH~Yc~RK~t~r~Y~~~L~~ed~l~~~~~y~raa~~ai~iYl~l~d~~  392 (517)
T PF12569_consen  327 RFHAVLKHFDDFEEDQFDFHSYCLRKMTLRAYVDMLRWEDKLRSHPFYRRAAKGAIRIYLELHDKP  392 (517)
T ss_pred             HHHHHHHHHHHHhcccccHHHHHHhhccHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHhcCc
Confidence            77655432  010000  001110000000      011223567777777777777666666554

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 [], [].

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=98.78  E-value=5.6e-06  Score=69.50  Aligned_cols=195  Identities=12%  Similarity=0.066  Sum_probs=147.0

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHH
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAI  119 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~  119 (410)
                      +..-+.-.|...|+...|+.-++..++.. +.+..++..+...|.+.|+.+.|.+-|++..+   .+-...|.--.-+|.
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~  115 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLAPNNGDVLNNYGAFLCA  115 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcCCCccchhhhhhHHHHh
Confidence            45566777888899999999999998875 45677888888899999999999999987653   345566777777788


Q ss_pred             cCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHH
Q 040371          120 HGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAY  198 (410)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~  198 (410)
                      .|++++|...|++....-.-| -..||..+.-+..+.|+.+.|+.+|++..+.  .+-...+.-.+.....+.|++..|.
T Consensus       116 qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~--dp~~~~~~l~~a~~~~~~~~y~~Ar  193 (250)
T COG3063         116 QGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALEL--DPQFPPALLELARLHYKAGDYAPAR  193 (250)
T ss_pred             CCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHh--CcCCChHHHHHHHHHHhcccchHHH
Confidence            889999999998887753222 2456777777777889999999999988752  2223556777888888899999998


Q ss_pred             HHHHhC--CCCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhccCC
Q 040371          199 GLITSM--TMEPDVVVWRALLSACRTFKRLELGEVA---IVNISRLM  240 (410)
Q Consensus       199 ~~~~~m--~~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~  240 (410)
                      .++++.  ...++..+.-..|.--...|+.+.+.+.   +.+..|..
T Consensus       194 ~~~~~~~~~~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL~r~fP~s  240 (250)
T COG3063         194 LYLERYQQRGGAQAESLLLGIRIAKRLGDRAAAQRYQAQLQRLFPYS  240 (250)
T ss_pred             HHHHHHHhcccccHHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCc
Confidence            888877  3336777766777777888888888887   44555544

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

Probab=98.76  E-value=6.7e-06  Score=81.31  Aligned_cols=183  Identities=15%  Similarity=0.147  Sum_probs=143.4

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      ..|+.++|.+++.+.++.. +-+...|-+|...+-..|+.+.+...+-.+.... +.|...|-.+.+...+.|.++.|+-
T Consensus       151 arg~~eeA~~i~~EvIkqd-p~~~~ay~tL~~IyEqrGd~eK~l~~~llAAHL~-p~d~e~W~~ladls~~~~~i~qA~~  228 (895)
T KOG2076|consen  151 ARGDLEEAEEILMEVIKQD-PRNPIAYYTLGEIYEQRGDIEKALNFWLLAAHLN-PKDYELWKRLADLSEQLGNINQARY  228 (895)
T ss_pred             HhCCHHHHHHHHHHHHHhC-ccchhhHHHHHHHHHHcccHHHHHHHHHHHHhcC-CCChHHHHHHHHHHHhcccHHHHHH
Confidence            3499999999999999863 5578899999999999999999988776555543 5678999999999999999999999


Q ss_pred             HHHhcccCChhhHH---HHHHHHHHcCChHHHHHHHHHHHHCCCCCCH-----HHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371           98 VFDTVQRNDVSVWN---AMISGVAIHGLAADASAIFTKMEMFNVLPDS-----ITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus        98 ~f~~m~~~~~~~~~---~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~-----~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      .|.+..+.+..-|-   --+..|-+.|+...|++.|.++..... |..     .+.-.++..+...+.-+.|.+.++...
T Consensus       229 cy~rAI~~~p~n~~~~~ers~L~~~~G~~~~Am~~f~~l~~~~p-~~d~er~~d~i~~~~~~~~~~~~~e~a~~~le~~~  307 (895)
T KOG2076|consen  229 CYSRAIQANPSNWELIYERSSLYQKTGDLKRAMETFLQLLQLDP-PVDIERIEDLIRRVAHYFITHNERERAAKALEGAL  307 (895)
T ss_pred             HHHHHHhcCCcchHHHHHHHHHHHHhChHHHHHHHHHHHHhhCC-chhHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence            99988765443333   345678899999999999999988632 322     233345667777888899999998887


Q ss_pred             hhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371          170 SRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITS  203 (410)
Q Consensus       170 ~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  203 (410)
                      .+.+-..+...++.++..|.+...++.|...+..
T Consensus       308 s~~~~~~~~ed~ni~ael~l~~~q~d~~~~~i~~  341 (895)
T KOG2076|consen  308 SKEKDEASLEDLNILAELFLKNKQSDKALMKIVD  341 (895)
T ss_pred             hhccccccccHHHHHHHHHHHhHHHHHhhHHHHH
Confidence            6555555667788888888888888887665543

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.73  E-value=1.5e-06  Score=89.19  Aligned_cols=206  Identities=12%  Similarity=0.122  Sum_probs=167.5

Q ss_pred             HHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccC--------ChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           64 HNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRN--------DVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        64 ~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~--------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      |++.+... +-....|-..|......+++++|++++++....        -...|-++++.-...|.-+...++|++..+
T Consensus      1447 ferlvrss-PNSSi~WI~YMaf~LelsEiekAR~iaerAL~tIN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcq 1525 (1710)
T KOG1070|consen 1447 FERLVRSS-PNSSILWIRYMAFHLELSEIEKARKIAERALKTINFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQ 1525 (1710)
T ss_pred             HHHHHhcC-CCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhCCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHH
Confidence            44444432 445778999999999999999999999987632        345788888888888988999999999877


Q ss_pred             CCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC---CHH
Q 040371          136 FNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP---DVV  211 (410)
Q Consensus       136 ~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p---~~~  211 (410)
                      .-  -....|..|...|.+.+..++|.++|+.|.++++  .....|...++.+.+..+-++|..++.+. ..-|   ...
T Consensus      1526 yc--d~~~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~--q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~ 1601 (1710)
T KOG1070|consen 1526 YC--DAYTVHLKLLGIYEKSEKNDEADELLRLMLKKFG--QTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVE 1601 (1710)
T ss_pred             hc--chHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhc--chhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHH
Confidence            42  1235588999999999999999999999999877  56778999999999999999999998876 2223   344


Q ss_pred             HHHHHHHHHHhcCchhHHHHHHH---hhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcC
Q 040371          212 VWRALLSACRTFKRLELGEVAIV---NISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRK  274 (410)
Q Consensus       212 ~~~~li~~~~~~g~~~~a~~~~~---~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~  274 (410)
                      ...-.+..-.+.|+.+.|..++.   .-.|.....|+..+++-.+.|..+.++.+|++....++.+
T Consensus      1602 ~IskfAqLEFk~GDaeRGRtlfEgll~ayPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~ 1667 (1710)
T KOG1070|consen 1602 FISKFAQLEFKYGDAERGRTLFEGLLSAYPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSI 1667 (1710)
T ss_pred             HHHHHHHHHhhcCCchhhHHHHHHHHhhCccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCCh
Confidence            55556666689999999999944   4467778899999999999999999999999999988753

>PF12854 PPR_1: PPR repeat

Probab=98.71  E-value=2.4e-08  Score=58.29  Aligned_cols=32  Identities=28%  Similarity=0.625  Sum_probs=25.5

Q ss_pred             CCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          173 SIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       173 ~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      |+.||..+|++||++|++.|++++|.++|++|
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            67788888888888888888888888888777

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

Probab=98.70  E-value=2.6e-05  Score=74.74  Aligned_cols=252  Identities=15%  Similarity=0.101  Sum_probs=144.4

Q ss_pred             HHHHHcCCHhHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCC
Q 040371           14 GGFVRNARFDEALRFFREMLSSKVEPD--KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK   91 (410)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~g~~pd--~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~   91 (410)
                      -.|-..|..-.+..+....+.-|+.-.  ..||..-...|.+.+.++-++.+|...++- ++.+..+|......=-.-|.
T Consensus       487 e~~e~agsv~TcQAIi~avigigvEeed~~~tw~~da~~~~k~~~~~carAVya~alqv-fp~k~slWlra~~~ek~hgt  565 (913)
T KOG0495|consen  487 EACEDAGSVITCQAIIRAVIGIGVEEEDRKSTWLDDAQSCEKRPAIECARAVYAHALQV-FPCKKSLWLRAAMFEKSHGT  565 (913)
T ss_pred             HHHhhcCChhhHHHHHHHHHhhccccchhHhHHhhhHHHHHhcchHHHHHHHHHHHHhh-ccchhHHHHHHHHHHHhcCc
Confidence            334444555555555555554443321  236666666666666677777777666665 34455666665555555566


Q ss_pred             HHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040371           92 IQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHM  168 (410)
Q Consensus        92 ~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  168 (410)
                      .++-..+|++...   ...+.|-....-+-..|+...|..++.+.-+.. +-+...+...+..-.....++.|+.+|...
T Consensus       566 ~Esl~Allqkav~~~pkae~lwlM~ake~w~agdv~~ar~il~~af~~~-pnseeiwlaavKle~en~e~eraR~llaka  644 (913)
T KOG0495|consen  566 RESLEALLQKAVEQCPKAEILWLMYAKEKWKAGDVPAARVILDQAFEAN-PNSEEIWLAAVKLEFENDELERARDLLAKA  644 (913)
T ss_pred             HHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCcHHHHHHHHHHHHhC-CCcHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence            6666666665542   233445555555555666666666666665542 124455555666666666666666666665


Q ss_pred             hhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCchhHHHHHH---HhhccCCCch
Q 040371          169 RSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDV-VVWRALLSACRTFKRLELGEVAI---VNISRLMGGD  243 (410)
Q Consensus       169 ~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~-~~~~~li~~~~~~g~~~~a~~~~---~~~~~~~~~~  243 (410)
                      .   +..|+..+|.--+...--.+..++|++++++. ..-|+- ..|..+-+.+-+.++++.|....   .+..|..+..
T Consensus       645 r---~~sgTeRv~mKs~~~er~ld~~eeA~rllEe~lk~fp~f~Kl~lmlGQi~e~~~~ie~aR~aY~~G~k~cP~~ipL  721 (913)
T KOG0495|consen  645 R---SISGTERVWMKSANLERYLDNVEEALRLLEEALKSFPDFHKLWLMLGQIEEQMENIEMAREAYLQGTKKCPNSIPL  721 (913)
T ss_pred             h---ccCCcchhhHHHhHHHHHhhhHHHHHHHHHHHHHhCCchHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCchH
Confidence            4   34556666666666666666666666666554 333443 34555555566666666666662   2333555556


Q ss_pred             HHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          244 YVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       244 ~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      |..|...-.+.|....|+.++++-+-+
T Consensus       722 WllLakleEk~~~~~rAR~ildrarlk  748 (913)
T KOG0495|consen  722 WLLLAKLEEKDGQLVRARSILDRARLK  748 (913)
T ss_pred             HHHHHHHHHHhcchhhHHHHHHHHHhc
Confidence            666666666666666666666655444

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

Probab=98.69  E-value=3.3e-06  Score=84.07  Aligned_cols=262  Identities=11%  Similarity=0.023  Sum_probs=185.9

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHC---CCCCCH------HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSS---KVEPDK------FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNF   76 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~---g~~pd~------~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~   76 (410)
                      +..-|.+.+-+...|.+++|...|......   ...+|.      .+--.+....-..++.+.|.+.|..+++.. +.-+
T Consensus       452 ~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~l~~~~~A~e~Yk~Ilkeh-p~YI  530 (1018)
T KOG2002|consen  452 PEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEELHDTEVAEEMYKSILKEH-PGYI  530 (1018)
T ss_pred             HHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHhhhhhhHHHHHHHHHHHHC-chhH
Confidence            456677778888888888888888877653   122333      122234444556678888888888887753 2223


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhcc---cCChhhHHHHHHHHHHcCChHHHHHHHHHHHHC-CCCCCHHHHHHHHHHH
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQ---RNDVSVWNAMISGVAIHGLAADASAIFTKMEMF-NVLPDSITFLGLLTAC  152 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~---~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~~t~~~ll~a~  152 (410)
                      ..|--|.-+-...+...+|...+....   +.|...|+.+-..|.....+..|.+-|...... ...+|.++..+|.+.|
T Consensus       531 d~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~~i~~~~~~~~D~YsliaLGN~~  610 (1018)
T KOG2002|consen  531 DAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFETILKKTSTKTDAYSLIALGNVY  610 (1018)
T ss_pred             HHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHHHHHhhhccCCchhHHHHhhHHH
Confidence            333333333333466778888887665   356778888888888888888888877766554 2347888888888866


Q ss_pred             Hc------------cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCC--CCCCHHHHHHHHH
Q 040371          153 SH------------CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMT--MEPDVVVWRALLS  218 (410)
Q Consensus       153 ~~------------~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~--~~p~~~~~~~li~  218 (410)
                      ..            .+..++|.++|..+.+  .-+-|...-|-+.-.++..|++.+|.++|....  ..-+..+|..+..
T Consensus       611 ~~~l~~~~rn~ek~kk~~~KAlq~y~kvL~--~dpkN~yAANGIgiVLA~kg~~~~A~dIFsqVrEa~~~~~dv~lNlah  688 (1018)
T KOG2002|consen  611 IQALHNPSRNPEKEKKHQEKALQLYGKVLR--NDPKNMYAANGIGIVLAEKGRFSEARDIFSQVREATSDFEDVWLNLAH  688 (1018)
T ss_pred             HHHhcccccChHHHHHHHHHHHHHHHHHHh--cCcchhhhccchhhhhhhccCchHHHHHHHHHHHHHhhCCceeeeHHH
Confidence            53            3567889999998885  334466777778888999999999999999882  2225578889999


Q ss_pred             HHHhcCchhHHHHH----HHhhc-cCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          219 ACRTFKRLELGEVA----IVNIS-RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       219 ~~~~~g~~~~a~~~----~~~~~-~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      .|...|++..|.+.    +.+.. ..++.+...|..++.+.|++.+|.+........
T Consensus       689 ~~~e~~qy~~AIqmYe~~lkkf~~~~~~~vl~~Lara~y~~~~~~eak~~ll~a~~~  745 (1018)
T KOG2002|consen  689 CYVEQGQYRLAIQMYENCLKKFYKKNRSEVLHYLARAWYEAGKLQEAKEALLKARHL  745 (1018)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHhhhHHHHHHHHHHHHHh
Confidence            99999999999998    33333 334566778999999999999999988766554

>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=98.68  E-value=1.6e-05  Score=66.88  Aligned_cols=192  Identities=12%  Similarity=0.054  Sum_probs=159.9

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYS   87 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~   87 (410)
                      +.--|--+|.+.|+...|..-+++.++.. +-+..+|..+...|.+.|..+.|.+-|++.++.. +-+-.+.|.....++
T Consensus        37 arlqLal~YL~~gd~~~A~~nlekAL~~D-Ps~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl~-p~~GdVLNNYG~FLC  114 (250)
T COG3063          37 ARLQLALGYLQQGDYAQAKKNLEKALEHD-PSYYLAHLVRAHYYQKLGENDLADESYRKALSLA-PNNGDVLNNYGAFLC  114 (250)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCChhhHHHHHHHHHhcC-CCccchhhhhhHHHH
Confidence            45667789999999999999999999853 3356699999999999999999999999999875 457789999999999


Q ss_pred             hcCCHHHHHHHHHhcc-cCC----hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040371           88 KCGKIQMAKEVFDTVQ-RND----VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGR  162 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~-~~~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  162 (410)
                      ..|++++|...|++.. .|+    ..+|..+.-+..+.|+.+.|.+.|++-.+.. +-...+...+.....+.|++..|.
T Consensus       115 ~qg~~~eA~q~F~~Al~~P~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~d-p~~~~~~l~~a~~~~~~~~y~~Ar  193 (250)
T COG3063         115 AQGRPEEAMQQFERALADPAYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELD-PQFPPALLELARLHYKAGDYAPAR  193 (250)
T ss_pred             hCCChHHHHHHHHHHHhCCCCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhC-cCCChHHHHHHHHHHhcccchHHH
Confidence            9999999999999765 443    4588888888899999999999999998753 223567778888889999999999


Q ss_pred             HHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          163 KYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       163 ~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      .+++.....  ..++..+.-..|..--+.|+-+.+.+.=..+
T Consensus       194 ~~~~~~~~~--~~~~A~sL~L~iriak~~gd~~~a~~Y~~qL  233 (250)
T COG3063         194 LYLERYQQR--GGAQAESLLLGIRIAKRLGDRAAAQRYQAQL  233 (250)
T ss_pred             HHHHHHHhc--ccccHHHHHHHHHHHHHhccHHHHHHHHHHH
Confidence            999998864  3478888777888888889888876554433

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

Probab=98.67  E-value=2.1e-05  Score=72.86  Aligned_cols=254  Identities=14%  Similarity=0.113  Sum_probs=171.8

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc-HHHHHHHHHHH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPD-KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN-FILSAALIDMY   86 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~-~~~~~~li~~y   86 (410)
                      +-..-+-|.++|.+++|+..|.+.+.  +.|| ++-|....-+|...|+++.+.+.--..++.  .|+ +..+.--..++
T Consensus       118 lK~~GN~~f~~kkY~eAIkyY~~AI~--l~p~epiFYsNraAcY~~lgd~~~Vied~TkALEl--~P~Y~KAl~RRA~A~  193 (606)
T KOG0547|consen  118 LKTKGNKFFRNKKYDEAIKYYTQAIE--LCPDEPIFYSNRAACYESLGDWEKVIEDCTKALEL--NPDYVKALLRRASAH  193 (606)
T ss_pred             HHhhhhhhhhcccHHHHHHHHHHHHh--cCCCCchhhhhHHHHHHHHhhHHHHHHHHHHHhhc--CcHHHHHHHHHHHHH
Confidence            44455667889999999999999887  4777 677888888888999998887766655553  333 33444444455


Q ss_pred             HhcCCHHHHHH----------------------HHHh---------ccc---C---C-----------------------
Q 040371           87 SKCGKIQMAKE----------------------VFDT---------VQR---N---D-----------------------  106 (410)
Q Consensus        87 ~~~g~~~~A~~----------------------~f~~---------m~~---~---~-----------------------  106 (410)
                      -+.|++++|..                      ++..         +.+   |   .                       
T Consensus       194 E~lg~~~eal~D~tv~ci~~~F~n~s~~~~~eR~Lkk~a~~ka~e~~k~nr~p~lPS~~fi~syf~sF~~~~~~~~~~~~  273 (606)
T KOG0547|consen  194 EQLGKFDEALFDVTVLCILEGFQNASIEPMAERVLKKQAMKKAKEKLKENRPPVLPSATFIASYFGSFHADPKPLFDNKS  273 (606)
T ss_pred             HhhccHHHHHHhhhHHHHhhhcccchhHHHHHHHHHHHHHHHHHHhhcccCCCCCCcHHHHHHHHhhccccccccccCCC
Confidence            55555555432                      1110         110   0   0                       


Q ss_pred             --------------------------------------hhhHH------------HHHH--HHHHcCChHHHHHHHHHHH
Q 040371          107 --------------------------------------VSVWN------------AMIS--GVAIHGLAADASAIFTKME  134 (410)
Q Consensus       107 --------------------------------------~~~~~------------~li~--~~~~~g~~~~A~~l~~~m~  134 (410)
                                                            ..++|            .++.  -+.-.|+.-.|.+-|+...
T Consensus       274 ~ksDa~l~~~l~~l~~~~~e~Y~~a~~~~te~~~~~~~~~~~n~~d~~le~~A~al~~~gtF~fL~g~~~~a~~d~~~~I  353 (606)
T KOG0547|consen  274 DKSDAALAEALEALEKGLEEGYLKAYDKATEECLGSESSLSVNEIDAELEYMAEALLLRGTFHFLKGDSLGAQEDFDAAI  353 (606)
T ss_pred             ccchhhHHHHHHHHHhhCchhHHHHHHHHHHHhhhhhhhccccccchhHHHHHHHHHHhhhhhhhcCCchhhhhhHHHHH
Confidence                                                  00011            0011  1223567777777777777


Q ss_pred             HCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHH
Q 040371          135 MFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVV  212 (410)
Q Consensus       135 ~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~  212 (410)
                      .....++. .|.-+..+|....+.++.++.|+...+-  -+-++.+|..-..++.-.+++++|..=|++. .+.| +...
T Consensus       354 ~l~~~~~~-lyI~~a~~y~d~~~~~~~~~~F~~A~~l--dp~n~dvYyHRgQm~flL~q~e~A~aDF~Kai~L~pe~~~~  430 (606)
T KOG0547|consen  354 KLDPAFNS-LYIKRAAAYADENQSEKMWKDFNKAEDL--DPENPDVYYHRGQMRFLLQQYEEAIADFQKAISLDPENAYA  430 (606)
T ss_pred             hcCcccch-HHHHHHHHHhhhhccHHHHHHHHHHHhc--CCCCCchhHhHHHHHHHHHHHHHHHHHHHHHhhcChhhhHH
Confidence            65433332 2777778889999999999999998742  1224566766667777788999999999887 5666 3456


Q ss_pred             HHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040371          213 WRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       213 ~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                      |.-+--+.-+.+.++++...   ..+..|..+..|+....++...+++++|.+.++...+
T Consensus       431 ~iQl~~a~Yr~~k~~~~m~~Fee~kkkFP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~  490 (606)
T KOG0547|consen  431 YIQLCCALYRQHKIAESMKTFEEAKKKFPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIE  490 (606)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHh
Confidence            66665565677788888887   4456688899999999999999999999999997765

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=98.67  E-value=2.3e-06  Score=77.23  Aligned_cols=144  Identities=13%  Similarity=0.115  Sum_probs=74.1

Q ss_pred             HHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----cCCH
Q 040371           83 IDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSH----CGLV  158 (410)
Q Consensus        83 i~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~----~g~~  158 (410)
                      ..+|...|++++|.+++.+-  .+.......+..|.+.++++.|.+.++.|.+.  ..| .+...+..++..    ...+
T Consensus       109 A~i~~~~~~~~~AL~~l~~~--~~lE~~al~Vqi~L~~~R~dlA~k~l~~~~~~--~eD-~~l~qLa~awv~l~~g~e~~  183 (290)
T PF04733_consen  109 ATILFHEGDYEEALKLLHKG--GSLELLALAVQILLKMNRPDLAEKELKNMQQI--DED-SILTQLAEAWVNLATGGEKY  183 (290)
T ss_dssp             HHHHCCCCHHHHHHCCCTTT--TCHHHHHHHHHHHHHTT-HHHHHHHHHHHHCC--SCC-HHHHHHHHHHHHHHHTTTCC
T ss_pred             HHHHHHcCCHHHHHHHHHcc--CcccHHHHHHHHHHHcCCHHHHHHHHHHHHhc--CCc-HHHHHHHHHHHHHHhCchhH
Confidence            34555566666666666554  34445555566666666666666666666543  222 333334343332    2346


Q ss_pred             HHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCch-hHHHHHH
Q 040371          159 EEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRL-ELGEVAI  233 (410)
Q Consensus       159 ~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~-~~a~~~~  233 (410)
                      .+|..+|+++.++  ..+++.+.+.+..++...|++++|.+++.+. ...| |..+...++......|+. +.+.+.+
T Consensus       184 ~~A~y~f~El~~~--~~~t~~~lng~A~~~l~~~~~~eAe~~L~~al~~~~~~~d~LaNliv~~~~~gk~~~~~~~~l  259 (290)
T PF04733_consen  184 QDAFYIFEELSDK--FGSTPKLLNGLAVCHLQLGHYEEAEELLEEALEKDPNDPDTLANLIVCSLHLGKPTEAAERYL  259 (290)
T ss_dssp             CHHHHHHHHHHCC--S--SHHHHHHHHHHHHHCT-HHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHTT-TCHHHHHHH
T ss_pred             HHHHHHHHHHHhc--cCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCCChhHHHHHH
Confidence            6666666666542  3445556666666666666666666665553 3333 334444555555555555 3344443

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.

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

Probab=98.67  E-value=3.2e-05  Score=70.98  Aligned_cols=179  Identities=13%  Similarity=0.132  Sum_probs=120.2

Q ss_pred             cCCHHHHHHHHHhcccCChhhHHHHHH---HHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040371           89 CGKIQMAKEVFDTVQRNDVSVWNAMIS---GVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYF  165 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~~~~~~~~~li~---~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  165 (410)
                      .|++++|.+.+.+....|...-.+|.+   .+-..|+.++|++.|-++..- +.-+.....-+.+.|-...+..+|.+++
T Consensus       503 ngd~dka~~~ykeal~ndasc~ealfniglt~e~~~~ldeald~f~klh~i-l~nn~evl~qianiye~led~aqaie~~  581 (840)
T KOG2003|consen  503 NGDLDKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAI-LLNNAEVLVQIANIYELLEDPAQAIELL  581 (840)
T ss_pred             cCcHHHHHHHHHHHHcCchHHHHHHHHhcccHHHhcCHHHHHHHHHHHHHH-HHhhHHHHHHHHHHHHHhhCHHHHHHHH
Confidence            456666666666666555443333222   244567777777777665432 2224455556666777777777888877


Q ss_pred             HHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHHHHh--hccCCC
Q 040371          166 DHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVAIVN--ISRLMG  241 (410)
Q Consensus       166 ~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~--~~~~~~  241 (410)
                      .+...  -++.|+...+.|.+.|-+.|+-.+|.+..-.- ..-| |..+...|..-|....-.+.++.++.+  +-.++.
T Consensus       582 ~q~~s--lip~dp~ilskl~dlydqegdksqafq~~ydsyryfp~nie~iewl~ayyidtqf~ekai~y~ekaaliqp~~  659 (840)
T KOG2003|consen  582 MQANS--LIPNDPAILSKLADLYDQEGDKSQAFQCHYDSYRYFPCNIETIEWLAAYYIDTQFSEKAINYFEKAALIQPNQ  659 (840)
T ss_pred             HHhcc--cCCCCHHHHHHHHHHhhcccchhhhhhhhhhcccccCcchHHHHHHHHHHHhhHHHHHHHHHHHHHHhcCccH
Confidence            76652  45556788889999999999999888764433 3333 677777788888888888888888443  334455


Q ss_pred             chHHHHH-HHHHhcCChhHHHHHHHHHHhC
Q 040371          242 GDYVLLS-NMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       242 ~~~~~l~-~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      .-|..++ +++-+.|++.+|.++++...++
T Consensus       660 ~kwqlmiasc~rrsgnyqka~d~yk~~hrk  689 (840)
T KOG2003|consen  660 SKWQLMIASCFRRSGNYQKAFDLYKDIHRK  689 (840)
T ss_pred             HHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence            6676665 4556789999999999988654

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

Probab=98.63  E-value=3.8e-05  Score=71.02  Aligned_cols=249  Identities=14%  Similarity=0.055  Sum_probs=191.4

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      .++++..|.++|++.+.-. .-+...|.--+.+=.+...+..|+.++++.+.. ++.-...|--.+.|=-..|++..|++
T Consensus        85 sq~e~~RARSv~ERALdvd-~r~itLWlkYae~Emknk~vNhARNv~dRAvt~-lPRVdqlWyKY~ymEE~LgNi~gaRq  162 (677)
T KOG1915|consen   85 SQKEIQRARSVFERALDVD-YRNITLWLKYAEFEMKNKQVNHARNVWDRAVTI-LPRVDQLWYKYIYMEEMLGNIAGARQ  162 (677)
T ss_pred             hHHHHHHHHHHHHHHHhcc-cccchHHHHHHHHHHhhhhHhHHHHHHHHHHHh-cchHHHHHHHHHHHHHHhcccHHHHH
Confidence            3566778999999988653 446667777777778899999999999999886 33344567777888888999999999


Q ss_pred             HHHhcc--cCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCC
Q 040371           98 VFDTVQ--RNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQ  175 (410)
Q Consensus        98 ~f~~m~--~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~  175 (410)
                      +|++-.  +|+..+|++.|.-=.+....+.|..++++..-  +.|+..+|.-...-=-+.|++..+..+|....+..|-.
T Consensus       163 iferW~~w~P~eqaW~sfI~fElRykeieraR~IYerfV~--~HP~v~~wikyarFE~k~g~~~~aR~VyerAie~~~~d  240 (677)
T KOG1915|consen  163 IFERWMEWEPDEQAWLSFIKFELRYKEIERARSIYERFVL--VHPKVSNWIKYARFEEKHGNVALARSVYERAIEFLGDD  240 (677)
T ss_pred             HHHHHHcCCCcHHHHHHHHHHHHHhhHHHHHHHHHHHHhe--ecccHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHhhhH
Confidence            999865  79999999999999999999999999999987  56999999988888889999999999999998765532


Q ss_pred             C-ChhHHHHHHHHHHhcCCHHHHHHHHHhC----CCCCCHHHHHHHHHHHHhcCchhHHHHH-----------HHhhccC
Q 040371          176 P-QLEHYGAMVDLLGRAGHIEEAYGLITSM----TMEPDVVVWRALLSACRTFKRLELGEVA-----------IVNISRL  239 (410)
Q Consensus       176 ~-~~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~p~~~~~~~li~~~~~~g~~~~a~~~-----------~~~~~~~  239 (410)
                      . +...+.+...-=.++..++.|.-+|+-.    |.......|..+..-=.+.|+....+.+           .....|.
T Consensus       241 ~~~e~lfvaFA~fEe~qkE~ERar~iykyAld~~pk~raeeL~k~~~~fEKqfGd~~gIEd~Iv~KRk~qYE~~v~~np~  320 (677)
T KOG1915|consen  241 EEAEILFVAFAEFEERQKEYERARFIYKYALDHIPKGRAEELYKKYTAFEKQFGDKEGIEDAIVGKRKFQYEKEVSKNPY  320 (677)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHhcchhhhHHHHhhhhhhHHHHHHHhCCC
Confidence            1 1223444444444567788888777654    3222355666666666667776655555           2334566


Q ss_pred             CCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          240 MGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       240 ~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      |..++.-.+..-...|+.+...+++++...+
T Consensus       321 nYDsWfdylrL~e~~g~~~~Ire~yErAIan  351 (677)
T KOG1915|consen  321 NYDSWFDYLRLEESVGDKDRIRETYERAIAN  351 (677)
T ss_pred             CchHHHHHHHHHHhcCCHHHHHHHHHHHHcc
Confidence            7778888888888999999999999987654

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=98.63  E-value=0.00016  Score=67.86  Aligned_cols=307  Identities=9%  Similarity=0.043  Sum_probs=186.8

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCC-CCCCHHH-HHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHH---
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSK-VEPDKFT-FASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSA---   80 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g-~~pd~~t-~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~---   80 (410)
                      ...|..+...+...|+.+++...+.+..+.. ..++... .......+...|+++.+.++++...+.. +.|...++   
T Consensus         6 ~~a~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~~~   84 (355)
T cd05804           6 ALGHAAAALLLLLGGERPAAAAKAAAAAQALAARATERERAHVEALSAWIAGDLPKALALLEQLLDDY-PRDLLALKLHL   84 (355)
T ss_pred             HHHHHHHHHHHHhcCCcchHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHhH
Confidence            4567777788888899999877777765432 1223322 2222344567899999999999998863 44554544   


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcccCC---hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQRND---VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGL  157 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~~~---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~  157 (410)
                      .+.......|..+.+.+.++.....+   ...+..+...+...|++++|.+.+++..+.. +.+...+..+...+...|+
T Consensus        85 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al~~~-p~~~~~~~~la~i~~~~g~  163 (355)
T cd05804          85 GAFGLGDFSGMRDHVARVLPLWAPENPDYWYLLGMLAFGLEEAGQYDRAEEAARRALELN-PDDAWAVHAVAHVLEMQGR  163 (355)
T ss_pred             HHHHhcccccCchhHHHHHhccCcCCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCC
Confidence            22222333566677777776533222   2344455567888999999999999998853 3345667788889999999


Q ss_pred             HHHHHHHHHHhhhhcCCCCCh--hHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC--CHHH-H-H--HHHHHHHhcCchhH
Q 040371          158 VEEGRKYFDHMRSRYSIQPQL--EHYGAMVDLLGRAGHIEEAYGLITSM-TMEP--DVVV-W-R--ALLSACRTFKRLEL  228 (410)
Q Consensus       158 ~~~a~~~~~~m~~~~~~~~~~--~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p--~~~~-~-~--~li~~~~~~g~~~~  228 (410)
                      +++|..+++...+.....|+.  ..|..+...+...|++++|.+++++. ...|  .... . +  .++.-+...|..+.
T Consensus       164 ~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~  243 (355)
T cd05804         164 FKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAALAIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDV  243 (355)
T ss_pred             HHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHHHHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCCh
Confidence            999999999987532222332  34557888999999999999999986 2233  2111 1 1  33444455565555


Q ss_pred             HHHH--HHhh-c---cCCCchHH--HHHHHHHhcCChhHHHHHHHHHHhCCCcCC-CceeEEEECCEEEEEEeCCCCCcc
Q 040371          229 GEVA--IVNI-S---RLMGGDYV--LLSNMYCYLKRWDTAENVREIMKKKGVRKS-QGKSWLELAGVIHQFKAGDRSHPE  299 (410)
Q Consensus       229 a~~~--~~~~-~---~~~~~~~~--~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~-~~~s~~~~~~~~~~~~~~~~~~~~  299 (410)
                      +.+.  +... .   +.....+.  ....++...|+.++|..+++.+........ .+..|..+...+- ........|+
T Consensus       244 ~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l-~A~~~~~~g~  322 (355)
T cd05804         244 GDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLA-EALYAFAEGN  322 (355)
T ss_pred             HHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHH-HHHHHHHcCC
Confidence            5554  2211 1   11111222  456677889999999999999876433210 0111111100000 0011234567


Q ss_pred             HHHHHHHHHHHHHHHH
Q 040371          300 AQAIDKILGSLIQRTK  315 (410)
Q Consensus       300 ~~~~~~~l~~l~~~m~  315 (410)
                      .+++...|.+......
T Consensus       323 ~~~A~~~L~~al~~a~  338 (355)
T cd05804         323 YATALELLGPVRDDLA  338 (355)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            7777777765554443

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.

>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment

Probab=98.60  E-value=1.8e-06  Score=77.97  Aligned_cols=242  Identities=10%  Similarity=0.012  Sum_probs=156.5

Q ss_pred             HHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHH
Q 040371           14 GGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQ   93 (410)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~   93 (410)
                      +-+.-.|++..++.-.+ .....-..+..+..-+.+++..+|..+.+.   ..+.+.. .|.......+...+...++-+
T Consensus         9 rn~fy~G~Y~~~i~e~~-~~~~~~~~~~e~~~~~~Rs~iAlg~~~~vl---~ei~~~~-~~~l~av~~la~y~~~~~~~e   83 (290)
T PF04733_consen    9 RNQFYLGNYQQCINEAS-LKSFSPENKLERDFYQYRSYIALGQYDSVL---SEIKKSS-SPELQAVRLLAEYLSSPSDKE   83 (290)
T ss_dssp             HHHHCTT-HHHHCHHHH-CHTSTCHHHHHHHHHHHHHHHHTT-HHHHH---HHS-TTS-SCCCHHHHHHHHHHCTSTTHH
T ss_pred             HHHHHhhhHHHHHHHhh-ccCCCchhHHHHHHHHHHHHHHcCChhHHH---HHhccCC-ChhHHHHHHHHHHHhCccchH
Confidence            44455788888887665 222221223445667778888899876543   3333333 566666655554444435556


Q ss_pred             HHHHHHHhcc-cCC---hhhHHHH-HHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040371           94 MAKEVFDTVQ-RND---VSVWNAM-ISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHM  168 (410)
Q Consensus        94 ~A~~~f~~m~-~~~---~~~~~~l-i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  168 (410)
                      .+..-+++.. ++.   -.++..+ ...|...|++++|++++++-      .+.......+..+.+.+++|.|.+.++.|
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            6665555433 221   1122222 23455679999999988642      35566777889999999999999999999


Q ss_pred             hhhcCCCCChhHHHHHHHHHH----hcCCHHHHHHHHHhC--CCCCCHHHHHHHHHHHHhcCchhHHHHHH---HhhccC
Q 040371          169 RSRYSIQPQLEHYGAMVDLLG----RAGHIEEAYGLITSM--TMEPDVVVWRALLSACRTFKRLELGEVAI---VNISRL  239 (410)
Q Consensus       169 ~~~~~~~~~~~~~~~li~~~~----~~g~~~~A~~~~~~m--~~~p~~~~~~~li~~~~~~g~~~~a~~~~---~~~~~~  239 (410)
                      .+   +..| .+...+..++.    -.+.+.+|.-+|+++  ...++..+.+.+..+....|++++|+.++   ...+|.
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            84   2334 33333444433    345799999999999  34578888899999999999999999993   445677


Q ss_pred             CCchHHHHHHHHHhcCCh-hHHHHHHHHHHhC
Q 040371          240 MGGDYVLLSNMYCYLKRW-DTAENVREIMKKK  270 (410)
Q Consensus       240 ~~~~~~~l~~~~~~~g~~-~~a~~~~~~m~~~  270 (410)
                      ++.+...++-+....|+. +.+.+.+.+++..
T Consensus       234 ~~d~LaNliv~~~~~gk~~~~~~~~l~qL~~~  265 (290)
T PF04733_consen  234 DPDTLANLIVCSLHLGKPTEAAERYLSQLKQS  265 (290)
T ss_dssp             HHHHHHHHHHHHHHTT-TCHHHHHHHHHCHHH
T ss_pred             CHHHHHHHHHHHHHhCCChhHHHHHHHHHHHh
Confidence            777888888888888988 6677888887764

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.

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

Probab=98.60  E-value=2.2e-05  Score=78.32  Aligned_cols=270  Identities=14%  Similarity=0.100  Sum_probs=131.5

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCC-C-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKV-E-PDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAAL   82 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~-~-pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l   82 (410)
                      |++.-|.|-+-|.-.|++..++.+...+...-. . .-...|--+..++-..|+++.|...|....+..-..-+..+-.|
T Consensus       269 nP~~l~~LAn~fyfK~dy~~v~~la~~ai~~t~~~~~~aes~Y~~gRs~Ha~Gd~ekA~~yY~~s~k~~~d~~~l~~~Gl  348 (1018)
T KOG2002|consen  269 NPVALNHLANHFYFKKDYERVWHLAEHAIKNTENKSIKAESFYQLGRSYHAQGDFEKAFKYYMESLKADNDNFVLPLVGL  348 (1018)
T ss_pred             CcHHHHHHHHHHhhcccHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHccCCCCccccccch
Confidence            455556666666666666666666665554320 0 11234555666666666666666666555554322112333455


Q ss_pred             HHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHc-------------------------------------CC
Q 040371           83 IDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIH-------------------------------------GL  122 (410)
Q Consensus        83 i~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~-------------------------------------g~  122 (410)
                      ..+|.+.|+++.|...|+....  | +..+-..+...|+..                                     ++
T Consensus       349 gQm~i~~~dle~s~~~fEkv~k~~p~~~etm~iLG~Lya~~~~~~~~~d~a~~~l~K~~~~~~~d~~a~l~laql~e~~d  428 (1018)
T KOG2002|consen  349 GQMYIKRGDLEESKFCFEKVLKQLPNNYETMKILGCLYAHSAKKQEKRDKASNVLGKVLEQTPVDSEAWLELAQLLEQTD  428 (1018)
T ss_pred             hHHHHHhchHHHHHHHHHHHHHhCcchHHHHHHHHhHHHhhhhhhHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHhcC
Confidence            6666666666666666665542  1 222333333333333                                     22


Q ss_pred             hHHHHHHHHHHH----HCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcC--CCCCh------hHHHHHHHHHHh
Q 040371          123 AADASAIFTKME----MFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYS--IQPQL------EHYGAMVDLLGR  190 (410)
Q Consensus       123 ~~~A~~l~~~m~----~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~--~~~~~------~~~~~li~~~~~  190 (410)
                      +..++..|....    ..+..+.....+.+.......|+++.|...|.....+..  ..++.      .+--.+...+-.
T Consensus       429 ~~~sL~~~~~A~d~L~~~~~~ip~E~LNNvaslhf~~g~~~~A~~~f~~A~~~~~~~~n~de~~~~~lt~~YNlarl~E~  508 (1018)
T KOG2002|consen  429 PWASLDAYGNALDILESKGKQIPPEVLNNVASLHFRLGNIEKALEHFKSALGKLLEVANKDEGKSTNLTLKYNLARLLEE  508 (1018)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCCCHHHHHhHHHHHHHhcChHHHHHHHHHHhhhhhhhcCccccccchhHHHHHHHHHHHh
Confidence            222233333221    222334444455555555555555555555555443200  01111      111223333344


Q ss_pred             cCCHHHHHHHHHhC-CCCCCHH-HHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHH
Q 040371          191 AGHIEEAYGLITSM-TMEPDVV-VWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVRE  265 (410)
Q Consensus       191 ~g~~~~A~~~~~~m-~~~p~~~-~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  265 (410)
                      .++++.|.+.++.+ ...|... .|.-+.......++..+|...   ....+..++.....+.+.|.+...|..|.+-|.
T Consensus       509 l~~~~~A~e~Yk~Ilkehp~YId~ylRl~~ma~~k~~~~ea~~~lk~~l~~d~~np~arsl~G~~~l~k~~~~~a~k~f~  588 (1018)
T KOG2002|consen  509 LHDTEVAEEMYKSILKEHPGYIDAYLRLGCMARDKNNLYEASLLLKDALNIDSSNPNARSLLGNLHLKKSEWKPAKKKFE  588 (1018)
T ss_pred             hhhhhHHHHHHHHHHHHCchhHHHHHHhhHHHHhccCcHHHHHHHHHHHhcccCCcHHHHHHHHHHHhhhhhcccccHHH
Confidence            44555555555554 2334322 222222222233444555554   444555667777777778888888888888777


Q ss_pred             HHHhCCCcC
Q 040371          266 IMKKKGVRK  274 (410)
Q Consensus       266 ~m~~~g~~~  274 (410)
                      ...++-...
T Consensus       589 ~i~~~~~~~  597 (1018)
T KOG2002|consen  589 TILKKTSTK  597 (1018)
T ss_pred             HHHhhhccC
Confidence            665554333

>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals

Probab=98.59  E-value=7.9e-05  Score=70.03  Aligned_cols=256  Identities=12%  Similarity=-0.017  Sum_probs=159.7

Q ss_pred             HHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh----hCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh
Q 040371           13 IGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCAR----LGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK   88 (410)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~----~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~   88 (410)
                      ...+...|++++|.+.+++..+.. +.|...+.. ...+..    .+..+.+.+.+.. .....+.+......+...+..
T Consensus        50 a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~-~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~~a~~~~~  126 (355)
T cd05804          50 ALSAWIAGDLPKALALLEQLLDDY-PRDLLALKL-HLGAFGLGDFSGMRDHVARVLPL-WAPENPDYWYLLGMLAFGLEE  126 (355)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHH-hHHHHHhcccccCchhHHHHHhc-cCcCCCCcHHHHHHHHHHHHH
Confidence            345667899999999999988752 334444442 222222    3445555555544 111223334555667788999


Q ss_pred             cCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCC-CCCH--HHHHHHHHHHHccCCHHHHH
Q 040371           89 CGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNV-LPDS--ITFLGLLTACSHCGLVEEGR  162 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~~--~t~~~ll~a~~~~g~~~~a~  162 (410)
                      .|++++|...+++..+   .+...+..+...|...|++++|...+++...... .|+.  ..+..+...+...|+.++|.
T Consensus       127 ~G~~~~A~~~~~~al~~~p~~~~~~~~la~i~~~~g~~~eA~~~l~~~l~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~  206 (355)
T cd05804         127 AGQYDRAEEAARRALELNPDDAWAVHAVAHVLEMQGRFKEGIAFMESWRDTWDCSSMLRGHNWWHLALFYLERGDYEAAL  206 (355)
T ss_pred             cCCHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHhhhhccCCCcchhHHHHHHHHHHHHHCCCHHHHH
Confidence            9999999999998764   3566788888999999999999999998876532 2332  24556788889999999999


Q ss_pred             HHHHHhhhhcCCCCChhHH-H--HHHHHHHhcCCHHHHHHH---HHhC-CCCC---CHHHHHHHHHHHHhcCchhHHHHH
Q 040371          163 KYFDHMRSRYSIQPQLEHY-G--AMVDLLGRAGHIEEAYGL---ITSM-TMEP---DVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       163 ~~~~~m~~~~~~~~~~~~~-~--~li~~~~~~g~~~~A~~~---~~~m-~~~p---~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      .+++.........+..... +  .++.-+...|..+.+.++   ...- +..|   ..........++...|+.+.|..+
T Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~a~~~  286 (355)
T cd05804         207 AIYDTHIAPSAESDPALDLLDAASLLWRLELAGHVDVGDRWEDLADYAAWHFPDHGLAFNDLHAALALAGAGDKDALDKL  286 (355)
T ss_pred             HHHHHHhccccCCChHHHHhhHHHHHHHHHhcCCCChHHHHHHHHHHHHhhcCcccchHHHHHHHHHHhcCCCHHHHHHH
Confidence            9999976321111222111 1  233334444533333332   1111 1101   122223566667888999999988


Q ss_pred             HHhhcc---C---------CCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          233 IVNISR---L---------MGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       233 ~~~~~~---~---------~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      +..+..   .         .........-++...|++++|.+.+......+
T Consensus       287 L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~~a  337 (355)
T cd05804         287 LAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRDDL  337 (355)
T ss_pred             HHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            443322   1         11223344556779999999999998876543

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.

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.58  E-value=1e-07  Score=56.35  Aligned_cols=35  Identities=43%  Similarity=0.861  Sum_probs=32.9

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDK   41 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~   41 (410)
                      ++||+||.+|++.|++++|.++|++|.+.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            48999999999999999999999999999999983

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.

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

Probab=98.57  E-value=7.6e-06  Score=75.73  Aligned_cols=211  Identities=16%  Similarity=0.108  Sum_probs=164.0

Q ss_pred             HhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHH
Q 040371           52 ARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASA  128 (410)
Q Consensus        52 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~  128 (410)
                      .-.|+.-.+.+-|+..++.... +...|--+..+|+...+-++..+.|+....   .|..+|..-...+.-.+++++|..
T Consensus       337 fL~g~~~~a~~d~~~~I~l~~~-~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dvYyHRgQm~flL~q~e~A~a  415 (606)
T KOG0547|consen  337 FLKGDSLGAQEDFDAAIKLDPA-FNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDVYYHRGQMRFLLQQYEEAIA  415 (606)
T ss_pred             hhcCCchhhhhhHHHHHhcCcc-cchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCchhHhHHHHHHHHHHHHHHHH
Confidence            4567888899999999887543 333366677789999999999999987763   356677777777777889999999


Q ss_pred             HHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CC
Q 040371          129 IFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TM  206 (410)
Q Consensus       129 l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~  206 (410)
                      =|++.+.  +.| +...|.-+-.+..+.+.+++++..|++..++  ++.-+..|+-....+...++++.|.+.|+.. .+
T Consensus       416 DF~Kai~--L~pe~~~~~iQl~~a~Yr~~k~~~~m~~Fee~kkk--FP~~~Evy~~fAeiLtDqqqFd~A~k~YD~ai~L  491 (606)
T KOG0547|consen  416 DFQKAIS--LDPENAYAYIQLCCALYRQHKIAESMKTFEEAKKK--FPNCPEVYNLFAEILTDQQQFDKAVKQYDKAIEL  491 (606)
T ss_pred             HHHHHhh--cChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--CCCCchHHHHHHHHHhhHHhHHHHHHHHHHHHhh
Confidence            9999887  455 4566777777777899999999999999975  4445778998999999999999999999876 44


Q ss_pred             CCC---------HHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          207 EPD---------VVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       207 ~p~---------~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                      +|+         ..+-.+++-. .=.+++..|..+   ..+++|.....|..|...-.+.|+.++|.++|++-.
T Consensus       492 E~~~~~~~v~~~plV~Ka~l~~-qwk~d~~~a~~Ll~KA~e~Dpkce~A~~tlaq~~lQ~~~i~eAielFEksa  564 (606)
T KOG0547|consen  492 EPREHLIIVNAAPLVHKALLVL-QWKEDINQAENLLRKAIELDPKCEQAYETLAQFELQRGKIDEAIELFEKSA  564 (606)
T ss_pred             ccccccccccchhhhhhhHhhh-chhhhHHHHHHHHHHHHccCchHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            443         1222222222 223888999998   566778777899999999999999999999998643

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

Probab=98.50  E-value=2.4e-05  Score=73.70  Aligned_cols=208  Identities=15%  Similarity=0.110  Sum_probs=102.9

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCC-ccHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD-KFTFASVIYGCARLGALNHAYWVHNLIIEKKIE-LNFILSAALI   83 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~-~~~~~~~~li   83 (410)
                      .+||-++-..|.-.|+..+|.+.|.+...-  .|. ...|.....+++..+.-|+|...+..+-+.=.. .-+..|.  .
T Consensus       312 a~sW~aVg~YYl~i~k~seARry~SKat~l--D~~fgpaWl~fghsfa~e~EhdQAmaaY~tAarl~~G~hlP~LYl--g  387 (611)
T KOG1173|consen  312 ALSWFAVGCYYLMIGKYSEARRYFSKATTL--DPTFGPAWLAFGHSFAGEGEHDQAMAAYFTAARLMPGCHLPSLYL--G  387 (611)
T ss_pred             CcchhhHHHHHHHhcCcHHHHHHHHHHhhc--CccccHHHHHHhHHhhhcchHHHHHHHHHHHHHhccCCcchHHHH--H
Confidence            345555555555555555555555554321  111 234555555555555555555555544443100 0111121  1


Q ss_pred             HHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHC--CC---CC-CHHHHHHHHHHHHc
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMF--NV---LP-DSITFLGLLTACSH  154 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~--g~---~p-~~~t~~~ll~a~~~  154 (410)
                      -=|.+.++++.|.++|.+...   .|+...+-+.-.....+.+.+|..+|+..+..  .+   ++ -..+++.|..+|.+
T Consensus       388 mey~~t~n~kLAe~Ff~~A~ai~P~Dplv~~Elgvvay~~~~y~~A~~~f~~~l~~ik~~~~e~~~w~p~~~NLGH~~Rk  467 (611)
T KOG1173|consen  388 MEYMRTNNLKLAEKFFKQALAIAPSDPLVLHELGVVAYTYEEYPEALKYFQKALEVIKSVLNEKIFWEPTLNNLGHAYRK  467 (611)
T ss_pred             HHHHHhccHHHHHHHHHHHHhcCCCcchhhhhhhheeehHhhhHHHHHHHHHHHHHhhhccccccchhHHHHhHHHHHHH
Confidence            234455555566655554431   24445555544444455566666666554421  00   11 22345555566666


Q ss_pred             cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHH
Q 040371          155 CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLSA  219 (410)
Q Consensus       155 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~  219 (410)
                      .+.+++|...|+....  -.+.+..++.++.-.|...|+++.|.+.|.+. .++||..+...+++.
T Consensus       468 l~~~~eAI~~~q~aL~--l~~k~~~~~asig~iy~llgnld~Aid~fhKaL~l~p~n~~~~~lL~~  531 (611)
T KOG1173|consen  468 LNKYEEAIDYYQKALL--LSPKDASTHASIGYIYHLLGNLDKAIDHFHKALALKPDNIFISELLKL  531 (611)
T ss_pred             HhhHHHHHHHHHHHHH--cCCCchhHHHHHHHHHHHhcChHHHHHHHHHHHhcCCccHHHHHHHHH
Confidence            6666666666665553  22334555556555566666666666655554 555555555555543

>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif)

Probab=98.47  E-value=2.8e-07  Score=54.35  Aligned_cols=35  Identities=26%  Similarity=0.455  Sum_probs=31.9

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH
Q 040371          108 SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS  142 (410)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~  142 (410)
                      .+||+||.+|++.|++++|.++|++|.+.|++||.
T Consensus         1 ~~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~p~~   35 (35)
T TIGR00756         1 VTYNTLIDGLCKAGRVEEALELFKEMLERGIEPDV   35 (35)
T ss_pred             CcHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCCC
Confidence            47999999999999999999999999999999973

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.

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.46  E-value=3.2e-05  Score=68.12  Aligned_cols=180  Identities=12%  Similarity=0.017  Sum_probs=101.4

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCH---HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCC-cc-HHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDK---FTFASVIYGCARLGALNHAYWVHNLIIEKKIE-LN-FILSA   80 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~---~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~-~~-~~~~~   80 (410)
                      ...+-.+...|.+.|++++|...|++..... +.+.   .++..+..++...|+++.|...++.+++.... +. ..++.
T Consensus        33 ~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~  111 (235)
T TIGR03302        33 AEELYEEAKEALDSGDYTEAIKYFEALESRY-PFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYY  111 (235)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHH
Confidence            4455566666677777777777777666532 1111   34555666666777777777777777654321 11 11334


Q ss_pred             HHHHHHHhc--------CCHHHHHHHHHhcccC--Ch-hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040371           81 ALIDMYSKC--------GKIQMAKEVFDTVQRN--DV-SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLL  149 (410)
Q Consensus        81 ~li~~y~~~--------g~~~~A~~~f~~m~~~--~~-~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll  149 (410)
                      .+...|.+.        |+.++|.+.|+++...  +. ..+.++.....    .....             . .....+.
T Consensus       112 ~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~~~~----~~~~~-------------~-~~~~~~a  173 (235)
T TIGR03302       112 LRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEYAPDAKKRMDY----LRNRL-------------A-GKELYVA  173 (235)
T ss_pred             HHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChhHHHHHHHHHH----HHHHH-------------H-HHHHHHH
Confidence            444444443        5566666666665432  11 12211111000    00000             0 0012345


Q ss_pred             HHHHccCCHHHHHHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          150 TACSHCGLVEEGRKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       150 ~a~~~~g~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      ..+.+.|++++|...++...+.+.-.| ....+..+..+|.+.|++++|...++.+
T Consensus       174 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l  229 (235)
T TIGR03302       174 RFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVL  229 (235)
T ss_pred             HHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            667888888888888888876533223 3567888888888888888888888776

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).

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.46  E-value=3.4e-07  Score=53.69  Aligned_cols=34  Identities=29%  Similarity=0.527  Sum_probs=31.2

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCC
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEP   39 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~p   39 (410)
                      +.+||++|.+|++.|+++.|.++|++|.+.|++|
T Consensus         1 v~ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~P   34 (34)
T PF13812_consen    1 VHTYNALLRACAKAGDPDAALQLFDEMKEQGVKP   34 (34)
T ss_pred             CcHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC
Confidence            4689999999999999999999999999999887

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.44  E-value=0.00017  Score=62.94  Aligned_cols=251  Identities=15%  Similarity=0.094  Sum_probs=163.1

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHH-HHHHH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAAL-IDMYS   87 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l-i~~y~   87 (410)
                      +++.+..+.+..++.+|++++..-.+.. +-+....+.+..+|-...++..|-.-++++-..-  |...-|... .....
T Consensus        13 ftaviy~lI~d~ry~DaI~~l~s~~Er~-p~~rAgLSlLgyCYY~~Q~f~~AA~CYeQL~ql~--P~~~qYrlY~AQSLY   89 (459)
T KOG4340|consen   13 FTAVVYRLIRDARYADAIQLLGSELERS-PRSRAGLSLLGYCYYRLQEFALAAECYEQLGQLH--PELEQYRLYQAQSLY   89 (459)
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC--hHHHHHHHHHHHHHH
Confidence            5667777778888999999887766652 2266777777788888888888888887776542  222222110 11223


Q ss_pred             hcCCHHHHHHHH----------------------------------Hhcc-cCChhhHHHHHHHHHHcCChHHHHHHHHH
Q 040371           88 KCGKIQMAKEVF----------------------------------DTVQ-RNDVSVWNAMISGVAIHGLAADASAIFTK  132 (410)
Q Consensus        88 ~~g~~~~A~~~f----------------------------------~~m~-~~~~~~~~~li~~~~~~g~~~~A~~l~~~  132 (410)
                      +.+.+.+|.++.                                  ++.+ +.+..+.+.......+.|++++|++-|+.
T Consensus        90 ~A~i~ADALrV~~~~~D~~~L~~~~lqLqaAIkYse~Dl~g~rsLveQlp~en~Ad~~in~gCllykegqyEaAvqkFqa  169 (459)
T KOG4340|consen   90 KACIYADALRVAFLLLDNPALHSRVLQLQAAIKYSEGDLPGSRSLVEQLPSENEADGQINLGCLLYKEGQYEAAVQKFQA  169 (459)
T ss_pred             HhcccHHHHHHHHHhcCCHHHHHHHHHHHHHHhcccccCcchHHHHHhccCCCccchhccchheeeccccHHHHHHHHHH
Confidence            334444444444                                  4433 22334444444556678999999999998


Q ss_pred             HHHC-CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCC-------------CCh--------hHHHHHHHH---
Q 040371          133 MEMF-NVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQ-------------PQL--------EHYGAMVDL---  187 (410)
Q Consensus       133 m~~~-g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~-------------~~~--------~~~~~li~~---  187 (410)
                      ..+- |.. ....|+..+. ..+.|+.+.|.++..++.++ |+.             ||+        -+-+.++.+   
T Consensus       170 AlqvsGyq-pllAYniALa-Hy~~~qyasALk~iSEIieR-G~r~HPElgIGm~tegiDvrsvgNt~~lh~Sal~eAfNL  246 (459)
T KOG4340|consen  170 ALQVSGYQ-PLLAYNLALA-HYSSRQYASALKHISEIIER-GIRQHPELGIGMTTEGIDVRSVGNTLVLHQSALVEAFNL  246 (459)
T ss_pred             HHhhcCCC-chhHHHHHHH-HHhhhhHHHHHHHHHHHHHh-hhhcCCccCccceeccCchhcccchHHHHHHHHHHHhhh
Confidence            8775 444 4567776654 45568999999999988865 543             221        123444443   


Q ss_pred             ----HHhcCCHHHHHHHHHhCCC----CCCHHHHHHHHHHHHhcCchhHH---HHHHHhhccCCCchHHHHHHHHHhcCC
Q 040371          188 ----LGRAGHIEEAYGLITSMTM----EPDVVVWRALLSACRTFKRLELG---EVAIVNISRLMGGDYVLLSNMYCYLKR  256 (410)
Q Consensus       188 ----~~~~g~~~~A~~~~~~m~~----~p~~~~~~~li~~~~~~g~~~~a---~~~~~~~~~~~~~~~~~l~~~~~~~g~  256 (410)
                          +.+.|+++.|.+-+-.||-    +.|.+|...+.-.= ..+++..+   .+.+.+..|..+.+|..++-.|++..-
T Consensus       247 KaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n-~~~~p~~g~~KLqFLL~~nPfP~ETFANlLllyCKNey  325 (459)
T KOG4340|consen  247 KAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMN-MDARPTEGFEKLQFLLQQNPFPPETFANLLLLYCKNEY  325 (459)
T ss_pred             hhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhc-ccCCccccHHHHHHHHhcCCCChHHHHHHHHHHhhhHH
Confidence                5578999999999999952    24666654433221 12223222   233777788888999999999999999


Q ss_pred             hhHHHHHHHH
Q 040371          257 WDTAENVREI  266 (410)
Q Consensus       257 ~~~a~~~~~~  266 (410)
                      ++-|..++-+
T Consensus       326 f~lAADvLAE  335 (459)
T KOG4340|consen  326 FDLAADVLAE  335 (459)
T ss_pred             HhHHHHHHhh
Confidence            9999988754

>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]

Probab=98.42  E-value=7.5e-05  Score=77.27  Aligned_cols=225  Identities=12%  Similarity=0.141  Sum_probs=164.3

Q ss_pred             CCC-hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccH
Q 040371            3 DKD-VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD-----KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNF   76 (410)
Q Consensus         3 ~~~-~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-----~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~   76 (410)
                      .|| .+.|-..|+-..+.+..++|.+++++.+.. +.+.     ...|.++++.-..-|.-+...++|+++.+..  .-.
T Consensus      1454 sPNSSi~WI~YMaf~LelsEiekAR~iaerAL~t-IN~REeeEKLNiWiA~lNlEn~yG~eesl~kVFeRAcqyc--d~~ 1530 (1710)
T KOG1070|consen 1454 SPNSSILWIRYMAFHLELSEIEKARKIAERALKT-INFREEEEKLNIWIAYLNLENAYGTEESLKKVFERACQYC--DAY 1530 (1710)
T ss_pred             CCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhh-CCcchhHHHHHHHHHHHhHHHhhCcHHHHHHHHHHHHHhc--chH
Confidence            344 356888899999999999999999988764 3222     2357777777677777888889999988864  235


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhcccC---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHH-HHHHHHH
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQRN---DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITF-LGLLTAC  152 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~-~~ll~a~  152 (410)
                      .+|..|...|.+.++.++|-++|+.|.++   ....|...+..+.++.+.++|..++.+.++.=.+-..+-+ .-.+..-
T Consensus      1531 ~V~~~L~~iy~k~ek~~~A~ell~~m~KKF~q~~~vW~~y~~fLl~~ne~~aa~~lL~rAL~~lPk~eHv~~IskfAqLE 1610 (1710)
T KOG1070|consen 1531 TVHLKLLGIYEKSEKNDEADELLRLMLKKFGQTRKVWIMYADFLLRQNEAEAARELLKRALKSLPKQEHVEFISKFAQLE 1610 (1710)
T ss_pred             HHHHHHHHHHHHhhcchhHHHHHHHHHHHhcchhhHHHHHHHHHhcccHHHHHHHHHHHHHhhcchhhhHHHHHHHHHHH
Confidence            67889999999999999999999999754   5568998999999999889999999888774222123322 2333444


Q ss_pred             HccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC---CCCC--CHHHHHHHHHHHHhcCchh
Q 040371          153 SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM---TMEP--DVVVWRALLSACRTFKRLE  227 (410)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m---~~~p--~~~~~~~li~~~~~~g~~~  227 (410)
                      .+.|+.+.|+.+|+.....  .+-....|+..|++-.+.|..+.+.++|++.   ++.|  --..|...+.-=..+|+-+
T Consensus      1611 Fk~GDaeRGRtlfEgll~a--yPKRtDlW~VYid~eik~~~~~~vR~lfeRvi~l~l~~kkmKfffKkwLeyEk~~Gde~ 1688 (1710)
T KOG1070|consen 1611 FKYGDAERGRTLFEGLLSA--YPKRTDLWSVYIDMEIKHGDIKYVRDLFERVIELKLSIKKMKFFFKKWLEYEKSHGDEK 1688 (1710)
T ss_pred             hhcCCchhhHHHHHHHHhh--CccchhHHHHHHHHHHccCCHHHHHHHHHHHHhcCCChhHhHHHHHHHHHHHHhcCchh
Confidence            5789999999999988854  2335678999999999999999999999987   3333  2345555555555666655


Q ss_pred             HHHHH
Q 040371          228 LGEVA  232 (410)
Q Consensus       228 ~a~~~  232 (410)
                      .++.+
T Consensus      1689 ~vE~V 1693 (1710)
T KOG1070|consen 1689 NVEYV 1693 (1710)
T ss_pred             hHHHH
Confidence            55444

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.41  E-value=1.3e-05  Score=75.77  Aligned_cols=214  Identities=12%  Similarity=0.018  Sum_probs=167.5

Q ss_pred             HhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccC---ChhhHHHHHHHHHHcCChHHHHH
Q 040371           52 ARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRN---DVSVWNAMISGVAIHGLAADASA  128 (410)
Q Consensus        52 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~  128 (410)
                      .+.|++..|.-.|+..++.. +.+...|.-|....+..++-..|+..+.+..+-   |....-+|.-.|...|.-.+|+.
T Consensus       296 m~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~LdP~NleaLmaLAVSytNeg~q~~Al~  374 (579)
T KOG1125|consen  296 MKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLELDPTNLEALMALAVSYTNEGLQNQALK  374 (579)
T ss_pred             HhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhHHHHHH
Confidence            57788889988999888875 557888999988889888888898888877643   56677777778888999999999


Q ss_pred             HHHHHHHCCCC--------CCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHH
Q 040371          129 IFTKMEMFNVL--------PDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGL  200 (410)
Q Consensus       129 l~~~m~~~g~~--------p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~  200 (410)
                      .++.-.....+        ++..+-..  ........+....++|-.+....+.++|..++..|.-.|--.|.+++|.+.
T Consensus       375 ~L~~Wi~~~p~y~~l~~a~~~~~~~~~--~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiDc  452 (579)
T KOG1125|consen  375 MLDKWIRNKPKYVHLVSAGENEDFENT--KSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVDC  452 (579)
T ss_pred             HHHHHHHhCccchhccccCccccccCC--cCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHHH
Confidence            99887654211        01000000  122223345566677777766557668888999999999999999999999


Q ss_pred             HHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          201 ITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       201 ~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                      |+.. .++| |..+||-|-..++...+.++|..+   ..++.|.-..+...|.-.|...|.+++|.+.|-...
T Consensus       453 f~~AL~v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~hlL~AL  525 (579)
T KOG1125|consen  453 FEAALQVKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKHLLEAL  525 (579)
T ss_pred             HHHHHhcCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHHHHHHH
Confidence            9987 7788 678999999999999999999999   778889888888899999999999999999876543

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=98.36  E-value=0.0011  Score=60.51  Aligned_cols=180  Identities=11%  Similarity=0.012  Sum_probs=96.1

Q ss_pred             HHHHHH--cCCHhHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHH-HHHHHHHHHh
Q 040371           13 IGGFVR--NARFDEALRFFREMLSS-KVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFIL-SAALIDMYSK   88 (410)
Q Consensus        13 i~~~~~--~g~~~~a~~l~~~m~~~-g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~-~~~li~~y~~   88 (410)
                      |.+|++  .++...|..+|--.... -++-|......+...+...|+.+++.-.|+.....  .|+... -....-.+.+
T Consensus       201 ika~Aq~~~~~hs~a~~t~l~le~~~~lr~NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~--dpy~i~~MD~Ya~LL~~  278 (564)
T KOG1174|consen  201 IKALAQMFNFKHSDASQTFLMLHDNTTLRCNEHLMMALGKCLYYNGDYFQAEDIFSSTLCA--NPDNVEAMDLYAVLLGQ  278 (564)
T ss_pred             HHHHHHHHhcccchhhhHHHHHHhhccCCccHHHHHHHhhhhhhhcCchHHHHHHHHHhhC--ChhhhhhHHHHHHHHHh
Confidence            444443  44444555544433332 24556667777888888888888888888877654  232211 1111222345


Q ss_pred             cCCHHHHHHHHHhcccC---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHH
Q 040371           89 CGKIQMAKEVFDTVQRN---DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKY  164 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~  164 (410)
                      .|+++....+-..+-..   ....|-.-.......++++.|+.+-++-.+.  .| +...|..-..++...|+.++|.-.
T Consensus       279 eg~~e~~~~L~~~Lf~~~~~ta~~wfV~~~~l~~~K~~~rAL~~~eK~I~~--~~r~~~alilKG~lL~~~~R~~~A~Ia  356 (564)
T KOG1174|consen  279 EGGCEQDSALMDYLFAKVKYTASHWFVHAQLLYDEKKFERALNFVEKCIDS--EPRNHEALILKGRLLIALERHTQAVIA  356 (564)
T ss_pred             ccCHhhHHHHHHHHHhhhhcchhhhhhhhhhhhhhhhHHHHHHHHHHHhcc--CcccchHHHhccHHHHhccchHHHHHH
Confidence            66666665555544322   2334444444444555666666666555442  22 223333334455556666666666


Q ss_pred             HHHhhhhcCCC-CChhHHHHHHHHHHhcCCHHHHHH
Q 040371          165 FDHMRSRYSIQ-PQLEHYGAMVDLLGRAGHIEEAYG  199 (410)
Q Consensus       165 ~~~m~~~~~~~-~~~~~~~~li~~~~~~g~~~~A~~  199 (410)
                      |....   .+. .+...|.-|+..|...|++.||.-
T Consensus       357 FR~Aq---~Lap~rL~~Y~GL~hsYLA~~~~kEA~~  389 (564)
T KOG1174|consen  357 FRTAQ---MLAPYRLEIYRGLFHSYLAQKRFKEANA  389 (564)
T ss_pred             HHHHH---hcchhhHHHHHHHHHHHHhhchHHHHHH
Confidence            66554   222 245566666666666666666543

>PF13812 PPR_3: Pentatricopeptide repeat domain

Probab=98.32  E-value=1.1e-06  Score=51.53  Aligned_cols=33  Identities=27%  Similarity=0.396  Sum_probs=27.3

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC
Q 040371          108 SVWNAMISGVAIHGLAADASAIFTKMEMFNVLP  140 (410)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  140 (410)
                      .+||++|.+|++.|+++.|.++|++|++.|++|
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            578888888888888888888888888888877

>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO

Probab=98.27  E-value=0.00013  Score=64.28  Aligned_cols=176  Identities=12%  Similarity=-0.008  Sum_probs=111.3

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCC-c-cHHHHHHHHHHHHhcCCHHHHHHHHHhccc--CC-hh---hHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIE-L-NFILSAALIDMYSKCGKIQMAKEVFDTVQR--ND-VS---VWN  111 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~-~-~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~-~~---~~~  111 (410)
                      ....+......+...|+++.|...++.+.+.... | ....+..+...|.+.|++++|...|+++.+  |+ ..   +|.
T Consensus        32 ~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~  111 (235)
T TIGR03302        32 PAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYY  111 (235)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHH
Confidence            3456666777777888888888888887765311 1 124566777788888888888888887753  21 11   344


Q ss_pred             HHHHHHHHc--------CChHHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHH
Q 040371          112 AMISGVAIH--------GLAADASAIFTKMEMFNVLPDSI-TFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYG  182 (410)
Q Consensus       112 ~li~~~~~~--------g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  182 (410)
                      .+..++.+.        |+.++|.+.|+++...  .|+.. ....+... .   ..      .....         ....
T Consensus       112 ~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~p~~~~~~~a~~~~-~---~~------~~~~~---------~~~~  170 (235)
T TIGR03302       112 LRGLSNYNQIDRVDRDQTAAREAFEAFQELIRR--YPNSEYAPDAKKRM-D---YL------RNRLA---------GKEL  170 (235)
T ss_pred             HHHHHHHHhcccccCCHHHHHHHHHHHHHHHHH--CCCChhHHHHHHHH-H---HH------HHHHH---------HHHH
Confidence            444455443        6677778777777654  33321 11111110 0   00      00000         1123


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCchhHHHHHHHhh
Q 040371          183 AMVDLLGRAGHIEEAYGLITSM----TMEP-DVVVWRALLSACRTFKRLELGEVAIVNI  236 (410)
Q Consensus       183 ~li~~~~~~g~~~~A~~~~~~m----~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~  236 (410)
                      .+...|.+.|++++|...+++.    +-.| ....|..+..++...|++++|...+..+
T Consensus       171 ~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~a~~~l~~~~~~lg~~~~A~~~~~~l  229 (235)
T TIGR03302       171 YVARFYLKRGAYVAAINRFETVVENYPDTPATEEALARLVEAYLKLGLKDLAQDAAAVL  229 (235)
T ss_pred             HHHHHHHHcCChHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            5667899999999999998887    2233 3568889999999999999999985544

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).

>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=98.26  E-value=5.3e-05  Score=70.92  Aligned_cols=128  Identities=14%  Similarity=0.062  Sum_probs=105.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCG  156 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g  156 (410)
                      ..-.+|+..+...++++.|..+|+++.+.+...+..++..+...++..+|++++++.... .+-|...+..-...|.+.+
T Consensus       170 yLv~~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  170 YLVDTLLKYLSLTQRYDEAIELLEKLRERDPEVAVLLARVYLLMNEEVEAIRLLNEALKE-NPQDSELLNLQAEFLLSKK  248 (395)
T ss_pred             HHHHHHHHHHhhcccHHHHHHHHHHHHhcCCcHHHHHHHHHHhcCcHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhcC
Confidence            344566777778899999999999999888777778889998899999999999998864 2335555666667788999


Q ss_pred             CHHHHHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhCCCCC
Q 040371          157 LVEEGRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSMTMEP  208 (410)
Q Consensus       157 ~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p  208 (410)
                      +.+.|..+.+++..   ..|+ ..+|..|...|.+.|++++|+..++.+|+.|
T Consensus       249 ~~~lAL~iAk~av~---lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~Pm~~  298 (395)
T PF09295_consen  249 KYELALEIAKKAVE---LSPSEFETWYQLAECYIQLGDFENALLALNSCPMLT  298 (395)
T ss_pred             CHHHHHHHHHHHHH---hCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCcCCC
Confidence            99999999999984   3555 5699999999999999999999999997655

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=98.25  E-value=1.2e-06  Score=50.03  Aligned_cols=31  Identities=39%  Similarity=0.763  Sum_probs=28.3

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCC
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKV   37 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~   37 (410)
                      ++||+||++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            5899999999999999999999999998774

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.

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.25  E-value=0.00011  Score=71.54  Aligned_cols=217  Identities=17%  Similarity=0.158  Sum_probs=165.1

Q ss_pred             CCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040371           71 KIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLT  150 (410)
Q Consensus        71 g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  150 (410)
                      +++|-...-..+.+.+.++|-...|..+|+++     ..|.-.|.+|...|+..+|..+..+-.+  -+||...|..+..
T Consensus       393 ~lpp~Wq~q~~laell~slGitksAl~I~Erl-----emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGD  465 (777)
T KOG1128|consen  393 HLPPIWQLQRLLAELLLSLGITKSALVIFERL-----EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGD  465 (777)
T ss_pred             CCCCcchHHHHHHHHHHHcchHHHHHHHHHhH-----HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhh
Confidence            45666667778899999999999999999986     5688899999999999999999988776  5789999999999


Q ss_pred             HHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhH
Q 040371          151 ACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLEL  228 (410)
Q Consensus       151 a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~  228 (410)
                      ......-+++|+++++....+        .-..+.....+.++++++.+.|+.- .+.| -..+|-.+-.+..+.++++.
T Consensus       466 v~~d~s~yEkawElsn~~sar--------A~r~~~~~~~~~~~fs~~~~hle~sl~~nplq~~~wf~~G~~ALqlek~q~  537 (777)
T KOG1128|consen  466 VLHDPSLYEKAWELSNYISAR--------AQRSLALLILSNKDFSEADKHLERSLEINPLQLGTWFGLGCAALQLEKEQA  537 (777)
T ss_pred             hccChHHHHHHHHHhhhhhHH--------HHHhhccccccchhHHHHHHHHHHHhhcCccchhHHHhccHHHHHHhhhHH
Confidence            988888899999999886643        1111222233478899998888764 5555 46788777777788888888


Q ss_pred             HHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHH
Q 040371          229 GEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDK  305 (410)
Q Consensus       229 a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~  305 (410)
                      |.+.   -..++|++...|+.+..+|.+.|+-.+|...+++..+-+..     +|..+.+..  +++  ..-|+.+++..
T Consensus       538 av~aF~rcvtL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~-----~w~iWENym--lvs--vdvge~eda~~  608 (777)
T KOG1128|consen  538 AVKAFHRCVTLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQ-----HWQIWENYM--LVS--VDVGEFEDAIK  608 (777)
T ss_pred             HHHHHHHHhhcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCC-----CCeeeechh--hhh--hhcccHHHHHH
Confidence            8888   45678999999999999999999999999999988776632     344333322  111  23456677776


Q ss_pred             HHHHHH
Q 040371          306 ILGSLI  311 (410)
Q Consensus       306 ~l~~l~  311 (410)
                      ...++.
T Consensus       609 A~~rll  614 (777)
T KOG1128|consen  609 AYHRLL  614 (777)
T ss_pred             HHHHHH
Confidence            666543

>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala

Probab=98.24  E-value=0.0008  Score=65.57  Aligned_cols=256  Identities=10%  Similarity=0.043  Sum_probs=165.5

Q ss_pred             HHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCC--hh-hHHHHHHHHHHc----
Q 040371           48 IYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRND--VS-VWNAMISGVAIH----  120 (410)
Q Consensus        48 l~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~--~~-~~~~li~~~~~~----  120 (410)
                      ...+...|++++|.+.+..-.+. +.....+.......|.+.|+.++|..+|..+.++|  -. -|..+..+....    
T Consensus        11 ~~il~e~g~~~~AL~~L~~~~~~-I~Dk~~~~E~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~   89 (517)
T PF12569_consen   11 NSILEEAGDYEEALEHLEKNEKQ-ILDKLAVLEKRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQLQLS   89 (517)
T ss_pred             HHHHHHCCCHHHHHHHHHhhhhh-CCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhhcccc
Confidence            34567889999999999775554 33456777888999999999999999999998543  33 344444444222    


Q ss_pred             -CChHHHHHHHHHHHHCCCC---C--------CH--------------------HHHHHHHHHHHccCCHHHHHHHHHHh
Q 040371          121 -GLAADASAIFTKMEMFNVL---P--------DS--------------------ITFLGLLTACSHCGLVEEGRKYFDHM  168 (410)
Q Consensus       121 -g~~~~A~~l~~~m~~~g~~---p--------~~--------------------~t~~~ll~a~~~~g~~~~a~~~~~~m  168 (410)
                       ...+...++|+++...-.+   |        +.                    .+|+.|-..|......+-..+++...
T Consensus        90 ~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~l~KgvPslF~~lk~Ly~d~~K~~~i~~l~~~~  169 (517)
T PF12569_consen   90 DEDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQLRKGVPSLFSNLKPLYKDPEKAAIIESLVEEY  169 (517)
T ss_pred             cccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHcChhHHHHHHHHHHHH
Confidence             2456666777766443100   0        11                    23333333334344444444454444


Q ss_pred             hhhc-------------CCCCChhHH--HHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCchhHHHH
Q 040371          169 RSRY-------------SIQPQLEHY--GAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRALLSACRTFKRLELGEV  231 (410)
Q Consensus       169 ~~~~-------------~~~~~~~~~--~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~li~~~~~~g~~~~a~~  231 (410)
                      ....             .-.|+...|  .-+...|-..|++++|++.+++. ...|+ +..|..-...+...|++++|..
T Consensus       170 ~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~KarilKh~G~~~~Aa~  249 (517)
T PF12569_consen  170 VNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKARILKHAGDLKEAAE  249 (517)
T ss_pred             HHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHCCCHHHHHH
Confidence            3211             112444334  55567788999999999999976 56676 5677777788999999999999


Q ss_pred             H---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCC-----ceeEEEECCEEEEEEeCCCCCccHHHH
Q 040371          232 A---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQ-----GKSWLELAGVIHQFKAGDRSHPEAQAI  303 (410)
Q Consensus       232 ~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~-----~~s~~~~~~~~~~~~~~~~~~~~~~~~  303 (410)
                      .   ...+++.|...-+-.+..+.++|++++|.+++....+.+..|..     .+.|.++..     ..++...|....|
T Consensus       250 ~~~~Ar~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~~~~~~L~~mQc~Wf~~e~-----a~a~~r~~~~~~A  324 (517)
T PF12569_consen  250 AMDEARELDLADRYINSKCAKYLLRAGRIEEAEKTASLFTREDVDPLSNLNDMQCMWFETEC-----AEAYLRQGDYGLA  324 (517)
T ss_pred             HHHHHHhCChhhHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCCCcccCHHHHHHHHHHHHH-----HHHHHHHhhHHHH
Confidence            8   66777777666677888889999999999999988877763332     234643211     1223334555555


Q ss_pred             HHHHHH
Q 040371          304 DKILGS  309 (410)
Q Consensus       304 ~~~l~~  309 (410)
                      +..+..
T Consensus       325 Lk~~~~  330 (517)
T PF12569_consen  325 LKRFHA  330 (517)
T ss_pred             HHHHHH
Confidence            555543

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 [], [].

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.23  E-value=6.3e-05  Score=64.13  Aligned_cols=159  Identities=9%  Similarity=0.102  Sum_probs=116.4

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCC
Q 040371           12 MIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK   91 (410)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~   91 (410)
                      -+..|.+.|++..+..-.+.+..    |. .       .+...++.+++...++..++.. +.|...|..|...|...|+
T Consensus        22 ~~~~Y~~~g~~~~v~~~~~~~~~----~~-~-------~~~~~~~~~~~i~~l~~~L~~~-P~~~~~w~~Lg~~~~~~g~   88 (198)
T PRK10370         22 CVGSYLLSPKWQAVRAEYQRLAD----PL-H-------QFASQQTPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWRND   88 (198)
T ss_pred             HHHHHHHcchHHHHHHHHHHHhC----cc-c-------cccCchhHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCC
Confidence            34678899999887544433221    11 0       1123566777777788777765 6688999999999999999


Q ss_pred             HHHHHHHHHhccc---CChhhHHHHHHH-HHHcCC--hHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040371           92 IQMAKEVFDTVQR---NDVSVWNAMISG-VAIHGL--AADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYF  165 (410)
Q Consensus        92 ~~~A~~~f~~m~~---~~~~~~~~li~~-~~~~g~--~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  165 (410)
                      +++|...|++...   .+...|..+..+ |.+.|+  .++|.+++++..+... -+...+..+..++...|++++|...|
T Consensus        89 ~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~dP-~~~~al~~LA~~~~~~g~~~~Ai~~~  167 (198)
T PRK10370         89 YDNALLAYRQALQLRGENAELYAALATVLYYQAGQHMTPQTREMIDKALALDA-NEVTALMLLASDAFMQADYAQAIELW  167 (198)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCC-CChhHHHHHHHHHHHcCCHHHHHHHH
Confidence            9999999998763   366788887776 467777  5999999999988532 25667788888889999999999999


Q ss_pred             HHhhhhcCCCCChhHHHHHHHH
Q 040371          166 DHMRSRYSIQPQLEHYGAMVDL  187 (410)
Q Consensus       166 ~~m~~~~~~~~~~~~~~~li~~  187 (410)
                      +.+.+  ..+|+..-+ .+|..
T Consensus       168 ~~aL~--l~~~~~~r~-~~i~~  186 (198)
T PRK10370        168 QKVLD--LNSPRVNRT-QLVES  186 (198)
T ss_pred             HHHHh--hCCCCccHH-HHHHH
Confidence            99985  455555444 44454

>PLN02789 farnesyltranstransferase

Probab=98.20  E-value=0.00091  Score=61.35  Aligned_cols=143  Identities=10%  Similarity=0.042  Sum_probs=85.8

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHhhC-CHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPD-KFTFASVIYGCARLG-ALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~a~~~~~-~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      +++.+-..+...++.++|+.+..++++.  .|+ ..+|+.--.++...+ +++++...++.+++.. +.+..+|+..--.
T Consensus        39 a~~~~ra~l~~~e~serAL~lt~~aI~l--nP~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~n-pknyqaW~~R~~~  115 (320)
T PLN02789         39 AMDYFRAVYASDERSPRALDLTADVIRL--NPGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDN-PKNYQIWHHRRWL  115 (320)
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHC-CcchHHhHHHHHH
Confidence            4555556666677777777777777763  343 335555555555555 4677777777777664 3455566655555


Q ss_pred             HHhcCCH--HHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040371           86 YSKCGKI--QMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSH  154 (410)
Q Consensus        86 y~~~g~~--~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~  154 (410)
                      +.+.|+.  +++..+++++.+   +|..+|+-..-.+...|+++++++.++++.+.+.. |...|+.....+.+
T Consensus       116 l~~l~~~~~~~el~~~~kal~~dpkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~d~~-N~sAW~~R~~vl~~  188 (320)
T PLN02789        116 AEKLGPDAANKELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEEDVR-NNSAWNQRYFVITR  188 (320)
T ss_pred             HHHcCchhhHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHCCC-chhHHHHHHHHHHh
Confidence            5555552  455666665543   35566776666666677777777777777665432 33444444444433

>KOG1125 consensus TPR repeat-containing protein [General function prediction only]

Probab=98.18  E-value=0.00018  Score=68.17  Aligned_cols=213  Identities=15%  Similarity=0.116  Sum_probs=165.0

Q ss_pred             HHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHH
Q 040371           15 GFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQM   94 (410)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~   94 (410)
                      -+.++|++.+|.-.|+...+.. +-+...|--|..+-+..++=..|+..+.+.++.. +.+..+.-+|.-.|...|.-..
T Consensus       294 ~lm~nG~L~~A~LafEAAVkqd-P~haeAW~~LG~~qaENE~E~~ai~AL~rcl~Ld-P~NleaLmaLAVSytNeg~q~~  371 (579)
T KOG1125|consen  294 NLMKNGDLSEAALAFEAAVKQD-PQHAEAWQKLGITQAENENEQNAISALRRCLELD-PTNLEALMALAVSYTNEGLQNQ  371 (579)
T ss_pred             HHHhcCCchHHHHHHHHHHhhC-hHHHHHHHHhhhHhhhccchHHHHHHHHHHHhcC-CccHHHHHHHHHHHhhhhhHHH
Confidence            4678999999999999988764 4467799999999999999999999999999875 4478888899999999999999


Q ss_pred             HHHHHHhcccCC-hhhHHHHH---------HHHHHcCChHHHHHHHHHHHH-CCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 040371           95 AKEVFDTVQRND-VSVWNAMI---------SGVAIHGLAADASAIFTKMEM-FNVLPDSITFLGLLTACSHCGLVEEGRK  163 (410)
Q Consensus        95 A~~~f~~m~~~~-~~~~~~li---------~~~~~~g~~~~A~~l~~~m~~-~g~~p~~~t~~~ll~a~~~~g~~~~a~~  163 (410)
                      |.+.|+.-.... ...|...-         ..+..........++|-++.. .+.++|......|--.|.-.|.+++|..
T Consensus       372 Al~~L~~Wi~~~p~y~~l~~a~~~~~~~~~~s~~~~~~l~~i~~~fLeaa~~~~~~~DpdvQ~~LGVLy~ls~efdraiD  451 (579)
T KOG1125|consen  372 ALKMLDKWIRNKPKYVHLVSAGENEDFENTKSFLDSSHLAHIQELFLEAARQLPTKIDPDVQSGLGVLYNLSGEFDRAVD  451 (579)
T ss_pred             HHHHHHHHHHhCccchhccccCccccccCCcCCCCHHHHHHHHHHHHHHHHhCCCCCChhHHhhhHHHHhcchHHHHHHH
Confidence            999998753110 00000000         122222334566677766654 3545777777778888888999999999


Q ss_pred             HHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCchhHHHHH
Q 040371          164 YFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDV-VVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       164 ~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~-~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      .|+.+..   +.|+ ...||.|...++...+.++|..-|.+. .++|+- ..+..|--+|...|.+++|.+.
T Consensus       452 cf~~AL~---v~Pnd~~lWNRLGAtLAN~~~s~EAIsAY~rALqLqP~yVR~RyNlgIS~mNlG~ykEA~~h  520 (579)
T KOG1125|consen  452 CFEAALQ---VKPNDYLLWNRLGATLANGNRSEEAISAYNRALQLQPGYVRVRYNLGISCMNLGAYKEAVKH  520 (579)
T ss_pred             HHHHHHh---cCCchHHHHHHhhHHhcCCcccHHHHHHHHHHHhcCCCeeeeehhhhhhhhhhhhHHHHHHH
Confidence            9999884   4565 679999999999999999999999987 788874 4666677788999999999988

>PLN02789 farnesyltranstransferase

Probab=98.18  E-value=0.0024  Score=58.57  Aligned_cols=213  Identities=10%  Similarity=0.036  Sum_probs=150.8

Q ss_pred             HhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC-CHHHHHHHHHhccc---CChhhHHHHHHHHHHcCCh--HH
Q 040371           52 ARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG-KIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLA--AD  125 (410)
Q Consensus        52 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g-~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~--~~  125 (410)
                      ...+..++|..+...+++.. +-+..+|+..-.++.+.| ++++++..++++.+   ++..+|+-.--.+.+.|..  ++
T Consensus        48 ~~~e~serAL~lt~~aI~ln-P~~ytaW~~R~~iL~~L~~~l~eeL~~~~~~i~~npknyqaW~~R~~~l~~l~~~~~~~  126 (320)
T PLN02789         48 ASDERSPRALDLTADVIRLN-PGNYTVWHFRRLCLEALDADLEEELDFAEDVAEDNPKNYQIWHHRRWLAEKLGPDAANK  126 (320)
T ss_pred             HcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHcchhHHHHHHHHHHHHHHCCcchHHhHHHHHHHHHcCchhhHH
Confidence            34466778888888888864 445677887777778888 58999999998774   3556788665556666653  67


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhc---CCH----HHHH
Q 040371          126 ASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRA---GHI----EEAY  198 (410)
Q Consensus       126 A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~---g~~----~~A~  198 (410)
                      ++++++++.+.. .-|..++....-++.+.|.++++.+.++.+.+. . ..+...|+.....+.+.   |.+    +++.
T Consensus       127 el~~~~kal~~d-pkNy~AW~~R~w~l~~l~~~~eeL~~~~~~I~~-d-~~N~sAW~~R~~vl~~~~~l~~~~~~~e~el  203 (320)
T PLN02789        127 ELEFTRKILSLD-AKNYHAWSHRQWVLRTLGGWEDELEYCHQLLEE-D-VRNNSAWNQRYFVITRSPLLGGLEAMRDSEL  203 (320)
T ss_pred             HHHHHHHHHHhC-cccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH-C-CCchhHHHHHHHHHHhccccccccccHHHHH
Confidence            899999998754 236788888888888999999999999999864 3 33566777666555544   323    4566


Q ss_pred             HHHHh-CCCCC-CHHHHHHHHHHHHhcC----chhHHHHH---HHhhccCCCchHHHHHHHHHhcC--------------
Q 040371          199 GLITS-MTMEP-DVVVWRALLSACRTFK----RLELGEVA---IVNISRLMGGDYVLLSNMYCYLK--------------  255 (410)
Q Consensus       199 ~~~~~-m~~~p-~~~~~~~li~~~~~~g----~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g--------------  255 (410)
                      +...+ +...| |...|+-+-..+...+    ...+|...   +....+.++.....|++.|+...              
T Consensus       204 ~y~~~aI~~~P~N~SaW~Yl~~ll~~~~~~l~~~~~~~~~~~~~~~~~~~s~~al~~l~d~~~~~~~~~~~~~~~~~~~~  283 (320)
T PLN02789        204 KYTIDAILANPRNESPWRYLRGLFKDDKEALVSDPEVSSVCLEVLSKDSNHVFALSDLLDLLCEGLQPTAEFRDTVDTLA  283 (320)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHHhcCCcccccchhHHHHHHHhhcccCCcHHHHHHHHHHHHhhhccchhhhhhhhccc
Confidence            66644 45566 5678888888877633    34556666   33445666667778999998643              


Q ss_pred             ----ChhHHHHHHHHHH
Q 040371          256 ----RWDTAENVREIMK  268 (410)
Q Consensus       256 ----~~~~a~~~~~~m~  268 (410)
                          ..++|.++++.+.
T Consensus       284 ~~~~~~~~a~~~~~~l~  300 (320)
T PLN02789        284 EELSDSTLAQAVCSELE  300 (320)
T ss_pred             cccccHHHHHHHHHHHH
Confidence                3467999999884

>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional

Probab=98.17  E-value=0.00037  Score=59.41  Aligned_cols=157  Identities=8%  Similarity=0.009  Sum_probs=109.7

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCC
Q 040371           46 SVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGL  122 (410)
Q Consensus        46 ~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~  122 (410)
                      ..+..|...|+++.+....+.+..    |.        .-|...++.+++...++...+   .|...|..+...|...|+
T Consensus        21 ~~~~~Y~~~g~~~~v~~~~~~~~~----~~--------~~~~~~~~~~~~i~~l~~~L~~~P~~~~~w~~Lg~~~~~~g~   88 (198)
T PRK10370         21 LCVGSYLLSPKWQAVRAEYQRLAD----PL--------HQFASQQTPEAQLQALQDKIRANPQNSEQWALLGEYYLWRND   88 (198)
T ss_pred             HHHHHHHHcchHHHHHHHHHHHhC----cc--------ccccCchhHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCC
Confidence            344567788888877555433221    10        022236667777777776553   477899999999999999


Q ss_pred             hHHHHHHHHHHHHCCCCC-CHHHHHHHHHHH-HccCC--HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHH
Q 040371          123 AADASAIFTKMEMFNVLP-DSITFLGLLTAC-SHCGL--VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAY  198 (410)
Q Consensus       123 ~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~-~~~g~--~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~  198 (410)
                      +++|...|++..+.  .| |...+..+..++ ...|+  .++|.+++++..+.  -+-+...+..+...+.+.|++++|.
T Consensus        89 ~~~A~~a~~~Al~l--~P~~~~~~~~lA~aL~~~~g~~~~~~A~~~l~~al~~--dP~~~~al~~LA~~~~~~g~~~~Ai  164 (198)
T PRK10370         89 YDNALLAYRQALQL--RGENAELYAALATVLYYQAGQHMTPQTREMIDKALAL--DANEVTALMLLASDAFMQADYAQAI  164 (198)
T ss_pred             HHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHh--CCCChhHHHHHHHHHHHcCCHHHHH
Confidence            99999999988875  34 556666666653 66676  59999999998853  2335678888888999999999999


Q ss_pred             HHHHhC-C-CCCCHHHHHHHHHH
Q 040371          199 GLITSM-T-MEPDVVVWRALLSA  219 (410)
Q Consensus       199 ~~~~~m-~-~~p~~~~~~~li~~  219 (410)
                      ..|+++ . ..|+.. ...+|.+
T Consensus       165 ~~~~~aL~l~~~~~~-r~~~i~~  186 (198)
T PRK10370        165 ELWQKVLDLNSPRVN-RTQLVES  186 (198)
T ss_pred             HHHHHHHhhCCCCcc-HHHHHHH
Confidence            999998 3 334443 3344444

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.16  E-value=7.9e-05  Score=60.06  Aligned_cols=92  Identities=12%  Similarity=-0.108  Sum_probs=47.4

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHH
Q 040371          110 WNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLG  189 (410)
Q Consensus       110 ~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~  189 (410)
                      +......+.+.|++++|...|+...... +.+...+..+..++...|++++|...|+....  --+.+...+..+..++.
T Consensus        27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~--l~p~~~~a~~~lg~~l~  103 (144)
T PRK15359         27 VYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALM--LDASHPEPVYQTGVCLK  103 (144)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHh--cCCCCcHHHHHHHHHHH
Confidence            3344444555555555555555554431 22344455555555555555555555555553  12223455555555555


Q ss_pred             hcCCHHHHHHHHHhC
Q 040371          190 RAGHIEEAYGLITSM  204 (410)
Q Consensus       190 ~~g~~~~A~~~~~~m  204 (410)
                      +.|++++|...|++.
T Consensus       104 ~~g~~~eAi~~~~~A  118 (144)
T PRK15359        104 MMGEPGLAREAFQTA  118 (144)
T ss_pred             HcCCHHHHHHHHHHH
Confidence            555555555555554

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=98.13  E-value=0.0013  Score=61.45  Aligned_cols=145  Identities=13%  Similarity=0.063  Sum_probs=103.1

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-hhHHHHHH
Q 040371          108 SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD-SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAMV  185 (410)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~li  185 (410)
                      ..+.-..-.+.+.|+.++|+..++.+...  .|| ..-.......+...++..+|.+.++.+...   .|+ ...+-.+.
T Consensus       307 aa~YG~A~~~~~~~~~d~A~~~l~~L~~~--~P~N~~~~~~~~~i~~~~nk~~~A~e~~~kal~l---~P~~~~l~~~~a  381 (484)
T COG4783         307 AAQYGRALQTYLAGQYDEALKLLQPLIAA--QPDNPYYLELAGDILLEANKAKEAIERLKKALAL---DPNSPLLQLNLA  381 (484)
T ss_pred             HHHHHHHHHHHHhcccchHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhc---CCCccHHHHHHH
Confidence            33444444456678888888888887764  454 444445556777888888888888888743   455 55666777


Q ss_pred             HHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHH
Q 040371          186 DLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENV  263 (410)
Q Consensus       186 ~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~  263 (410)
                      .+|.+.|++.+|..++++. .-.| |...|..|-.+|...|+..++...              ....|.-.|+|++|...
T Consensus       382 ~all~~g~~~eai~~L~~~~~~~p~dp~~w~~LAqay~~~g~~~~a~~A--------------~AE~~~~~G~~~~A~~~  447 (484)
T COG4783         382 QALLKGGKPQEAIRILNRYLFNDPEDPNGWDLLAQAYAELGNRAEALLA--------------RAEGYALAGRLEQAIIF  447 (484)
T ss_pred             HHHHhcCChHHHHHHHHHHhhcCCCCchHHHHHHHHHHHhCchHHHHHH--------------HHHHHHhCCCHHHHHHH
Confidence            8888888888888888776 2233 677888888888888887776544              34457778888888888


Q ss_pred             HHHHHhCC
Q 040371          264 REIMKKKG  271 (410)
Q Consensus       264 ~~~m~~~g  271 (410)
                      +...++..
T Consensus       448 l~~A~~~~  455 (484)
T COG4783         448 LMRASQQV  455 (484)
T ss_pred             HHHHHHhc
Confidence            88777653

>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat

Probab=98.11  E-value=3.7e-06  Score=47.96  Aligned_cols=31  Identities=26%  Similarity=0.427  Sum_probs=23.7

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHHHHCCC
Q 040371          108 SVWNAMISGVAIHGLAADASAIFTKMEMFNV  138 (410)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~  138 (410)
                      ++||+||++|++.|++++|.++|++|.+.|+
T Consensus         1 v~y~~li~~~~~~~~~~~a~~~~~~M~~~g~   31 (31)
T PF01535_consen    1 VTYNSLISGYCKMGQFEEALEVFDEMRERGI   31 (31)
T ss_pred             CcHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence            4678888888888888888888888877663

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.11  E-value=0.0025  Score=67.85  Aligned_cols=258  Identities=13%  Similarity=0.063  Sum_probs=166.8

Q ss_pred             HHHHHcCCHhHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHhhCCHHHHHHHHHHHHHc----CC-CccHHHHHHHHH
Q 040371           14 GGFVRNARFDEALRFFREMLSSKVEPDK----FTFASVIYGCARLGALNHAYWVHNLIIEK----KI-ELNFILSAALID   84 (410)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~----~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~-~~~~~~~~~li~   84 (410)
                      ..+...|++++|...+++....--..+.    ...+.+..++...|+++.|...+......    |- .....+...+..
T Consensus       460 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~  539 (903)
T PRK04841        460 QVAINDGDPEEAERLAELALAELPLTWYYSRIVATSVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSE  539 (903)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHH
Confidence            4456789999999999988763111122    23455566677899999999998887653    21 112345566777


Q ss_pred             HHHhcCCHHHHHHHHHhccc-------CC----hhhHHHHHHHHHHcCChHHHHHHHHHHHHC--CCCCC--HHHHHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQR-------ND----VSVWNAMISGVAIHGLAADASAIFTKMEMF--NVLPD--SITFLGLL  149 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~-------~~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~--g~~p~--~~t~~~ll  149 (410)
                      .+...|+++.|...+++...       ++    ...+..+...+...|++++|...+.+....  ...|.  ...+..+.
T Consensus       540 ~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la  619 (903)
T PRK04841        540 ILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEFLLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLA  619 (903)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHH
Confidence            88899999999998876542       11    123445555677789999999999887553  11222  23344455


Q ss_pred             HHHHccCCHHHHHHHHHHhhhhcCCCCChhHH-----HHHHHHHHhcCCHHHHHHHHHhCCC-C-CCH----HHHHHHHH
Q 040371          150 TACSHCGLVEEGRKYFDHMRSRYSIQPQLEHY-----GAMVDLLGRAGHIEEAYGLITSMTM-E-PDV----VVWRALLS  218 (410)
Q Consensus       150 ~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~-----~~li~~~~~~g~~~~A~~~~~~m~~-~-p~~----~~~~~li~  218 (410)
                      ......|+.++|.+.++....-.........+     ...+..+...|+.+.|..++..... . ...    ..+..+..
T Consensus       620 ~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~  699 (903)
T PRK04841        620 KISLARGDLDNARRYLNRLENLLGNGRYHSDWIANADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIAR  699 (903)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhHHHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHH
Confidence            67778999999999998875321111111111     1122445668999999999877621 1 111    11345556


Q ss_pred             HHHhcCchhHHHHHHHhhc----c-----CCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          219 ACRTFKRLELGEVAIVNIS----R-----LMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       219 ~~~~~g~~~~a~~~~~~~~----~-----~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      ++...|+.++|...+.+..    .     ....+...+..+|.+.|+.++|...+.+..+..
T Consensus       700 ~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~~~la~a~~~~G~~~~A~~~L~~Al~la  761 (903)
T PRK04841        700 AQILLGQFDEAEIILEELNENARSLRLMSDLNRNLILLNQLYWQQGRKSEAQRVLLEALKLA  761 (903)
T ss_pred             HHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence            6788899999988732211    1     112345567788999999999999999887654

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=98.10  E-value=0.00063  Score=68.77  Aligned_cols=144  Identities=8%  Similarity=-0.033  Sum_probs=115.2

Q ss_pred             CCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccC---ChhhHHHH
Q 040371           37 VEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRN---DVSVWNAM  113 (410)
Q Consensus        37 ~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~---~~~~~~~l  113 (410)
                      ...+...+..|..+..+.|.+++|..+++...+.. +-+......+...+.+.+++++|...+++....   +....+.+
T Consensus        82 ~~~~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~~-Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~p~~~~~~~~~  160 (694)
T PRK15179         82 YPHTELFQVLVARALEAAHRSDEGLAVWRGIHQRF-PDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGGSSSAREILLE  160 (694)
T ss_pred             ccccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcCCCCHHHHHHH
Confidence            45567888888899999999999999999998863 335677788888999999999999999988753   44567777


Q ss_pred             HHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHH
Q 040371          114 ISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAM  184 (410)
Q Consensus       114 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~l  184 (410)
                      ..++.+.|++++|.++|++....+ .-+..++.++..++-..|+.++|...|+...+  ...|....|+.+
T Consensus       161 a~~l~~~g~~~~A~~~y~~~~~~~-p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~--~~~~~~~~~~~~  228 (694)
T PRK15179        161 AKSWDEIGQSEQADACFERLSRQH-PEFENGYVGWAQSLTRRGALWRARDVLQAGLD--AIGDGARKLTRR  228 (694)
T ss_pred             HHHHHHhcchHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--hhCcchHHHHHH
Confidence            888889999999999999998732 23478888888999999999999999999885  334445555443

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.10  E-value=0.00054  Score=58.97  Aligned_cols=162  Identities=15%  Similarity=0.108  Sum_probs=128.7

Q ss_pred             CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHH
Q 040371           38 EPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMI  114 (410)
Q Consensus        38 ~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li  114 (410)
                      .|+.......-.++...|+-+....+.....-. .+.|..+.++++....+.|++..|...|.+...   +|...||.+-
T Consensus        63 ~p~d~~i~~~a~a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p~d~~~~~~lg  141 (257)
T COG5010          63 NPEDLSIAKLATALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAPTDWEAWNLLG  141 (257)
T ss_pred             CcchHHHHHHHHHHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccCCCChhhhhHHH
Confidence            453332266677777788877777766664432 356777888899999999999999999998764   4788999999


Q ss_pred             HHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCC
Q 040371          115 SGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGH  193 (410)
Q Consensus       115 ~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~  193 (410)
                      .+|.+.|+.++|..-|.+..+.  .| +...++.+.-.+.-.|+.+.|..++.....  .-.-|..+-..+.-..+..|+
T Consensus       142 aaldq~Gr~~~Ar~ay~qAl~L--~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l--~~~ad~~v~~NLAl~~~~~g~  217 (257)
T COG5010         142 AALDQLGRFDEARRAYRQALEL--APNEPSIANNLGMSLLLRGDLEDAETLLLPAYL--SPAADSRVRQNLALVVGLQGD  217 (257)
T ss_pred             HHHHHccChhHHHHHHHHHHHh--ccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHh--CCCCchHHHHHHHHHHhhcCC
Confidence            9999999999999999988874  44 345577788888889999999999998874  333367788888999999999


Q ss_pred             HHHHHHHHHhC
Q 040371          194 IEEAYGLITSM  204 (410)
Q Consensus       194 ~~~A~~~~~~m  204 (410)
                      +++|.++...-
T Consensus       218 ~~~A~~i~~~e  228 (257)
T COG5010         218 FREAEDIAVQE  228 (257)
T ss_pred             hHHHHhhcccc
Confidence            99999987764

>PRK15359 type III secretion system chaperone protein SscB; Provisional

Probab=98.09  E-value=0.00017  Score=58.12  Aligned_cols=109  Identities=12%  Similarity=0.105  Sum_probs=77.3

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--
Q 040371           27 RFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--  104 (410)
Q Consensus        27 ~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--  104 (410)
                      .+|++..+  +.|+.  +.....++...|+++.|...+...+... +.+..++..+..++.+.|++++|...|++...  
T Consensus        14 ~~~~~al~--~~p~~--~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~   88 (144)
T PRK15359         14 DILKQLLS--VDPET--VYASGYASWQEGDYSRAVIDFSWLVMAQ-PWSWRAHIALAGTWMMLKEYTTAINFYGHALMLD   88 (144)
T ss_pred             HHHHHHHH--cCHHH--HHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            34555544  24443  4456667778888888888888877764 44677778888888888888888888887664  


Q ss_pred             -CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH
Q 040371          105 -NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS  142 (410)
Q Consensus       105 -~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~  142 (410)
                       .+...|..+..++.+.|+.++|...|++....  .|+.
T Consensus        89 p~~~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~--~p~~  125 (144)
T PRK15359         89 ASHPEPVYQTGVCLKMMGEPGLAREAFQTAIKM--SYAD  125 (144)
T ss_pred             CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCC
Confidence             25567777778888888888888888887763  4543

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

Probab=98.08  E-value=0.0026  Score=62.59  Aligned_cols=245  Identities=17%  Similarity=0.089  Sum_probs=163.9

Q ss_pred             HhHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040371           22 FDEALRFFREMLSSK-VEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFD  100 (410)
Q Consensus        22 ~~~a~~l~~~m~~~g-~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~  100 (410)
                      ..++++.+++..+.+ -.|+..-|.++  -++..++++.|.+...+.++.+-..+...|.-|.-.+.-.+++.+|+.+.+
T Consensus       460 h~kslqale~av~~d~~dp~~if~lal--q~A~~R~l~sAl~~~~eaL~l~~~~~~~~whLLALvlSa~kr~~~Al~vvd  537 (799)
T KOG4162|consen  460 HKKSLQALEEAVQFDPTDPLVIFYLAL--QYAEQRQLTSALDYAREALALNRGDSAKAWHLLALVLSAQKRLKEALDVVD  537 (799)
T ss_pred             HHHHHHHHHHHHhcCCCCchHHHHHHH--HHHHHHhHHHHHHHHHHHHHhcCCccHHHHHHHHHHHhhhhhhHHHHHHHH
Confidence            457788888887653 34444444433  456778999999999999998767789999999999999999999998877


Q ss_pred             hcccC--C---------------------hhhHHHHHHHHH------HcC-----------------ChHHHHHHHHHHH
Q 040371          101 TVQRN--D---------------------VSVWNAMISGVA------IHG-----------------LAADASAIFTKME  134 (410)
Q Consensus       101 ~m~~~--~---------------------~~~~~~li~~~~------~~g-----------------~~~~A~~l~~~m~  134 (410)
                      ...+.  +                     +.|...++..+-      +.+                 +..+|....++..
T Consensus       538 ~al~E~~~N~~l~~~~~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk~~l~la~~q~~~a~s~sr~ls  617 (799)
T KOG4162|consen  538 AALEEFGDNHVLMDGKIHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLKAGLHLALSQPTDAISTSRYLS  617 (799)
T ss_pred             HHHHHhhhhhhhchhhhhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhhcccccCcccccccchhhHHHH
Confidence            54321  0                     111111111111      001                 1111111111110


Q ss_pred             --------HCC---------CC--CCH------HHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHH
Q 040371          135 --------MFN---------VL--PDS------ITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLG  189 (410)
Q Consensus       135 --------~~g---------~~--p~~------~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~  189 (410)
                              ..|         +.  |+.      ..+......+.+.+..++|...+.+..+  -.......|.-....+.
T Consensus       618 ~l~a~~~~~~~se~~Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea~~--~~~l~~~~~~~~G~~~~  695 (799)
T KOG4162|consen  618 SLVASQLKSAGSELKLPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEASK--IDPLSASVYYLRGLLLE  695 (799)
T ss_pred             HHHHhhhhhcccccccCcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHh--cchhhHHHHHHhhHHHH
Confidence                    000         11  111      1223444556677788888877777663  22233556666667788


Q ss_pred             hcCCHHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCchhHHHH--H---HHhhccCCCchHHHHHHHHHhcCChhHHHH
Q 040371          190 RAGHIEEAYGLITSM-TMEPD-VVVWRALLSACRTFKRLELGEV--A---IVNISRLMGGDYVLLSNMYCYLKRWDTAEN  262 (410)
Q Consensus       190 ~~g~~~~A~~~~~~m-~~~p~-~~~~~~li~~~~~~g~~~~a~~--~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~  262 (410)
                      ..|++++|...|... -+.|+ +.+.+++-..+.+.|+...|..  +   ..+.+|.++..|..|..++-+.|+.++|.+
T Consensus       696 ~~~~~~EA~~af~~Al~ldP~hv~s~~Ala~~lle~G~~~la~~~~~L~dalr~dp~n~eaW~~LG~v~k~~Gd~~~Aae  775 (799)
T KOG4162|consen  696 VKGQLEEAKEAFLVALALDPDHVPSMTALAELLLELGSPRLAEKRSLLSDALRLDPLNHEAWYYLGEVFKKLGDSKQAAE  775 (799)
T ss_pred             HHHhhHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHhCCcchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHccchHHHHH
Confidence            899999999887765 67785 5678888889999999888888  4   678899999999999999999999999999


Q ss_pred             HHHHHHhC
Q 040371          263 VREIMKKK  270 (410)
Q Consensus       263 ~~~~m~~~  270 (410)
                      .|....+-
T Consensus       776 cf~aa~qL  783 (799)
T KOG4162|consen  776 CFQAALQL  783 (799)
T ss_pred             HHHHHHhh
Confidence            99876553

>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]

Probab=98.08  E-value=0.00017  Score=61.92  Aligned_cols=157  Identities=14%  Similarity=0.079  Sum_probs=125.7

Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhc
Q 040371           10 NSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKC   89 (410)
Q Consensus        10 n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~   89 (410)
                      ..+-..+...|+-+.++.+..+.... .+-|............+.|++..|...+.+..... ++|..+|+.+.-.|.+.
T Consensus        70 ~~~a~a~~~~G~a~~~l~~~~~~~~~-~~~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~-p~d~~~~~~lgaaldq~  147 (257)
T COG5010          70 AKLATALYLRGDADSSLAVLQKSAIA-YPKDRELLAAQGKNQIRNGNFGEAVSVLRKAARLA-PTDWEAWNLLGAALDQL  147 (257)
T ss_pred             HHHHHHHHhcccccchHHHHhhhhcc-CcccHHHHHHHHHHHHHhcchHHHHHHHHHHhccC-CCChhhhhHHHHHHHHc
Confidence            45667777888888888887775432 23355566678889999999999999999988765 78999999999999999


Q ss_pred             CCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH
Q 040371           90 GKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFD  166 (410)
Q Consensus        90 g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~  166 (410)
                      |+.+.|+.-|.+..+   .+....|.|.-.|.-.|+.+.|..++......+.. |...-..+..+....|++++|+.+-.
T Consensus       148 Gr~~~Ar~ay~qAl~L~~~~p~~~nNlgms~~L~gd~~~A~~lll~a~l~~~a-d~~v~~NLAl~~~~~g~~~~A~~i~~  226 (257)
T COG5010         148 GRFDEARRAYRQALELAPNEPSIANNLGMSLLLRGDLEDAETLLLPAYLSPAA-DSRVRQNLALVVGLQGDFREAEDIAV  226 (257)
T ss_pred             cChhHHHHHHHHHHHhccCCchhhhhHHHHHHHcCCHHHHHHHHHHHHhCCCC-chHHHHHHHHHHhhcCChHHHHhhcc
Confidence            999999999987653   46677888888888899999999999988876533 55566667778889999999999876


Q ss_pred             Hhh
Q 040371          167 HMR  169 (410)
Q Consensus       167 ~m~  169 (410)
                      .-.
T Consensus       227 ~e~  229 (257)
T COG5010         227 QEL  229 (257)
T ss_pred             ccc
Confidence            543

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=98.07  E-value=0.0029  Score=54.72  Aligned_cols=159  Identities=14%  Similarity=0.062  Sum_probs=98.9

Q ss_pred             HHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHH
Q 040371           64 HNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSI  143 (410)
Q Consensus        64 ~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~  143 (410)
                      .+.+.......+......-...|.+.|++++|.+.......-+....|.  ..+.+..+.+-|.+.+++|++-   -+..
T Consensus        96 ~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~~~lE~~Al~V--qI~lk~~r~d~A~~~lk~mq~i---ded~  170 (299)
T KOG3081|consen   96 YELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLGENLEAAALNV--QILLKMHRFDLAEKELKKMQQI---DEDA  170 (299)
T ss_pred             HHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhccchHHHHHHHH--HHHHHHHHHHHHHHHHHHHHcc---chHH
Confidence            3333333333343444444556778888888888877744333333333  3355667778888888888753   3556


Q ss_pred             HHHHHHHHHHc----cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC--CCCCCHHHHHHHH
Q 040371          144 TFLGLLTACSH----CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM--TMEPDVVVWRALL  217 (410)
Q Consensus       144 t~~~ll~a~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m--~~~p~~~~~~~li  217 (410)
                      |.+-|..++.+    .+.+.+|.-+|++|.+  ...|++.+.+-+..+....|++++|..+++..  ....+..+...+|
T Consensus       171 tLtQLA~awv~la~ggek~qdAfyifeE~s~--k~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd~~dpetL~Nli  248 (299)
T KOG3081|consen  171 TLTQLAQAWVKLATGGEKIQDAFYIFEELSE--KTPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKDAKDPETLANLI  248 (299)
T ss_pred             HHHHHHHHHHHHhccchhhhhHHHHHHHHhc--ccCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhccCCCHHHHHHHH
Confidence            67666666654    4567788888888875  35677777777777778888888888887776  2223555555555


Q ss_pred             HHHHhcCchhHH
Q 040371          218 SACRTFKRLELG  229 (410)
Q Consensus       218 ~~~~~~g~~~~a  229 (410)
                      -..-..|...++
T Consensus       249 v~a~~~Gkd~~~  260 (299)
T KOG3081|consen  249 VLALHLGKDAEV  260 (299)
T ss_pred             HHHHHhCCChHH
Confidence            555555554333

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=98.05  E-value=0.00024  Score=56.46  Aligned_cols=93  Identities=11%  Similarity=0.037  Sum_probs=55.9

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHH
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVA  118 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~  118 (410)
                      .....+...+...|+++.|.+.++.+...+ +.+...+..+...|.+.|++++|...|++...   .+...|..+...|.
T Consensus        18 ~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~la~~~~   96 (135)
T TIGR02552        18 EQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPYFHAAECLL   96 (135)
T ss_pred             HHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHH
Confidence            344455555566666666666666666553 33556666666666666666666666665532   23445555556666


Q ss_pred             HcCChHHHHHHHHHHHH
Q 040371          119 IHGLAADASAIFTKMEM  135 (410)
Q Consensus       119 ~~g~~~~A~~l~~~m~~  135 (410)
                      ..|+.++|+..|++..+
T Consensus        97 ~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        97 ALGEPESALKALDLAIE  113 (135)
T ss_pred             HcCCHHHHHHHHHHHHH
Confidence            66666666666666655

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.05  E-value=0.0034  Score=56.40  Aligned_cols=116  Identities=12%  Similarity=0.093  Sum_probs=77.3

Q ss_pred             CHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCC-CCHHHHHHHHHH-HHhcCchhHHHHHH
Q 040371          157 LVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TME-PDVVVWRALLSA-CRTFKRLELGEVAI  233 (410)
Q Consensus       157 ~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~-p~~~~~~~li~~-~~~~g~~~~a~~~~  233 (410)
                      ++|+..-+++.+.. +-...|...+ .+..+++..|.+.+|+++|-++ +.+ .|..+|.+++.- |...+.++.|..++
T Consensus       374 qFddVl~YlnSi~s-YF~NdD~Fn~-N~AQAk~atgny~eaEelf~~is~~~ikn~~~Y~s~LArCyi~nkkP~lAW~~~  451 (557)
T KOG3785|consen  374 QFDDVLTYLNSIES-YFTNDDDFNL-NLAQAKLATGNYVEAEELFIRISGPEIKNKILYKSMLARCYIRNKKPQLAWDMM  451 (557)
T ss_pred             HHHHHHHHHHHHHH-HhcCcchhhh-HHHHHHHHhcChHHHHHHHhhhcChhhhhhHHHHHHHHHHHHhcCCchHHHHHH
Confidence            34555555555442 2222333333 3567788889999999999887 222 377788776654 57889999999996


Q ss_pred             HhhccCC-Cc-hHHHHHHHHHhcCChhHHHHHHHHHHhCCCcC
Q 040371          234 VNISRLM-GG-DYVLLSNMYCYLKRWDTAENVREIMKKKGVRK  274 (410)
Q Consensus       234 ~~~~~~~-~~-~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~  274 (410)
                      .+.+.+. .. ....+.+.|.+++.+--|.+.|+.++..+-.|
T Consensus       452 lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKAFd~lE~lDP~p  494 (557)
T KOG3785|consen  452 LKTNTPSERFSLLQLIANDCYKANEFYYAAKAFDELEILDPTP  494 (557)
T ss_pred             HhcCCchhHHHHHHHHHHHHHHHHHHHHHHHhhhHHHccCCCc
Confidence            6665332 22 23345678899999999999999988765433

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=98.01  E-value=0.00052  Score=66.90  Aligned_cols=190  Identities=14%  Similarity=0.200  Sum_probs=111.9

Q ss_pred             HhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHH
Q 040371           52 ARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFT  131 (410)
Q Consensus        52 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~  131 (410)
                      .....+..|..+++.+.....  -..-|.-+.+.|+..|+++.|.++|.+..     .++-.|..|.++|+|+.|.++-.
T Consensus       743 i~akew~kai~ildniqdqk~--~s~yy~~iadhyan~~dfe~ae~lf~e~~-----~~~dai~my~k~~kw~da~kla~  815 (1636)
T KOG3616|consen  743 IGAKEWKKAISILDNIQDQKT--ASGYYGEIADHYANKGDFEIAEELFTEAD-----LFKDAIDMYGKAGKWEDAFKLAE  815 (1636)
T ss_pred             hhhhhhhhhHhHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHhcc-----hhHHHHHHHhccccHHHHHHHHH
Confidence            344455556666655544321  22335556677777777777777776542     34556677777777777777665


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHH
Q 040371          132 KMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVV  211 (410)
Q Consensus       132 ~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~  211 (410)
                      +..  |.......|.+-..-.-..|.+.+|++++-.+.     .|+     ..|.+|-+.|..+..+++.++-.-..-..
T Consensus       816 e~~--~~e~t~~~yiakaedldehgkf~eaeqlyiti~-----~p~-----~aiqmydk~~~~ddmirlv~k~h~d~l~d  883 (1636)
T KOG3616|consen  816 ECH--GPEATISLYIAKAEDLDEHGKFAEAEQLYITIG-----EPD-----KAIQMYDKHGLDDDMIRLVEKHHGDHLHD  883 (1636)
T ss_pred             Hhc--CchhHHHHHHHhHHhHHhhcchhhhhheeEEcc-----Cch-----HHHHHHHhhCcchHHHHHHHHhChhhhhH
Confidence            542  223333445444455556677777776654332     223     24667777777777777776652111234


Q ss_pred             HHHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHH
Q 040371          212 VWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVRE  265 (410)
Q Consensus       212 ~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  265 (410)
                      |...+..-+-..|++..|+.-+.+-     .-|.+.+++|-..+.|++|.++-+
T Consensus       884 t~~~f~~e~e~~g~lkaae~~flea-----~d~kaavnmyk~s~lw~dayriak  932 (1636)
T KOG3616|consen  884 THKHFAKELEAEGDLKAAEEHFLEA-----GDFKAAVNMYKASELWEDAYRIAK  932 (1636)
T ss_pred             HHHHHHHHHHhccChhHHHHHHHhh-----hhHHHHHHHhhhhhhHHHHHHHHh
Confidence            5555666666677777776664432     345666777777777877776654

>KOG1128 consensus Uncharacterized conserved protein, contains TPR repeats [General function prediction only]

Probab=98.01  E-value=0.0003  Score=68.53  Aligned_cols=204  Identities=15%  Similarity=0.102  Sum_probs=136.2

Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC
Q 040371           11 SMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG   90 (410)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g   90 (410)
                      .+...+...|-...|+.+|++.         ..|..++.+|...|+...|..+..+-++  -+||...|..|.+....--
T Consensus       403 ~laell~slGitksAl~I~Erl---------emw~~vi~CY~~lg~~~kaeei~~q~le--k~~d~~lyc~LGDv~~d~s  471 (777)
T KOG1128|consen  403 LLAELLLSLGITKSALVIFERL---------EMWDPVILCYLLLGQHGKAEEINRQELE--KDPDPRLYCLLGDVLHDPS  471 (777)
T ss_pred             HHHHHHHHcchHHHHHHHHHhH---------HHHHHHHHHHHHhcccchHHHHHHHHhc--CCCcchhHHHhhhhccChH
Confidence            3455666778888888888764         3466777788888888888888777776  3677888888877776666


Q ss_pred             CHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhh
Q 040371           91 KIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRS  170 (410)
Q Consensus        91 ~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~  170 (410)
                      -+++|.++++....+--..|+..+   .++++++++.+.|+.-.+.. ..-..||-..-.+..+.++++.|.+.|.... 
T Consensus       472 ~yEkawElsn~~sarA~r~~~~~~---~~~~~fs~~~~hle~sl~~n-plq~~~wf~~G~~ALqlek~q~av~aF~rcv-  546 (777)
T KOG1128|consen  472 LYEKAWELSNYISARAQRSLALLI---LSNKDFSEADKHLERSLEIN-PLQLGTWFGLGCAALQLEKEQAAVKAFHRCV-  546 (777)
T ss_pred             HHHHHHHHhhhhhHHHHHhhcccc---ccchhHHHHHHHHHHHhhcC-ccchhHHHhccHHHHHHhhhHHHHHHHHHHh-
Confidence            678888887766544222222222   23677777777777655432 1234566666666667777888777777766 


Q ss_pred             hcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcCchhHHHHH
Q 040371          171 RYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM-TM-EPDVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       171 ~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m-~~-~p~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                        ...|+ ...||.+-.+|.+.|+-.+|...+.+. .. .-+-..|...+-...+.|.++.|.++
T Consensus       547 --tL~Pd~~eaWnNls~ayi~~~~k~ra~~~l~EAlKcn~~~w~iWENymlvsvdvge~eda~~A  609 (777)
T KOG1128|consen  547 --TLEPDNAEAWNNLSTAYIRLKKKKRAFRKLKEALKCNYQHWQIWENYMLVSVDVGEFEDAIKA  609 (777)
T ss_pred             --hcCCCchhhhhhhhHHHHHHhhhHHHHHHHHHHhhcCCCCCeeeechhhhhhhcccHHHHHHH
Confidence              33444 567888888888888888887777766 21 12345566666666777777777777

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=98.01  E-value=0.0067  Score=58.71  Aligned_cols=115  Identities=11%  Similarity=0.147  Sum_probs=71.6

Q ss_pred             CCHHHHHHHHHHhhhhcCCCCC------hhHHHHHHHHHHhcCCHHHHHHHHHhCCCC--CC----HHHHHHHHHHHHhc
Q 040371          156 GLVEEGRKYFDHMRSRYSIQPQ------LEHYGAMVDLLGRAGHIEEAYGLITSMTME--PD----VVVWRALLSACRTF  223 (410)
Q Consensus       156 g~~~~a~~~~~~m~~~~~~~~~------~~~~~~li~~~~~~g~~~~A~~~~~~m~~~--p~----~~~~~~li~~~~~~  223 (410)
                      |+..+-...+.++.+  .+.|.      -..|..+.+.|-..|+++.|..+|++.-.-  +.    ..+|..-...=.++
T Consensus       361 ~~~~~~i~tyteAv~--~vdP~ka~Gs~~~Lw~~faklYe~~~~l~~aRvifeka~~V~y~~v~dLa~vw~~waemElrh  438 (835)
T KOG2047|consen  361 GNAAEQINTYTEAVK--TVDPKKAVGSPGTLWVEFAKLYENNGDLDDARVIFEKATKVPYKTVEDLAEVWCAWAEMELRH  438 (835)
T ss_pred             CChHHHHHHHHHHHH--ccCcccCCCChhhHHHHHHHHHHhcCcHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHhh
Confidence            445555556666553  34442      235788889999999999999999987211  11    34566655666788


Q ss_pred             CchhHHHHHHHhhc--cCC-------------------CchHHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 040371          224 KRLELGEVAIVNIS--RLM-------------------GGDYVLLSNMYCYLKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       224 g~~~~a~~~~~~~~--~~~-------------------~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  272 (410)
                      .+++.|.+++..-.  |.+                   ...|...++.-...|-++....+++++.+-.+
T Consensus       439 ~~~~~Al~lm~~A~~vP~~~~~~~yd~~~pvQ~rlhrSlkiWs~y~DleEs~gtfestk~vYdriidLri  508 (835)
T KOG2047|consen  439 ENFEAALKLMRRATHVPTNPELEYYDNSEPVQARLHRSLKIWSMYADLEESLGTFESTKAVYDRIIDLRI  508 (835)
T ss_pred             hhHHHHHHHHHhhhcCCCchhhhhhcCCCcHHHHHHHhHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhc
Confidence            88888888832211  111                   12344445555566777777777777765544

>KOG3616 consensus Selective LIM binding factor [Transcription]

Probab=97.99  E-value=0.00084  Score=65.55  Aligned_cols=132  Identities=15%  Similarity=0.121  Sum_probs=85.5

Q ss_pred             HHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHH
Q 040371          116 GVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIE  195 (410)
Q Consensus       116 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~  195 (410)
                      +-.....|.+|+.+++.++....  -.--|..+..-|+..|+++.|+++|-+.-          .++-.|++|.++|+++
T Consensus       741 aai~akew~kai~ildniqdqk~--~s~yy~~iadhyan~~dfe~ae~lf~e~~----------~~~dai~my~k~~kw~  808 (1636)
T KOG3616|consen  741 AAIGAKEWKKAISILDNIQDQKT--ASGYYGEIADHYANKGDFEIAEELFTEAD----------LFKDAIDMYGKAGKWE  808 (1636)
T ss_pred             HHhhhhhhhhhHhHHHHhhhhcc--ccccchHHHHHhccchhHHHHHHHHHhcc----------hhHHHHHHHhccccHH
Confidence            34445677777877777766432  22346677788888999999998886542          3566788999999999


Q ss_pred             HHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHH
Q 040371          196 EAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVR  264 (410)
Q Consensus       196 ~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  264 (410)
                      .|.++-.+. +-+.....|.+-..-.-.+|++.+|+++......++     ..|.+|-+.|..++..++.
T Consensus       809 da~kla~e~~~~e~t~~~yiakaedldehgkf~eaeqlyiti~~p~-----~aiqmydk~~~~ddmirlv  873 (1636)
T KOG3616|consen  809 DAFKLAEECHGPEATISLYIAKAEDLDEHGKFAEAEQLYITIGEPD-----KAIQMYDKHGLDDDMIRLV  873 (1636)
T ss_pred             HHHHHHHHhcCchhHHHHHHHhHHhHHhhcchhhhhheeEEccCch-----HHHHHHHhhCcchHHHHHH
Confidence            998887775 433344556665666778888888888733333222     2344455555555444443

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.96  E-value=0.0021  Score=65.03  Aligned_cols=235  Identities=16%  Similarity=0.236  Sum_probs=152.7

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC---------------
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSK--VEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKK---------------   71 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g--~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g---------------   71 (410)
                      -+.-+.++..++-+.+-++++++..-.+  ..-+...-+.++-... ..+.....+..+++-...               
T Consensus       987 vS~tVkAfMtadLp~eLIELLEKIvL~~S~Fse~~nLQnLLiLtAi-kad~trVm~YI~rLdnyDa~~ia~iai~~~LyE 1065 (1666)
T KOG0985|consen  987 VSVTVKAFMTADLPNELIELLEKIVLDNSVFSENRNLQNLLILTAI-KADRTRVMEYINRLDNYDAPDIAEIAIENQLYE 1065 (1666)
T ss_pred             HHHHHHHHHhcCCcHHHHHHHHHHhcCCcccccchhhhhhHHHHHh-hcChHHHHHHHHHhccCCchhHHHHHhhhhHHH
Confidence            3455788888899999999998886322  1111122222222222 223333333333332221               


Q ss_pred             --------CCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHH
Q 040371           72 --------IELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSI  143 (410)
Q Consensus        72 --------~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~  143 (410)
                              +..+....+.||+   ..+.+|.|.++-++..  ....|+.+..+-.+.|...+|++-|-+.      -|..
T Consensus      1066 EAF~ifkkf~~n~~A~~VLie---~i~~ldRA~efAe~~n--~p~vWsqlakAQL~~~~v~dAieSyika------dDps 1134 (1666)
T KOG0985|consen 1066 EAFAIFKKFDMNVSAIQVLIE---NIGSLDRAYEFAERCN--EPAVWSQLAKAQLQGGLVKDAIESYIKA------DDPS 1134 (1666)
T ss_pred             HHHHHHHHhcccHHHHHHHHH---HhhhHHHHHHHHHhhC--ChHHHHHHHHHHHhcCchHHHHHHHHhc------CCcH
Confidence                    1112222222221   2234444444444433  3357999999999999999999988542      2567


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 040371          144 TFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTF  223 (410)
Q Consensus       144 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~  223 (410)
                      .|.-++..+.+.|.+++-.+++.-.+++ .-+|.+  -+.||-+|++.+++.+-++++.    .||......+-.-|...
T Consensus      1135 ~y~eVi~~a~~~~~~edLv~yL~MaRkk-~~E~~i--d~eLi~AyAkt~rl~elE~fi~----gpN~A~i~~vGdrcf~~ 1207 (1666)
T KOG0985|consen 1135 NYLEVIDVASRTGKYEDLVKYLLMARKK-VREPYI--DSELIFAYAKTNRLTELEEFIA----GPNVANIQQVGDRCFEE 1207 (1666)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHh-hcCccc--hHHHHHHHHHhchHHHHHHHhc----CCCchhHHHHhHHHhhh
Confidence            7999999999999999999999887765 555554  4589999999999999877764    37888888888889999


Q ss_pred             CchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHH
Q 040371          224 KRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIM  267 (410)
Q Consensus       224 g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  267 (410)
                      |.++.|.-+..     +.+.|..|...+...|.+..|...-++.
T Consensus      1208 ~~y~aAkl~y~-----~vSN~a~La~TLV~LgeyQ~AVD~aRKA 1246 (1666)
T KOG0985|consen 1208 KMYEAAKLLYS-----NVSNFAKLASTLVYLGEYQGAVDAARKA 1246 (1666)
T ss_pred             hhhHHHHHHHH-----HhhhHHHHHHHHHHHHHHHHHHHHhhhc
Confidence            98888876633     2356677777777778777776655443

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=97.96  E-value=0.001  Score=53.70  Aligned_cols=124  Identities=8%  Similarity=0.042  Sum_probs=79.9

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc--HHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD---KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN--FILSAA   81 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd---~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~--~~~~~~   81 (410)
                      ..|..++..+ ..++...+...++.+.... +.+   ....-.+...+...|++++|...|+.+......++  ....-.
T Consensus        13 ~~y~~~~~~~-~~~~~~~~~~~~~~l~~~~-~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~   90 (145)
T PF09976_consen   13 ALYEQALQAL-QAGDPAKAEAAAEQLAKDY-PSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLR   90 (145)
T ss_pred             HHHHHHHHHH-HCCCHHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHH
Confidence            3466666666 3777888877788777652 222   12333344666777888888888888877653332  223445


Q ss_pred             HHHHHHhcCCHHHHHHHHHhcccC--ChhhHHHHHHHHHHcCChHHHHHHHHH
Q 040371           82 LIDMYSKCGKIQMAKEVFDTVQRN--DVSVWNAMISGVAIHGLAADASAIFTK  132 (410)
Q Consensus        82 li~~y~~~g~~~~A~~~f~~m~~~--~~~~~~~li~~~~~~g~~~~A~~l~~~  132 (410)
                      |...+...|++++|...++....+  ....+......|.+.|+.++|...|++
T Consensus        91 LA~~~~~~~~~d~Al~~L~~~~~~~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   91 LARILLQQGQYDEALATLQQIPDEAFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHHHcCCHHHHHHHHHhccCcchHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            666777778888888877765433  233555566677777777777777765

>KOG1174 consensus Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=97.93  E-value=0.0033  Score=57.63  Aligned_cols=282  Identities=10%  Similarity=-0.018  Sum_probs=145.5

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKF-TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~-t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      |+....++...|..+|+.++|+..|++.+..  .|+.. ......-.+...|+++....+-..+.... +....-|-.-.
T Consensus       231 NvhLl~~lak~~~~~Gdn~~a~~~Fe~~~~~--dpy~i~~MD~Ya~LL~~eg~~e~~~~L~~~Lf~~~-~~ta~~wfV~~  307 (564)
T KOG1174|consen  231 NEHLMMALGKCLYYNGDYFQAEDIFSSTLCA--NPDNVEAMDLYAVLLGQEGGCEQDSALMDYLFAKV-KYTASHWFVHA  307 (564)
T ss_pred             cHHHHHHHhhhhhhhcCchHHHHHHHHHhhC--ChhhhhhHHHHHHHHHhccCHhhHHHHHHHHHhhh-hcchhhhhhhh
Confidence            4445566666667777777777777666542  33322 11111222345566666555555554332 11111121112


Q ss_pred             HHHHhcCCHHHHHHHHHhcccC---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQRN---DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVE  159 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~  159 (410)
                      .......+++.|..+-++-.+-   ++..|-.--..+.+.|++++|.-.|+..+.  +.| +...|..|+..|...|.+.
T Consensus       308 ~~l~~~K~~~rAL~~~eK~I~~~~r~~~alilKG~lL~~~~R~~~A~IaFR~Aq~--Lap~rL~~Y~GL~hsYLA~~~~k  385 (564)
T KOG1174|consen  308 QLLYDEKKFERALNFVEKCIDSEPRNHEALILKGRLLIALERHTQAVIAFRTAQM--LAPYRLEIYRGLFHSYLAQKRFK  385 (564)
T ss_pred             hhhhhhhhHHHHHHHHHHHhccCcccchHHHhccHHHHhccchHHHHHHHHHHHh--cchhhHHHHHHHHHHHHhhchHH
Confidence            2223344566666665554432   333333333455566677777777766654  333 4566777777777777777


Q ss_pred             HHHHHHHHhhhhcCCCCChhHHHHHH-HHHH-hcCCHHHHHHHHHhC-CCCCCH-HHHHHHHHHHHhcCchhHHHHHHHh
Q 040371          160 EGRKYFDHMRSRYSIQPQLEHYGAMV-DLLG-RAGHIEEAYGLITSM-TMEPDV-VVWRALLSACRTFKRLELGEVAIVN  235 (410)
Q Consensus       160 ~a~~~~~~m~~~~~~~~~~~~~~~li-~~~~-~~g~~~~A~~~~~~m-~~~p~~-~~~~~li~~~~~~g~~~~a~~~~~~  235 (410)
                      +|.-.-+...+  -+..+..+.+.+. +.+. ...--++|.+++++- .++|+. ...+.+...|...|..+.+..++.+
T Consensus       386 EA~~~An~~~~--~~~~sA~~LtL~g~~V~~~dp~~rEKAKkf~ek~L~~~P~Y~~AV~~~AEL~~~Eg~~~D~i~LLe~  463 (564)
T KOG1174|consen  386 EANALANWTIR--LFQNSARSLTLFGTLVLFPDPRMREKAKKFAEKSLKINPIYTPAVNLIAELCQVEGPTKDIIKLLEK  463 (564)
T ss_pred             HHHHHHHHHHH--HhhcchhhhhhhcceeeccCchhHHHHHHHHHhhhccCCccHHHHHHHHHHHHhhCccchHHHHHHH
Confidence            66666555543  2222333333221 1111 112245666666654 555653 3445555556666666666666332


Q ss_pred             h--ccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHH
Q 040371          236 I--SRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQR  313 (410)
Q Consensus       236 ~--~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  313 (410)
                      -  ..+|....+.|.+.+...+.+.+|.+.|....                          +..|+.+.+.+-++.|.++
T Consensus       464 ~L~~~~D~~LH~~Lgd~~~A~Ne~Q~am~~y~~AL--------------------------r~dP~~~~sl~Gl~~lEK~  517 (564)
T KOG1174|consen  464 HLIIFPDVNLHNHLGDIMRAQNEPQKAMEYYYKAL--------------------------RQDPKSKRTLRGLRLLEKS  517 (564)
T ss_pred             HHhhccccHHHHHHHHHHHHhhhHHHHHHHHHHHH--------------------------hcCccchHHHHHHHHHHhc
Confidence            2  12333455666666666666666666654433                          3355666777777755444


Q ss_pred             HHHCCcccCC
Q 040371          314 TKSEGFLPAT  323 (410)
Q Consensus       314 m~~~g~~pd~  323 (410)
                      |.    .||.
T Consensus       518 ~~----~~DA  523 (564)
T KOG1174|consen  518 DD----ESDA  523 (564)
T ss_pred             cC----CCCc
Confidence            44    5555

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.93  E-value=0.017  Score=61.60  Aligned_cols=302  Identities=11%  Similarity=0.052  Sum_probs=185.6

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHHHC--CC----CCCHH--HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc----HHHH
Q 040371           12 MIGGFVRNARFDEALRFFREMLSS--KV----EPDKF--TFASVIYGCARLGALNHAYWVHNLIIEKKIELN----FILS   79 (410)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~--g~----~pd~~--t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~----~~~~   79 (410)
                      ....+...|++++|...+......  ..    .|...  ....+...+...|+++.+...++...+.-...+    ....
T Consensus       415 ~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~a~  494 (903)
T PRK04841        415 QAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAELPLTWYYSRIVAT  494 (903)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccHHHHHHHH
Confidence            344556789999999998877542  11    11111  122223445678999999999998876421112    2345


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhccc-------CC--hhhHHHHHHHHHHcCChHHHHHHHHHHHHC----CCC--C-CHH
Q 040371           80 AALIDMYSKCGKIQMAKEVFDTVQR-------ND--VSVWNAMISGVAIHGLAADASAIFTKMEMF----NVL--P-DSI  143 (410)
Q Consensus        80 ~~li~~y~~~g~~~~A~~~f~~m~~-------~~--~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~--p-~~~  143 (410)
                      +.+...+...|+++.|...+++...       +.  ..+++.+...+...|++++|...+++....    +..  | ...
T Consensus       495 ~~lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~  574 (903)
T PRK04841        495 SVLGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQHLEQLPMHEF  574 (903)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccccccHHHH
Confidence            6677778889999999999887652       11  234555667788899999999998876552    211  1 223


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhhhhc-CCCCC--hhHHHHHHHHHHhcCCHHHHHHHHHhC----CCCCCHHHHHH-
Q 040371          144 TFLGLLTACSHCGLVEEGRKYFDHMRSRY-SIQPQ--LEHYGAMVDLLGRAGHIEEAYGLITSM----TMEPDVVVWRA-  215 (410)
Q Consensus       144 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~-~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~p~~~~~~~-  215 (410)
                      .+..+...+...|++++|...+....... ...+.  ...+..+...+...|++++|.+.+.+.    ........+.. 
T Consensus       575 ~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la~~~~~~G~~~~A~~~l~~a~~~~~~~~~~~~~~~~  654 (903)
T PRK04841        575 LLRIRAQLLWEWARLDEAEQCARKGLEVLSNYQPQQQLQCLAMLAKISLARGDLDNARRYLNRLENLLGNGRYHSDWIAN  654 (903)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHhHHhhhccCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccHhHhhH
Confidence            34445556677899999999988875421 11121  334445666788899999998887765    11111111111 


Q ss_pred             ----HHHHHHhcCchhHHHHHHHhhccCC-Cch------HHHHHHHHHhcCChhHHHHHHHHHHhC----CCcCCCceeE
Q 040371          216 ----LLSACRTFKRLELGEVAIVNISRLM-GGD------YVLLSNMYCYLKRWDTAENVREIMKKK----GVRKSQGKSW  280 (410)
Q Consensus       216 ----li~~~~~~g~~~~a~~~~~~~~~~~-~~~------~~~l~~~~~~~g~~~~a~~~~~~m~~~----g~~~~~~~s~  280 (410)
                          .+..+...|+.+.|...+....... ...      ...+..++...|++++|...+++....    |.........
T Consensus       655 ~~~~~~~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~l~~al~~~~~~g~~~~~a~~~  734 (903)
T PRK04841        655 ADKVRLIYWQMTGDKEAAANWLRQAPKPEFANNHFLQGQWRNIARAQILLGQFDEAEIILEELNENARSLRLMSDLNRNL  734 (903)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCchHHHHHHH
Confidence                2234456788888888854433221 111      345777889999999999999887653    2211110000


Q ss_pred             EEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHHHCCcc
Q 040371          281 LELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFL  320 (410)
Q Consensus       281 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~  320 (410)
                      .       .+...+...|+.++|...+.+..+.-...|+.
T Consensus       735 ~-------~la~a~~~~G~~~~A~~~L~~Al~la~~~g~~  767 (903)
T PRK04841        735 I-------LLNQLYWQQGRKSEAQRVLLEALKLANRTGFI  767 (903)
T ss_pred             H-------HHHHHHHHcCCHHHHHHHHHHHHHHhCccchh
Confidence            0       01223455688889988888776666666663

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=97.91  E-value=0.006  Score=59.01  Aligned_cols=162  Identities=10%  Similarity=0.128  Sum_probs=98.8

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      +-..-|-.++..| ..+++...+.+.+..++ +.+-...|.....-.+...|+-++|....+..++..+ .+.+.|..+.
T Consensus         6 KE~~lF~~~lk~y-E~kQYkkgLK~~~~iL~-k~~eHgeslAmkGL~L~~lg~~~ea~~~vr~glr~d~-~S~vCwHv~g   82 (700)
T KOG1156|consen    6 KENALFRRALKCY-ETKQYKKGLKLIKQILK-KFPEHGESLAMKGLTLNCLGKKEEAYELVRLGLRNDL-KSHVCWHVLG   82 (700)
T ss_pred             HHHHHHHHHHHHH-HHHHHHhHHHHHHHHHH-hCCccchhHHhccchhhcccchHHHHHHHHHHhccCc-ccchhHHHHH
Confidence            3445566777776 45788888888888877 3444556666666667778888888888887777653 3566777777


Q ss_pred             HHHHhcCCHHHHHHHHHhcc---cCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQ---RNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVE  159 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~---~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~  159 (410)
                      -.+-...++++|++.|....   ..|...|.-+--.-++.|+++.......+..+.  .| ....|..+..+.--.|+..
T Consensus        83 l~~R~dK~Y~eaiKcy~nAl~~~~dN~qilrDlslLQ~QmRd~~~~~~tr~~LLql--~~~~ra~w~~~Avs~~L~g~y~  160 (700)
T KOG1156|consen   83 LLQRSDKKYDEAIKCYRNALKIEKDNLQILRDLSLLQIQMRDYEGYLETRNQLLQL--RPSQRASWIGFAVAQHLLGEYK  160 (700)
T ss_pred             HHHhhhhhHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHHhhhhHHHHHHHHHHh--hhhhHHHHHHHHHHHHHHHHHH
Confidence            77777788889988887643   223444444444444445555544444444432  22 2333444444444455555


Q ss_pred             HHHHHHHHhhh
Q 040371          160 EGRKYFDHMRS  170 (410)
Q Consensus       160 ~a~~~~~~m~~  170 (410)
                      .|..+.+...+
T Consensus       161 ~A~~il~ef~~  171 (700)
T KOG1156|consen  161 MALEILEEFEK  171 (700)
T ss_pred             HHHHHHHHHHH
Confidence            55555555443

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=97.91  E-value=0.0038  Score=64.17  Aligned_cols=144  Identities=12%  Similarity=0.106  Sum_probs=70.6

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHH-HHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFT-FASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t-~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      +...|-.|+..|...+++++|.++.+.-.+.  .|+... |..+...+.+.++.+.+..+  .+..              
T Consensus        30 n~~a~~~Li~~~~~~~~~deai~i~~~~l~~--~P~~i~~yy~~G~l~~q~~~~~~~~lv--~~l~--------------   91 (906)
T PRK14720         30 KFKELDDLIDAYKSENLTDEAKDICEEHLKE--HKKSISALYISGILSLSRRPLNDSNLL--NLID--------------   91 (906)
T ss_pred             hHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh--CCcceehHHHHHHHHHhhcchhhhhhh--hhhh--------------
Confidence            4567888888888888899888888866553  455432 22222344555555444333  2211              


Q ss_pred             HHHHhcCCHHHHHHHHHhccc--CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR--NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~--~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a  161 (410)
                       ...+..++....-+...|..  .+..++-.+..+|-+.|+.++|..+|+++.+.. .-|....+.+...++.. ++++|
T Consensus        92 -~~~~~~~~~~ve~~~~~i~~~~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~D-~~n~~aLNn~AY~~ae~-dL~KA  168 (906)
T PRK14720         92 -SFSQNLKWAIVEHICDKILLYGENKLALRTLAEAYAKLNENKKLKGVWERLVKAD-RDNPEIVKKLATSYEEE-DKEKA  168 (906)
T ss_pred             -hcccccchhHHHHHHHHHHhhhhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHh-hHHHH
Confidence             11111111111111111111  011234445555555555555555555555543 22344455555555555 55555


Q ss_pred             HHHHHHhh
Q 040371          162 RKYFDHMR  169 (410)
Q Consensus       162 ~~~~~~m~  169 (410)
                      .+++....
T Consensus       169 ~~m~~KAV  176 (906)
T PRK14720        169 ITYLKKAI  176 (906)
T ss_pred             HHHHHHHH
Confidence            55555544

>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD

Probab=97.87  E-value=0.00037  Score=55.39  Aligned_cols=98  Identities=13%  Similarity=0.105  Sum_probs=84.5

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +......+...+.+.|++++|.+.|++....+ +.+...+..+..++...|+++.|...++...+.+ +.+..++..+..
T Consensus        16 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~la~   93 (135)
T TIGR02552        16 QLEQIYALAYNLYQQGRYDEALKLFQLLAAYD-PYNSRYWLGLAACCQMLKEYEEAIDAYALAAALD-PDDPRPYFHAAE   93 (135)
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCChHHHHHHHH
Confidence            44556678888999999999999999998754 4477888899999999999999999999998875 557888888999


Q ss_pred             HHHhcCCHHHHHHHHHhccc
Q 040371           85 MYSKCGKIQMAKEVFDTVQR  104 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~  104 (410)
                      .|...|+.++|.+.|+...+
T Consensus        94 ~~~~~g~~~~A~~~~~~al~  113 (135)
T TIGR02552        94 CLLALGEPESALKALDLAIE  113 (135)
T ss_pred             HHHHcCCHHHHHHHHHHHHH
Confidence            99999999999999988764

ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=97.83  E-value=0.0029  Score=62.76  Aligned_cols=205  Identities=15%  Similarity=0.090  Sum_probs=124.6

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHC-C--------CCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSS-K--------VEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN   75 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~-g--------~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~   75 (410)
                      +-..|..|.+.|.+..+.+-|.-.+-.|... |        -.|+ .+=.-+.-....+|.+++|+.+|.+-.+..    
T Consensus       756 S~~vW~nmA~McVkT~RLDVAkVClGhm~~aRgaRAlR~a~q~~~-e~eakvAvLAieLgMlEeA~~lYr~ckR~D----  830 (1416)
T KOG3617|consen  756 SDSVWDNMASMCVKTRRLDVAKVCLGHMKNARGARALRRAQQNGE-EDEAKVAVLAIELGMLEEALILYRQCKRYD----  830 (1416)
T ss_pred             hhHHHHHHHHHhhhhccccHHHHhhhhhhhhhhHHHHHHHHhCCc-chhhHHHHHHHHHhhHHHHHHHHHHHHHHH----
Confidence            4567999999999988888777666666321 1        1222 222233333467889999999998887743    


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhcccCC-hhhHHHHHHHHHHcCChHHHHHHHHHH----------HHCC-------
Q 040371           76 FILSAALIDMYSKCGKIQMAKEVFDTVQRND-VSVWNAMISGVAIHGLAADASAIFTKM----------EMFN-------  137 (410)
Q Consensus        76 ~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~-~~~~~~li~~~~~~g~~~~A~~l~~~m----------~~~g-------  137 (410)
                           .|=..|-..|.+++|.++-+.-..-. ..||..-..-+-..++.+.|++.|++-          +.+.       
T Consensus       831 -----LlNKlyQs~g~w~eA~eiAE~~DRiHLr~Tyy~yA~~Lear~Di~~AleyyEK~~~hafev~rmL~e~p~~~e~Y  905 (1416)
T KOG3617|consen  831 -----LLNKLYQSQGMWSEAFEIAETKDRIHLRNTYYNYAKYLEARRDIEAALEYYEKAGVHAFEVFRMLKEYPKQIEQY  905 (1416)
T ss_pred             -----HHHHHHHhcccHHHHHHHHhhccceehhhhHHHHHHHHHhhccHHHHHHHHHhcCChHHHHHHHHHhChHHHHHH
Confidence                 44456778899999988766432211 124444444444456777777766653          1111       


Q ss_pred             --CCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHH
Q 040371          138 --VLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRA  215 (410)
Q Consensus       138 --~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~  215 (410)
                        -+.|...|.--....-..|++|.|+.++....+          |-++++..|-.|+.++|-++-++-+   |......
T Consensus       906 v~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D----------~fs~VrI~C~qGk~~kAa~iA~esg---d~AAcYh  972 (1416)
T KOG3617|consen  906 VRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD----------YFSMVRIKCIQGKTDKAARIAEESG---DKAACYH  972 (1416)
T ss_pred             HHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh----------hhhheeeEeeccCchHHHHHHHhcc---cHHHHHH
Confidence              112333333344444567888888888877663          5566666667777777776666654   4445555


Q ss_pred             HHHHHHhcCchhHHHHH
Q 040371          216 LLSACRTFKRLELGEVA  232 (410)
Q Consensus       216 li~~~~~~g~~~~a~~~  232 (410)
                      |..-|-..|++.+|...
T Consensus       973 laR~YEn~g~v~~Av~F  989 (1416)
T KOG3617|consen  973 LARMYENDGDVVKAVKF  989 (1416)
T ss_pred             HHHHhhhhHHHHHHHHH
Confidence            55556666666655555

>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function

Probab=97.82  E-value=0.0011  Score=53.59  Aligned_cols=122  Identities=14%  Similarity=0.087  Sum_probs=76.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhcccCChh------hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH--HHHHHHH
Q 040371           78 LSAALIDMYSKCGKIQMAKEVFDTVQRNDVS------VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS--ITFLGLL  149 (410)
Q Consensus        78 ~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~------~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~--~t~~~ll  149 (410)
                      .|..++..+ ..++.+.+...++.+......      ..-.+...+...|++++|...|+........|+.  .....+.
T Consensus        14 ~y~~~~~~~-~~~~~~~~~~~~~~l~~~~~~s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA   92 (145)
T PF09976_consen   14 LYEQALQAL-QAGDPAKAEAAAEQLAKDYPSSPYAALAALQLAKAAYEQGDYDEAKAALEKALANAPDPELKPLARLRLA   92 (145)
T ss_pred             HHHHHHHHH-HCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHH
Confidence            344444444 367777777777766643221      2223445667778888888888888776522321  2344456


Q ss_pred             HHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371          150 TACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITS  203 (410)
Q Consensus       150 ~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  203 (410)
                      ..+...|++++|...++.....   ......+....+.|.+.|+.++|...|++
T Consensus        93 ~~~~~~~~~d~Al~~L~~~~~~---~~~~~~~~~~Gdi~~~~g~~~~A~~~y~~  143 (145)
T PF09976_consen   93 RILLQQGQYDEALATLQQIPDE---AFKALAAELLGDIYLAQGDYDEARAAYQK  143 (145)
T ss_pred             HHHHHcCCHHHHHHHHHhccCc---chHHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            6777788888888888664321   23345666777888888888888887764

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=97.81  E-value=0.0066  Score=54.42  Aligned_cols=212  Identities=11%  Similarity=0.083  Sum_probs=131.7

Q ss_pred             HHHHcCCHhHHHHHHHHHHHCCCCCCH--------------HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHH
Q 040371           15 GFVRNARFDEALRFFREMLSSKVEPDK--------------FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSA   80 (410)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~~g~~pd~--------------~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (410)
                      .+.++|.+++|..=|+..++....-+.              ......+..+...|+...++.....+++.. +.|...+.
T Consensus       115 vllK~Gele~A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~-~Wda~l~~  193 (504)
T KOG0624|consen  115 VLLKQGELEQAEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQ-PWDASLRQ  193 (504)
T ss_pred             hhhhcccHHHHHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcC-cchhHHHH
Confidence            456789999999999988875311110              112334555667788888888888888874 56888888


Q ss_pred             HHHHHHHhcCCHHHHHHHHH---hcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHH---------
Q 040371           81 ALIDMYSKCGKIQMAKEVFD---TVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGL---------  148 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~---~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~l---------  148 (410)
                      .-..+|...|++.+|+.=+.   ++.+.++.+..-+-..+...|+.+.++...++.++  +.||....-..         
T Consensus       194 ~Rakc~i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLK--ldpdHK~Cf~~YKklkKv~K  271 (504)
T KOG0624|consen  194 ARAKCYIAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEIRECLK--LDPDHKLCFPFYKKLKKVVK  271 (504)
T ss_pred             HHHHHHHhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHHHHHHc--cCcchhhHHHHHHHHHHHHH
Confidence            88999999999999876554   44456777777788888889999999999988876  56775432111         


Q ss_pred             ----HHHHHccCCHHHHHHHHHHhhhhcCCCCC-----hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHHH
Q 040371          149 ----LTACSHCGLVEEGRKYFDHMRSRYSIQPQ-----LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRALL  217 (410)
Q Consensus       149 ----l~a~~~~g~~~~a~~~~~~m~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~li  217 (410)
                          +......+.+.++..-.+...+.   .|.     ...+..+-.+|...|++.+|++.-.+. .+.|| +.++.-=.
T Consensus       272 ~les~e~~ie~~~~t~cle~ge~vlk~---ep~~~~ir~~~~r~~c~C~~~d~~~~eAiqqC~evL~~d~~dv~~l~dRA  348 (504)
T KOG0624|consen  272 SLESAEQAIEEKHWTECLEAGEKVLKN---EPEETMIRYNGFRVLCTCYREDEQFGEAIQQCKEVLDIDPDDVQVLCDRA  348 (504)
T ss_pred             HHHHHHHHHhhhhHHHHHHHHHHHHhc---CCcccceeeeeeheeeecccccCCHHHHHHHHHHHHhcCchHHHHHHHHH
Confidence                11112234444444444444322   222     122333444555566666666655554 44454 44554444


Q ss_pred             HHHHhcCchhHHHHH
Q 040371          218 SACRTFKRLELGEVA  232 (410)
Q Consensus       218 ~~~~~~g~~~~a~~~  232 (410)
                      .+|.....++.|+.-
T Consensus       349 eA~l~dE~YD~AI~d  363 (504)
T KOG0624|consen  349 EAYLGDEMYDDAIHD  363 (504)
T ss_pred             HHHhhhHHHHHHHHH
Confidence            555555555555554

>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]

Probab=97.77  E-value=0.0042  Score=58.23  Aligned_cols=177  Identities=14%  Similarity=0.007  Sum_probs=116.5

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      |+...+...+.+.........+-.++- +... -.-...-|...+. ....|+++.|+..+..+++. .+-|+..+....
T Consensus       272 ~~~~~~~~r~~~~~~~~~~~~~~~~~~-~~~~-~~~~aa~YG~A~~-~~~~~~~d~A~~~l~~L~~~-~P~N~~~~~~~~  347 (484)
T COG4783         272 PDFQLARARIRAKYEALPNQQAADLLA-KRSK-RGGLAAQYGRALQ-TYLAGQYDEALKLLQPLIAA-QPDNPYYLELAG  347 (484)
T ss_pred             ccHHHHHHHHHHHhccccccchHHHHH-HHhC-ccchHHHHHHHHH-HHHhcccchHHHHHHHHHHh-CCCCHHHHHHHH
Confidence            344455555554443333333333332 2222 1112334444443 34678888888888887776 355677777788


Q ss_pred             HHHHhcCCHHHHHHHHHhccc--CC-hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR--ND-VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~--~~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      +.+.+.++.++|.+.|+++..  |+ ...+-.+..+|.+.|++.+|+.+++..... .+-|...|..|..+|...|+..+
T Consensus       348 ~i~~~~nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g~~~eai~~L~~~~~~-~p~dp~~w~~LAqay~~~g~~~~  426 (484)
T COG4783         348 DILLEANKAKEAIERLKKALALDPNSPLLQLNLAQALLKGGKPQEAIRILNRYLFN-DPEDPNGWDLLAQAYAELGNRAE  426 (484)
T ss_pred             HHHHHcCChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCChHHHHHHHHHHhhc-CCCCchHHHHHHHHHHHhCchHH
Confidence            888888888888888888764  43 456666778888888888888888887765 34577888888888888888777


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      +.....+                   .|...|++++|..+....
T Consensus       427 a~~A~AE-------------------~~~~~G~~~~A~~~l~~A  451 (484)
T COG4783         427 ALLARAE-------------------GYALAGRLEQAIIFLMRA  451 (484)
T ss_pred             HHHHHHH-------------------HHHhCCCHHHHHHHHHHH
Confidence            6654433                   356677777777776655

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.77  E-value=0.001  Score=60.07  Aligned_cols=127  Identities=13%  Similarity=0.138  Sum_probs=75.8

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHH-HHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYG-CARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a-~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      .+|-.++...-+.+..+.|..+|.+.++.+ ..+...|...... +...++.+.|..+|+..++. ++.+...|...++.
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            357777777777777777777777776432 2223334333333 22245566677777777665 45566777777777


Q ss_pred             HHhcCCHHHHHHHHHhcccC------ChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           86 YSKCGKIQMAKEVFDTVQRN------DVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~~------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      +.+.|+.+.|+.+|++....      -...|...+.-=.+.|+.+.+.++.+++.+
T Consensus        80 l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~~  135 (280)
T PF05843_consen   80 LIKLNDINNARALFERAISSLPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAEE  135 (280)
T ss_dssp             HHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHHH
T ss_pred             HHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            77777777777777766532      223666666666666666666666666655

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.

>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional

Probab=97.76  E-value=0.0023  Score=64.84  Aligned_cols=140  Identities=12%  Similarity=0.076  Sum_probs=115.9

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDK-FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~-~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      ++..+-.|.....+.|++++|..+++...+.  .||. .....+..++.+.+.+++|....++.+... +.+....+.+.
T Consensus        85 ~~~~~~~La~i~~~~g~~~ea~~~l~~~~~~--~Pd~~~a~~~~a~~L~~~~~~eeA~~~~~~~l~~~-p~~~~~~~~~a  161 (694)
T PRK15179         85 TELFQVLVARALEAAHRSDEGLAVWRGIHQR--FPDSSEAFILMLRGVKRQQGIEAGRAEIELYFSGG-SSSAREILLEA  161 (694)
T ss_pred             cHHHHHHHHHHHHHcCCcHHHHHHHHHHHhh--CCCcHHHHHHHHHHHHHhccHHHHHHHHHHHhhcC-CCCHHHHHHHH
Confidence            3566777888889999999999999999874  6654 578888899999999999999999999875 44677888899


Q ss_pred             HHHHhcCCHHHHHHHHHhcccCC---hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQRND---VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGL  148 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~~~---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~l  148 (410)
                      ..+.+.|++++|..+|++...++   ..+|......+-..|+.++|...|++..+. ..|....|+..
T Consensus       162 ~~l~~~g~~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~~G~~~~A~~~~~~a~~~-~~~~~~~~~~~  228 (694)
T PRK15179        162 KSWDEIGQSEQADACFERLSRQHPEFENGYVGWAQSLTRRGALWRARDVLQAGLDA-IGDGARKLTRR  228 (694)
T ss_pred             HHHHHhcchHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-hCcchHHHHHH
Confidence            99999999999999999998543   568888888889999999999999998775 23333444433

>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=97.76  E-value=0.00064  Score=49.29  Aligned_cols=94  Identities=18%  Similarity=0.174  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYS   87 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~   87 (410)
                      +|..+...+.+.|++++|+..|++..+.. +.+...+..+..++...++++.|.+.+....+.. +.+..++..+...+.
T Consensus         2 ~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~   79 (100)
T cd00189           2 ALLNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALELD-PDNAKAYYNLGLAYY   79 (100)
T ss_pred             HHHHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CcchhHHHHHHHHHH
Confidence            45567777778888888888888877642 3344566667777777777777777777776654 334456666666777


Q ss_pred             hcCCHHHHHHHHHhcc
Q 040371           88 KCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~  103 (410)
                      ..|+.++|...|+...
T Consensus        80 ~~~~~~~a~~~~~~~~   95 (100)
T cd00189          80 KLGKYEEALEAYEKAL   95 (100)
T ss_pred             HHHhHHHHHHHHHHHH
Confidence            7777777776666543

>KOG2047 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.75  E-value=0.027  Score=54.68  Aligned_cols=45  Identities=18%  Similarity=0.375  Sum_probs=29.4

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCAR   53 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~   53 (410)
                      ..|++|...|.+.|++++|.++|++-.+.  .....-|..+.++|+.
T Consensus       249 ~Lw~SLAdYYIr~g~~ekarDvyeeai~~--v~tvrDFt~ifd~Ya~  293 (835)
T KOG2047|consen  249 FLWCSLADYYIRSGLFEKARDVYEEAIQT--VMTVRDFTQIFDAYAQ  293 (835)
T ss_pred             HHHHHHHHHHHHhhhhHHHHHHHHHHHHh--heehhhHHHHHHHHHH
Confidence            35888888888888888888888776653  2233445555555543

>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=97.71  E-value=0.00078  Score=63.18  Aligned_cols=118  Identities=18%  Similarity=0.119  Sum_probs=73.5

Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhc
Q 040371          146 LGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTF  223 (410)
Q Consensus       146 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~  223 (410)
                      .+++..+...++++.|..+|+++.+.   .|+  ....++..+...++-.+|.+++++. ...| +......-...|...
T Consensus       173 ~~Ll~~l~~t~~~~~ai~lle~L~~~---~pe--v~~~LA~v~l~~~~E~~AI~ll~~aL~~~p~d~~LL~~Qa~fLl~k  247 (395)
T PF09295_consen  173 DTLLKYLSLTQRYDEAIELLEKLRER---DPE--VAVLLARVYLLMNEEVEAIRLLNEALKENPQDSELLNLQAEFLLSK  247 (395)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHhc---CCc--HHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhc
Confidence            34555566666777777777776654   233  3444666666666666776666665 2223 444444444556667


Q ss_pred             CchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          224 KRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       224 g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                      ++++.|..+   .....|.+-.+|..|..+|.+.|+++.|...++.+.
T Consensus       248 ~~~~lAL~iAk~av~lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs~P  295 (395)
T PF09295_consen  248 KKYELALEIAKKAVELSPSEFETWYQLAECYIQLGDFENALLALNSCP  295 (395)
T ss_pred             CCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhcCCHHHHHHHHhcCc
Confidence            777777777   444556666677777777777777777777776654

They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].

>KOG0985 consensus Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.71  E-value=0.0085  Score=60.86  Aligned_cols=164  Identities=12%  Similarity=0.149  Sum_probs=81.4

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccC--ChhhHHHHHHHHHH
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRN--DVSVWNAMISGVAI  119 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~--~~~~~~~li~~~~~  119 (410)
                      ..|+.+..|-...|.+.+|.+-|=   +   ..|+..|.-.++...+.|.+++-.+.+....++  ....=+.+|-+|++
T Consensus      1105 ~vWsqlakAQL~~~~v~dAieSyi---k---adDps~y~eVi~~a~~~~~~edLv~yL~MaRkk~~E~~id~eLi~AyAk 1178 (1666)
T KOG0985|consen 1105 AVWSQLAKAQLQGGLVKDAIESYI---K---ADDPSNYLEVIDVASRTGKYEDLVKYLLMARKKVREPYIDSELIFAYAK 1178 (1666)
T ss_pred             HHHHHHHHHHHhcCchHHHHHHHH---h---cCCcHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhcCccchHHHHHHHHH
Confidence            445555555555555555544331   1   124445555555555555555555544432221  11222345555555


Q ss_pred             cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHH
Q 040371          120 HGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYG  199 (410)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~  199 (410)
                      .++..+..++.       ..||......+..-|...|.++.|.-+|....          .|..|...+...|.+..|.+
T Consensus      1179 t~rl~elE~fi-------~gpN~A~i~~vGdrcf~~~~y~aAkl~y~~vS----------N~a~La~TLV~LgeyQ~AVD 1241 (1666)
T KOG0985|consen 1179 TNRLTELEEFI-------AGPNVANIQQVGDRCFEEKMYEAAKLLYSNVS----------NFAKLASTLVYLGEYQGAVD 1241 (1666)
T ss_pred             hchHHHHHHHh-------cCCCchhHHHHhHHHhhhhhhHHHHHHHHHhh----------hHHHHHHHHHHHHHHHHHHH
Confidence            55555444333       34555555555556666666665555554432          24555555555555555555


Q ss_pred             HHHhCCCCCCHHHHHHHHHHHHhcCchhHHHH
Q 040371          200 LITSMTMEPDVVVWRALLSACRTFKRLELGEV  231 (410)
Q Consensus       200 ~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~  231 (410)
                      --++.   .+..||.-+-.+|...+.+..|.-
T Consensus      1242 ~aRKA---ns~ktWK~VcfaCvd~~EFrlAQi 1270 (1666)
T KOG0985|consen 1242 AARKA---NSTKTWKEVCFACVDKEEFRLAQI 1270 (1666)
T ss_pred             Hhhhc---cchhHHHHHHHHHhchhhhhHHHh
Confidence            44443   244555555555555555544443

>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]

Probab=97.69  E-value=0.02  Score=55.57  Aligned_cols=252  Identities=13%  Similarity=0.056  Sum_probs=166.7

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      ..|+-++|.+..+.-.+..++ ..+-|..+.-.+-...++++|...|..+++.+ +.|..++.-|--.-++.|+++....
T Consensus        53 ~lg~~~ea~~~vr~glr~d~~-S~vCwHv~gl~~R~dK~Y~eaiKcy~nAl~~~-~dN~qilrDlslLQ~QmRd~~~~~~  130 (700)
T KOG1156|consen   53 CLGKKEEAYELVRLGLRNDLK-SHVCWHVLGLLQRSDKKYDEAIKCYRNALKIE-KDNLQILRDLSLLQIQMRDYEGYLE  130 (700)
T ss_pred             cccchHHHHHHHHHHhccCcc-cchhHHHHHHHHhhhhhHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHHHhhhhHHH
Confidence            347888888887776654333 56778887777788889999999999999986 5578888888777788888887766


Q ss_pred             HHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCC-CCCCHHHHHHHH------HHHHccCCHHHHHHHHHH
Q 040371           98 VFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFN-VLPDSITFLGLL------TACSHCGLVEEGRKYFDH  167 (410)
Q Consensus        98 ~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~t~~~ll------~a~~~~g~~~~a~~~~~~  167 (410)
                      .-....+   .....|.....++.-.|+...|..+.++..... -.|+...|....      ......|.+++|.+.+..
T Consensus       131 tr~~LLql~~~~ra~w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~  210 (700)
T KOG1156|consen  131 TRNQLLQLRPSQRASWIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLD  210 (700)
T ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHh
Confidence            6655543   356789999999999999999999999988764 356666554332      233467888888888776


Q ss_pred             hhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHH-hcCchhHHH-HHHHhh---ccCCC
Q 040371          168 MRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLSACR-TFKRLELGE-VAIVNI---SRLMG  241 (410)
Q Consensus       168 m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~-~~g~~~~a~-~~~~~~---~~~~~  241 (410)
                      -..  .+.-....-..-.+.+.+.+++++|..++..+ ...||..-|.-.+..+. +..+.-++. .++...   -|...
T Consensus       211 ~e~--~i~Dkla~~e~ka~l~~kl~~lEeA~~~y~~Ll~rnPdn~~Yy~~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e  288 (700)
T KOG1156|consen  211 NEK--QIVDKLAFEETKADLLMKLGQLEEAVKVYRRLLERNPDNLDYYEGLEKALGKIKDMLEALKALYAILSEKYPRHE  288 (700)
T ss_pred             hhh--HHHHHHHHhhhHHHHHHHHhhHHhHHHHHHHHHhhCchhHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhcCcccc
Confidence            553  22222333446677889999999999999988 45687776665555444 344444444 222221   12111


Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHHhCCCc
Q 040371          242 GDYVLLSNMYCYLKRWDTAENVREIMKKKGVR  273 (410)
Q Consensus       242 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  273 (410)
                      ..-..=++......-.+...+++..+.++|++
T Consensus       289 ~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p  320 (700)
T KOG1156|consen  289 CPRRLPLSVLNGEELKEIVDKYLRPLLSKGVP  320 (700)
T ss_pred             cchhccHHHhCcchhHHHHHHHHHHHhhcCCC
Confidence            11111112222223344455566667777774

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=97.68  E-value=0.022  Score=52.27  Aligned_cols=110  Identities=12%  Similarity=0.148  Sum_probs=80.4

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh
Q 040371          143 ITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRT  222 (410)
Q Consensus       143 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~  222 (410)
                      .+.+..+.-|...|....|.++-.    ++.+ |+..-|-..+.+|+..+++++-.++...   +..+..|..++.+|..
T Consensus       178 ~Sl~~Ti~~li~~~~~k~A~kl~k----~Fkv-~dkrfw~lki~aLa~~~~w~eL~~fa~s---kKsPIGyepFv~~~~~  249 (319)
T PF04840_consen  178 LSLNDTIRKLIEMGQEKQAEKLKK----EFKV-PDKRFWWLKIKALAENKDWDELEKFAKS---KKSPIGYEPFVEACLK  249 (319)
T ss_pred             CCHHHHHHHHHHCCCHHHHHHHHH----HcCC-cHHHHHHHHHHHHHhcCCHHHHHHHHhC---CCCCCChHHHHHHHHH
Confidence            345555666777888777776643    3444 6788888889999999999888876654   2244778888889999


Q ss_pred             cCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHHH
Q 040371          223 FKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREI  266 (410)
Q Consensus       223 ~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  266 (410)
                      .|+..+|..++.+.      .+..-+.+|.++|+|.+|.+.--+
T Consensus       250 ~~~~~eA~~yI~k~------~~~~rv~~y~~~~~~~~A~~~A~~  287 (319)
T PF04840_consen  250 YGNKKEASKYIPKI------PDEERVEMYLKCGDYKEAAQEAFK  287 (319)
T ss_pred             CCCHHHHHHHHHhC------ChHHHHHHHHHCCCHHHHHHHHHH
Confidence            99988888886652      335677888899999988776543

Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.67  E-value=0.0011  Score=49.47  Aligned_cols=79  Identities=14%  Similarity=0.138  Sum_probs=67.6

Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHhhC--------CHHHHHHHHHHHHHcCCCccHHHHH
Q 040371           10 NSMIGGFVRNARFDEALRFFREMLSSKV-EPDKFTFASVIYGCARLG--------ALNHAYWVHNLIIEKKIELNFILSA   80 (410)
Q Consensus        10 n~li~~~~~~g~~~~a~~l~~~m~~~g~-~pd~~t~~~ll~a~~~~~--------~~~~a~~~~~~~~~~g~~~~~~~~~   80 (410)
                      ...|..+..++++...-.+|+.+++.|+ .|+..+|+.++.+.++..        .+-....+|+.|+..+++|+..+|+
T Consensus        29 i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~~lKP~~etYn  108 (120)
T PF08579_consen   29 IDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSNKLKPNDETYN  108 (120)
T ss_pred             HHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHhccCCcHHHHH
Confidence            4566777778999999999999999999 999999999999987654        2445678899999999999999999


Q ss_pred             HHHHHHHh
Q 040371           81 ALIDMYSK   88 (410)
Q Consensus        81 ~li~~y~~   88 (410)
                      .++....+
T Consensus       109 ivl~~Llk  116 (120)
T PF08579_consen  109 IVLGSLLK  116 (120)
T ss_pred             HHHHHHHH
Confidence            99887664

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 [, , ].

>KOG3081 consensus Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.64  E-value=0.0083  Score=51.95  Aligned_cols=168  Identities=14%  Similarity=0.122  Sum_probs=116.7

Q ss_pred             HHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCC-
Q 040371           28 FFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRND-  106 (410)
Q Consensus        28 l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~-  106 (410)
                      +.+.+.......|......-...|...++++.|.......    -  +......=+..+.|..+.|-|.+.+++|.+-| 
T Consensus        95 l~E~~a~~~~~sn~i~~l~aa~i~~~~~~~deAl~~~~~~----~--~lE~~Al~VqI~lk~~r~d~A~~~lk~mq~ide  168 (299)
T KOG3081|consen   95 LYELVADSTDGSNLIDLLLAAIIYMHDGDFDEALKALHLG----E--NLEAAALNVQILLKMHRFDLAEKELKKMQQIDE  168 (299)
T ss_pred             HHHHHHhhccchhHHHHHHhhHHhhcCCChHHHHHHHhcc----c--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHccch
Confidence            3444444444545455555667788999999998877652    1  23333333455678888999999999998754 


Q ss_pred             hhhHHHHHHHHHH----cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHH
Q 040371          107 VSVWNAMISGVAI----HGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYG  182 (410)
Q Consensus       107 ~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  182 (410)
                      -.+.+-|..++.+    .++..+|.-+|++|-+. ..|+..+.+....++...|++++|..+++....+.  .-++.+..
T Consensus       169 d~tLtQLA~awv~la~ggek~qdAfyifeE~s~k-~~~T~~llnG~Av~~l~~~~~eeAe~lL~eaL~kd--~~dpetL~  245 (299)
T KOG3081|consen  169 DATLTQLAQAWVKLATGGEKIQDAFYIFEELSEK-TPPTPLLLNGQAVCHLQLGRYEEAESLLEEALDKD--AKDPETLA  245 (299)
T ss_pred             HHHHHHHHHHHHHHhccchhhhhHHHHHHHHhcc-cCCChHHHccHHHHHHHhcCHHHHHHHHHHHHhcc--CCCHHHHH
Confidence            3455555555544    45789999999999764 68999999999999999999999999999988652  23455666


Q ss_pred             HHHHHHHhcCCHHHH-HHHHHhC
Q 040371          183 AMVDLLGRAGHIEEA-YGLITSM  204 (410)
Q Consensus       183 ~li~~~~~~g~~~~A-~~~~~~m  204 (410)
                      .+|-+-...|...++ .+.+..+
T Consensus       246 Nliv~a~~~Gkd~~~~~r~l~QL  268 (299)
T KOG3081|consen  246 NLIVLALHLGKDAEVTERNLSQL  268 (299)
T ss_pred             HHHHHHHHhCCChHHHHHHHHHH
Confidence            666555556655443 3444444

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.60  E-value=0.0033  Score=52.37  Aligned_cols=110  Identities=12%  Similarity=0.068  Sum_probs=51.5

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc--HHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHH
Q 040371           44 FASVIYGCARLGALNHAYWVHNLIIEKKIELN--FILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVA  118 (410)
Q Consensus        44 ~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~--~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~  118 (410)
                      +..+...+...|++++|...+++.++....+.  ...+..+...|.+.|++++|...+++..+   .+...+..+...|.
T Consensus        38 ~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~  117 (172)
T PRK02603         38 YYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQALELNPKQPSALNNIAVIYH  117 (172)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence            44444444444555555555554444321111  23444445555555555555555544332   12333433444444


Q ss_pred             HcCC--------------hHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 040371          119 IHGL--------------AADASAIFTKMEMFNVLPDSITFLGLLTACSHCGL  157 (410)
Q Consensus       119 ~~g~--------------~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~  157 (410)
                      ..|+              +++|++.+++...  ..|+.  +..++.-+...|.
T Consensus       118 ~~g~~~~a~~~~~~A~~~~~~A~~~~~~a~~--~~p~~--~~~~~~~~~~~~~  166 (172)
T PRK02603        118 KRGEKAEEAGDQDEAEALFDKAAEYWKQAIR--LAPNN--YIEAQNWLKTTGR  166 (172)
T ss_pred             HcCChHhHhhCHHHHHHHHHHHHHHHHHHHh--hCchh--HHHHHHHHHhcCc
Confidence            4333              4667777777655  33443  5555555554443

>PF08579 RPM2: Mitochondrial ribonuclease P subunit (RPM2); InterPro: IPR013888 Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends

Probab=97.59  E-value=0.0017  Score=48.54  Aligned_cols=81  Identities=11%  Similarity=0.131  Sum_probs=65.6

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHccC--------CHHHHHHHHHHhhhhcCCCCChh
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNV-LPDSITFLGLLTACSHCG--------LVEEGRKYFDHMRSRYSIQPQLE  179 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~~~t~~~ll~a~~~~g--------~~~~a~~~~~~m~~~~~~~~~~~  179 (410)
                      +....|.-+...+++.....+|+.+++.|+ .|+..+|+.++.+..+..        .+-+.+.+++.|... +++|+..
T Consensus        27 t~i~~I~~~~~~~d~N~I~~lYqslkRN~i~lPsv~~Yn~VL~Si~~R~lD~~~ie~kl~~LLtvYqDiL~~-~lKP~~e  105 (120)
T PF08579_consen   27 TQIDNINSCFENEDYNIINPLYQSLKRNGITLPSVELYNKVLKSIAKRELDSEDIENKLTNLLTVYQDILSN-KLKPNDE  105 (120)
T ss_pred             HHHHHHHHHHhhcchHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHccccchhHHHHHHHHHHHHHHHHHh-ccCCcHH
Confidence            445566667777999999999999999999 899999999999887643        345677788888865 8899999


Q ss_pred             HHHHHHHHHHh
Q 040371          180 HYGAMVDLLGR  190 (410)
Q Consensus       180 ~~~~li~~~~~  190 (410)
                      +|+.++..+.+
T Consensus       106 tYnivl~~Llk  116 (120)
T PF08579_consen  106 TYNIVLGSLLK  116 (120)
T ss_pred             HHHHHHHHHHH
Confidence            99988887754

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 [, , ].

>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional

Probab=97.58  E-value=0.014  Score=60.16  Aligned_cols=150  Identities=7%  Similarity=-0.016  Sum_probs=108.5

Q ss_pred             CCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHH
Q 040371           36 KVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMI  114 (410)
Q Consensus        36 g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li  114 (410)
                      +..| +...+..|++++...+++++|.++.+..++.. +.....|-.+...|.+.++.+++..+             .++
T Consensus        25 ~~~p~n~~a~~~Li~~~~~~~~~deai~i~~~~l~~~-P~~i~~yy~~G~l~~q~~~~~~~~lv-------------~~l   90 (906)
T PRK14720         25 NYSLSKFKELDDLIDAYKSENLTDEAKDICEEHLKEH-KKSISALYISGILSLSRRPLNDSNLL-------------NLI   90 (906)
T ss_pred             cCCcchHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CcceehHHHHHHHHHhhcchhhhhhh-------------hhh
Confidence            3455 45588889999999999999999999776653 33344444444477888887666544             344


Q ss_pred             HHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCH
Q 040371          115 SGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHI  194 (410)
Q Consensus       115 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~  194 (410)
                      .......++.-+..+...|...  .-+...+..+..+|-+.|+.+++..+++++.+- . +-++...|.+...|+.. ++
T Consensus        91 ~~~~~~~~~~~ve~~~~~i~~~--~~~k~Al~~LA~~Ydk~g~~~ka~~~yer~L~~-D-~~n~~aLNn~AY~~ae~-dL  165 (906)
T PRK14720         91 DSFSQNLKWAIVEHICDKILLY--GENKLALRTLAEAYAKLNENKKLKGVWERLVKA-D-RDNPEIVKKLATSYEEE-DK  165 (906)
T ss_pred             hhcccccchhHHHHHHHHHHhh--hhhhHHHHHHHHHHHHcCChHHHHHHHHHHHhc-C-cccHHHHHHHHHHHHHh-hH
Confidence            4444555564445555566553  234557888999999999999999999999953 4 44688889999999998 99


Q ss_pred             HHHHHHHHhC
Q 040371          195 EEAYGLITSM  204 (410)
Q Consensus       195 ~~A~~~~~~m  204 (410)
                      ++|..++.+.
T Consensus       166 ~KA~~m~~KA  175 (906)
T PRK14720        166 EKAITYLKKA  175 (906)
T ss_pred             HHHHHHHHHH
Confidence            9998888765

>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=97.54  E-value=0.0016  Score=47.06  Aligned_cols=90  Identities=14%  Similarity=0.052  Sum_probs=43.3

Q ss_pred             HHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHh
Q 040371          111 NAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGR  190 (410)
Q Consensus       111 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~  190 (410)
                      ..+...+...|++++|...|++..+.. +.+...+..+...+...+++++|.+.|+...+.  .+.+...+..+...+..
T Consensus         4 ~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~~~~   80 (100)
T cd00189           4 LNLGNLYYKLGDYDEALEYYEKALELD-PDNADAYYNLAAAYYKLGKYEEALEDYEKALEL--DPDNAKAYYNLGLAYYK   80 (100)
T ss_pred             HHHHHHHHHHhcHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC--CCcchhHHHHHHHHHHH
Confidence            334444555555555555555554431 112234444445555555555555555554431  12222345555555555


Q ss_pred             cCCHHHHHHHHHh
Q 040371          191 AGHIEEAYGLITS  203 (410)
Q Consensus       191 ~g~~~~A~~~~~~  203 (410)
                      .|++++|...+.+
T Consensus        81 ~~~~~~a~~~~~~   93 (100)
T cd00189          81 LGKYEEALEAYEK   93 (100)
T ss_pred             HHhHHHHHHHHHH
Confidence            5555555555544

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

Probab=97.51  E-value=0.039  Score=53.11  Aligned_cols=119  Identities=13%  Similarity=0.162  Sum_probs=73.1

Q ss_pred             HHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHH--HHHHH--Hh
Q 040371           13 IGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAA--LIDMY--SK   88 (410)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~--li~~y--~~   88 (410)
                      ++.+.++|++++|+....+++..+ +-|...+..-+-+....+.++.|..+.+   ..+.   ..+++.  +=.+|  .+
T Consensus        19 ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ik---k~~~---~~~~~~~~fEKAYc~Yr   91 (652)
T KOG2376|consen   19 LNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIK---KNGA---LLVINSFFFEKAYCEYR   91 (652)
T ss_pred             HHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHH---hcch---hhhcchhhHHHHHHHHH
Confidence            456667778888888888887654 4455566666777777777777764332   2221   111121  22333  46


Q ss_pred             cCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCC
Q 040371           89 CGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNV  138 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~  138 (410)
                      .+..|+|...++....-+..+...-...+.+.|++++|+++|+.+.+.+.
T Consensus        92 lnk~Dealk~~~~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~  141 (652)
T KOG2376|consen   92 LNKLDEALKTLKGLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNS  141 (652)
T ss_pred             cccHHHHHHHHhcccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCC
Confidence            77777777777755544444555555566677777777777777766543

>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins

Probab=97.49  E-value=0.0013  Score=59.45  Aligned_cols=126  Identities=14%  Similarity=0.110  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh-cCCHHHHHHHHHhccc---CChhhHHHHHHHH
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK-CGKIQMAKEVFDTVQR---NDVSVWNAMISGV  117 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~-~g~~~~A~~~f~~m~~---~~~~~~~~li~~~  117 (410)
                      .+|..+++..-+.+.++.|+.+|.++.+.+ ..+..+|-....+-.+ .++.+.|.++|+...+   .+...|..-+.-+
T Consensus         2 ~v~i~~m~~~~r~~g~~~aR~vF~~a~~~~-~~~~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~~~~~~~~~Y~~~l   80 (280)
T PF05843_consen    2 LVWIQYMRFMRRTEGIEAARKVFKRARKDK-RCTYHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYLDFL   80 (280)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CS-THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCChHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence            345556666666666666666666665432 1122233333333222 2334446666655442   2444555555555


Q ss_pred             HHcCChHHHHHHHHHHHHCCCCCCH---HHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          118 AIHGLAADASAIFTKMEMFNVLPDS---ITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~~g~~p~~---~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      ...|+.+.|..+|++.... +.++.   ..|...+..=.+.|+++.+..+.+++.
T Consensus        81 ~~~~d~~~aR~lfer~i~~-l~~~~~~~~iw~~~i~fE~~~Gdl~~v~~v~~R~~  134 (280)
T PF05843_consen   81 IKLNDINNARALFERAISS-LPKEKQSKKIWKKFIEFESKYGDLESVRKVEKRAE  134 (280)
T ss_dssp             HHTT-HHHHHHHHHHHCCT-SSCHHHCHHHHHHHHHHHHHHS-HHHHHHHHHHHH
T ss_pred             HHhCcHHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            5555555555555555443 22111   244444444444455555554444444

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.

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.49  E-value=0.0082  Score=51.61  Aligned_cols=149  Identities=14%  Similarity=0.072  Sum_probs=69.3

Q ss_pred             HHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHH-HHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHH
Q 040371          117 VAIHGLAADASAIFTKMEMFNVLPDSITFLGLL-TACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIE  195 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll-~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~  195 (410)
                      ....|+.+.|...++++...-  |.+.-...+= --+-..|++++|.++++...++  -+.|..+|-.-+...-..|+--
T Consensus        62 Ald~~~~~lAq~C~~~L~~~f--p~S~RV~~lkam~lEa~~~~~~A~e~y~~lL~d--dpt~~v~~KRKlAilka~GK~l  137 (289)
T KOG3060|consen   62 ALDTGRDDLAQKCINQLRDRF--PGSKRVGKLKAMLLEATGNYKEAIEYYESLLED--DPTDTVIRKRKLAILKAQGKNL  137 (289)
T ss_pred             HHHhcchHHHHHHHHHHHHhC--CCChhHHHHHHHHHHHhhchhhHHHHHHHHhcc--CcchhHHHHHHHHHHHHcCCcH
Confidence            334455556666666555432  3222111110 1112345566666666665543  1333444444444444455544


Q ss_pred             HHHHHHHhC--CCCCCHHHHHHHHHHHHhcCchhHHHHHH---HhhccCCCchHHHHHHHHHhcCC---hhHHHHHHHHH
Q 040371          196 EAYGLITSM--TMEPDVVVWRALLSACRTFKRLELGEVAI---VNISRLMGGDYVLLSNMYCYLKR---WDTAENVREIM  267 (410)
Q Consensus       196 ~A~~~~~~m--~~~p~~~~~~~li~~~~~~g~~~~a~~~~---~~~~~~~~~~~~~l~~~~~~~g~---~~~a~~~~~~m  267 (410)
                      +|++-+.+.  .+-.|...|.-+-.-|...|+++.|.-.+   .-..|.++..+..+.+.+...|.   .+-|.+.+.+.
T Consensus       138 ~aIk~ln~YL~~F~~D~EAW~eLaeiY~~~~~f~kA~fClEE~ll~~P~n~l~f~rlae~~Yt~gg~eN~~~arkyy~~a  217 (289)
T KOG3060|consen  138 EAIKELNEYLDKFMNDQEAWHELAEIYLSEGDFEKAAFCLEELLLIQPFNPLYFQRLAEVLYTQGGAENLELARKYYERA  217 (289)
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhHhHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence            554433333  23345566666666666666666655552   22345555445555555443332   33344444444


Q ss_pred             Hh
Q 040371          268 KK  269 (410)
Q Consensus       268 ~~  269 (410)
                      .+
T Consensus       218 lk  219 (289)
T KOG3060|consen  218 LK  219 (289)
T ss_pred             HH
Confidence            33

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.48  E-value=0.0064  Score=46.92  Aligned_cols=108  Identities=17%  Similarity=0.118  Sum_probs=73.9

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCC--ccHHHHHHHHHHHH
Q 040371           12 MIGGFVRNARFDEALRFFREMLSSKVEPD--KFTFASVIYGCARLGALNHAYWVHNLIIEKKIE--LNFILSAALIDMYS   87 (410)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~g~~pd--~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~--~~~~~~~~li~~y~   87 (410)
                      +-.++-..|+.++|+.+|++....|+...  ...+..+.+++...|++++|..+++........  .+..+...+..++.
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHH
Confidence            45567778999999999999888776654  336667778888889999998888888765211  12233333444667


Q ss_pred             hcCCHHHHHHHHHhcccCChhhHHHHHHHHHH
Q 040371           88 KCGKIQMAKEVFDTVQRNDVSVWNAMISGVAI  119 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~  119 (410)
                      ..|+.++|.+.+-....++...|.--|..|+.
T Consensus        87 ~~gr~~eAl~~~l~~la~~~~~y~ra~~~ya~  118 (120)
T PF12688_consen   87 NLGRPKEALEWLLEALAETLPRYRRAIRFYAD  118 (120)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            77888888887766655555566665655543

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.47  E-value=0.0059  Score=50.57  Aligned_cols=91  Identities=15%  Similarity=0.026  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCc--cHHHHHHHHHHHHhcCCHHHHHHHHHhcccC---ChhhHHHHHHH
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIEL--NFILSAALIDMYSKCGKIQMAKEVFDTVQRN---DVSVWNAMISG  116 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~--~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~  116 (410)
                      ..|..+...+...|++++|...+...+.....+  ...++..+...|.+.|+.++|+..|++....   ...+++.+...
T Consensus        36 ~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~~~~~~~la~i  115 (168)
T CHL00033         36 FTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQALERNPFLPQALNNMAVI  115 (168)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHH
Confidence            344555555555666666666666665542221  1235566666666666666666666654421   23344555444


Q ss_pred             HH-------HcCChHHHHHHHHH
Q 040371          117 VA-------IHGLAADASAIFTK  132 (410)
Q Consensus       117 ~~-------~~g~~~~A~~l~~~  132 (410)
                      |.       ..|++++|+..+++
T Consensus       116 ~~~~~~~~~~~g~~~~A~~~~~~  138 (168)
T CHL00033        116 CHYRGEQAIEQGDSEIAEAWFDQ  138 (168)
T ss_pred             HHHhhHHHHHcccHHHHHHHHHH
Confidence            44       56666655444443

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.47  E-value=0.00036  Score=50.40  Aligned_cols=80  Identities=14%  Similarity=0.204  Sum_probs=38.6

Q ss_pred             cCCHhHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           19 NARFDEALRFFREMLSSKV-EPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        19 ~g~~~~a~~l~~~m~~~g~-~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      +|+++.|+.+|+++.+... .|+...+-.+..++.+.|+++.|..+++. .+.+. .+....-.+..+|.+.|++++|++
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~-~~~~~~~l~a~~~~~l~~y~eAi~   79 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDP-SNPDIHYLLARCLLKLGKYEEAIK   79 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHH-CHHHHHHHHHHHHHHTT-HHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCC-CCHHHHHHHHHHHHHhCCHHHHHH
Confidence            4566666666666655321 11233333455555666666666666655 22211 122333344555555666666655


Q ss_pred             HHH
Q 040371           98 VFD  100 (410)
Q Consensus        98 ~f~  100 (410)
                      +|+
T Consensus        80 ~l~   82 (84)
T PF12895_consen   80 ALE   82 (84)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            554

>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]

Probab=97.44  E-value=0.084  Score=47.59  Aligned_cols=188  Identities=13%  Similarity=0.091  Sum_probs=131.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHH---HHHHHcCChHHHHHHHHHHHHCCCCCCHHHH-HHHHHHHHc
Q 040371           79 SAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMI---SGVAIHGLAADASAIFTKMEMFNVLPDSITF-LGLLTACSH  154 (410)
Q Consensus        79 ~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li---~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~-~~ll~a~~~  154 (410)
                      .--|...+...|++.+|+.-|....+-|...|-++.   ..|...|+...|+.=|.+.++  ++||-..- .--...+.+
T Consensus        41 hlElGk~lla~~Q~sDALt~yHaAve~dp~~Y~aifrRaT~yLAmGksk~al~Dl~rVle--lKpDF~~ARiQRg~vllK  118 (504)
T KOG0624|consen   41 HLELGKELLARGQLSDALTHYHAAVEGDPNNYQAIFRRATVYLAMGKSKAALQDLSRVLE--LKPDFMAARIQRGVVLLK  118 (504)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHcCCchhHHHHHHHHHHHhhhcCCccchhhHHHHHh--cCccHHHHHHHhchhhhh
Confidence            334555566678888888888887777776666653   467778888888888888776  57774321 112234567


Q ss_pred             cCCHHHHHHHHHHhhhhcCC------------CCChhHHH--HHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHH
Q 040371          155 CGLVEEGRKYFDHMRSRYSI------------QPQLEHYG--AMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLS  218 (410)
Q Consensus       155 ~g~~~~a~~~~~~m~~~~~~------------~~~~~~~~--~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~  218 (410)
                      .|.+++|..=|+.+... .-            .+...+|+  ..+..+.-.|+...|+..+..+ .+.| |...+..=..
T Consensus       119 ~Gele~A~~DF~~vl~~-~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~~~GD~~~ai~~i~~llEi~~Wda~l~~~Rak  197 (504)
T KOG0624|consen  119 QGELEQAEADFDQVLQH-EPSNGLVLEAQSKLALIQEHWVLVQQLKSASGSGDCQNAIEMITHLLEIQPWDASLRQARAK  197 (504)
T ss_pred             cccHHHHHHHHHHHHhc-CCCcchhHHHHHHHHhHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHhcCcchhHHHHHHHH
Confidence            88888888888887743 11            01111222  2333455678888888888776 5555 6777777778


Q ss_pred             HHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040371          219 ACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       219 ~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                      +|...|.+..|+.-   ..++..++...+.-+...+...|+.+.+....++-.+
T Consensus       198 c~i~~~e~k~AI~Dlk~askLs~DnTe~~ykis~L~Y~vgd~~~sL~~iRECLK  251 (504)
T KOG0624|consen  198 CYIAEGEPKKAIHDLKQASKLSQDNTEGHYKISQLLYTVGDAENSLKEIRECLK  251 (504)
T ss_pred             HHHhcCcHHHHHHHHHHHHhccccchHHHHHHHHHHHhhhhHHHHHHHHHHHHc
Confidence            88899999988876   5667778888888889999999999988887776654

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=97.43  E-value=0.039  Score=49.99  Aligned_cols=196  Identities=13%  Similarity=0.087  Sum_probs=97.4

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHH----CCCCCCH-HHHHHHHHHHHhhCCHHHHHHHHHHHHHc----CCCc-cHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLS----SKVEPDK-FTFASVIYGCARLGALNHAYWVHNLIIEK----KIEL-NFI   77 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~----~g~~pd~-~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~~~-~~~   77 (410)
                      .|+.....|...|++++|.+.|.+...    .+-+.+. ..|......+.+ .+++.|.+.+.+....    |-.. -..
T Consensus        37 ~y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~-~~~~~Ai~~~~~A~~~y~~~G~~~~aA~  115 (282)
T PF14938_consen   37 LYEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKK-GDPDEAIECYEKAIEIYREAGRFSQAAK  115 (282)
T ss_dssp             HHHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHHHHHCT-HHHHHH
T ss_pred             HHHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHh-hCHHHHHHHHHHHHHHHHhcCcHHHHHH
Confidence            477777778888888888888877633    2211111 234444444433 3777777766665432    3111 123


Q ss_pred             HHHHHHHHHHhc-CCHHHHHHHHHhccc----CC-----hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCC-----CCH
Q 040371           78 LSAALIDMYSKC-GKIQMAKEVFDTVQR----ND-----VSVWNAMISGVAIHGLAADASAIFTKMEMFNVL-----PDS  142 (410)
Q Consensus        78 ~~~~li~~y~~~-g~~~~A~~~f~~m~~----~~-----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-----p~~  142 (410)
                      .+..+...|-+. |++++|.+.|++..+    .+     ...+..+...+.+.|++++|.++|++....-..     ++.
T Consensus       116 ~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~  195 (282)
T PF14938_consen  116 CLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEGSPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSA  195 (282)
T ss_dssp             HHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhH
Confidence            455556666666 666666666655431    11     124445556666666666777666666543221     111


Q ss_pred             H-HHHHHHHHHHccCCHHHHHHHHHHhhhh-cCCCCC--hhHHHHHHHHHHhc--CCHHHHHHHHHhC
Q 040371          143 I-TFLGLLTACSHCGLVEEGRKYFDHMRSR-YSIQPQ--LEHYGAMVDLLGRA--GHIEEAYGLITSM  204 (410)
Q Consensus       143 ~-t~~~ll~a~~~~g~~~~a~~~~~~m~~~-~~~~~~--~~~~~~li~~~~~~--g~~~~A~~~~~~m  204 (410)
                      . .|...+-.+...|++..|.+.|+..... .++..+  -.....||.++-..  ..+++|..-|+.+
T Consensus       196 ~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~d~~  263 (282)
T PF14938_consen  196 KEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVAEYDSI  263 (282)
T ss_dssp             HHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCHHHTTS
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHHHHccc
Confidence            1 1222233444556666666666665422 122222  22344455554432  3455555556555

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.42  E-value=0.0021  Score=51.61  Aligned_cols=93  Identities=13%  Similarity=0.009  Sum_probs=76.8

Q ss_pred             hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHH
Q 040371          178 LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYC  252 (410)
Q Consensus       178 ~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~  252 (410)
                      ....-.+-..+...|++++|.++|+-. .+.| +..-|-.|-..|...|++++|+..   ...+.|+++.++..+..+|.
T Consensus        35 l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~L  114 (157)
T PRK15363         35 LNTLYRYAMQLMEVKEFAGAARLFQLLTIYDAWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECYL  114 (157)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHH
Confidence            334445566678899999999999987 4556 456777888888889999999998   66778999999999999999


Q ss_pred             hcCChhHHHHHHHHHHhC
Q 040371          253 YLKRWDTAENVREIMKKK  270 (410)
Q Consensus       253 ~~g~~~~a~~~~~~m~~~  270 (410)
                      ..|+.+.|++.|+.....
T Consensus       115 ~lG~~~~A~~aF~~Ai~~  132 (157)
T PRK15363        115 ACDNVCYAIKALKAVVRI  132 (157)
T ss_pred             HcCCHHHHHHHHHHHHHH
Confidence            999999999999977653

>KOG4340 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.40  E-value=0.017  Score=50.83  Aligned_cols=158  Identities=13%  Similarity=0.053  Sum_probs=104.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhccc----CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCC-----------
Q 040371           75 NFILSAALIDMYSKCGKIQMAKEVFDTVQR----NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVL-----------  139 (410)
Q Consensus        75 ~~~~~~~li~~y~~~g~~~~A~~~f~~m~~----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-----------  139 (410)
                      +..+.+...-...+.|+.+.|.+-|+...+    .....||..+..|. .|+...|++...++.+.|++           
T Consensus       143 ~Ad~~in~gCllykegqyEaAvqkFqaAlqvsGyqpllAYniALaHy~-~~qyasALk~iSEIieRG~r~HPElgIGm~t  221 (459)
T KOG4340|consen  143 EADGQINLGCLLYKEGQYEAAVQKFQAALQVSGYQPLLAYNLALAHYS-SRQYASALKHISEIIERGIRQHPELGIGMTT  221 (459)
T ss_pred             ccchhccchheeeccccHHHHHHHHHHHHhhcCCCchhHHHHHHHHHh-hhhHHHHHHHHHHHHHhhhhcCCccCcccee
Confidence            344444455556788999999999998764    25678998877664 68999999999999887743           


Q ss_pred             --CCHH--------HHHHHHHHH-------HccCCHHHHHHHHHHhhhhcCCCCChhHHHHHH--HHHHhcCCHHHHHHH
Q 040371          140 --PDSI--------TFLGLLTAC-------SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMV--DLLGRAGHIEEAYGL  200 (410)
Q Consensus       140 --p~~~--------t~~~ll~a~-------~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li--~~~~~~g~~~~A~~~  200 (410)
                        ||..        .-+.++.++       .+.|+.+.|.+.+-.|..+..-+.|+.|...+.  ++=++-+.--+-+.+
T Consensus       222 egiDvrsvgNt~~lh~Sal~eAfNLKaAIeyq~~n~eAA~eaLtDmPPRaE~elDPvTLHN~Al~n~~~~p~~g~~KLqF  301 (459)
T KOG4340|consen  222 EGIDVRSVGNTLVLHQSALVEAFNLKAAIEYQLRNYEAAQEALTDMPPRAEEELDPVTLHNQALMNMDARPTEGFEKLQF  301 (459)
T ss_pred             ccCchhcccchHHHHHHHHHHHhhhhhhhhhhcccHHHHHHHhhcCCCcccccCCchhhhHHHHhcccCCccccHHHHHH
Confidence              2211        112333333       467899999999988875544445555554433  333322222222333


Q ss_pred             HHhCCCCC-CHHHHHHHHHHHHhcCchhHHHHHHHh
Q 040371          201 ITSMTMEP-DVVVWRALLSACRTFKRLELGEVAIVN  235 (410)
Q Consensus       201 ~~~m~~~p-~~~~~~~li~~~~~~g~~~~a~~~~~~  235 (410)
                      +-.  +.| ...||..++-.|+++.-++.|-.++.+
T Consensus       302 LL~--~nPfP~ETFANlLllyCKNeyf~lAADvLAE  335 (459)
T KOG4340|consen  302 LLQ--QNPFPPETFANLLLLYCKNEYFDLAADVLAE  335 (459)
T ss_pred             HHh--cCCCChHHHHHHHHHHhhhHHHhHHHHHHhh
Confidence            333  344 457899999999999999999888544

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=97.40  E-value=0.035  Score=52.91  Aligned_cols=201  Identities=13%  Similarity=0.103  Sum_probs=113.2

Q ss_pred             HhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC---CHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHH
Q 040371           22 FDEALRFFREMLSSKVEPDKFTFASVIYGCARLG---ALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEV   98 (410)
Q Consensus        22 ~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~---~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~   98 (410)
                      .+++.+++++....-..-+..+|..+..-=-..-   ..+....+++.+++.-...-..+|..+|+.--|..-+..|+.+
T Consensus       309 t~e~~~~yEr~I~~l~~~~~~Ly~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~i  388 (656)
T KOG1914|consen  309 TDEAASIYERAIEGLLKENKLLYFALADYEESRYDDNKEKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKI  388 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhcccchhhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHH
Confidence            4555555555544323334445444433222111   2445555555555443222234566667766777777777777


Q ss_pred             HHhccc----C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHccCCHHHHHHHHHHhhhhc
Q 040371           99 FDTVQR----N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS-ITFLGLLTACSHCGLVEEGRKYFDHMRSRY  172 (410)
Q Consensus        99 f~~m~~----~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~  172 (410)
                      |.+..+    + ++...++++.-|+ .++.+-|..+|+-=++.  -+|. .-....+.-+.+.++-..++.+|+..... 
T Consensus       389 F~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkk--f~d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s-  464 (656)
T KOG1914|consen  389 FKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKK--FGDSPEYVLKYLDFLSHLNDDNNARALFERVLTS-  464 (656)
T ss_pred             HHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHh--cCCChHHHHHHHHHHHHhCcchhHHHHHHHHHhc-
Confidence            776653    1 5566677777665 46667777777643332  1222 22344566666777777777777777764 


Q ss_pred             CCCCC--hhHHHHHHHHHHhcCCHHHHHHHHHhC----C--CCCCHHHHHHHHHHHHhcCch
Q 040371          173 SIQPQ--LEHYGAMVDLLGRAGHIEEAYGLITSM----T--MEPDVVVWRALLSACRTFKRL  226 (410)
Q Consensus       173 ~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m----~--~~p~~~~~~~li~~~~~~g~~  226 (410)
                      ++.|+  ...|..+|+-=..-|++..+.++-+++    +  ..|....-..+++-|...+..
T Consensus       465 ~l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY~~~d~~  526 (656)
T KOG1914|consen  465 VLSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRYGILDLY  526 (656)
T ss_pred             cCChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHHhhcccc
Confidence            55555  467777777777777777777776665    2  223333344455555555443

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.39  E-value=0.0037  Score=59.10  Aligned_cols=119  Identities=13%  Similarity=0.045  Sum_probs=65.9

Q ss_pred             CCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc--CCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc----CChhhH
Q 040371           37 VEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK--KIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR----NDVSVW  110 (410)
Q Consensus        37 ~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~--g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~----~~~~~~  110 (410)
                      .+.+......+++.+....+++.+..++-+....  ....-..+..++|..|.+.|..+.+..++..=..    ||-.++
T Consensus        62 ~~vS~~dld~fvn~~~~~~~~d~~~~~L~k~R~s~~~~~~~~~t~ha~vR~~l~~~~~~~~l~~L~n~~~yGiF~D~~s~  141 (429)
T PF10037_consen   62 KPVSSLDLDIFVNNVESKDDLDEVEDVLYKFRHSPNCSYLLPSTHHALVRQCLELGAEDELLELLKNRLQYGIFPDNFSF  141 (429)
T ss_pred             CCCcHHHHHHHHhhcCCHhHHHHHHHHHHHHHcCcccccccCccHHHHHHHHHhcCCHHHHHHHHhChhhcccCCChhhH
Confidence            3445555666666666666666666655555443  1112223344666666666666666665554332    455666


Q ss_pred             HHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc
Q 040371          111 NAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHC  155 (410)
Q Consensus       111 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~  155 (410)
                      |.+|+.+.+.|++..|.++..+|...+...+..|+...+.+|.+.
T Consensus       142 n~Lmd~fl~~~~~~~A~~V~~~~~lQe~~~~~~t~~L~l~~~~~~  186 (429)
T PF10037_consen  142 NLLMDHFLKKGNYKSAAKVATEMMLQEEFDNPSTQALALYSCYKY  186 (429)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHHHhhccCCchHHHHHHHHHHHh
Confidence            666666666666666666666665555555555555555555443

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 [].

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

Probab=97.37  E-value=0.077  Score=51.14  Aligned_cols=215  Identities=10%  Similarity=-0.040  Sum_probs=139.4

Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHH--HHHHH--HHc
Q 040371           45 ASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNA--MISGV--AIH  120 (410)
Q Consensus        45 ~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~--li~~~--~~~  120 (410)
                      -+=++-+...+++++|.+.-.+++..+ +.|...+..=+-+..+.+++++|.++.+.-..-  .+++.  +=.+|  .+.
T Consensus        16 ~t~ln~~~~~~e~e~a~k~~~Kil~~~-pdd~~a~~cKvValIq~~ky~~ALk~ikk~~~~--~~~~~~~fEKAYc~Yrl   92 (652)
T KOG2376|consen   16 LTDLNRHGKNGEYEEAVKTANKILSIV-PDDEDAIRCKVVALIQLDKYEDALKLIKKNGAL--LVINSFFFEKAYCEYRL   92 (652)
T ss_pred             HHHHHHhccchHHHHHHHHHHHHHhcC-CCcHhhHhhhHhhhhhhhHHHHHHHHHHhcchh--hhcchhhHHHHHHHHHc
Confidence            344556677889999999999999887 556777777777889999999999776654321  22222  23444  468


Q ss_pred             CChHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHH
Q 040371          121 GLAADASAIFTKMEMFNVLPDS-ITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYG  199 (410)
Q Consensus       121 g~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~  199 (410)
                      ++.++|+..++     |..++. .+...-...|.+.|++++|..+|+.+.+...-..+...-..++..    +---.+. 
T Consensus        93 nk~Dealk~~~-----~~~~~~~~ll~L~AQvlYrl~~ydealdiY~~L~kn~~dd~d~~~r~nl~a~----~a~l~~~-  162 (652)
T KOG2376|consen   93 NKLDEALKTLK-----GLDRLDDKLLELRAQVLYRLERYDEALDIYQHLAKNNSDDQDEERRANLLAV----AAALQVQ-  162 (652)
T ss_pred             ccHHHHHHHHh-----cccccchHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCchHHHHHHHHHHHH----HHhhhHH-
Confidence            99999999988     344433 355555677889999999999999998641111122222222221    1112222 


Q ss_pred             HHHhCCCCCCHHHHHHHH---HHHHhcCchhHHHHHHHhh--------ccCCC----------chHHHHHHHHHhcCChh
Q 040371          200 LITSMTMEPDVVVWRALL---SACRTFKRLELGEVAIVNI--------SRLMG----------GDYVLLSNMYCYLKRWD  258 (410)
Q Consensus       200 ~~~~m~~~p~~~~~~~li---~~~~~~g~~~~a~~~~~~~--------~~~~~----------~~~~~l~~~~~~~g~~~  258 (410)
                      +.+..+..| ..+|..+-   ..+...|++..|++++..-        ...+.          ..-.-|..++...|+.+
T Consensus       163 ~~q~v~~v~-e~syel~yN~Ac~~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~  241 (652)
T KOG2376|consen  163 LLQSVPEVP-EDSYELLYNTACILIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTA  241 (652)
T ss_pred             HHHhccCCC-cchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchH
Confidence            566667666 33333333   3456789999999983332        22211          12334667788999999


Q ss_pred             HHHHHHHHHHhCCCc
Q 040371          259 TAENVREIMKKKGVR  273 (410)
Q Consensus       259 ~a~~~~~~m~~~g~~  273 (410)
                      +|..++.....++..
T Consensus       242 ea~~iy~~~i~~~~~  256 (652)
T KOG2376|consen  242 EASSIYVDIIKRNPA  256 (652)
T ss_pred             HHHHHHHHHHHhcCC
Confidence            999999998887653

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.35  E-value=0.0052  Score=47.24  Aligned_cols=22  Identities=23%  Similarity=0.196  Sum_probs=9.0

Q ss_pred             HHHHHHHcCChHHHHHHHHHHH
Q 040371          113 MISGVAIHGLAADASAIFTKME  134 (410)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~  134 (410)
                      +...+.+.|++++|...|++..
T Consensus        45 l~~~~~~~~~~~~A~~~~~~~~   66 (119)
T TIGR02795        45 LGEAYYAQGKYADAAKAFLAVV   66 (119)
T ss_pred             HHHHHHhhccHHHHHHHHHHHH
Confidence            3333444444444444444433

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.

>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A

Probab=97.35  E-value=0.0013  Score=47.37  Aligned_cols=79  Identities=16%  Similarity=0.143  Sum_probs=42.9

Q ss_pred             hCCHHHHHHHHHHHHHcCCC-ccHHHHHHHHHHHHhcCCHHHHHHHHHhcc--cCChhhHHHHHHHHHHcCChHHHHHHH
Q 040371           54 LGALNHAYWVHNLIIEKKIE-LNFILSAALIDMYSKCGKIQMAKEVFDTVQ--RNDVSVWNAMISGVAIHGLAADASAIF  130 (410)
Q Consensus        54 ~~~~~~a~~~~~~~~~~g~~-~~~~~~~~li~~y~~~g~~~~A~~~f~~m~--~~~~~~~~~li~~~~~~g~~~~A~~l~  130 (410)
                      .|+++.|..+++++.+.... ++...+-.+..+|.+.|++++|..++++..  ..+....-.+..+|.+.|++++|++.|
T Consensus         2 ~~~y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~~~~y~~A~~~~~~~~~~~~~~~~~~l~a~~~~~l~~y~eAi~~l   81 (84)
T PF12895_consen    2 QGNYENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQQGKYEEAIELLQKLKLDPSNPDIHYLLARCLLKLGKYEEAIKAL   81 (84)
T ss_dssp             TT-HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHHTTHHHHHHHHHHCHTHHHCHHHHHHHHHHHHHHTT-HHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHHCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhCCHHHHHHHH
Confidence            35666666666666665431 234444446666666666666666665521  122233334455566666666666666


Q ss_pred             HH
Q 040371          131 TK  132 (410)
Q Consensus       131 ~~  132 (410)
                      ++
T Consensus        82 ~~   83 (84)
T PF12895_consen   82 EK   83 (84)
T ss_dssp             HH
T ss_pred             hc
Confidence            54

>PF10037 MRP-S27: Mitochondrial 28S ribosomal protein S27; InterPro: IPR019266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.34  E-value=0.0037  Score=59.07  Aligned_cols=120  Identities=10%  Similarity=0.071  Sum_probs=94.0

Q ss_pred             CCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc-C-----ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHH
Q 040371           71 KIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR-N-----DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSIT  144 (410)
Q Consensus        71 g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-~-----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t  144 (410)
                      +.+.+......+++......+++.+..++-+... |     -..|..++|..|...|..++++.+++.=..-|+-||..|
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            3445566666777777777888889888877653 2     123567999999999999999999999889999999999


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhc
Q 040371          145 FLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRA  191 (410)
Q Consensus       145 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~  191 (410)
                      |+.|+..+.+.|++..|.++...|... ....+..++.-.+..+.+.
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            999999999999999999999998865 5555556655544444443

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 [].

>KOG3060 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.32  E-value=0.09  Score=45.43  Aligned_cols=82  Identities=13%  Similarity=0.106  Sum_probs=36.9

Q ss_pred             cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHH
Q 040371          120 HGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYG  199 (410)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~  199 (410)
                      .|++++|+++++...+.. +.|.+++--=+...-..|.--+|++-+....+  .+..|...|.-+-+.|...|++++|.-
T Consensus        99 ~~~~~~A~e~y~~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~--~F~~D~EAW~eLaeiY~~~~~f~kA~f  175 (289)
T KOG3060|consen   99 TGNYKEAIEYYESLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLD--KFMNDQEAWHELAEIYLSEGDFEKAAF  175 (289)
T ss_pred             hhchhhHHHHHHHHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHH--HhcCcHHHHHHHHHHHHhHhHHHHHHH
Confidence            344555555555544443 22333333333333334444444444444443  233345555555555555555555544


Q ss_pred             HHHhC
Q 040371          200 LITSM  204 (410)
Q Consensus       200 ~~~~m  204 (410)
                      .++++
T Consensus       176 ClEE~  180 (289)
T KOG3060|consen  176 CLEEL  180 (289)
T ss_pred             HHHHH
Confidence            44444

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.31  E-value=0.014  Score=57.38  Aligned_cols=140  Identities=9%  Similarity=0.012  Sum_probs=84.2

Q ss_pred             CCCCCHHHHHHHHHHHHhhC-----CHHHHHHHHHHHHHcCCCcc-HHHHHHHHHHHHhc--------CCHHHHHHHHHh
Q 040371           36 KVEPDKFTFASVIYGCARLG-----ALNHAYWVHNLIIEKKIELN-FILSAALIDMYSKC--------GKIQMAKEVFDT  101 (410)
Q Consensus        36 g~~pd~~t~~~ll~a~~~~~-----~~~~a~~~~~~~~~~g~~~~-~~~~~~li~~y~~~--------g~~~~A~~~f~~  101 (410)
                      +.+.|...|...+.+.....     +.+.|..+|+++++..  |+ ...+..+..+|...        +++..+.+..++
T Consensus       332 ~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ld--P~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~  409 (517)
T PRK10153        332 GLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSE--PDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDN  409 (517)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHH
Confidence            34566677777776654322     2556777777777653  33 33343333323221        123344444443


Q ss_pred             cc-----cCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCC
Q 040371          102 VQ-----RNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP  176 (410)
Q Consensus       102 m~-----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~  176 (410)
                      ..     ..+...|.++.......|++++|...|++....  .|+...|..+...+...|+.++|.+.++...   .+.|
T Consensus       410 a~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~L--~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~---~L~P  484 (517)
T PRK10153        410 IVALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAIDL--EMSWLNYVLLGKVYELKGDNRLAADAYSTAF---NLRP  484 (517)
T ss_pred             hhhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHHc--CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH---hcCC
Confidence            21     224456777766666678888888888888774  3677778888888888888888888888776   3345


Q ss_pred             ChhHHH
Q 040371          177 QLEHYG  182 (410)
Q Consensus       177 ~~~~~~  182 (410)
                      ...+|.
T Consensus       485 ~~pt~~  490 (517)
T PRK10153        485 GENTLY  490 (517)
T ss_pred             CCchHH
Confidence            444443

>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=97.30  E-value=0.0025  Score=53.70  Aligned_cols=97  Identities=21%  Similarity=0.308  Sum_probs=72.1

Q ss_pred             HHHHHhc--ccCChhhHHHHHHHHHHc-----CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc-------------
Q 040371           96 KEVFDTV--QRNDVSVWNAMISGVAIH-----GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHC-------------  155 (410)
Q Consensus        96 ~~~f~~m--~~~~~~~~~~li~~~~~~-----g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~-------------  155 (410)
                      ...|+..  ..+|..+|..++..|.+.     |..+=....++.|.+-|+.-|..+|+.||..+=+.             
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            4455555  456777777777777653     66777777778888888888888888888776542             


Q ss_pred             ---CCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCC
Q 040371          156 ---GLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGH  193 (410)
Q Consensus       156 ---g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~  193 (410)
                         .+.+-|.+++++|.. +|+-||.+++..+++.+++.+.
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               235778888999885 5899999999988888887664

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>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=97.25  E-value=0.0041  Score=52.42  Aligned_cols=87  Identities=10%  Similarity=0.090  Sum_probs=43.6

Q ss_pred             CChhHHHHHHHHHHHc-----CCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC----------------CHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRN-----ARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLG----------------ALNHAYW   62 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~-----g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~----------------~~~~a~~   62 (410)
                      +|-.+|..+|..|.+.     |+.+=....++.|.+.|+.-|..+|+.||+.+=+..                +-+-|.+
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            3445555555555543     344444444555555555555555555555443211                2234455


Q ss_pred             HHHHHHHcCCCccHHHHHHHHHHHHhcC
Q 040371           63 VHNLIIEKKIELNFILSAALIDMYSKCG   90 (410)
Q Consensus        63 ~~~~~~~~g~~~~~~~~~~li~~y~~~g   90 (410)
                      ++++|...|+-||..++..|++.+++.+
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            5555555555555555555555554444

ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].

>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF

Probab=97.24  E-value=0.0099  Score=45.63  Aligned_cols=92  Identities=13%  Similarity=0.054  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCC--ccHHHHHHH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPD----KFTFASVIYGCARLGALNHAYWVHNLIIEKKIE--LNFILSAAL   82 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd----~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~--~~~~~~~~l   82 (410)
                      +-.+...+.+.|++++|.+.|.++....  |+    ...+..+..++.+.|+++.|...++.+.+....  ....++..+
T Consensus         5 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~   82 (119)
T TIGR02795         5 YYDAALLVLKAGDYADAIQAFQAFLKKY--PKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKL   82 (119)
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC--CCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHH
Confidence            3444555555666666666665555421  11    123333444455555555555555554443111  112333344


Q ss_pred             HHHHHhcCCHHHHHHHHHhc
Q 040371           83 IDMYSKCGKIQMAKEVFDTV  102 (410)
Q Consensus        83 i~~y~~~g~~~~A~~~f~~m  102 (410)
                      ..+|.+.|+.++|.+.|+++
T Consensus        83 ~~~~~~~~~~~~A~~~~~~~  102 (119)
T TIGR02795        83 GMSLQELGDKEKAKATLQQV  102 (119)
T ss_pred             HHHHHHhCChHHHHHHHHHH
Confidence            44444444444444444433

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.

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.24  E-value=0.0089  Score=56.04  Aligned_cols=84  Identities=15%  Similarity=0.074  Sum_probs=35.7

Q ss_pred             HHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHH
Q 040371           16 FVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMA   95 (410)
Q Consensus        16 ~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A   95 (410)
                      +...|++++|+++|++.++.. +-+...|..+..++...|+++.|...++++++.. +.+...|..+..+|...|++++|
T Consensus        12 a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~-P~~~~a~~~lg~~~~~lg~~~eA   89 (356)
T PLN03088         12 AFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELD-PSLAKAYLRKGTACMKLEEYQTA   89 (356)
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhCCHHHH
Confidence            334455555555555544431 2233344444444444444444444444444432 12333334444444444444444


Q ss_pred             HHHHHh
Q 040371           96 KEVFDT  101 (410)
Q Consensus        96 ~~~f~~  101 (410)
                      ...|++
T Consensus        90 ~~~~~~   95 (356)
T PLN03088         90 KAALEK   95 (356)
T ss_pred             HHHHHH
Confidence            444443

>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional

Probab=97.21  E-value=0.01  Score=47.68  Aligned_cols=89  Identities=8%  Similarity=-0.111  Sum_probs=52.9

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc---cCChhhHHHHHHHHHHcCC
Q 040371           46 SVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ---RNDVSVWNAMISGVAIHGL  122 (410)
Q Consensus        46 ~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~---~~~~~~~~~li~~~~~~g~  122 (410)
                      .+...+...|+++.|..+|+.+.... +.+..-|-.|.-++-..|++++|+..|....   ..|..++-.+..+|...|+
T Consensus        40 ~~A~~ly~~G~l~~A~~~f~~L~~~D-p~~~~y~~gLG~~~Q~~g~~~~AI~aY~~A~~L~~ddp~~~~~ag~c~L~lG~  118 (157)
T PRK15363         40 RYAMQLMEVKEFAGAARLFQLLTIYD-AWSFDYWFRLGECCQAQKHWGEAIYAYGRAAQIKIDAPQAPWAAAECYLACDN  118 (157)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHcCC
Confidence            33344456666666666666666653 2345555666666666666666666666543   2245555556666666666


Q ss_pred             hHHHHHHHHHHHH
Q 040371          123 AADASAIFTKMEM  135 (410)
Q Consensus       123 ~~~A~~l~~~m~~  135 (410)
                      .+.|.+-|+....
T Consensus       119 ~~~A~~aF~~Ai~  131 (157)
T PRK15363        119 VCYAIKALKAVVR  131 (157)
T ss_pred             HHHHHHHHHHHHH
Confidence            6666666665544

>KOG3617 consensus WD40 and TPR repeat-containing protein [General function prediction only]

Probab=97.20  E-value=0.056  Score=54.09  Aligned_cols=212  Identities=10%  Similarity=0.079  Sum_probs=127.3

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      +.|-.++|+.+|++-.+         |..+=..|-..|.+++|.++-+.=-+..+.   .+|.....-+-..++.+.|++
T Consensus       812 eLgMlEeA~~lYr~ckR---------~DLlNKlyQs~g~w~eA~eiAE~~DRiHLr---~Tyy~yA~~Lear~Di~~Ale  879 (1416)
T KOG3617|consen  812 ELGMLEEALILYRQCKR---------YDLLNKLYQSQGMWSEAFEIAETKDRIHLR---NTYYNYAKYLEARRDIEAALE  879 (1416)
T ss_pred             HHhhHHHHHHHHHHHHH---------HHHHHHHHHhcccHHHHHHHHhhccceehh---hhHHHHHHHHHhhccHHHHHH
Confidence            45777888888877654         233344556677788777765433222222   234344444445666777777


Q ss_pred             HHHhcccC-----------------------ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040371           98 VFDTVQRN-----------------------DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSH  154 (410)
Q Consensus        98 ~f~~m~~~-----------------------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~  154 (410)
                      .|++...+                       |...|.=...-.-..|+.+.|+.+|...+.         |-+++...+-
T Consensus       880 yyEK~~~hafev~rmL~e~p~~~e~Yv~~~~d~~L~~WWgqYlES~GemdaAl~~Y~~A~D---------~fs~VrI~C~  950 (1416)
T KOG3617|consen  880 YYEKAGVHAFEVFRMLKEYPKQIEQYVRRKRDESLYSWWGQYLESVGEMDAALSFYSSAKD---------YFSMVRIKCI  950 (1416)
T ss_pred             HHHhcCChHHHHHHHHHhChHHHHHHHHhccchHHHHHHHHHHhcccchHHHHHHHHHhhh---------hhhheeeEee
Confidence            77654321                       333333333333446778888887776543         4556677778


Q ss_pred             cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHH
Q 040371          155 CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIV  234 (410)
Q Consensus       155 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~  234 (410)
                      .|+.++|-++-++-.       |....-.|.+.|-..|++.+|..+|-+.      .++...|..|..++--++-..+..
T Consensus       951 qGk~~kAa~iA~esg-------d~AAcYhlaR~YEn~g~v~~Av~FfTrA------qafsnAIRlcKEnd~~d~L~nlal 1017 (1416)
T KOG3617|consen  951 QGKTDKAARIAEESG-------DKAACYHLARMYENDGDVVKAVKFFTRA------QAFSNAIRLCKENDMKDRLANLAL 1017 (1416)
T ss_pred             ccCchHHHHHHHhcc-------cHHHHHHHHHHhhhhHHHHHHHHHHHHH------HHHHHHHHHHHhcCHHHHHHHHHh
Confidence            899999999876643       5556777899999999999999999875      244555555555544333333311


Q ss_pred             hhccCC-----------CchHHHHHHHHHhcCChhHHHHH
Q 040371          235 NISRLM-----------GGDYVLLSNMYCYLKRWDTAENV  263 (410)
Q Consensus       235 ~~~~~~-----------~~~~~~l~~~~~~~g~~~~a~~~  263 (410)
                      -..+.+           +....-.+..|-++|.+.+|.++
T Consensus      1018 ~s~~~d~v~aArYyEe~g~~~~~AVmLYHkAGm~~kALel 1057 (1416)
T KOG3617|consen 1018 MSGGSDLVSAARYYEELGGYAHKAVMLYHKAGMIGKALEL 1057 (1416)
T ss_pred             hcCchhHHHHHHHHHHcchhhhHHHHHHHhhcchHHHHHH
Confidence            111111           11223455678888888888775

>KOG3785 consensus Uncharacterized conserved protein [Function unknown]

Probab=97.19  E-value=0.0075  Score=54.28  Aligned_cols=121  Identities=14%  Similarity=0.122  Sum_probs=68.8

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHH-HHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYG-AMVDL  187 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~-~li~~  187 (410)
                      --.+|.+.+.-..++++++-.+.....--..-|.+.| .+..|.+..|++.+|+++|-.+... .++ |..+|- .|.++
T Consensus       361 GRQsmAs~fFL~~qFddVl~YlnSi~sYF~NdD~Fn~-N~AQAk~atgny~eaEelf~~is~~-~ik-n~~~Y~s~LArC  437 (557)
T KOG3785|consen  361 GRQSMASYFFLSFQFDDVLTYLNSIESYFTNDDDFNL-NLAQAKLATGNYVEAEELFIRISGP-EIK-NKILYKSMLARC  437 (557)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchhhh-HHHHHHHHhcChHHHHHHHhhhcCh-hhh-hhHHHHHHHHHH
Confidence            3445555555556666666666666554333333333 3566777777777777777666531 222 334443 34466


Q ss_pred             HHhcCCHHHHHHHHHhCCCCCCHHHHHHHH-HHHHhcCchhHHHHH
Q 040371          188 LGRAGHIEEAYGLITSMTMEPDVVVWRALL-SACRTFKRLELGEVA  232 (410)
Q Consensus       188 ~~~~g~~~~A~~~~~~m~~~p~~~~~~~li-~~~~~~g~~~~a~~~  232 (410)
                      |.++++++-|.+++-++.-..+..+.-.+| .-|-+.+.+=-|-++
T Consensus       438 yi~nkkP~lAW~~~lk~~t~~e~fsLLqlIAn~CYk~~eFyyaaKA  483 (557)
T KOG3785|consen  438 YIRNKKPQLAWDMMLKTNTPSERFSLLQLIANDCYKANEFYYAAKA  483 (557)
T ss_pred             HHhcCCchHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            777777777777777764333444433333 346666666555555

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=97.14  E-value=0.37  Score=48.92  Aligned_cols=211  Identities=12%  Similarity=0.121  Sum_probs=132.0

Q ss_pred             HHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHH--HhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHH
Q 040371           17 VRNARFDEALRFFREMLSSKVEPDKFTFASVIYGC--ARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQM   94 (410)
Q Consensus        17 ~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~--~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~   94 (410)
                      ...+++.+|+....++.+.  .|| ..|..++.|+  .+.|..++|..+++.....+.. |..+...+-.+|...|+.++
T Consensus        20 ld~~qfkkal~~~~kllkk--~Pn-~~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~   95 (932)
T KOG2053|consen   20 LDSSQFKKALAKLGKLLKK--HPN-ALYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDE   95 (932)
T ss_pred             hhhHHHHHHHHHHHHHHHH--CCC-cHHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhH
Confidence            4567889999988888765  344 3455666666  5788899998887777665533 88888999999999999999


Q ss_pred             HHHHHHhccc--CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC----------CHHHHH
Q 040371           95 AKEVFDTVQR--NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCG----------LVEEGR  162 (410)
Q Consensus        95 A~~~f~~m~~--~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g----------~~~~a~  162 (410)
                      |..+|++..+  |+......+..+|++.+.+.+-.+.=-+|.+. ++-+.+.|-++++.....-          .+..|.
T Consensus        96 ~~~~Ye~~~~~~P~eell~~lFmayvR~~~yk~qQkaa~~LyK~-~pk~~yyfWsV~Slilqs~~~~~~~~~~i~l~LA~  174 (932)
T KOG2053|consen   96 AVHLYERANQKYPSEELLYHLFMAYVREKSYKKQQKAALQLYKN-FPKRAYYFWSVISLILQSIFSENELLDPILLALAE  174 (932)
T ss_pred             HHHHHHHHHhhCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCcccchHHHHHHHHHHhccCCcccccchhHHHHH
Confidence            9999998875  44444555666777777665444333333332 3445677777777665421          245677


Q ss_pred             HHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHh-C-CCCC--CHHHHHHHHHHHHhcCchhHHHHH
Q 040371          163 KYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITS-M-TMEP--DVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       163 ~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~-m-~~~p--~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      +.++.+.++.|-.-+..-.---...+...|++++|.+++.. . ...+  +...-+--+.-+...+++.+-.++
T Consensus       175 ~m~~~~l~~~gk~~s~aE~~Lyl~iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l  248 (932)
T KOG2053|consen  175 KMVQKLLEKKGKIESEAEIILYLLILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFEL  248 (932)
T ss_pred             HHHHHHhccCCccchHHHHHHHHHHHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHH
Confidence            77777776543111211112222335567888898888733 2 1111  333333444555566666666666

>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional

Probab=97.12  E-value=0.014  Score=54.65  Aligned_cols=102  Identities=15%  Similarity=0.004  Sum_probs=85.7

Q ss_pred             HHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChH
Q 040371           48 IYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAA  124 (410)
Q Consensus        48 l~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~  124 (410)
                      ...+...|+++.|.+.+.++++.. +.+...+..+..+|.+.|++++|...+++...  | +...|..+..+|...|+++
T Consensus         9 a~~a~~~~~~~~Ai~~~~~Al~~~-P~~~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~lg~~~   87 (356)
T PLN03088          9 AKEAFVDDDFALAVDLYTQAIDLD-PNNAELYADRAQANIKLGNFTEAVADANKAIELDPSLAKAYLRKGTACMKLEEYQ   87 (356)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHhCCHH
Confidence            455668899999999999999875 45788899999999999999999999998864  3 5668999999999999999


Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040371          125 DASAIFTKMEMFNVLPDSITFLGLLTAC  152 (410)
Q Consensus       125 ~A~~l~~~m~~~g~~p~~~t~~~ll~a~  152 (410)
                      +|+..|++...  +.|+...+...+..|
T Consensus        88 eA~~~~~~al~--l~P~~~~~~~~l~~~  113 (356)
T PLN03088         88 TAKAALEKGAS--LAPGDSRFTKLIKEC  113 (356)
T ss_pred             HHHHHHHHHHH--hCCCCHHHHHHHHHH
Confidence            99999999987  457666666666555

>PF12688 TPR_5: Tetratrico peptide repeat

Probab=97.11  E-value=0.022  Score=44.02  Aligned_cols=108  Identities=9%  Similarity=0.080  Sum_probs=71.7

Q ss_pred             HHHHHHHcCChHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCC-ChhHHHHHHHHHH
Q 040371          113 MISGVAIHGLAADASAIFTKMEMFNVLPD--SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP-QLEHYGAMVDLLG  189 (410)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~  189 (410)
                      +..++-..|+.++|+.+|++....|...+  ...+..+.+.+...|++++|..+|+.....+.-.+ +......+..++.
T Consensus         7 ~A~a~d~~G~~~~Ai~~Y~~Al~~gL~~~~~~~a~i~lastlr~LG~~deA~~~L~~~~~~~p~~~~~~~l~~f~Al~L~   86 (120)
T PF12688_consen    7 LAWAHDSLGREEEAIPLYRRALAAGLSGADRRRALIQLASTLRNLGRYDEALALLEEALEEFPDDELNAALRVFLALALY   86 (120)
T ss_pred             HHHHHHhcCCHHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHH
Confidence            44567778999999999999988876654  34566778888899999999999998876422111 1222223344677


Q ss_pred             hcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 040371          190 RAGHIEEAYGLITSMTMEPDVVVWRALLSACR  221 (410)
Q Consensus       190 ~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~  221 (410)
                      ..|+.++|...+-.. +.++...|.--|..|+
T Consensus        87 ~~gr~~eAl~~~l~~-la~~~~~y~ra~~~ya  117 (120)
T PF12688_consen   87 NLGRPKEALEWLLEA-LAETLPRYRRAIRFYA  117 (120)
T ss_pred             HCCCHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence            889999988776543 1234445555555543

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=97.11  E-value=0.0042  Score=56.96  Aligned_cols=253  Identities=10%  Similarity=0.007  Sum_probs=158.3

Q ss_pred             HHHHcCCHhHHHHHHHHHHHCCCCCCHH----HHHHHHHHHHhhCCHHHHHHHHHHHH--Hc--CCC-ccHHHHHHHHHH
Q 040371           15 GFVRNARFDEALRFFREMLSSKVEPDKF----TFASVIYGCARLGALNHAYWVHNLII--EK--KIE-LNFILSAALIDM   85 (410)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~~g~~pd~~----t~~~ll~a~~~~~~~~~a~~~~~~~~--~~--g~~-~~~~~~~~li~~   85 (410)
                      -+++.|+.+..+.+|+..++.|.. |..    .|..+-+||.-++++++|.++|..=+  ..  |-+ -.......|.+.
T Consensus        26 RLck~gdcraGv~ff~aA~qvGTe-Dl~tLSAIYsQLGNAyfyL~DY~kAl~yH~hDltlar~lgdklGEAKssgNLGNt  104 (639)
T KOG1130|consen   26 RLCKMGDCRAGVDFFKAALQVGTE-DLSTLSAIYSQLGNAYFYLKDYEKALKYHTHDLTLARLLGDKLGEAKSSGNLGNT  104 (639)
T ss_pred             HHHhccchhhhHHHHHHHHHhcch-HHHHHHHHHHHhcchhhhHhhHHHHHhhhhhhHHHHHHhcchhccccccccccch
Confidence            467899999999999999987733 443    46667788888999999999875322  11  100 012223344445


Q ss_pred             HHhcCCHHHHHHHHHh-cc------cC--ChhhHHHHHHHHHHcCC--------------------hHHHHHHHHHHHH-
Q 040371           86 YSKCGKIQMAKEVFDT-VQ------RN--DVSVWNAMISGVAIHGL--------------------AADASAIFTKMEM-  135 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~-m~------~~--~~~~~~~li~~~~~~g~--------------------~~~A~~l~~~m~~-  135 (410)
                      +--.|.+++|.-.-.+ +.      .+  ...++..+...|...|+                    ++.|.++|.+=++ 
T Consensus       105 lKv~G~fdeA~~cc~rhLd~areLgDrv~e~RAlYNlgnvYhakGk~~g~~~pee~g~f~~ev~~al~~Av~fy~eNL~l  184 (639)
T KOG1130|consen  105 LKVKGAFDEALTCCFRHLDFARELGDRVLESRALYNLGNVYHAKGKCTGLEAPEEKGAFNAEVTSALENAVKFYMENLEL  184 (639)
T ss_pred             hhhhcccchHHHHHHHHhHHHHHHhHHHhhhHHHhhhhhhhhhcccccCCCChhhcccccHHHHHHHHHHHHHHHHHHHH
Confidence            5556677776543322 11      11  12244445666655543                    2344455543222 


Q ss_pred             ---CCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHh---hhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC---
Q 040371          136 ---FNVL-PDSITFLGLLTACSHCGLVEEGRKYFDHM---RSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM---  204 (410)
Q Consensus       136 ---~g~~-p~~~t~~~ll~a~~~~g~~~~a~~~~~~m---~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m---  204 (410)
                         .|-. .-...|..|-+.|.-.|+++.|...++.-   .+.+|-... -..+..+..++.-.|+++.|.+.++..   
T Consensus       185 ~~~lgDr~aqGRa~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~L  264 (639)
T KOG1130|consen  185 SEKLGDRLAQGRAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNL  264 (639)
T ss_pred             HHHhhhHHhhcchhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHH
Confidence               1110 11234666666667789999999887753   233453322 357788888999999999998888765   


Q ss_pred             ----CCC-CCHHHHHHHHHHHHhcCchhHHHHH-------HHhhcc--CCCchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          205 ----TME-PDVVVWRALLSACRTFKRLELGEVA-------IVNISR--LMGGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       205 ----~~~-p~~~~~~~li~~~~~~g~~~~a~~~-------~~~~~~--~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                          +-+ ....+..+|-..|....+++.|+.+       ..++..  .....+-+|.++|...|..++|..+.+.-.
T Consensus       265 Aielg~r~vEAQscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~hl  342 (639)
T KOG1130|consen  265 AIELGNRTVEAQSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELHL  342 (639)
T ss_pred             HHHhcchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence                211 2455677888888888899999888       222222  123568889999999999999987766543

>PRK02603 photosystem I assembly protein Ycf3; Provisional

Probab=97.11  E-value=0.017  Score=48.01  Aligned_cols=61  Identities=13%  Similarity=0.136  Sum_probs=26.8

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPD--SITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      .|..+...|...|++++|...|++.......|+  ...+..+...+.+.|++++|...+....
T Consensus        37 ~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al   99 (172)
T PRK02603         37 VYYRDGMSAQADGEYAEALENYEEALKLEEDPNDRSYILYNMGIIYASNGEHDKALEYYHQAL   99 (172)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            334444444444455555554444443221111  1334444444455555555555555444

>PRK10153 DNA-binding transcriptional activator CadC; Provisional

Probab=97.07  E-value=0.061  Score=52.93  Aligned_cols=141  Identities=9%  Similarity=0.041  Sum_probs=92.9

Q ss_pred             cCCCccHHHHHHHHHHHHh--cCC---HHHHHHHHHhccc--CC-hhhHHHHHHHHHHcC--------ChHHHHHHHHHH
Q 040371           70 KKIELNFILSAALIDMYSK--CGK---IQMAKEVFDTVQR--ND-VSVWNAMISGVAIHG--------LAADASAIFTKM  133 (410)
Q Consensus        70 ~g~~~~~~~~~~li~~y~~--~g~---~~~A~~~f~~m~~--~~-~~~~~~li~~~~~~g--------~~~~A~~l~~~m  133 (410)
                      ...+.+...|...+.+...  .++   .+.|+.+|++..+  || ...|..+..+|....        +...+.+...+.
T Consensus       331 ~~~~~~~~Ay~~~lrg~~~~~~~~~~~~~~A~~lle~Ai~ldP~~a~a~A~la~~~~~~~~~~~~~~~~l~~a~~~~~~a  410 (517)
T PRK10153        331 QGLPHQGAALTLFYQAHHYLNSGDAKSLNKASDLLEEILKSEPDFTYAQAEKALADIVRHSQQPLDEKQLAALSTELDNI  410 (517)
T ss_pred             ccCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHh
Confidence            3456777888888776543  333   7789999998875  43 345555444443321        123334444433


Q ss_pred             HHC-CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHH
Q 040371          134 EMF-NVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVV  211 (410)
Q Consensus       134 ~~~-g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~  211 (410)
                      ... ....+...+..+.-.....|++++|...++++.+   +.|+...|..+...+...|+.++|.+.+++. .+.|...
T Consensus       411 ~al~~~~~~~~~~~ala~~~~~~g~~~~A~~~l~rAl~---L~ps~~a~~~lG~~~~~~G~~~eA~~~~~~A~~L~P~~p  487 (517)
T PRK10153        411 VALPELNVLPRIYEILAVQALVKGKTDEAYQAINKAID---LEMSWLNYVLLGKVYELKGDNRLAADAYSTAFNLRPGEN  487 (517)
T ss_pred             hhcccCcCChHHHHHHHHHHHhcCCHHHHHHHHHHHHH---cCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCc
Confidence            332 1233456676665666677999999999999884   3578889999999999999999999998875 4555544


Q ss_pred             HH
Q 040371          212 VW  213 (410)
Q Consensus       212 ~~  213 (410)
                      +|
T Consensus       488 t~  489 (517)
T PRK10153        488 TL  489 (517)
T ss_pred             hH
Confidence            44

>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]

Probab=97.07  E-value=0.14  Score=49.02  Aligned_cols=208  Identities=15%  Similarity=0.110  Sum_probs=145.5

Q ss_pred             HHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhc---CCHHHHHHHHHhcccC----ChhhHHHHHHHHHHcCChHHHHHH
Q 040371           57 LNHAYWVHNLIIEKKIELNFILSAALIDMYSKC---GKIQMAKEVFDTVQRN----DVSVWNAMISGVAIHGLAADASAI  129 (410)
Q Consensus        57 ~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~---g~~~~A~~~f~~m~~~----~~~~~~~li~~~~~~g~~~~A~~l  129 (410)
                      -+++..++++.+..-...+..+|.++.+-=-..   ...+.....++++...    -..+|-..++.-.+..-.+.|..+
T Consensus       309 t~e~~~~yEr~I~~l~~~~~~Ly~~~a~~eE~~~~~n~~~~~~~~~~~ll~~~~~~~tLv~~~~mn~irR~eGlkaaR~i  388 (656)
T KOG1914|consen  309 TDEAASIYERAIEGLLKENKLLYFALADYEESRYDDNKEKKVHEIYNKLLKIEDIDLTLVYCQYMNFIRRAEGLKAARKI  388 (656)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHhcccchhhhhHHHHHHHHhhhccCCceehhHHHHHHHHhhhHHHHHHH
Confidence            356677777776654445666666665422111   1355666666666532    234788888888888889999999


Q ss_pred             HHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC---C
Q 040371          130 FTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM---T  205 (410)
Q Consensus       130 ~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m---~  205 (410)
                      |.+..+.+..+ +....++++.-++ .++..-|.++|+.-.+++|-  ++.--...++-+...++-..|..+|++.   .
T Consensus       389 F~kaR~~~r~~hhVfVa~A~mEy~c-skD~~~AfrIFeLGLkkf~d--~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~  465 (656)
T KOG1914|consen  389 FKKAREDKRTRHHVFVAAALMEYYC-SKDKETAFRIFELGLKKFGD--SPEYVLKYLDFLSHLNDDNNARALFERVLTSV  465 (656)
T ss_pred             HHHHhhccCCcchhhHHHHHHHHHh-cCChhHHHHHHHHHHHhcCC--ChHHHHHHHHHHHHhCcchhHHHHHHHHHhcc
Confidence            99999998888 6666777776655 57889999999997766553  3445568889999999999999999998   2


Q ss_pred             CCCC--HHHHHHHHHHHHhcCchhHHHHHHH---hhcc----CCCchHHHHHHHHHhcCChhHHHHHHHHH
Q 040371          206 MEPD--VVVWRALLSACRTFKRLELGEVAIV---NISR----LMGGDYVLLSNMYCYLKRWDTAENVREIM  267 (410)
Q Consensus       206 ~~p~--~~~~~~li~~~~~~g~~~~a~~~~~---~~~~----~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  267 (410)
                      +.||  ..+|..+|.-=...|++..+.++-.   ...|    .....-..+++.|.-.+....-..=++.|
T Consensus       466 l~~~ks~~Iw~r~l~yES~vGdL~si~~lekR~~~af~~~qe~~~~~~~~~v~RY~~~d~~~c~~~elk~l  536 (656)
T KOG1914|consen  466 LSADKSKEIWDRMLEYESNVGDLNSILKLEKRRFTAFPADQEYEGNETALFVDRYGILDLYPCSLDELKFL  536 (656)
T ss_pred             CChhhhHHHHHHHHHHHHhcccHHHHHHHHHHHHHhcchhhcCCCChHHHHHHHHhhcccccccHHHHHhh
Confidence            3443  4789999999999999999998811   1112    11234455677777777766555545444

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=97.04  E-value=0.049  Score=52.96  Aligned_cols=222  Identities=15%  Similarity=0.137  Sum_probs=132.6

Q ss_pred             HHHHHHHHHHHcCC--HhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNAR--FDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         8 ~~n~li~~~~~~g~--~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      .++..=.+|.+-.+  +-+.+.-+++|++.|-.||....   ...|+-.|.+.+|.++|.   +.|..      |-.+.|
T Consensus       600 ~f~~ARkAY~rVRdl~~L~li~EL~~~k~rge~P~~iLl---A~~~Ay~gKF~EAAklFk---~~G~e------nRAlEm  667 (1081)
T KOG1538|consen  600 DFETARKAYIRVRDLRYLELISELEERKKRGETPNDLLL---ADVFAYQGKFHEAAKLFK---RSGHE------NRALEM  667 (1081)
T ss_pred             hhHHHHHHHHHHhccHHHHHHHHHHHHHhcCCCchHHHH---HHHHHhhhhHHHHHHHHH---HcCch------hhHHHH
Confidence            35555567766554  34555566788888888887643   456777889999888875   34432      345667


Q ss_pred             HHhcCCHHHHHHHHHhcc---------cC-----ChhhHHHHHHHHHHcCChHHHHHHHHH-----H-HHCCCC---CCH
Q 040371           86 YSKCGKIQMAKEVFDTVQ---------RN-----DVSVWNAMISGVAIHGLAADASAIFTK-----M-EMFNVL---PDS  142 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~---------~~-----~~~~~~~li~~~~~~g~~~~A~~l~~~-----m-~~~g~~---p~~  142 (410)
                      |.....+|.|.++...-.         ++     |+.-=.+....+...|+.++|..+.-+     | .+-+-+   .+.
T Consensus       668 yTDlRMFD~aQE~~~~g~~~eKKmL~RKRA~WAr~~kePkaAAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~~er  747 (1081)
T KOG1538|consen  668 YTDLRMFDYAQEFLGSGDPKEKKMLIRKRADWARNIKEPKAAAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDKAER  747 (1081)
T ss_pred             HHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHhhhcCCcHHHHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcchhhh
Confidence            777777777777664321         11     111112233344456666666654321     1 111112   234


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCCHHHHHHHHHHHH
Q 040371          143 ITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMT-MEPDVVVWRALLSACR  221 (410)
Q Consensus       143 ~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~~~~~~li~~~~  221 (410)
                      .+...+..-+.+...+..|-++|..|-+          ...++++....+++++|.++-++.| ..||+..  ....-++
T Consensus       748 e~l~~~a~ylk~l~~~gLAaeIF~k~gD----------~ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~--pyaqwLA  815 (1081)
T KOG1538|consen  748 EPLLLCATYLKKLDSPGLAAEIFLKMGD----------LKSLVQLHVETQRWDEAFALAEKHPEFKDDVYM--PYAQWLA  815 (1081)
T ss_pred             hHHHHHHHHHhhccccchHHHHHHHhcc----------HHHHhhheeecccchHhHhhhhhCccccccccc--hHHHHhh
Confidence            4555555556677778888899988763          3467888999999999999999884 4455432  1222234


Q ss_pred             hcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          222 TFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       222 ~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      ...++++|.+                  +|.++|+-.+|.++++++....
T Consensus       816 E~DrFeEAqk------------------AfhkAGr~~EA~~vLeQLtnna  847 (1081)
T KOG1538|consen  816 ENDRFEEAQK------------------AFHKAGRQREAVQVLEQLTNNA  847 (1081)
T ss_pred             hhhhHHHHHH------------------HHHHhcchHHHHHHHHHhhhhh
Confidence            4445555543                  3556667777777776665443

>CHL00033 ycf3 photosystem I assembly protein Ycf3

Probab=97.01  E-value=0.018  Score=47.62  Aligned_cols=61  Identities=11%  Similarity=0.070  Sum_probs=29.4

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLP--DSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p--~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      .|..+...+...|++++|+..|++.......|  ...++..+...+.+.|+.++|...++...
T Consensus        37 ~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al   99 (168)
T CHL00033         37 TYYRDGMSAQSEGEYAEALQNYYEAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFQAL   99 (168)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhccccchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34444444555555555555555554332111  11244445555555555555555555544

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=96.95  E-value=0.24  Score=43.65  Aligned_cols=57  Identities=16%  Similarity=0.028  Sum_probs=38.6

Q ss_pred             HHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHH---HHHHHHHHhcCCHHHHHHHHHhccc
Q 040371           47 VIYGCARLGALNHAYWVHNLIIEKKIELNFILS---AALIDMYSKCGKIQMAKEVFDTVQR  104 (410)
Q Consensus        47 ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~---~~li~~y~~~g~~~~A~~~f~~m~~  104 (410)
                      ....+...|+++.|.+.|+.+...-..+ ....   -.+..+|.+.+++++|...|++..+
T Consensus        38 ~A~~~~~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~   97 (243)
T PRK10866         38 TAQQKLQDGNWKQAITQLEALDNRYPFG-PYSQQVQLDLIYAYYKNADLPLAQAAIDRFIR   97 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHhCCCC-hHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence            4444456788888888888887753222 2332   3456677888888888888887753

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.94  E-value=0.072  Score=46.26  Aligned_cols=140  Identities=15%  Similarity=0.063  Sum_probs=67.2

Q ss_pred             HhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371           22 FDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDT  101 (410)
Q Consensus        22 ~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~  101 (410)
                      .+..+++|++=.       .+...+++...-..+.+.-...++...++...+.++.....|+.+-.+.|+.+.|...|++
T Consensus       165 ~ESsv~lW~KRl-------~~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~  237 (366)
T KOG2796|consen  165 EESSIRLWRKRL-------GRVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQD  237 (366)
T ss_pred             hhhHHHHHHHHH-------HHHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHH
Confidence            345555555432       2334445555555555555555555555555455566666666666666666666666664


Q ss_pred             cccC----ChhhH-----HHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          102 VQRN----DVSVW-----NAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       102 m~~~----~~~~~-----~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      ..+.    |-...     -.+...|.-.+++.+|...|.+..... ..|.+..+.-.-...-.|+..+|.+..+.|.
T Consensus       238 vek~~~kL~~~q~~~~V~~n~a~i~lg~nn~a~a~r~~~~i~~~D-~~~~~a~NnKALcllYlg~l~DAiK~~e~~~  313 (366)
T KOG2796|consen  238 VEKVTQKLDGLQGKIMVLMNSAFLHLGQNNFAEAHRFFTEILRMD-PRNAVANNNKALCLLYLGKLKDALKQLEAMV  313 (366)
T ss_pred             HHHHHhhhhccchhHHHHhhhhhheecccchHHHHHHHhhccccC-CCchhhhchHHHHHHHHHHHHHHHHHHHHHh
Confidence            4321    11111     122233444455555555555554432 1122222322222233455666666666655

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=96.91  E-value=0.0075  Score=41.26  Aligned_cols=49  Identities=18%  Similarity=0.201  Sum_probs=24.7

Q ss_pred             hCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           54 LGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        54 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      .|++++|.++++.+.+.. +.+..+...+..+|.+.|++++|.++++++.
T Consensus         4 ~~~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~   52 (68)
T PF14559_consen    4 QGDYDEAIELLEKALQRN-PDNPEARLLLAQCYLKQGQYDEAEELLERLL   52 (68)
T ss_dssp             TTHHHHHHHHHHHHHHHT-TTSHHHHHHHHHHHHHTT-HHHHHHHHHCCH
T ss_pred             ccCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            445555555555554442 2244445555555555555555555555554

...

>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=96.89  E-value=0.015  Score=45.34  Aligned_cols=51  Identities=16%  Similarity=0.296  Sum_probs=36.1

Q ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHH
Q 040371          137 NVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDL  187 (410)
Q Consensus       137 g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~  187 (410)
                      ...|+..+..+++.+|+..|++..|.++.+...+.|+++.+...|..|+.-
T Consensus        47 pl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~W   97 (126)
T PF12921_consen   47 PLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLEW   97 (126)
T ss_pred             CCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            456677777777777777777777777777777777776666677666654

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.87  E-value=0.016  Score=51.10  Aligned_cols=98  Identities=20%  Similarity=0.233  Sum_probs=80.1

Q ss_pred             HHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCH
Q 040371          117 VAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHI  194 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~  194 (410)
                      ..+.+++++|+..|.+.++.  .| |.+-|..=..+|++.|.++.|++--+...   .+.|. ..+|..|-.+|...|++
T Consensus        91 ~m~~~~Y~eAv~kY~~AI~l--~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al---~iDp~yskay~RLG~A~~~~gk~  165 (304)
T KOG0553|consen   91 LMKNKDYQEAVDKYTEAIEL--DPTNAVYYCNRAAAYSKLGEYEDAVKDCESAL---SIDPHYSKAYGRLGLAYLALGKY  165 (304)
T ss_pred             HHHhhhHHHHHHHHHHHHhc--CCCcchHHHHHHHHHHHhcchHHHHHHHHHHH---hcChHHHHHHHHHHHHHHccCcH
Confidence            56689999999999999884  55 66778888899999999999998777766   33444 67899999999999999


Q ss_pred             HHHHHHHHhC-CCCCCHHHHHHHHHH
Q 040371          195 EEAYGLITSM-TMEPDVVVWRALLSA  219 (410)
Q Consensus       195 ~~A~~~~~~m-~~~p~~~~~~~li~~  219 (410)
                      ++|.+.|++. .+.|+-.+|-.=|..
T Consensus       166 ~~A~~aykKaLeldP~Ne~~K~nL~~  191 (304)
T KOG0553|consen  166 EEAIEAYKKALELDPDNESYKSNLKI  191 (304)
T ss_pred             HHHHHHHHhhhccCCCcHHHHHHHHH
Confidence            9999999886 788988777665544

>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A

Probab=96.86  E-value=0.0054  Score=41.99  Aligned_cols=59  Identities=17%  Similarity=0.215  Sum_probs=28.7

Q ss_pred             cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHH
Q 040371          155 CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRA  215 (410)
Q Consensus       155 ~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~  215 (410)
                      .|++++|.++|+.+...  .+-+...+..+..+|.+.|++++|..+++++ ...|+...|..
T Consensus         4 ~~~~~~A~~~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~~~~   63 (68)
T PF14559_consen    4 QGDYDEAIELLEKALQR--NPDNPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDNPEYQQ   63 (68)
T ss_dssp             TTHHHHHHHHHHHHHHH--TTTSHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCHHHHHH
Confidence            45555555555555432  1123444555555555555555555555555 33344433333

...

>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex

Probab=96.84  E-value=0.38  Score=44.20  Aligned_cols=107  Identities=15%  Similarity=0.128  Sum_probs=72.1

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLL  188 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~  188 (410)
                      +.+..|.-+...|+...|.++-++.+    -||..-|-..+.+++..+++++-.++-..  ++     ++..|...++.+
T Consensus       179 Sl~~Ti~~li~~~~~k~A~kl~k~Fk----v~dkrfw~lki~aLa~~~~w~eL~~fa~s--kK-----sPIGyepFv~~~  247 (319)
T PF04840_consen  179 SLNDTIRKLIEMGQEKQAEKLKKEFK----VPDKRFWWLKIKALAENKDWDELEKFAKS--KK-----SPIGYEPFVEAC  247 (319)
T ss_pred             CHHHHHHHHHHCCCHHHHHHHHHHcC----CcHHHHHHHHHHHHHhcCCHHHHHHHHhC--CC-----CCCChHHHHHHH
Confidence            44555666677787777777766552    46777777788888888888776665432  11     346677888888


Q ss_pred             HhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHH
Q 040371          189 GRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAI  233 (410)
Q Consensus       189 ~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~  233 (410)
                      .+.|+..+|..++.+++   +    ..-+..|.+.|++.+|.+..
T Consensus       248 ~~~~~~~eA~~yI~k~~---~----~~rv~~y~~~~~~~~A~~~A  285 (319)
T PF04840_consen  248 LKYGNKKEASKYIPKIP---D----EERVEMYLKCGDYKEAAQEA  285 (319)
T ss_pred             HHCCCHHHHHHHHHhCC---h----HHHHHHHHHCCCHHHHHHHH
Confidence            88888888888877753   2    23445566777777776663

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

>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=96.80  E-value=0.018  Score=44.91  Aligned_cols=83  Identities=18%  Similarity=0.267  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHHHHh--------------hhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC----
Q 040371          143 ITFLGLLTACSHCGLVEEGRKYFDHM--------------RSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM----  204 (410)
Q Consensus       143 ~t~~~ll~a~~~~g~~~~a~~~~~~m--------------~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m----  204 (410)
                      .++..++.++++.|+++....+.+..              .....+.|+..+..+++.+|+..|++..|+++++..    
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            44444455555555554444444322              223356788889999999999999999998888776    


Q ss_pred             CCCCCHHHHHHHHHHHHhcCc
Q 040371          205 TMEPDVVVWRALLSACRTFKR  225 (410)
Q Consensus       205 ~~~p~~~~~~~li~~~~~~g~  225 (410)
                      ++.-+...|..|+.=+...-+
T Consensus        83 ~I~i~~~~W~~Ll~W~~v~s~  103 (126)
T PF12921_consen   83 PIPIPKEFWRRLLEWAYVLSS  103 (126)
T ss_pred             CCCCCHHHHHHHHHHHHHhcC
Confidence            666678889888876554443

The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.77  E-value=0.22  Score=49.16  Aligned_cols=218  Identities=13%  Similarity=0.080  Sum_probs=112.5

Q ss_pred             CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc-CCCc--------cHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChh
Q 040371           38 EPDKFTFASVIYGCARLGALNHAYWVHNLIIEK-KIEL--------NFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVS  108 (410)
Q Consensus        38 ~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~-g~~~--------~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~  108 (410)
                      .|.+..|..+.......-+++.|+..|-+.... |++.        +...-.+=+.+|  -|++++|++++-+|..+|..
T Consensus       689 nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~--~g~feeaek~yld~drrDLA  766 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAF--YGEFEEAEKLYLDADRRDLA  766 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhh--hcchhHhhhhhhccchhhhh
Confidence            566777777776666666666666655444322 2211        111112223333  37777777777777766542


Q ss_pred             hHHHHHHHHHHcCChHHHHHHHH----------------HHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHH------
Q 040371          109 VWNAMISGVAIHGLAADASAIFT----------------KMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFD------  166 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~----------------~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~------  166 (410)
                           |..+.+.|++-...++++                .|-+  .-.+...|......|..+|+.+.-.+.+-      
T Consensus       767 -----ielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~--~fa~~~~We~A~~yY~~~~~~e~~~ecly~le~f~  839 (1189)
T KOG2041|consen  767 -----IELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGE--TFAEMMEWEEAAKYYSYCGDTENQIECLYRLELFG  839 (1189)
T ss_pred             -----HHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHH--HHHHHHHHHHHHHHHHhccchHhHHHHHHHHHhhh
Confidence                 222333333333333222                1111  00111222333334444443332222111      


Q ss_pred             Hhhh-hcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCc---
Q 040371          167 HMRS-RYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGG---  242 (410)
Q Consensus       167 ~m~~-~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~---  242 (410)
                      .+.. ...++-+....-.|.+++.+.|.-++|.+.+-+-+..      .+.+..|...+++.+|.++..+..-+...   
T Consensus       840 ~LE~la~~Lpe~s~llp~~a~mf~svGMC~qAV~a~Lr~s~p------kaAv~tCv~LnQW~~avelaq~~~l~qv~tli  913 (1189)
T KOG2041|consen  840 ELEVLARTLPEDSELLPVMADMFTSVGMCDQAVEAYLRRSLP------KAAVHTCVELNQWGEAVELAQRFQLPQVQTLI  913 (1189)
T ss_pred             hHHHHHHhcCcccchHHHHHHHHHhhchHHHHHHHHHhccCc------HHHHHHHHHHHHHHHHHHHHHhccchhHHHHH
Confidence            1110 0023445667778889999999999998877666422      13455677777777776663332222111   


Q ss_pred             -----------hHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          243 -----------DYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       243 -----------~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                                 -..--|..+-++|+.-+|.+++.+|.++
T Consensus       914 ak~aaqll~~~~~~eaIe~~Rka~~~~daarll~qmae~  952 (1189)
T KOG2041|consen  914 AKQAAQLLADANHMEAIEKDRKAGRHLDAARLLSQMAER  952 (1189)
T ss_pred             HHHHHHHHhhcchHHHHHHhhhcccchhHHHHHHHHhHH
Confidence                       1223467788999999999988888654

>KOG2053 consensus Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton]

Probab=96.75  E-value=0.36  Score=48.99  Aligned_cols=193  Identities=16%  Similarity=0.148  Sum_probs=129.9

Q ss_pred             HHHHHHHHHH--HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            8 SWNSMIGGFV--RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         8 ~~n~li~~~~--~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      .|...+.++.  |.|+.++|..+++.....+.. |..|...+-..|-..+.++++..+|+++.+.  -|+......+..+
T Consensus        43 ~~a~vLkaLsl~r~gk~~ea~~~Le~~~~~~~~-D~~tLq~l~~~y~d~~~~d~~~~~Ye~~~~~--~P~eell~~lFma  119 (932)
T KOG2053|consen   43 LYAKVLKALSLFRLGKGDEALKLLEALYGLKGT-DDLTLQFLQNVYRDLGKLDEAVHLYERANQK--YPSEELLYHLFMA  119 (932)
T ss_pred             HHHHHHHHHHHHHhcCchhHHHHHhhhccCCCC-chHHHHHHHHHHHHHhhhhHHHHHHHHHHhh--CCcHHHHHHHHHH
Confidence            4555666654  789999999888887655433 7889999999999999999999999999886  4567888888889


Q ss_pred             HHhcCCHHH----HHHHHHhcccCChhhHHHHHHHHHHc-CC---------hHHHHHHHHHHHHCC-CCCCHHHHHHHHH
Q 040371           86 YSKCGKIQM----AKEVFDTVQRNDVSVWNAMISGVAIH-GL---------AADASAIFTKMEMFN-VLPDSITFLGLLT  150 (410)
Q Consensus        86 y~~~g~~~~----A~~~f~~m~~~~~~~~~~li~~~~~~-g~---------~~~A~~l~~~m~~~g-~~p~~~t~~~ll~  150 (410)
                      |.+.+++.+    |.+++...+++--.-|+.+ +.+.+. ..         ..-|...++.+.+.+ -.-+..-...-+.
T Consensus       120 yvR~~~yk~qQkaa~~LyK~~pk~~yyfWsV~-Slilqs~~~~~~~~~~i~l~LA~~m~~~~l~~~gk~~s~aE~~Lyl~  198 (932)
T KOG2053|consen  120 YVREKSYKKQQKAALQLYKNFPKRAYYFWSVI-SLILQSIFSENELLDPILLALAEKMVQKLLEKKGKIESEAEIILYLL  198 (932)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCcccchHHHHH-HHHHHhccCCcccccchhHHHHHHHHHHHhccCCccchHHHHHHHHH
Confidence            999888754    6667776666555566643 333332 11         224556666666554 2112222333334


Q ss_pred             HHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          151 ACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       151 a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      .....|..++|..++..-....-...+...-+--++.+...+++.+..++-.++
T Consensus       199 iL~~~~k~~eal~~l~~~la~~l~~~~~~l~~~~~dllk~l~~w~~l~~l~~~L  252 (932)
T KOG2053|consen  199 ILELQGKYQEALEFLAITLAEKLTSANLYLENKKLDLLKLLNRWQELFELSSRL  252 (932)
T ss_pred             HHHhcccHHHHHHHHHHHHHHhccccchHHHHHHHHHHHHhcChHHHHHHHHHH
Confidence            456788899999999443222122334445556778888999998876665555

>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A

Probab=96.71  E-value=0.12  Score=46.79  Aligned_cols=158  Identities=10%  Similarity=0.041  Sum_probs=77.4

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHc----CCCcc-HHHHHHHHHHHHhcCCHHHHHHHHHhccc-------CC--hhh
Q 040371           44 FASVIYGCARLGALNHAYWVHNLIIEK----KIELN-FILSAALIDMYSKCGKIQMAKEVFDTVQR-------ND--VSV  109 (410)
Q Consensus        44 ~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~~~~-~~~~~~li~~y~~~g~~~~A~~~f~~m~~-------~~--~~~  109 (410)
                      |.-..+.|...+++++|.+.|.+....    +-+.+ ...|.....+|.+. ++++|...+++..+       ++  ...
T Consensus        38 y~~Aa~~fk~~~~~~~A~~ay~kAa~~~~~~~~~~~Aa~~~~~Aa~~~k~~-~~~~Ai~~~~~A~~~y~~~G~~~~aA~~  116 (282)
T PF14938_consen   38 YEKAANCFKLAKDWEKAAEAYEKAADCYEKLGDKFEAAKAYEEAANCYKKG-DPDEAIECYEKAIEIYREAGRFSQAAKC  116 (282)
T ss_dssp             HHHHHHHHHHTT-CHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHCT-HHHHHHH
T ss_pred             HHHHHHHHHHHhccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhh-CHHHHHHHHHHHHHHHHhcCcHHHHHHH
Confidence            334444455555555555555544321    11111 12223333334333 55555555544321       11  123


Q ss_pred             HHHHHHHHHHc-CChHHHHHHHHHHHHC----CCCCC--HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCC-----CC
Q 040371          110 WNAMISGVAIH-GLAADASAIFTKMEMF----NVLPD--SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQ-----PQ  177 (410)
Q Consensus       110 ~~~li~~~~~~-g~~~~A~~l~~~m~~~----g~~p~--~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~-----~~  177 (410)
                      +..+...|-.. |++++|++.|++..+.    | .+.  ...+..+...+.+.|++++|.++|++.... ...     .+
T Consensus       117 ~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~-~l~~~l~~~~  194 (282)
T PF14938_consen  117 LKELAEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKK-CLENNLLKYS  194 (282)
T ss_dssp             HHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHT-CCCHCTTGHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH-hhcccccchh
Confidence            44455566666 7788888777766542    2 221  234556667777888888888888876643 111     11


Q ss_pred             h-hHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          178 L-EHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       178 ~-~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      . ..+-..+-++...|++..|.+.+++.
T Consensus       195 ~~~~~l~a~l~~L~~~D~v~A~~~~~~~  222 (282)
T PF14938_consen  195 AKEYFLKAILCHLAMGDYVAARKALERY  222 (282)
T ss_dssp             HHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            1 12333344556667777777777765

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=96.68  E-value=0.14  Score=48.90  Aligned_cols=213  Identities=11%  Similarity=0.031  Sum_probs=112.9

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChh----------hHHHH
Q 040371           44 FASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVS----------VWNAM  113 (410)
Q Consensus        44 ~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~----------~~~~l  113 (410)
                      ...+.++.-+..+++.+.+-+.......  .+..-++....+|...|.+......-+.-.+.+-.          +..-+
T Consensus       227 ek~lgnaaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~rad~klIak~~~r~  304 (539)
T KOG0548|consen  227 EKELGNAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGRELRADYKLIAKALARL  304 (539)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHHHHHHHHHHHHHHHh
Confidence            4456666666777777777777777664  56666677777777777776665554443332111          12223


Q ss_pred             HHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChh-HHHHHHHHHHhcC
Q 040371          114 ISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLE-HYGAMVDLLGRAG  192 (410)
Q Consensus       114 i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~-~~~~li~~~~~~g  192 (410)
                      -.+|.+.++++.|+..|.+.......||..+-         ....+++........   -+.|... ---.-...+.+.|
T Consensus       305 g~a~~k~~~~~~ai~~~~kaLte~Rt~~~ls~---------lk~~Ek~~k~~e~~a---~~~pe~A~e~r~kGne~Fk~g  372 (539)
T KOG0548|consen  305 GNAYTKREDYEGAIKYYQKALTEHRTPDLLSK---------LKEAEKALKEAERKA---YINPEKAEEEREKGNEAFKKG  372 (539)
T ss_pred             hhhhhhHHhHHHHHHHHHHHhhhhcCHHHHHH---------HHHHHHHHHHHHHHH---hhChhHHHHHHHHHHHHHhcc
Confidence            34566667777777777776555444433211         112222222222211   1122210 0011133455566


Q ss_pred             CHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHH
Q 040371          193 HIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIM  267 (410)
Q Consensus       193 ~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  267 (410)
                      ++.+|.+.+.++ ...| |...|..-..+|.+.|++..|..-   ..+++|.....|.-=..++.-..+|++|.+.|.+-
T Consensus       373 dy~~Av~~YteAIkr~P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay~ea  452 (539)
T KOG0548|consen  373 DYPEAVKHYTEAIKRDPEDARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAYQEA  452 (539)
T ss_pred             CHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            666666666665 3334 345565555666666666666554   34445555555555455555556666666666554


Q ss_pred             HhC
Q 040371          268 KKK  270 (410)
Q Consensus       268 ~~~  270 (410)
                      .+.
T Consensus       453 le~  455 (539)
T KOG0548|consen  453 LEL  455 (539)
T ss_pred             Hhc
Confidence            443

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

Probab=96.66  E-value=0.84  Score=45.71  Aligned_cols=341  Identities=14%  Similarity=0.075  Sum_probs=171.2

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHH-hhCCHHHHHHHHHHHHHc--CC--CccHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEP-DKFTFASVIYGCA-RLGALNHAYWVHNLIIEK--KI--ELNFILSAA   81 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~-~~~~~~~a~~~~~~~~~~--g~--~~~~~~~~~   81 (410)
                      .|+.+-..|+-.|.-..|+.+.+.-....-.| |...+-..-..|. +.+.++++..+-.+++..  +.  ......+-.
T Consensus       359 ~w~~~als~saag~~s~Av~ll~~~~~~~~~ps~~s~~Lmasklc~e~l~~~eegldYA~kai~~~~~~~~~l~~~~~l~  438 (799)
T KOG4162|consen  359 RWYQLALSYSAAGSDSKAVNLLRESLKKSEQPSDISVLLMASKLCIERLKLVEEGLDYAQKAISLLGGQRSHLKPRGYLF  438 (799)
T ss_pred             HHHHHHHHHHHhccchHHHHHHHhhcccccCCCcchHHHHHHHHHHhchhhhhhHHHHHHHHHHHhhhhhhhhhhhHHHH
Confidence            35555555555555555555554433221113 3333333334443 445566666665555552  11  111223333


Q ss_pred             HHHHHHhc----C-------CHHHHHHHHHhccc-----CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHH
Q 040371           82 LIDMYSKC----G-------KIQMAKEVFDTVQR-----NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITF  145 (410)
Q Consensus        82 li~~y~~~----g-------~~~~A~~~f~~m~~-----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~  145 (410)
                      +.-+|...    .       ...++.+.+++..+     |++.-|-+  --|+..++.+.|++..++..+.+-+-+...+
T Consensus       439 lGi~y~~~A~~a~~~seR~~~h~kslqale~av~~d~~dp~~if~la--lq~A~~R~l~sAl~~~~eaL~l~~~~~~~~w  516 (799)
T KOG4162|consen  439 LGIAYGFQARQANLKSERDALHKKSLQALEEAVQFDPTDPLVIFYLA--LQYAEQRQLTSALDYAREALALNRGDSAKAW  516 (799)
T ss_pred             HHHHHHhHhhcCCChHHHHHHHHHHHHHHHHHHhcCCCCchHHHHHH--HHHHHHHhHHHHHHHHHHHHHhcCCccHHHH
Confidence            33333321    1       12344555555432     23333322  3366778899999999998887666677777


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhhhhcCCCC------------------ChhHHHHHHHHHHh---------cC------
Q 040371          146 LGLLTACSHCGLVEEGRKYFDHMRSRYSIQP------------------QLEHYGAMVDLLGR---------AG------  192 (410)
Q Consensus       146 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~------------------~~~~~~~li~~~~~---------~g------  192 (410)
                      ..+.-.++..+++.+|+.+.+.....+|...                  ...|...+++.+-.         .|      
T Consensus       517 hLLALvlSa~kr~~~Al~vvd~al~E~~~N~~l~~~~~~i~~~~~~~e~~l~t~~~~L~~we~~~~~q~~~~~g~~~~lk  596 (799)
T KOG4162|consen  517 HLLALVLSAQKRLKEALDVVDAALEEFGDNHVLMDGKIHIELTFNDREEALDTCIHKLALWEAEYGVQQTLDEGKLLRLK  596 (799)
T ss_pred             HHHHHHHhhhhhhHHHHHHHHHHHHHhhhhhhhchhhhhhhhhcccHHHHHHHHHHHHHHHHhhhhHhhhhhhhhhhhhh
Confidence            7777777888888888888887766554410                  11222223322220         00      


Q ss_pred             --------CHHHHHHHHHh-----------C------C---CC--CC------HHHHHHHHHHHHhcCchhHHHHH---H
Q 040371          193 --------HIEEAYGLITS-----------M------T---ME--PD------VVVWRALLSACRTFKRLELGEVA---I  233 (410)
Q Consensus       193 --------~~~~A~~~~~~-----------m------~---~~--p~------~~~~~~li~~~~~~g~~~~a~~~---~  233 (410)
                              +..+|....++           +      +   ..  |+      ...|......+...++.++|...   .
T Consensus       597 ~~l~la~~q~~~a~s~sr~ls~l~a~~~~~~~se~~Lp~s~~~~~~~~~~~~~~~lwllaa~~~~~~~~~~~a~~CL~Ea  676 (799)
T KOG4162|consen  597 AGLHLALSQPTDAISTSRYLSSLVASQLKSAGSELKLPSSTVLPGPDSLWYLLQKLWLLAADLFLLSGNDDEARSCLLEA  676 (799)
T ss_pred             cccccCcccccccchhhHHHHHHHHhhhhhcccccccCcccccCCCCchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHH
Confidence                    11111111000           0      0   11  22      23355555667788888888766   4


Q ss_pred             HhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHH
Q 040371          234 VNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQR  313 (410)
Q Consensus       234 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  313 (410)
                      .++.|..+..|......+...|.+++|.+.|.....-+  |+.--+...+...+  +-.|   ++...+...++.    .
T Consensus       677 ~~~~~l~~~~~~~~G~~~~~~~~~~EA~~af~~Al~ld--P~hv~s~~Ala~~l--le~G---~~~la~~~~~L~----d  745 (799)
T KOG4162|consen  677 SKIDPLSASVYYLRGLLLEVKGQLEEAKEAFLVALALD--PDHVPSMTALAELL--LELG---SPRLAEKRSLLS----D  745 (799)
T ss_pred             HhcchhhHHHHHHhhHHHHHHHhhHHHHHHHHHHHhcC--CCCcHHHHHHHHHH--HHhC---CcchHHHHHHHH----H
Confidence            45556666778888888889999999999887665432  22111110000000  0011   222222222333    2


Q ss_pred             HHHCCcccCCccccccCChH-HHhhhhhhhhHHHHHHHHhcCCCCCCcEEE
Q 040371          314 TKSEGFLPATELVLMDVSEE-EKEGNLYHHSEKLALAYGILKTSPGTEIRI  363 (410)
Q Consensus       314 m~~~g~~pd~~~~~~~~~~~-~~~~~l~~~~e~la~~~~~~~~~~~~~~~~  363 (410)
                      +-  .+.|+.--....++.. .+.++...-.+....+..+..+.|-.|..+
T Consensus       746 al--r~dp~n~eaW~~LG~v~k~~Gd~~~Aaecf~aa~qLe~S~PV~pFs~  794 (799)
T KOG4162|consen  746 AL--RLDPLNHEAWYYLGEVFKKLGDSKQAAECFQAALQLEESNPVLPFSN  794 (799)
T ss_pred             HH--hhCCCCHHHHHHHHHHHHHccchHHHHHHHHHHHhhccCCCcccccc
Confidence            22  2344432221222211 234555566778888888888888766544

>KOG2796 consensus Uncharacterized conserved protein [Function unknown]

Probab=96.65  E-value=0.12  Score=44.83  Aligned_cols=139  Identities=10%  Similarity=0.079  Sum_probs=94.0

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhcccC----ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHH--
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQRN----DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLT--  150 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~~~----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~--  150 (410)
                      .+-+.++....-.|.+.-....+.+..++    +...-..+.+.-.+.|+.+.|...|++..+..-+.|..+++.++.  
T Consensus       178 ~Vmy~~~~~llG~kEy~iS~d~~~~vi~~~~e~~p~L~s~Lgr~~MQ~GD~k~a~~yf~~vek~~~kL~~~q~~~~V~~n  257 (366)
T KOG2796|consen  178 RVMYSMANCLLGMKEYVLSVDAYHSVIKYYPEQEPQLLSGLGRISMQIGDIKTAEKYFQDVEKVTQKLDGLQGKIMVLMN  257 (366)
T ss_pred             HHHHHHHHHHhcchhhhhhHHHHHHHHHhCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhccchhHHHHhh
Confidence            45567777777777777777777766654    456667777777889999999999998877655666666665443  


Q ss_pred             ---HHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHH
Q 040371          151 ---ACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALL  217 (410)
Q Consensus       151 ---a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li  217 (410)
                         .+.-..++..|...|.+....  -..|+..-|.-.-.+...|+..+|.+.++.| +..|...+-++++
T Consensus       258 ~a~i~lg~nn~a~a~r~~~~i~~~--D~~~~~a~NnKALcllYlg~l~DAiK~~e~~~~~~P~~~l~es~~  326 (366)
T KOG2796|consen  258 SAFLHLGQNNFAEAHRFFTEILRM--DPRNAVANNNKALCLLYLGKLKDALKQLEAMVQQDPRHYLHESVL  326 (366)
T ss_pred             hhhheecccchHHHHHHHhhcccc--CCCchhhhchHHHHHHHHHHHHHHHHHHHHHhccCCccchhhhHH
Confidence               333456778888888777643  2234444444334445567899999999998 5667666555444

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=96.62  E-value=0.15  Score=52.36  Aligned_cols=153  Identities=13%  Similarity=0.022  Sum_probs=110.6

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC---HHHHHHHH
Q 040371           76 FILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD---SITFLGLL  149 (410)
Q Consensus        76 ~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~---~~t~~~ll  149 (410)
                      ...|..|.+.|...-+...|.+.|+..-+   .|..+|......|+....+++|..+.-.--+  ..|-   ...+..+-
T Consensus       492 apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLDatdaeaaaa~adtyae~~~we~a~~I~l~~~q--ka~a~~~k~nW~~rG  569 (1238)
T KOG1127|consen  492 APAFAFLGQIYRDSDDMKRAKKCFDKAFELDATDAEAAAASADTYAEESTWEEAFEICLRAAQ--KAPAFACKENWVQRG  569 (1238)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhhHHHHHHHhhccccHHHHHHHHHHHhh--hchHHHHHhhhhhcc
Confidence            45788999999988899999999987654   4678999999999999999999998322211  1111   11222334


Q ss_pred             HHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHH-HHHhcCchh
Q 040371          150 TACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLS-ACRTFKRLE  227 (410)
Q Consensus       150 ~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~-~~~~~g~~~  227 (410)
                      -.+...++...+..-|+...+  --+-|...|..+..+|.++|++..|.++|.+. .++|+..--.-.+. .-+..|.++
T Consensus       570 ~yyLea~n~h~aV~~fQsALR--~dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs~LrP~s~y~~fk~A~~ecd~GkYk  647 (1238)
T KOG1127|consen  570 PYYLEAHNLHGAVCEFQSALR--TDPKDYNLWLGLGEAYPESGRYSHALKVFTKASLLRPLSKYGRFKEAVMECDNGKYK  647 (1238)
T ss_pred             ccccCccchhhHHHHHHHHhc--CCchhHHHHHHHHHHHHhcCceehHHHhhhhhHhcCcHhHHHHHHHHHHHHHhhhHH
Confidence            456678888999999988773  22346789999999999999999999999988 46665432221222 235678888


Q ss_pred             HHHHH
Q 040371          228 LGEVA  232 (410)
Q Consensus       228 ~a~~~  232 (410)
                      ++...
T Consensus       648 eald~  652 (1238)
T KOG1127|consen  648 EALDA  652 (1238)
T ss_pred             HHHHH
Confidence            88776

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=96.60  E-value=0.32  Score=40.14  Aligned_cols=122  Identities=16%  Similarity=0.155  Sum_probs=71.3

Q ss_pred             CCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc----CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCC---CCCCHHH
Q 040371           72 IELNFILSAALIDMYSKCGKIQMAKEVFDTVQR----NDVSVWNAMISGVAIHGLAADASAIFTKMEMFN---VLPDSIT  144 (410)
Q Consensus        72 ~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g---~~p~~~t  144 (410)
                      ..|++.---.|.....+.|+..+|...|++...    .|....-.+..+....+++.+|..+++++-+..   -.||  +
T Consensus        85 ~ApTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~pa~r~pd--~  162 (251)
T COG4700          85 IAPTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPD--G  162 (251)
T ss_pred             hchhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCccCCCC--c
Confidence            345555556666666777777777777766542    255555555555566677777777776665532   2333  2


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHH
Q 040371          145 FLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAY  198 (410)
Q Consensus       145 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~  198 (410)
                      ...+...+...|...+|+..|+...+-   .|+...-...-.++.+.|+.++|.
T Consensus       163 ~Ll~aR~laa~g~~a~Aesafe~a~~~---ypg~~ar~~Y~e~La~qgr~~ea~  213 (251)
T COG4700         163 HLLFARTLAAQGKYADAESAFEVAISY---YPGPQARIYYAEMLAKQGRLREAN  213 (251)
T ss_pred             hHHHHHHHHhcCCchhHHHHHHHHHHh---CCCHHHHHHHHHHHHHhcchhHHH
Confidence            333556666677777777777776632   444444444444556666665553

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=96.58  E-value=0.014  Score=40.08  Aligned_cols=65  Identities=11%  Similarity=0.274  Sum_probs=42.4

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHc
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLG-ALNHAYWVHNLIIEK   70 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~-~~~~a~~~~~~~~~~   70 (410)
                      +..+|..+-..+.+.|++++|+..|.+..+.. +-+...|..+..++...| ++++|.+.+++.++.
T Consensus         2 ~a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~al~l   67 (69)
T PF13414_consen    2 NAEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKALKL   67 (69)
T ss_dssp             SHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHHHHc
Confidence            45567777777777777777777777776642 224556666666666666 567777766666553

...

>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]

Probab=96.55  E-value=0.31  Score=50.16  Aligned_cols=143  Identities=17%  Similarity=0.048  Sum_probs=87.0

Q ss_pred             HhHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040371           22 FDEALRFFREMLSSKVEPD-KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFD  100 (410)
Q Consensus        22 ~~~a~~l~~~m~~~g~~pd-~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~  100 (410)
                      ...|+..|-+-.+.  .|+ ...|..+...|....+...|.+-|+...+.. +.|...+.+..+.|++..+++.|..+.-
T Consensus       474 ~~~al~ali~alrl--d~~~apaf~~LG~iYrd~~Dm~RA~kCf~KAFeLD-atdaeaaaa~adtyae~~~we~a~~I~l  550 (1238)
T KOG1127|consen  474 SALALHALIRALRL--DVSLAPAFAFLGQIYRDSDDMKRAKKCFDKAFELD-ATDAEAAAASADTYAEESTWEEAFEICL  550 (1238)
T ss_pred             HHHHHHHHHHHHhc--ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chhhhhHHHHHHHhhccccHHHHHHHHH
Confidence            56666666555443  222 3467777777777667777888888877764 4567778888888888888888887743


Q ss_pred             hcccCCh---h--hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          101 TVQRNDV---S--VWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       101 ~m~~~~~---~--~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      ...+.+.   .  .|--.--.|...++...|+.-|+...+.  .| |...+..+..+|..+|.+..|.++|....
T Consensus       551 ~~~qka~a~~~k~nW~~rG~yyLea~n~h~aV~~fQsALR~--dPkD~n~W~gLGeAY~~sGry~~AlKvF~kAs  623 (1238)
T KOG1127|consen  551 RAAQKAPAFACKENWVQRGPYYLEAHNLHGAVCEFQSALRT--DPKDYNLWLGLGEAYPESGRYSHALKVFTKAS  623 (1238)
T ss_pred             HHhhhchHHHHHhhhhhccccccCccchhhHHHHHHHHhcC--CchhHHHHHHHHHHHHhcCceehHHHhhhhhH
Confidence            3333211   1  2222222344555666666666655542  33 44556666666666666666666665554

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=96.50  E-value=0.0094  Score=40.38  Aligned_cols=24  Identities=17%  Similarity=0.248  Sum_probs=9.1

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHH
Q 040371          110 WNAMISGVAIHGLAADASAIFTKM  133 (410)
Q Consensus       110 ~~~li~~~~~~g~~~~A~~l~~~m  133 (410)
                      |..+...+.+.|++++|...|++.
T Consensus        34 ~~~lg~~~~~~g~~~~A~~~~~~a   57 (65)
T PF13432_consen   34 WYLLGRILYQQGRYDEALAYYERA   57 (65)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHH
Confidence            333333333444444444444333

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=96.49  E-value=0.52  Score=49.41  Aligned_cols=26  Identities=19%  Similarity=0.331  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHcC--CHhHHHHHHHHHHH
Q 040371            9 WNSMIGGFVRNA--RFDEALRFFREMLS   34 (410)
Q Consensus         9 ~n~li~~~~~~g--~~~~a~~l~~~m~~   34 (410)
                      .-.+|++|++.+  ..++|+....+.+.
T Consensus       793 ~~~ilTs~vk~~~~~ie~aL~kI~~l~~  820 (1265)
T KOG1920|consen  793 NLFILTSYVKSNPPEIEEALQKIKELQL  820 (1265)
T ss_pred             hHHHHHHHHhcCcHHHHHHHHHHHHHHh
Confidence            446888999988  77888888877764

>KOG0553 consensus TPR repeat-containing protein [General function prediction only]

Probab=96.42  E-value=0.047  Score=48.28  Aligned_cols=100  Identities=16%  Similarity=0.118  Sum_probs=76.6

Q ss_pred             HHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCCHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD-SITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~  160 (410)
                      -..+.+++.+|...|.+..+   .|.+-|..-..+|.+.|.++.|++-.+..+.  +.|. ..+|..|-.+|...|++++
T Consensus        90 ~~m~~~~Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg~~~~AVkDce~Al~--iDp~yskay~RLG~A~~~~gk~~~  167 (304)
T KOG0553|consen   90 KLMKNKDYQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLGEYEDAVKDCESALS--IDPHYSKAYGRLGLAYLALGKYEE  167 (304)
T ss_pred             HHHHhhhHHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhcchHHHHHHHHHHHh--cChHHHHHHHHHHHHHHccCcHHH
Confidence            34678888888888887653   4677788888889999998888888777665  4453 4678888889999999999


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHH
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLG  189 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~  189 (410)
                      |.+.|+...   .+.|+-.+|-.=++.--
T Consensus       168 A~~aykKaL---eldP~Ne~~K~nL~~Ae  193 (304)
T KOG0553|consen  168 AIEAYKKAL---ELDPDNESYKSNLKIAE  193 (304)
T ss_pred             HHHHHHhhh---ccCCCcHHHHHHHHHHH
Confidence            998888776   56788777766555443

>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]

Probab=96.38  E-value=0.84  Score=43.77  Aligned_cols=213  Identities=14%  Similarity=0.074  Sum_probs=134.8

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHH-------HH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILS-------AA   81 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~-------~~   81 (410)
                      ...+.++..+..++..|++-+.......  -+..-++....++...|.+......-...++.|... ..-+       .-
T Consensus       227 ek~lgnaaykkk~f~~a~q~y~~a~el~--~~it~~~n~aA~~~e~~~~~~c~~~c~~a~E~gre~-rad~klIak~~~r  303 (539)
T KOG0548|consen  227 EKELGNAAYKKKDFETAIQHYAKALELA--TDITYLNNIAAVYLERGKYAECIELCEKAVEVGREL-RADYKLIAKALAR  303 (539)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHhHh--hhhHHHHHHHHHHHhccHHHHhhcchHHHHHHhHHH-HHHHHHHHHHHHH
Confidence            4456677778888999999998887653  344455566667788888877777766666655321 1112       22


Q ss_pred             HHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHccCCHHH
Q 040371           82 LIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSI-TFLGLLTACSHCGLVEE  160 (410)
Q Consensus        82 li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~ll~a~~~~g~~~~  160 (410)
                      +...|.+.++++.|+..|.+...+-..     =....+....++++.......-  +.|... -.-.-.+.+.+.|++..
T Consensus       304 ~g~a~~k~~~~~~ai~~~~kaLte~Rt-----~~~ls~lk~~Ek~~k~~e~~a~--~~pe~A~e~r~kGne~Fk~gdy~~  376 (539)
T KOG0548|consen  304 LGNAYTKREDYEGAIKYYQKALTEHRT-----PDLLSKLKEAEKALKEAERKAY--INPEKAEEEREKGNEAFKKGDYPE  376 (539)
T ss_pred             hhhhhhhHHhHHHHHHHHHHHhhhhcC-----HHHHHHHHHHHHHHHHHHHHHh--hChhHHHHHHHHHHHHHhccCHHH
Confidence            344778888999999999885432111     1112223344555555544433  334321 12223566778899999


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCchhHHHHHH
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRALLSACRTFKRLELGEVAI  233 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~li~~~~~~g~~~~a~~~~  233 (410)
                      |...+.+++++ . +-|...|..-.-+|.+.|.+.+|++=-+.. ...|+ ...|.-=..++....+++.|...+
T Consensus       377 Av~~YteAIkr-~-P~Da~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~mk~ydkAleay  449 (539)
T KOG0548|consen  377 AVKHYTEAIKR-D-PEDARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRAMKEYDKALEAY  449 (539)
T ss_pred             HHHHHHHHHhc-C-CchhHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999998864 2 446788888889999999998887755544 34454 334444445556666777777773

>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A

Probab=96.37  E-value=0.017  Score=39.60  Aligned_cols=61  Identities=20%  Similarity=0.025  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC-CHHHHHHHHHhc
Q 040371           41 KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG-KIQMAKEVFDTV  102 (410)
Q Consensus        41 ~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g-~~~~A~~~f~~m  102 (410)
                      ..+|..+...+...|++++|...|.+.++.. +.+..++..+..+|.+.| ++++|++.|++.
T Consensus         3 a~~~~~~g~~~~~~~~~~~A~~~~~~ai~~~-p~~~~~~~~~g~~~~~~~~~~~~A~~~~~~a   64 (69)
T PF13414_consen    3 AEAWYNLGQIYFQQGDYEEAIEYFEKAIELD-PNNAEAYYNLGLAYMKLGKDYEEAIEDFEKA   64 (69)
T ss_dssp             HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHTTTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhCccHHHHHHHHHHH
Confidence            4455555555566666666666666665553 334555555555566555 455555555543

...

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=96.36  E-value=0.84  Score=42.17  Aligned_cols=124  Identities=10%  Similarity=0.039  Sum_probs=63.7

Q ss_pred             HHHHHHHHHH--cCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHH--HhhCCHHHHHHHHHHHHHcCCCccHHH--HHHH
Q 040371            9 WNSMIGGFVR--NARFDEALRFFREMLSSKVEPDKFTFASVIYGC--ARLGALNHAYWVHNLIIEKKIELNFIL--SAAL   82 (410)
Q Consensus         9 ~n~li~~~~~--~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~--~~~~~~~~a~~~~~~~~~~g~~~~~~~--~~~l   82 (410)
                      |.+|-.++.-  .|+-..|.++-.+-.+. +..|...+..++.+-  .-.|+.+.|++-|+.|...   |....  ...|
T Consensus        85 yqALStGliAagAGda~lARkmt~~~~~l-lssDqepLIhlLeAQaal~eG~~~~Ar~kfeAMl~d---PEtRllGLRgL  160 (531)
T COG3898          85 YQALSTGLIAAGAGDASLARKMTARASKL-LSSDQEPLIHLLEAQAALLEGDYEDARKKFEAMLDD---PETRLLGLRGL  160 (531)
T ss_pred             HHHHhhhhhhhccCchHHHHHHHHHHHhh-hhccchHHHHHHHHHHHHhcCchHHHHHHHHHHhcC---hHHHHHhHHHH
Confidence            4444444443  34455554444433221 344555555555443  3456777777777777642   11111  1122


Q ss_pred             HHHHHhcCCHHHHHHHHHhccc--CC-hhhHHHHHHHHHHcCChHHHHHHHHHHHHC
Q 040371           83 IDMYSKCGKIQMAKEVFDTVQR--ND-VSVWNAMISGVAIHGLAADASAIFTKMEMF  136 (410)
Q Consensus        83 i~~y~~~g~~~~A~~~f~~m~~--~~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  136 (410)
                      .----+.|..+.|++.-++.-.  |. .-.|.+.+...+..|+++.|+++.+.-+..
T Consensus       161 yleAqr~GareaAr~yAe~Aa~~Ap~l~WA~~AtLe~r~~~gdWd~AlkLvd~~~~~  217 (531)
T COG3898         161 YLEAQRLGAREAARHYAERAAEKAPQLPWAARATLEARCAAGDWDGALKLVDAQRAA  217 (531)
T ss_pred             HHHHHhcccHHHHHHHHHHHHhhccCCchHHHHHHHHHHhcCChHHHHHHHHHHHHH
Confidence            2222345666666665554432  21 235666777777777777777777665443

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=96.32  E-value=1.1  Score=44.92  Aligned_cols=247  Identities=11%  Similarity=0.046  Sum_probs=131.9

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCC----CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC---------
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKV----EPDKFTFASVIYGCARLGALNHAYWVHNLIIEKK---------   71 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~----~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g---------   71 (410)
                      .-+||..+.+---+.|+++.|..+.+.=...+-    -.+..-+...+.-+...|+.+...+++-.+.+.-         
T Consensus       506 ~~iSy~~iA~~Ay~~GR~~LA~kLle~E~~~~~qV~lLL~m~~~~~AL~kaies~d~~Li~~Vllhlk~~~~~s~l~~~l  585 (829)
T KOG2280|consen  506 PGISYAAIARRAYQEGRFELARKLLELEPRSGEQVPLLLKMKDSSLALKKAIESGDTDLIIQVLLHLKNKLNRSSLFMTL  585 (829)
T ss_pred             CceeHHHHHHHHHhcCcHHHHHHHHhcCCCccchhHHHhccchHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHHHH
Confidence            346788888877889999999888764322211    0122345566777778888877777665554431         


Q ss_pred             --CCccHHHHHHHHH--------HHHhcCCHHHHHHHHH--hcc-----cCChhhHHHHHHHHHHcCC----------hH
Q 040371           72 --IELNFILSAALID--------MYSKCGKIQMAKEVFD--TVQ-----RNDVSVWNAMISGVAIHGL----------AA  124 (410)
Q Consensus        72 --~~~~~~~~~~li~--------~y~~~g~~~~A~~~f~--~m~-----~~~~~~~~~li~~~~~~g~----------~~  124 (410)
                        .+....+|.-++.        -+...++...+...|.  ...     +.-...-....+.+++...          ..
T Consensus       586 ~~~p~a~~lY~~~~r~~~~~~l~d~y~q~dn~~~~a~~~~q~~~~~~~~~~r~~~lk~~a~~~a~sk~~s~e~ka~ed~~  665 (829)
T KOG2280|consen  586 RNQPLALSLYRQFMRHQDRATLYDFYNQDDNHQALASFHLQASYAAETIEGRIPALKTAANAFAKSKEKSFEAKALEDQM  665 (829)
T ss_pred             HhchhhhHHHHHHHHhhchhhhhhhhhcccchhhhhhhhhhhhhhhhhhcccchhHHHHHHHHhhhhhhhhHHHHHHHHH
Confidence              1111122221111        0011111111211111  000     0111112222233333322          11


Q ss_pred             HHHHHHHHHHHC-CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371          125 DASAIFTKMEMF-NVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITS  203 (410)
Q Consensus       125 ~A~~l~~~m~~~-g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~  203 (410)
                      .-+.+++.+... |..-...|.+-.+.-+...|+-.+|.++-.+.+     -||-..|---+.+++..+++++-+++-+.
T Consensus       666 kLl~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fk-----ipdKr~~wLk~~aLa~~~kweeLekfAks  740 (829)
T KOG2280|consen  666 KLLKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFK-----IPDKRLWWLKLTALADIKKWEELEKFAKS  740 (829)
T ss_pred             HHHHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcC-----CcchhhHHHHHHHHHhhhhHHHHHHHHhc
Confidence            112222222221 222333445555666667777777777755443     35677777777888888888887777776


Q ss_pred             CCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHH
Q 040371          204 MTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVR  264 (410)
Q Consensus       204 m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~  264 (410)
                      +.   ...-|..+..+|.+.|+.++|.+++-+..+.     .-...+|.+.|++.+|.++-
T Consensus       741 kk---sPIGy~PFVe~c~~~~n~~EA~KYiprv~~l-----~ekv~ay~~~~~~~eAad~A  793 (829)
T KOG2280|consen  741 KK---SPIGYLPFVEACLKQGNKDEAKKYIPRVGGL-----QEKVKAYLRVGDVKEAADLA  793 (829)
T ss_pred             cC---CCCCchhHHHHHHhcccHHHHhhhhhccCCh-----HHHHHHHHHhccHHHHHHHH
Confidence            62   2344666778888888888888775444322     15677788888888877664

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=96.30  E-value=0.61  Score=43.46  Aligned_cols=72  Identities=17%  Similarity=0.064  Sum_probs=39.9

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcccC---Chh----hHHHHHHHHHH---cCChHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQRN---DVS----VWNAMISGVAI---HGLAADASAIFTKMEMFNVLPDSITFLGLLT  150 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~~---~~~----~~~~li~~~~~---~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  150 (410)
                      .|+-.|-...+++...++.+.++..   ++.    .-....-++-+   .|+.++|++++..+......++..||..+..
T Consensus       146 ~lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~gL~GR  225 (374)
T PF13281_consen  146 NLLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTLGLLGR  225 (374)
T ss_pred             HHHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHHHHHHH
Confidence            3444566677777777777766643   111    11122333444   5677777777776555555566666665555


Q ss_pred             HH
Q 040371          151 AC  152 (410)
Q Consensus       151 a~  152 (410)
                      .|
T Consensus       226 Iy  227 (374)
T PF13281_consen  226 IY  227 (374)
T ss_pred             HH
Confidence            44

>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=96.25  E-value=0.096  Score=42.10  Aligned_cols=71  Identities=15%  Similarity=0.213  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhh----hcCCCCChhH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRS----RYSIQPQLEH  180 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~----~~~~~~~~~~  180 (410)
                      +...++..+...|++++|+.+.+.+.... +-|...+..++.++...|+...|.++|+.+.+    ..|+.|+..+
T Consensus        64 ~~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   64 ALERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            44556666777788888888887777642 33667777788888888888888877776542    3466666544

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B

Probab=96.25  E-value=0.031  Score=37.76  Aligned_cols=57  Identities=14%  Similarity=0.124  Sum_probs=36.5

Q ss_pred             HHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc
Q 040371           13 IGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~   70 (410)
                      ...+.+.|++++|++.|++.++.. +-+...+..+..++...|++++|...++.+++.
T Consensus         4 a~~~~~~g~~~~A~~~~~~~l~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~   60 (65)
T PF13432_consen    4 ARALYQQGDYDEAIAAFEQALKQD-PDNPEAWYLLGRILYQQGRYDEALAYYERALEL   60 (65)
T ss_dssp             HHHHHHCTHHHHHHHHHHHHHCCS-TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            445667777777777777776653 224556666666667777777777777766654

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=96.22  E-value=0.67  Score=39.64  Aligned_cols=178  Identities=12%  Similarity=0.078  Sum_probs=86.6

Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh
Q 040371           11 SMIGGFVRNARFDEALRFFREMLSSKV--EPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK   88 (410)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~g~--~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~   88 (410)
                      .....+.+.|++.+|+..|+++...-.  +--....-.+..++-+.|+++.|...++..++.-......-+...+.+.+.
T Consensus        10 ~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~~   89 (203)
T PF13525_consen   10 QKALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLSY   89 (203)
T ss_dssp             HHHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHH
Confidence            445556688889999999988876421  112234556677788888888888888887775322111111111111111


Q ss_pred             cCCHHHHHHHHHhcccCCh-------hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 040371           89 CGKIQMAKEVFDTVQRNDV-------SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~~~~-------~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a  161 (410)
                      ......   .+  ...+|.       ..+..+|.-|=......+|...+..+...   .-... ..+..-|.+.|.+..|
T Consensus        90 ~~~~~~---~~--~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~---la~~e-~~ia~~Y~~~~~y~aA  160 (203)
T PF13525_consen   90 YKQIPG---IL--RSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNR---LAEHE-LYIARFYYKRGKYKAA  160 (203)
T ss_dssp             HHHHHH---HH---TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHH---HHHHH-HHHHHHHHCTT-HHHH
T ss_pred             HHhCcc---ch--hcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHH---HHHHH-HHHHHHHHHcccHHHH
Confidence            110100   00  111111       13333444444444455555444444321   00111 1245567777777777


Q ss_pred             HHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHH
Q 040371          162 RKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEA  197 (410)
Q Consensus       162 ~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A  197 (410)
                      ..-++.+.+++.-.+. ......|+.+|.+.|..+.|
T Consensus       161 ~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~a  197 (203)
T PF13525_consen  161 IIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQAA  197 (203)
T ss_dssp             HHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHHH
T ss_pred             HHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHHH
Confidence            7777777765322221 23445666677777766644

>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=96.17  E-value=0.046  Score=43.98  Aligned_cols=69  Identities=17%  Similarity=0.182  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHH-----cCCCccHHH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIE-----KKIELNFIL   78 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~-----~g~~~~~~~   78 (410)
                      ...++..+...|++++|+.+.+++.... +-|...|..+|.++...|+...|.++|+.+.+     .|+.|+..+
T Consensus        65 ~~~l~~~~~~~~~~~~a~~~~~~~l~~d-P~~E~~~~~lm~~~~~~g~~~~A~~~Y~~~~~~l~~elg~~Ps~~~  138 (146)
T PF03704_consen   65 LERLAEALLEAGDYEEALRLLQRALALD-PYDEEAYRLLMRALAAQGRRAEALRVYERYRRRLREELGIEPSPET  138 (146)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHHHHHHHS-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHS----HHH
T ss_pred             HHHHHHHHHhccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhCcCcCHHH
Confidence            4455556666777777777777766542 44666777777777777777777776666543     366665544

It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.17  E-value=0.076  Score=47.31  Aligned_cols=94  Identities=19%  Similarity=0.186  Sum_probs=61.3

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-hhHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS----ITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGA  183 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~----~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~  183 (410)
                      .|+..+..+.+.|++++|...|+.+...  .|+.    ..+..+..++...|++++|...|..+.+.+.-.|. ...+-.
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~--yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~k  222 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKK--YPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFK  222 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHH
Confidence            4555555455667888888888887764  3432    35556777777888888888888887755332222 334444


Q ss_pred             HHHHHHhcCCHHHHHHHHHhC
Q 040371          184 MVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       184 li~~~~~~g~~~~A~~~~~~m  204 (410)
                      +...|...|+.++|.+++++.
T Consensus       223 lg~~~~~~g~~~~A~~~~~~v  243 (263)
T PRK10803        223 VGVIMQDKGDTAKAKAVYQQV  243 (263)
T ss_pred             HHHHHHHcCCHHHHHHHHHHH
Confidence            556677778888887777765

>PRK10803 tol-pal system protein YbgF; Provisional

Probab=96.12  E-value=0.12  Score=46.10  Aligned_cols=94  Identities=14%  Similarity=0.022  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc--HHHHHHHHHHHHhcCCHHHHHHHHHhccc--CC----hhhHHHHH
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELN--FILSAALIDMYSKCGKIQMAKEVFDTVQR--ND----VSVWNAMI  114 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~--~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~----~~~~~~li  114 (410)
                      .|...+....+.|++++|...|+.+++.-....  ..++--+...|...|++++|...|+.+.+  |+    ..++-.+.
T Consensus       145 ~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg  224 (263)
T PRK10803        145 DYNAAIALVQDKSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVG  224 (263)
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHH
Confidence            344444333444556666655655555421111  23444555666666666666666666642  21    22344445


Q ss_pred             HHHHHcCChHHHHHHHHHHHHC
Q 040371          115 SGVAIHGLAADASAIFTKMEMF  136 (410)
Q Consensus       115 ~~~~~~g~~~~A~~l~~~m~~~  136 (410)
                      ..|...|+.++|..+|++..+.
T Consensus       225 ~~~~~~g~~~~A~~~~~~vi~~  246 (263)
T PRK10803        225 VIMQDKGDTAKAKAVYQQVIKK  246 (263)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHH
Confidence            5566667777777777766653

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=96.11  E-value=0.047  Score=47.82  Aligned_cols=100  Identities=16%  Similarity=0.187  Sum_probs=81.7

Q ss_pred             HHHHHHhcc--cCChhhHHHHHHHHHHc-----CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC-----------
Q 040371           95 AKEVFDTVQ--RNDVSVWNAMISGVAIH-----GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCG-----------  156 (410)
Q Consensus        95 A~~~f~~m~--~~~~~~~~~li~~~~~~-----g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g-----------  156 (410)
                      .++.|...+  ++|..+|-+++..|...     +..+-....++.|.+-|+.-|..+|..||+.+=+..           
T Consensus        53 ~e~~F~aa~~~~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F  132 (406)
T KOG3941|consen   53 VEKQFEAAEPEKRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVF  132 (406)
T ss_pred             hhhhhhccCcccccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHH
Confidence            456677776  67888999999888764     566777778889999999999999999999876532           


Q ss_pred             -----CHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHH
Q 040371          157 -----LVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIE  195 (410)
Q Consensus       157 -----~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~  195 (410)
                           +-+-+..++++|.. +|+.||-.+-..|+.++++.+..-
T Consensus       133 ~HYP~QQ~C~I~vLeqME~-hGVmPdkE~e~~lvn~FGr~~~p~  175 (406)
T KOG3941|consen  133 LHYPQQQNCAIKVLEQMEW-HGVMPDKEIEDILVNAFGRWNFPT  175 (406)
T ss_pred             hhCchhhhHHHHHHHHHHH-cCCCCchHHHHHHHHHhccccccH
Confidence                 34568899999995 699999999999999999988643

>KOG2041 consensus WD40 repeat protein [General function prediction only]

Probab=96.01  E-value=0.76  Score=45.58  Aligned_cols=182  Identities=12%  Similarity=0.074  Sum_probs=93.9

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHhccc-CCh------------hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCC
Q 040371           73 ELNFILSAALIDMYSKCGKIQMAKEVFDTVQR-NDV------------SVWNAMISGVAIHGLAADASAIFTKMEMFNVL  139 (410)
Q Consensus        73 ~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-~~~------------~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  139 (410)
                      .|.+..|..|.+.-.+.-.++-|+..|-+... +.+            ..-.+=|++|  -|.+++|.++|-+|.+..+.
T Consensus       689 nPHprLWrllAe~Al~Kl~l~tAE~AFVrc~dY~Gik~vkrl~~i~s~~~q~aei~~~--~g~feeaek~yld~drrDLA  766 (1189)
T KOG2041|consen  689 NPHPRLWRLLAEYALFKLALDTAEHAFVRCGDYAGIKLVKRLRTIHSKEQQRAEISAF--YGEFEEAEKLYLDADRRDLA  766 (1189)
T ss_pred             CCchHHHHHHHHHHHHHHhhhhHhhhhhhhccccchhHHHHhhhhhhHHHHhHhHhhh--hcchhHhhhhhhccchhhhh
Confidence            57788888888777777777888877766542 111            1122334444  58999999999888654321


Q ss_pred             C----CHHHHHHHHHHHHcc--CCHHH-HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHH-------------HHHH
Q 040371          140 P----DSITFLGLLTACSHC--GLVEE-GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIE-------------EAYG  199 (410)
Q Consensus       140 p----~~~t~~~ll~a~~~~--g~~~~-a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~-------------~A~~  199 (410)
                      .    ..--|..+...+...  +.-|+ -...|+.|-+.   -.+...|......|.++|+.+             +-+.
T Consensus       767 ielr~klgDwfrV~qL~r~g~~d~dD~~~e~A~r~ig~~---fa~~~~We~A~~yY~~~~~~e~~~ecly~le~f~~LE~  843 (1189)
T KOG2041|consen  767 IELRKKLGDWFRVYQLIRNGGSDDDDEGKEDAFRNIGET---FAEMMEWEEAAKYYSYCGDTENQIECLYRLELFGELEV  843 (1189)
T ss_pred             HHHHHhhhhHHHHHHHHHccCCCcchHHHHHHHHHHHHH---HHHHHHHHHHHHHHHhccchHhHHHHHHHHHhhhhHHH
Confidence            1    111122222222221  11111 11222222211   012223444444444444433             2222


Q ss_pred             HHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHHH
Q 040371          200 LITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREI  266 (410)
Q Consensus       200 ~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  266 (410)
                      +.+.++  -|....-.+...+...|.-++|.+...+...+.     ..+..|....+|.+|.++-+.
T Consensus       844 la~~Lp--e~s~llp~~a~mf~svGMC~qAV~a~Lr~s~pk-----aAv~tCv~LnQW~~avelaq~  903 (1189)
T KOG2041|consen  844 LARTLP--EDSELLPVMADMFTSVGMCDQAVEAYLRRSLPK-----AAVHTCVELNQWGEAVELAQR  903 (1189)
T ss_pred             HHHhcC--cccchHHHHHHHHHhhchHHHHHHHHHhccCcH-----HHHHHHHHHHHHHHHHHHHHh
Confidence            222221  244455566677788888888888744433222     345667777888777776554

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=95.91  E-value=0.035  Score=39.11  Aligned_cols=62  Identities=23%  Similarity=0.337  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHC--CCC---CC-HHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSS--KVE---PD-KFTFASVIYGCARLGALNHAYWVHNLII   68 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~--g~~---pd-~~t~~~ll~a~~~~~~~~~a~~~~~~~~   68 (410)
                      .+|+.+-..|...|++++|+..|++..+.  ...   |+ ..++..+..++...|++++|.+.+++..
T Consensus         6 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al   73 (78)
T PF13424_consen    6 NAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL   73 (78)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            46788888888888888888888877542  111   11 3355555666666666666666665554

...

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=95.90  E-value=0.51  Score=42.06  Aligned_cols=96  Identities=13%  Similarity=0.050  Sum_probs=54.2

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHhcc---cCChhhHHHHHHHHHHcC---ChHHHHHHHHHHHHCCCCCC-HHHH
Q 040371           73 ELNFILSAALIDMYSKCGKIQMAKEVFDTVQ---RNDVSVWNAMISGVAIHG---LAADASAIFTKMEMFNVLPD-SITF  145 (410)
Q Consensus        73 ~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~---~~~~~~~~~li~~~~~~g---~~~~A~~l~~~m~~~g~~p~-~~t~  145 (410)
                      +.|..-|--|...|...|+.+.|...|.+..   -+|...+..+..++....   ...++.++|+++...  .|+ ..+.
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~--D~~~iral  230 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLAGDNPEILLGLAEALYYQAGQQMTAKARALLRQALAL--DPANIRAL  230 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhc--CCccHHHH
Confidence            4466666666666666666666666666543   234444444444433321   344666666666653  343 3334


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhhh
Q 040371          146 LGLLTACSHCGLVEEGRKYFDHMRS  170 (410)
Q Consensus       146 ~~ll~a~~~~g~~~~a~~~~~~m~~  170 (410)
                      ..|...+...|++.+|...++.|.+
T Consensus       231 ~lLA~~afe~g~~~~A~~~Wq~lL~  255 (287)
T COG4235         231 SLLAFAAFEQGDYAEAAAAWQMLLD  255 (287)
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHh
Confidence            4444566666777777777766663

>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]

Probab=95.82  E-value=0.31  Score=47.69  Aligned_cols=240  Identities=13%  Similarity=0.138  Sum_probs=139.3

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHH---------HHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHH--HHHHHHHHcCCCcc
Q 040371            7 VSWNSMIGGFVRNARFDEALRFF---------REMLSSKVEPDKFTFASVIYGCARLGALNHAY--WVHNLIIEKKIELN   75 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~---------~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~--~~~~~~~~~g~~~~   75 (410)
                      +.+.+=+..|...|.+++|..+-         +.+-.+  ..+...++..=.||.+..++.--+  .-++.+.++|-.|+
T Consensus       557 vp~~~~m~q~Ieag~f~ea~~iaclgVv~~DW~~LA~~--ALeAL~f~~ARkAY~rVRdl~~L~li~EL~~~k~rge~P~  634 (1081)
T KOG1538|consen  557 VPQSAPMYQYIERGLFKEAYQIACLGVTDTDWRELAME--ALEALDFETARKAYIRVRDLRYLELISELEERKKRGETPN  634 (1081)
T ss_pred             ccccccchhhhhccchhhhhcccccceecchHHHHHHH--HHhhhhhHHHHHHHHHHhccHHHHHHHHHHHHHhcCCCch
Confidence            44555566777888888876542         111111  112334555556676666654333  33456677787677


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhcccC--ChhhHHHH-----HHHHHHcCChHHHHHHHHHHHHC--CC-CCCHHHH
Q 040371           76 FILSAALIDMYSKCGKIQMAKEVFDTVQRN--DVSVWNAM-----ISGVAIHGLAADASAIFTKMEMF--NV-LPDSITF  145 (410)
Q Consensus        76 ~~~~~~li~~y~~~g~~~~A~~~f~~m~~~--~~~~~~~l-----i~~~~~~g~~~~A~~l~~~m~~~--g~-~p~~~t~  145 (410)
                      ...   +.+.++-.|++.+|-++|.+--..  -...|+-|     ..-|...|..++-..+.++-.+-  .+ .|..   
T Consensus       635 ~iL---lA~~~Ay~gKF~EAAklFk~~G~enRAlEmyTDlRMFD~aQE~~~~g~~~eKKmL~RKRA~WAr~~kePka---  708 (1081)
T KOG1538|consen  635 DLL---LADVFAYQGKFHEAAKLFKRSGHENRALEMYTDLRMFDYAQEFLGSGDPKEKKMLIRKRADWARNIKEPKA---  708 (1081)
T ss_pred             HHH---HHHHHHhhhhHHHHHHHHHHcCchhhHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHHHhhhcCCcHH---
Confidence            654   344566678888888888765432  22233322     33445556665555554432211  12 2221   


Q ss_pred             HHHHHHHHccCCHHHHHHH-------------HHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHH
Q 040371          146 LGLLTACSHCGLVEEGRKY-------------FDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVV  212 (410)
Q Consensus       146 ~~ll~a~~~~g~~~~a~~~-------------~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~  212 (410)
                        ....+..+|+.++|..+             -..+..     .+..+...+..-+-+...+.-|-++|.+|+   |.  
T Consensus       709 --AAEmLiSaGe~~KAi~i~~d~gW~d~lidI~rkld~-----~ere~l~~~a~ylk~l~~~gLAaeIF~k~g---D~--  776 (1081)
T KOG1538|consen  709 --AAEMLISAGEHVKAIEICGDHGWVDMLIDIARKLDK-----AEREPLLLCATYLKKLDSPGLAAEIFLKMG---DL--  776 (1081)
T ss_pred             --HHHHhhcccchhhhhhhhhcccHHHHHHHHHhhcch-----hhhhHHHHHHHHHhhccccchHHHHHHHhc---cH--
Confidence              22333345555555543             222221     133444444445556677888899999985   22  


Q ss_pred             HHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHH
Q 040371          213 WRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIM  267 (410)
Q Consensus       213 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  267 (410)
                       .+++......+++++|..+..+.-..-+.+|.--..-++...++++|.+.|.+.
T Consensus       777 -ksiVqlHve~~~W~eAFalAe~hPe~~~dVy~pyaqwLAE~DrFeEAqkAfhkA  830 (1081)
T KOG1538|consen  777 -KSLVQLHVETQRWDEAFALAEKHPEFKDDVYMPYAQWLAENDRFEEAQKAFHKA  830 (1081)
T ss_pred             -HHHhhheeecccchHhHhhhhhCccccccccchHHHHhhhhhhHHHHHHHHHHh
Confidence             245666778899999998877665555667777888889999999999888654

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.78  E-value=0.75  Score=36.55  Aligned_cols=43  Identities=19%  Similarity=0.162  Sum_probs=25.9

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhc
Q 040371           46 SVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKC   89 (410)
Q Consensus        46 ~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~   89 (410)
                      .++..+...+.......+++.+.+.+ ..+....|.++..|++.
T Consensus        12 ~vv~~~~~~~~~~~l~~yLe~~~~~~-~~~~~~~~~li~ly~~~   54 (140)
T smart00299       12 EVVELFEKRNLLEELIPYLESALKLN-SENPALQTKLIELYAKY   54 (140)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHccC-ccchhHHHHHHHHHHHH
Confidence            44555555556666666666666655 34566666666666654

>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H

Probab=95.74  E-value=0.036  Score=39.06  Aligned_cols=22  Identities=18%  Similarity=0.403  Sum_probs=8.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHH
Q 040371           79 SAALIDMYSKCGKIQMAKEVFD  100 (410)
Q Consensus        79 ~~~li~~y~~~g~~~~A~~~f~  100 (410)
                      ++.+...|.+.|++++|+..|+
T Consensus         8 ~~~la~~~~~~~~~~~A~~~~~   29 (78)
T PF13424_consen    8 YNNLARVYRELGRYDEALDYYE   29 (78)
T ss_dssp             HHHHHHHHHHTT-HHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHH
Confidence            3344444444444444444443

...

>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]

Probab=95.67  E-value=0.38  Score=42.83  Aligned_cols=111  Identities=13%  Similarity=0.048  Sum_probs=83.2

Q ss_pred             CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC--C-HHHHHHHHHhcccC---ChhhHH
Q 040371           38 EPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG--K-IQMAKEVFDTVQRN---DVSVWN  111 (410)
Q Consensus        38 ~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g--~-~~~A~~~f~~m~~~---~~~~~~  111 (410)
                      +-|...|-.|..+|...|+++.|...|....+.. ++++..+..+...+....  . -.++..+|++....   |+.+-.
T Consensus       153 P~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~-g~n~~~~~g~aeaL~~~a~~~~ta~a~~ll~~al~~D~~~iral~  231 (287)
T COG4235         153 PGDAEGWDLLGRAYMALGRASDALLAYRNALRLA-GDNPEILLGLAEALYYQAGQQMTAKARALLRQALALDPANIRALS  231 (287)
T ss_pred             CCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhcCCccHHHHH
Confidence            5578899999999999999999999999998873 456666666666544432  2 45788999988743   566777


Q ss_pred             HHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040371          112 AMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTA  151 (410)
Q Consensus       112 ~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a  151 (410)
                      -+...+...|++.+|...|+.|.+.  -|.......++..
T Consensus       232 lLA~~afe~g~~~~A~~~Wq~lL~~--lp~~~~rr~~ie~  269 (287)
T COG4235         232 LLAFAAFEQGDYAEAAAAWQMLLDL--LPADDPRRSLIER  269 (287)
T ss_pred             HHHHHHHHcccHHHHHHHHHHHHhc--CCCCCchHHHHHH
Confidence            7788889999999999999999885  3333445555543

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=95.63  E-value=0.22  Score=47.09  Aligned_cols=64  Identities=13%  Similarity=0.037  Sum_probs=55.6

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHhhCCHHHHHHHHHHHHHc
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDK----FTFASVIYGCARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~----~t~~~ll~a~~~~~~~~~a~~~~~~~~~~   70 (410)
                      +...|+.+-.+|.+.|++++|+..|++.++.  .||.    .+|..+..+|+.+|++++|.+.+++.++.
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL--~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALel  141 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALEL--NPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALRD  141 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            4568999999999999999999999998874  5664    35899999999999999999999999885

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=95.62  E-value=0.12  Score=35.61  Aligned_cols=57  Identities=16%  Similarity=0.146  Sum_probs=44.6

Q ss_pred             HHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC
Q 040371           14 GGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKK   71 (410)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g   71 (410)
                      ..|.+++++++|+++++.+...+ +.+...+.....++...|++++|.+.++..++.+
T Consensus         3 ~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~   59 (73)
T PF13371_consen    3 QIYLQQEDYEEALEVLERALELD-PDDPELWLQRARCLFQLGRYEEALEDLERALELS   59 (73)
T ss_pred             HHHHhCCCHHHHHHHHHHHHHhC-cccchhhHHHHHHHHHhccHHHHHHHHHHHHHHC
Confidence            56788888888888888888753 3356677777788888888888888888888764

>smart00299 CLH Clathrin heavy chain repeat homology

Probab=95.59  E-value=0.9  Score=36.09  Aligned_cols=121  Identities=12%  Similarity=0.183  Sum_probs=72.2

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcccC---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQRN---DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGL  157 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~  157 (410)
                      .++..+.+.+.......+++.+...   +....|.+|..|++.+ ..+.++.++.      .++......++..|.+.+.
T Consensus        12 ~vv~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~li~ly~~~~-~~~ll~~l~~------~~~~yd~~~~~~~c~~~~l   84 (140)
T smart00299       12 EVVELFEKRNLLEELIPYLESALKLNSENPALQTKLIELYAKYD-PQKEIERLDN------KSNHYDIEKVGKLCEKAKL   84 (140)
T ss_pred             HHHHHHHhCCcHHHHHHHHHHHHccCccchhHHHHHHHHHHHHC-HHHHHHHHHh------ccccCCHHHHHHHHHHcCc
Confidence            4556666667777777777765433   3456777777777653 3444444442      2334445557777777777


Q ss_pred             HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhc-CCHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Q 040371          158 VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRA-GHIEEAYGLITSMTMEPDVVVWRALLSACR  221 (410)
Q Consensus       158 ~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-g~~~~A~~~~~~m~~~p~~~~~~~li~~~~  221 (410)
                      ++++..++..+..          |...++.+... ++++.|.+++.+-   .+...|..++..+.
T Consensus        85 ~~~~~~l~~k~~~----------~~~Al~~~l~~~~d~~~a~~~~~~~---~~~~lw~~~~~~~l  136 (140)
T smart00299       85 YEEAVELYKKDGN----------FKDAIVTLIEHLGNYEKAIEYFVKQ---NNPELWAEVLKALL  136 (140)
T ss_pred             HHHHHHHHHhhcC----------HHHHHHHHHHcccCHHHHHHHHHhC---CCHHHHHHHHHHHH
Confidence            7777777766542          33334444444 6677777777663   25567776666554

>COG4700 Uncharacterized protein conserved in bacteria containing a divergent form of TPR repeats [Function unknown]

Probab=95.51  E-value=1.2  Score=36.94  Aligned_cols=138  Identities=12%  Similarity=0.031  Sum_probs=84.9

Q ss_pred             HHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhc
Q 040371           93 QMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRY  172 (410)
Q Consensus        93 ~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~  172 (410)
                      .+|.+-|+..  |.+..--.+..+....|+..||...|++....-..-|......+.++....++...|...++.+.+-.
T Consensus        77 Rea~~~~~~A--pTvqnr~rLa~al~elGr~~EA~~hy~qalsG~fA~d~a~lLglA~Aqfa~~~~A~a~~tLe~l~e~~  154 (251)
T COG4700          77 REATEELAIA--PTVQNRYRLANALAELGRYHEAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYN  154 (251)
T ss_pred             HHHHHHHhhc--hhHHHHHHHHHHHHHhhhhhhhHHHHHHHhccccCCCHHHHHHHHHHHHhhccHHHHHHHHHHHhhcC
Confidence            3444444433  34555556777788888888888888887654445567777788888888888888888888876532


Q ss_pred             CCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHH
Q 040371          173 SIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       173 ~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      .--.++.+.-.+...|...|++++|+.-|+-. ..-|+...-.-.-.-+.+.|+.+++..-
T Consensus       155 pa~r~pd~~Ll~aR~laa~g~~a~Aesafe~a~~~ypg~~ar~~Y~e~La~qgr~~ea~aq  215 (251)
T COG4700         155 PAFRSPDGHLLFARTLAAQGKYADAESAFEVAISYYPGPQARIYYAEMLAKQGRLREANAQ  215 (251)
T ss_pred             CccCCCCchHHHHHHHHhcCCchhHHHHHHHHHHhCCCHHHHHHHHHHHHHhcchhHHHHH
Confidence            11112334455667788888888887777765 3344433222222223455655554443

>PRK15331 chaperone protein SicA; Provisional

Probab=95.29  E-value=0.14  Score=41.47  Aligned_cols=83  Identities=10%  Similarity=0.074  Sum_probs=64.5

Q ss_pred             HHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHH
Q 040371          187 LLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAE  261 (410)
Q Consensus       187 ~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  261 (410)
                      -+-..|++++|..+|+-+ -..| |..-|..|-..|-..++++.|...   ...+.+.|+.++.-....|...|+.+.|+
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~~~~~A~  125 (165)
T PRK15331         46 EFYNQGRLDEAETFFRFLCIYDFYNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKAAKAR  125 (165)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCHHHHH
Confidence            345678888888888876 2223 444566677777778888888888   44566788888999999999999999999


Q ss_pred             HHHHHHHh
Q 040371          262 NVREIMKK  269 (410)
Q Consensus       262 ~~~~~m~~  269 (410)
                      ..|....+
T Consensus       126 ~~f~~a~~  133 (165)
T PRK15331        126 QCFELVNE  133 (165)
T ss_pred             HHHHHHHh
Confidence            99988776

>KOG3941 consensus Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms]

Probab=95.28  E-value=0.3  Score=42.99  Aligned_cols=101  Identities=12%  Similarity=0.088  Sum_probs=71.0

Q ss_pred             CCChhHHHHHHHHHHHc-----CCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC----------------CHHHHH
Q 040371            3 DKDVVSWNSMIGGFVRN-----ARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLG----------------ALNHAY   61 (410)
Q Consensus         3 ~~~~~~~n~li~~~~~~-----g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~----------------~~~~a~   61 (410)
                      ++|-.+|-+++..+...     ++++=.-..++.|.+.|+.-|..+|..||+.+-+..                +-+-+.
T Consensus        64 ~RdK~sfl~~V~~F~E~sVr~R~HveFIy~ALk~m~eyGVerDl~vYk~LlnvfPKgkfiP~nvfQ~~F~HYP~QQ~C~I  143 (406)
T KOG3941|consen   64 KRDKDSFLAAVATFKEKSVRGRTHVEFIYTALKYMKEYGVERDLDVYKGLLNVFPKGKFIPQNVFQKVFLHYPQQQNCAI  143 (406)
T ss_pred             cccHHHHHHHHHHHHHhhhcccchHHHHHHHHHHHHHhcchhhHHHHHHHHHhCcccccccHHHHHHHHhhCchhhhHHH
Confidence            46777888888777654     455556666788888888888888888888765432                223467


Q ss_pred             HHHHHHHHcCCCccHHHHHHHHHHHHhcCC-HHHHHHHHHhcc
Q 040371           62 WVHNLIIEKKIELNFILSAALIDMYSKCGK-IQMAKEVFDTVQ  103 (410)
Q Consensus        62 ~~~~~~~~~g~~~~~~~~~~li~~y~~~g~-~~~A~~~f~~m~  103 (410)
                      .++++|...|+.||-.+-..|++.+++.|- ..+..++.--|+
T Consensus       144 ~vLeqME~hGVmPdkE~e~~lvn~FGr~~~p~~K~~Rm~yWmP  186 (406)
T KOG3941|consen  144 KVLEQMEWHGVMPDKEIEDILVNAFGRWNFPTKKVKRMLYWMP  186 (406)
T ss_pred             HHHHHHHHcCCCCchHHHHHHHHHhccccccHHHHHHHHHhhh
Confidence            788888888888888888888888887765 334444444443

>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=95.24  E-value=0.87  Score=42.38  Aligned_cols=250  Identities=11%  Similarity=0.047  Sum_probs=136.6

Q ss_pred             HHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHH
Q 040371           14 GGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQ   93 (410)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~   93 (410)
                      ..+.+..++.+|+..+....+.. +-+..-|..=+..+...++++.+.--.+.-++.. +-......-.-.++...++..
T Consensus        57 n~~yk~k~Y~nal~~yt~Ai~~~-pd~a~yy~nRAa~~m~~~~~~~a~~dar~~~r~k-d~~~k~~~r~~~c~~a~~~~i  134 (486)
T KOG0550|consen   57 NAFYKQKTYGNALKNYTFAIDMC-PDNASYYSNRAATLMMLGRFEEALGDARQSVRLK-DGFSKGQLREGQCHLALSDLI  134 (486)
T ss_pred             chHHHHhhHHHHHHHHHHHHHhC-ccchhhhchhHHHHHHHHhHhhcccchhhheecC-CCccccccchhhhhhhhHHHH
Confidence            44555667777777777777653 2234445555555555566655544333333221 000111111222223333333


Q ss_pred             HHHHHHH------------hcc---c-----CChhhHHHH-HHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHH--
Q 040371           94 MAKEVFD------------TVQ---R-----NDVSVWNAM-ISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLT--  150 (410)
Q Consensus        94 ~A~~~f~------------~m~---~-----~~~~~~~~l-i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~--  150 (410)
                      +|.+.|+            ...   .     |-..+|-.+ ...+.-.|+.++|.+.--..++..  ++ ..+..+++  
T Consensus       135 ~A~~~~~~~~~~~~anal~~~~~~~~s~s~~pac~~a~~lka~cl~~~~~~~~a~~ea~~ilkld--~~-n~~al~vrg~  211 (486)
T KOG0550|consen  135 EAEEKLKSKQAYKAANALPTLEKLAPSHSREPACFKAKLLKAECLAFLGDYDEAQSEAIDILKLD--AT-NAEALYVRGL  211 (486)
T ss_pred             HHHHHhhhhhhhHHhhhhhhhhcccccccCCchhhHHHHhhhhhhhhcccchhHHHHHHHHHhcc--cc-hhHHHHhccc
Confidence            3333222            111   0     111233322 233455678888887766655432  11 12222232  


Q ss_pred             HHHccCCHHHHHHHHHHhhhhcCCCCChhH-------------HHHHHHHHHhcCCHHHHHHHHHhC-CCCC-----CHH
Q 040371          151 ACSHCGLVEEGRKYFDHMRSRYSIQPQLEH-------------YGAMVDLLGRAGHIEEAYGLITSM-TMEP-----DVV  211 (410)
Q Consensus       151 a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~-------------~~~li~~~~~~g~~~~A~~~~~~m-~~~p-----~~~  211 (410)
                      ++.-.++.+.|...|++...   +.|+-..             +.-=.....+.|++.+|.+.+.+. .+.|     +..
T Consensus       212 ~~yy~~~~~ka~~hf~qal~---ldpdh~~sk~~~~~~k~le~~k~~gN~~fk~G~y~~A~E~Yteal~idP~n~~~nak  288 (486)
T KOG0550|consen  212 CLYYNDNADKAINHFQQALR---LDPDHQKSKSASMMPKKLEVKKERGNDAFKNGNYRKAYECYTEALNIDPSNKKTNAK  288 (486)
T ss_pred             ccccccchHHHHHHHhhhhc---cChhhhhHHhHhhhHHHHHHHHhhhhhHhhccchhHHHHHHHHhhcCCccccchhHH
Confidence            23346778888888887662   3333211             112223456789999999988876 4444     455


Q ss_pred             HHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          212 VWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       212 ~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      .|........+.|+.++|+.-   ...+++.-...|..-.+++...++|++|.+-++...+..
T Consensus       289 lY~nra~v~~rLgrl~eaisdc~~Al~iD~syikall~ra~c~l~le~~e~AV~d~~~a~q~~  351 (486)
T KOG0550|consen  289 LYGNRALVNIRLGRLREAISDCNEALKIDSSYIKALLRRANCHLALEKWEEAVEDYEKAMQLE  351 (486)
T ss_pred             HHHHhHhhhcccCCchhhhhhhhhhhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            566666667888999998887   555555555556666778888899999999888766543

>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=95.24  E-value=0.59  Score=45.03  Aligned_cols=162  Identities=20%  Similarity=0.185  Sum_probs=104.7

Q ss_pred             HHHHcCCHhHHHHHHH-HHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHH
Q 040371           15 GFVRNARFDEALRFFR-EMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQ   93 (410)
Q Consensus        15 ~~~~~g~~~~a~~l~~-~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~   93 (410)
                      ...-+++++++.+..+ .-.-..++  ..-...++.-+-+.|-.+.|.++-.         |+   ..-.+...++|+++
T Consensus       270 ~av~~~d~~~v~~~i~~~~ll~~i~--~~~~~~i~~fL~~~G~~e~AL~~~~---------D~---~~rFeLAl~lg~L~  335 (443)
T PF04053_consen  270 TAVLRGDFEEVLRMIAASNLLPNIP--KDQGQSIARFLEKKGYPELALQFVT---------DP---DHRFELALQLGNLD  335 (443)
T ss_dssp             HHHHTT-HHH-----HHHHTGGG----HHHHHHHHHHHHHTT-HHHHHHHSS----------H---HHHHHHHHHCT-HH
T ss_pred             HHHHcCChhhhhhhhhhhhhcccCC--hhHHHHHHHHHHHCCCHHHHHhhcC---------Ch---HHHhHHHHhcCCHH
Confidence            3445688888777664 11111122  4457788888888898988887643         22   13345667899999


Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcC
Q 040371           94 MAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYS  173 (410)
Q Consensus        94 ~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~  173 (410)
                      .|.++-++..  +...|..|.....+.|+.+-|.+.|.+...         |..|+-.|.-.|+.+.-.++.+....+ |
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            9988877766  667999999999999999999999987542         566777778888887777777666543 2


Q ss_pred             CCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCC
Q 040371          174 IQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEP  208 (410)
Q Consensus       174 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p  208 (410)
                            -++....++.-.|+.++..+++.+-+.-|
T Consensus       404 ------~~n~af~~~~~lgd~~~cv~lL~~~~~~~  432 (443)
T PF04053_consen  404 ------DINIAFQAALLLGDVEECVDLLIETGRLP  432 (443)
T ss_dssp             -------HHHHHHHHHHHT-HHHHHHHHHHTT-HH
T ss_pred             ------CHHHHHHHHHHcCCHHHHHHHHHHcCCch
Confidence                  25555666677788888888888775443

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.

>PF13371 TPR_9: Tetratricopeptide repeat

Probab=95.20  E-value=0.12  Score=35.71  Aligned_cols=50  Identities=16%  Similarity=0.140  Sum_probs=21.2

Q ss_pred             HHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           86 YSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      |.+.+++++|.++++++..  | +...|......|.+.|++++|.+.|++..+
T Consensus         5 ~~~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~   57 (73)
T PF13371_consen    5 YLQQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRYEEALEDLERALE   57 (73)
T ss_pred             HHhCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence            3444444444444444332  1 233344444444444444444444444443

>COG3898 Uncharacterized membrane-bound protein [Function unknown]

Probab=95.08  E-value=2.9  Score=38.86  Aligned_cols=241  Identities=16%  Similarity=0.155  Sum_probs=155.4

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      -.|++++|.+-|+.|...- .--..-+..|.-..-+.|+.+.|++.-+..-... +.=...+.+++...+..|+++.|++
T Consensus       132 ~eG~~~~Ar~kfeAMl~dP-EtRllGLRgLyleAqr~GareaAr~yAe~Aa~~A-p~l~WA~~AtLe~r~~~gdWd~Alk  209 (531)
T COG3898         132 LEGDYEDARKKFEAMLDDP-ETRLLGLRGLYLEAQRLGAREAARHYAERAAEKA-PQLPWAARATLEARCAAGDWDGALK  209 (531)
T ss_pred             hcCchHHHHHHHHHHhcCh-HHHHHhHHHHHHHHHhcccHHHHHHHHHHHHhhc-cCCchHHHHHHHHHHhcCChHHHHH
Confidence            4699999999999998631 1111233445555568899999998888776543 2235678899999999999999999


Q ss_pred             HHHhcc-----cCChh--hHHHHHHHHHH---cCChHHHHHHHHHHHHCCCCCCHHH-HHHHHHHHHccCCHHHHHHHHH
Q 040371           98 VFDTVQ-----RNDVS--VWNAMISGVAI---HGLAADASAIFTKMEMFNVLPDSIT-FLGLLTACSHCGLVEEGRKYFD  166 (410)
Q Consensus        98 ~f~~m~-----~~~~~--~~~~li~~~~~---~g~~~~A~~l~~~m~~~g~~p~~~t-~~~ll~a~~~~g~~~~a~~~~~  166 (410)
                      +.+.-.     ++|+.  .-..|+.+-+.   .-+...|.+.-.+..+  +.||-+- -.....++.+.|++.++-.+++
T Consensus       210 Lvd~~~~~~vie~~~aeR~rAvLLtAkA~s~ldadp~~Ar~~A~~a~K--L~pdlvPaav~AAralf~d~~~rKg~~ilE  287 (531)
T COG3898         210 LVDAQRAAKVIEKDVAERSRAVLLTAKAMSLLDADPASARDDALEANK--LAPDLVPAAVVAARALFRDGNLRKGSKILE  287 (531)
T ss_pred             HHHHHHHHHhhchhhHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHhh--cCCccchHHHHHHHHHHhccchhhhhhHHH
Confidence            998755     34443  23334433322   3456666665554433  5676433 3344578889999999999999


Q ss_pred             HhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhcc
Q 040371          167 HMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM----TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISR  238 (410)
Q Consensus       167 ~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~  238 (410)
                      .+-+.   +|.+..+...+  +.+.|+.  +++-+++.    .++| +..+--.+..+....|++..|..-   .....|
T Consensus       288 ~aWK~---ePHP~ia~lY~--~ar~gdt--a~dRlkRa~~L~slk~nnaes~~~va~aAlda~e~~~ARa~Aeaa~r~~p  360 (531)
T COG3898         288 TAWKA---EPHPDIALLYV--RARSGDT--ALDRLKRAKKLESLKPNNAESSLAVAEAALDAGEFSAARAKAEAAAREAP  360 (531)
T ss_pred             HHHhc---CCChHHHHHHH--HhcCCCc--HHHHHHHHHHHHhcCccchHHHHHHHHHHHhccchHHHHHHHHHHhhhCc
Confidence            98754   55555444333  4455543  22222222    3456 456677777888888998888776   333333


Q ss_pred             CCCchHHHHHHHHH-hcCChhHHHHHHHHHHhC
Q 040371          239 LMGGDYVLLSNMYC-YLKRWDTAENVREIMKKK  270 (410)
Q Consensus       239 ~~~~~~~~l~~~~~-~~g~~~~a~~~~~~m~~~  270 (410)
                       ....|..|.+.-. ..|+-.++...+-+-...
T Consensus       361 -res~~lLlAdIeeAetGDqg~vR~wlAqav~A  392 (531)
T COG3898         361 -RESAYLLLADIEEAETGDQGKVRQWLAQAVKA  392 (531)
T ss_pred             -hhhHHHHHHHHHhhccCchHHHHHHHHHHhcC
Confidence             3356777777654 448888888777655443

>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional

Probab=94.99  E-value=0.45  Score=45.09  Aligned_cols=63  Identities=11%  Similarity=-0.090  Sum_probs=38.7

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc-H---HHHHHHHHHHHhcCCHHHHHHHHHhccc
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN-F---ILSAALIDMYSKCGKIQMAKEVFDTVQR  104 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~-~---~~~~~li~~y~~~g~~~~A~~~f~~m~~  104 (410)
                      +...++.+..++...|++++|...|++.++..  |+ .   ..|..+..+|.+.|+.++|...|++..+
T Consensus        74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~--Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe  140 (453)
T PLN03098         74 TAEDAVNLGLSLFSKGRVKDALAQFETALELN--PNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR  140 (453)
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC--CCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            34466666666666666666666666666643  33 1   3466666666666666666666666543

>PRK15331 chaperone protein SicA; Provisional

Probab=94.86  E-value=0.28  Score=39.82  Aligned_cols=85  Identities=15%  Similarity=0.048  Sum_probs=63.5

Q ss_pred             HHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhc---ccCChhhHHHHHHHHHHcCChHHH
Q 040371           50 GCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTV---QRNDVSVWNAMISGVAIHGLAADA  126 (410)
Q Consensus        50 a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m---~~~~~~~~~~li~~~~~~g~~~~A  126 (410)
                      -+-..|++++|..+|..+...+. .+..-+..|..+|-..+++++|...|...   ...|....--+..+|...|+.+.|
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~~~~~A  124 (165)
T PRK15331         46 EFYNQGRLDEAETFFRFLCIYDF-YNPDYTMGLAAVCQLKKQFQKACDLYAVAFTLLKNDYRPVFFTGQCQLLMRKAAKA  124 (165)
T ss_pred             HHHHCCCHHHHHHHHHHHHHhCc-CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCCccchHHHHHHHhCCHHHH
Confidence            33577888888888888877653 35666788888888888888888888643   234555566667778888888888


Q ss_pred             HHHHHHHHH
Q 040371          127 SAIFTKMEM  135 (410)
Q Consensus       127 ~~l~~~m~~  135 (410)
                      ..-|.....
T Consensus       125 ~~~f~~a~~  133 (165)
T PRK15331        125 RQCFELVNE  133 (165)
T ss_pred             HHHHHHHHh
Confidence            888887766

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=94.43  E-value=1.8  Score=40.80  Aligned_cols=146  Identities=14%  Similarity=0.123  Sum_probs=110.9

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC-CCccHHHHHHHHHHHHhcCCHHHHHHHHHh-cc-cCChhhH-HHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKK-IELNFILSAALIDMYSKCGKIQMAKEVFDT-VQ-RNDVSVW-NAMIS  115 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g-~~~~~~~~~~li~~y~~~g~~~~A~~~f~~-m~-~~~~~~~-~~li~  115 (410)
                      =.+.|...+++..+..-++.|+.+|-++.+.| +.+++.+++++|..|+ .|+..-|.++|+- |. -+|...| +--+.
T Consensus       396 ~t~v~C~~~N~v~r~~Gl~aaR~~F~k~rk~~~~~h~vyi~~A~~E~~~-~~d~~ta~~ifelGl~~f~d~~~y~~kyl~  474 (660)
T COG5107         396 LTFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLKFPDSTLYKEKYLL  474 (660)
T ss_pred             hhhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHhCCCchHHHHHHHH
Confidence            35788889999999999999999999999998 6789999999999877 6788889999984 33 3555444 45566


Q ss_pred             HHHHcCChHHHHHHHHHHHHCCCCCC--HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHh
Q 040371          116 GVAIHGLAADASAIFTKMEMFNVLPD--SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGR  190 (410)
Q Consensus       116 ~~~~~g~~~~A~~l~~~m~~~g~~p~--~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~  190 (410)
                      -+..-++-+.|..+|+.-... +..+  ...|..+|..=+.-|++..+..+=+.|.+.   .|...+-......|+-
T Consensus       475 fLi~inde~naraLFetsv~r-~~~~q~k~iy~kmi~YEs~~G~lN~v~sLe~rf~e~---~pQen~~evF~Sry~i  547 (660)
T COG5107         475 FLIRINDEENARALFETSVER-LEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL---VPQENLIEVFTSRYAI  547 (660)
T ss_pred             HHHHhCcHHHHHHHHHHhHHH-HHHhhhhHHHHHHHHHHHhhcchHHHHhHHHHHHHH---cCcHhHHHHHHHHHhh
Confidence            677789999999999955432 2222  467899999999999999998888888754   3444444444555544

>PRK10866 outer membrane biogenesis protein BamD; Provisional

Probab=94.32  E-value=3.5  Score=36.37  Aligned_cols=176  Identities=11%  Similarity=-0.002  Sum_probs=92.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhcccC--Ch-h---hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040371           76 FILSAALIDMYSKCGKIQMAKEVFDTVQRN--DV-S---VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLL  149 (410)
Q Consensus        76 ~~~~~~li~~y~~~g~~~~A~~~f~~m~~~--~~-~---~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll  149 (410)
                      ....-.....+.+.|++++|.+.|+.+...  +. .   ..-.+..+|.+.+++++|...|++..+.-..-...-+...+
T Consensus        32 ~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~  111 (243)
T PRK10866         32 PSEIYATAQQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYM  111 (243)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHH
Confidence            333334455567789999999999998753  22 1   22345677888999999999999998753222223444444


Q ss_pred             HHHHc--c---------------CC---HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCC
Q 040371          150 TACSH--C---------------GL---VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPD  209 (410)
Q Consensus       150 ~a~~~--~---------------g~---~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~  209 (410)
                      .+.+.  .               .+   ..+|...|+.+.+++   |+.             .-..+|..-+..+..+.-
T Consensus       112 ~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~y---P~S-------------~ya~~A~~rl~~l~~~la  175 (243)
T PRK10866        112 RGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGY---PNS-------------QYTTDATKRLVFLKDRLA  175 (243)
T ss_pred             HHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHC---cCC-------------hhHHHHHHHHHHHHHHHH
Confidence            44331  1               11   234555666666542   222             222233222222210000


Q ss_pred             HHHHHHHHHHHHhcCchhHHHHH---HHhhccCCC---chHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          210 VVVWRALLSACRTFKRLELGEVA---IVNISRLMG---GDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       210 ~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~---~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                      ..-+ .+..-|.+.|.+.-|..-   +.+.-|..+   .....++.+|.+.|..++|..+...+.
T Consensus       176 ~~e~-~ia~~Y~~~~~y~AA~~r~~~v~~~Yp~t~~~~eal~~l~~ay~~lg~~~~a~~~~~~l~  239 (243)
T PRK10866        176 KYEL-SVAEYYTKRGAYVAVVNRVEQMLRDYPDTQATRDALPLMENAYRQLQLNAQADKVAKIIA  239 (243)
T ss_pred             HHHH-HHHHHHHHcCchHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHcCChHHHHHHHHHHh
Confidence            0000 122234444544444433   222233332   345567778888888888887776554

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=94.28  E-value=1.4  Score=40.03  Aligned_cols=48  Identities=13%  Similarity=-0.040  Sum_probs=20.6

Q ss_pred             CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       121 g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      |+..+|-..++++++. .+.|...+...=.+|...|+.+.-...++.+.
T Consensus       117 g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIi  164 (491)
T KOG2610|consen  117 GKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKII  164 (491)
T ss_pred             ccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhc
Confidence            4444444444444432 22233333334444444444444444444444

>COG5107 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

Probab=94.22  E-value=1.4  Score=41.48  Aligned_cols=122  Identities=13%  Similarity=0.085  Sum_probs=55.1

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhH-HHHH
Q 040371          107 VSVWNAMISGVAIHGLAADASAIFTKMEMFN-VLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEH-YGAM  184 (410)
Q Consensus       107 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~-~~~l  184 (410)
                      ..+|-..|+.-.+..-.+.|..+|-+..+.| +.++...+++.+..++ .|+...|..+|+.-...+   ||... -+-.
T Consensus       397 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         397 TFVFCVHLNYVLRKRGLEAARKLFIKLRKEGIVGHHVYIYCAFIEYYA-TGDRATAYNIFELGLLKF---PDSTLYKEKY  472 (660)
T ss_pred             hhHHHHHHHHHHHHhhHHHHHHHHHHHhccCCCCcceeeeHHHHHHHh-cCCcchHHHHHHHHHHhC---CCchHHHHHH
Confidence            3445555554444444555555555555555 3444445555444333 344445555555433221   12222 2233


Q ss_pred             HHHHHhcCCHHHHHHHHHhC--CCCCC--HHHHHHHHHHHHhcCchhHHHHH
Q 040371          185 VDLLGRAGHIEEAYGLITSM--TMEPD--VVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       185 i~~~~~~g~~~~A~~~~~~m--~~~p~--~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      +.-+.+.++-+.|..+|+..  .+..+  ...|..+|.--...|++..+..+
T Consensus       473 l~fLi~inde~naraLFetsv~r~~~~q~k~iy~kmi~YEs~~G~lN~v~sL  524 (660)
T COG5107         473 LLFLIRINDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSL  524 (660)
T ss_pred             HHHHHHhCcHHHHHHHHHHhHHHHHHhhhhHHHHHHHHHHHhhcchHHHHhH
Confidence            44444555555555555533  11112  23455555554555555444444

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=94.20  E-value=1.1  Score=34.85  Aligned_cols=49  Identities=12%  Similarity=-0.018  Sum_probs=23.0

Q ss_pred             HhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371           52 ARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDT  101 (410)
Q Consensus        52 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~  101 (410)
                      +..|+++.|.+.|.+.+..- +....+||.-..+|--.|+.++|..=+++
T Consensus        54 aE~g~Ld~AlE~F~qal~l~-P~raSayNNRAQa~RLq~~~e~ALdDLn~  102 (175)
T KOG4555|consen   54 AEAGDLDGALELFGQALCLA-PERASAYNNRAQALRLQGDDEEALDDLNK  102 (175)
T ss_pred             HhccchHHHHHHHHHHHHhc-ccchHhhccHHHHHHHcCChHHHHHHHHH
Confidence            44455555555555444431 23444455555555555555544444443

>PF09205 DUF1955: Domain of unknown function (DUF1955); InterPro: IPR015288 Members of this family are found in hypothetical proteins synthesised by the Archaeal organism Sulfolobus

Probab=94.10  E-value=1.3  Score=34.51  Aligned_cols=135  Identities=10%  Similarity=0.052  Sum_probs=73.7

Q ss_pred             cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHH
Q 040371          120 HGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYG  199 (410)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~  199 (410)
                      .|..++..++..+.....   +..-++-++.-....-+-+-..+.++.+-+-+.+.              .+|++.....
T Consensus        15 dG~V~qGveii~k~v~Ss---ni~E~NWvICNiiDaa~C~yvv~~LdsIGkiFDis--------------~C~NlKrVi~   77 (161)
T PF09205_consen   15 DGDVKQGVEIIEKTVNSS---NIKEYNWVICNIIDAADCDYVVETLDSIGKIFDIS--------------KCGNLKRVIE   77 (161)
T ss_dssp             TT-HHHHHHHHHHHHHHS----HHHHTHHHHHHHHH--HHHHHHHHHHHGGGS-GG--------------G-S-THHHHH
T ss_pred             hchHHHHHHHHHHHcCcC---CccccceeeeecchhhchhHHHHHHHHHhhhcCch--------------hhcchHHHHH
Confidence            566666666666665432   33445555544444445555555555544322221              2233333333


Q ss_pred             HHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhh---ccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCc
Q 040371          200 LITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNI---SRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVR  273 (410)
Q Consensus       200 ~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~---~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  273 (410)
                      -+-.++  .+..-....+......|.-+.-.++..++   ...++.....+.++|.+.|+..++.+++++.-++|++
T Consensus        78 C~~~~n--~~se~vD~ALd~lv~~~kkDqLdki~~~l~kn~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACekG~k  152 (161)
T PF09205_consen   78 CYAKRN--KLSEYVDLALDILVKQGKKDQLDKIYNELKKNEEINPEFLVKIANAYKKLGNTREANELLKEACEKGLK  152 (161)
T ss_dssp             HHHHTT-----HHHHHHHHHHHHTT-HHHHHHHHHHH-----S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT-H
T ss_pred             HHHHhc--chHHHHHHHHHHHHHhccHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHhchH
Confidence            333322  12333445566777788888777774444   3556677888999999999999999999999999874

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.03  E-value=1  Score=39.66  Aligned_cols=95  Identities=19%  Similarity=0.176  Sum_probs=76.1

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCCh-hHHHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVL--PDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQL-EHYGAMV  185 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~--p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~-~~~~~li  185 (410)
                      .|+.-+..| +.|++.+|.+.|....+....  -....+--|..++...|+++.|..+|..+.++++-.|.. ...--|.
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 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            488877754 578899999999999886311  112335558899999999999999999999887766664 7788888


Q ss_pred             HHHHhcCCHHHHHHHHHhC
Q 040371          186 DLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       186 ~~~~~~g~~~~A~~~~~~m  204 (410)
                      ....+.|+.++|...|++.
T Consensus       223 ~~~~~l~~~d~A~atl~qv  241 (262)
T COG1729         223 VSLGRLGNTDEACATLQQV  241 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHH
Confidence            8899999999999999887

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=93.98  E-value=5.1  Score=39.17  Aligned_cols=177  Identities=13%  Similarity=0.084  Sum_probs=111.8

Q ss_pred             hHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC-CCcc-----HHHHHHHHHHHHh----cCCH
Q 040371           23 DEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKK-IELN-----FILSAALIDMYSK----CGKI   92 (410)
Q Consensus        23 ~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g-~~~~-----~~~~~~li~~y~~----~g~~   92 (410)
                      .-..-+|.-+... +||   .+..+++..+-.||-+.|.+.+....+.+ +...     .-.|+..+..+.-    ....
T Consensus       174 ~~G~G~f~L~lSl-LPp---~~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~  249 (468)
T PF10300_consen  174 YFGFGLFNLVLSL-LPP---KVLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPL  249 (468)
T ss_pred             HHHHHHHHHHHHh-CCH---HHHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCH
Confidence            3344556666654 444   45667777777888888888888776643 2211     2334455554443    4568


Q ss_pred             HHHHHHHHhccc--CChhhHHHHH-HHHHHcCChHHHHHHHHHHHHCC--C-CCCHHHHHHHHHHHHccCCHHHHHHHHH
Q 040371           93 QMAKEVFDTVQR--NDVSVWNAMI-SGVAIHGLAADASAIFTKMEMFN--V-LPDSITFLGLLTACSHCGLVEEGRKYFD  166 (410)
Q Consensus        93 ~~A~~~f~~m~~--~~~~~~~~li-~~~~~~g~~~~A~~l~~~m~~~g--~-~p~~~t~~~ll~a~~~~g~~~~a~~~~~  166 (410)
                      +.|.++++.+.+  |+...|...- ..+...|+.++|++.|++.....  . +.....+--+.-.+.-.+++++|...|.
T Consensus       250 ~~a~~lL~~~~~~yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~f~  329 (468)
T PF10300_consen  250 EEAEELLEEMLKRYPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEYFL  329 (468)
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHHHH
Confidence            889999998876  6766665543 33456799999999998765321  1 1123344455556777889999999999


Q ss_pred             HhhhhcCCCCChhHHHHHHHHHHhcCCH-------HHHHHHHHhC
Q 040371          167 HMRSRYSIQPQLEHYGAMVDLLGRAGHI-------EEAYGLITSM  204 (410)
Q Consensus       167 ~m~~~~~~~~~~~~~~~li~~~~~~g~~-------~~A~~~~~~m  204 (410)
                      .+.+.....+...+|.. ..+|...|+.       ++|.++|++.
T Consensus       330 ~L~~~s~WSka~Y~Y~~-a~c~~~l~~~~~~~~~~~~a~~l~~~v  373 (468)
T PF10300_consen  330 RLLKESKWSKAFYAYLA-AACLLMLGREEEAKEHKKEAEELFRKV  373 (468)
T ss_pred             HHHhccccHHHHHHHHH-HHHHHhhccchhhhhhHHHHHHHHHHH
Confidence            98865333322333322 2345566766       8888888887

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.

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=93.73  E-value=3.8  Score=36.62  Aligned_cols=120  Identities=8%  Similarity=-0.011  Sum_probs=83.1

Q ss_pred             HHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHH---HHHHHHhcCch
Q 040371          150 TACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRA---LLSACRTFKRL  226 (410)
Q Consensus       150 ~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~---li~~~~~~g~~  226 (410)
                      ......|++.+|..+|+.....  .+-+...--.|..+|...|+.+.|..++..++.+-...-|..   =|..+.+....
T Consensus       142 ~~~~~~e~~~~a~~~~~~al~~--~~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~  219 (304)
T COG3118         142 KELIEAEDFGEAAPLLKQALQA--APENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAAT  219 (304)
T ss_pred             hhhhhccchhhHHHHHHHHHHh--CcccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcC
Confidence            3456788899999999887753  222356677788899999999999999999865533333333   23334444444


Q ss_pred             hHHHHH--HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          227 ELGEVA--IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       227 ~~a~~~--~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      .+...+  -...+|.|...-..|...|...|+.++|.+.+-.+.+++
T Consensus       220 ~~~~~l~~~~aadPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d  266 (304)
T COG3118         220 PEIQDLQRRLAADPDDVEAALALADQLHLVGRNEAALEHLLALLRRD  266 (304)
T ss_pred             CCHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhc
Confidence            444444  334467777778889999999999999988776665553

>PF10300 DUF3808: Protein of unknown function (DUF3808); InterPro: IPR019412 This entry represents a family of proteins conserved from fungi to humans

Probab=93.65  E-value=2.4  Score=41.46  Aligned_cols=171  Identities=14%  Similarity=0.089  Sum_probs=109.3

Q ss_pred             HHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc-CC---------hhhHHHHHHHHHH----cCCh
Q 040371           58 NHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR-ND---------VSVWNAMISGVAI----HGLA  123 (410)
Q Consensus        58 ~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-~~---------~~~~~~li~~~~~----~g~~  123 (410)
                      ..+.-+|..++.. +||   ....+++..+=.|+-+.+.+.+.+-.+ ++         ...|+.++..++-    ....
T Consensus       174 ~~G~G~f~L~lSl-LPp---~~~kll~~vGF~gdR~~GL~~L~~~~~~~~i~~~la~L~LL~y~~~~~~~~~~~~~~~~~  249 (468)
T PF10300_consen  174 YFGFGLFNLVLSL-LPP---KVLKLLSFVGFSGDRELGLRLLWEASKSENIRSPLAALVLLWYHLVVPSFLGIDGEDVPL  249 (468)
T ss_pred             HHHHHHHHHHHHh-CCH---HHHHHHhhcCcCCcHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHHcCCcccCCCH
Confidence            3445566666654 344   345666677777888888888776543 22         2357777766654    3567


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHH-HHHHHccCCHHHHHHHHHHhhhhcCCCC--ChhHHHHHHHHHHhcCCHHHHHHH
Q 040371          124 ADASAIFTKMEMFNVLPDSITFLGL-LTACSHCGLVEEGRKYFDHMRSRYSIQP--QLEHYGAMVDLLGRAGHIEEAYGL  200 (410)
Q Consensus       124 ~~A~~l~~~m~~~g~~p~~~t~~~l-l~a~~~~g~~~~a~~~~~~m~~~~~~~~--~~~~~~~li~~~~~~g~~~~A~~~  200 (410)
                      +.|.+++..+...  -|+...|... ...+...|++++|.+.|+.......--+  ....+--+.-.+.-.+++++|.+.
T Consensus       250 ~~a~~lL~~~~~~--yP~s~lfl~~~gR~~~~~g~~~~Ai~~~~~a~~~q~~~~Ql~~l~~~El~w~~~~~~~w~~A~~~  327 (468)
T PF10300_consen  250 EEAEELLEEMLKR--YPNSALFLFFEGRLERLKGNLEEAIESFERAIESQSEWKQLHHLCYFELAWCHMFQHDWEEAAEY  327 (468)
T ss_pred             HHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHhcCHHHHHHHHHHhccchhhHHhHHHHHHHHHHHHHHHHchHHHHHHH
Confidence            8899999999874  6887766543 3456678999999999997553111111  223445566678889999999999


Q ss_pred             HHhCC-CC-CCHHHHHHHHHHH-HhcCch-------hHHHHHHH
Q 040371          201 ITSMT-ME-PDVVVWRALLSAC-RTFKRL-------ELGEVAIV  234 (410)
Q Consensus       201 ~~~m~-~~-p~~~~~~~li~~~-~~~g~~-------~~a~~~~~  234 (410)
                      |.++. .. ....+|.-+..+| ...|+.       ++|..++.
T Consensus       328 f~~L~~~s~WSka~Y~Y~~a~c~~~l~~~~~~~~~~~~a~~l~~  371 (468)
T PF10300_consen  328 FLRLLKESKWSKAFYAYLAAACLLMLGREEEAKEHKKEAEELFR  371 (468)
T ss_pred             HHHHHhccccHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHH
Confidence            99983 22 2333444444433 456666       66666633

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.

>KOG2610 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.52  E-value=2.4  Score=38.49  Aligned_cols=148  Identities=13%  Similarity=0.039  Sum_probs=88.0

Q ss_pred             cCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc---CCCccHHHHHHHHHHHHhcCCHHHH
Q 040371           19 NARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK---KIELNFILSAALIDMYSKCGKIQMA   95 (410)
Q Consensus        19 ~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~---g~~~~~~~~~~li~~y~~~g~~~~A   95 (410)
                      +|++.+|-..++++++. .+.|...+...=.+|.-.|+.+.-+..+++++-.   +++...++-..+.-++..+|-+++|
T Consensus       116 ~g~~h~a~~~wdklL~d-~PtDlla~kfsh~a~fy~G~~~~~k~ai~kIip~wn~dlp~~sYv~GmyaFgL~E~g~y~dA  194 (491)
T KOG2610|consen  116 RGKHHEAAIEWDKLLDD-YPTDLLAVKFSHDAHFYNGNQIGKKNAIEKIIPKWNADLPCYSYVHGMYAFGLEECGIYDDA  194 (491)
T ss_pred             cccccHHHHHHHHHHHh-CchhhhhhhhhhhHHHhccchhhhhhHHHHhccccCCCCcHHHHHHHHHHhhHHHhccchhH
Confidence            46666777777777764 4557777777777888888877777777777543   3333344444444555677888888


Q ss_pred             HHHHHhcccCC---hhhHHHHHHHHHHcCChHHHHHHHHHHHHC---CCCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040371           96 KEVFDTVQRND---VSVWNAMISGVAIHGLAADASAIFTKMEMF---NVLPDSITFLGLLTACSHCGLVEEGRKYFDH  167 (410)
Q Consensus        96 ~~~f~~m~~~~---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~---g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~  167 (410)
                      ++.-++..+-|   .-+-.+....+-.+|+..++.++..+-...   +-..-..-|-...-.+...+.++.|+.+|+.
T Consensus       195 Ek~A~ralqiN~~D~Wa~Ha~aHVlem~~r~Keg~eFM~~ted~Wr~s~mlasHNyWH~Al~~iE~aeye~aleIyD~  272 (491)
T KOG2610|consen  195 EKQADRALQINRFDCWASHAKAHVLEMNGRHKEGKEFMYKTEDDWRQSWMLASHNYWHTALFHIEGAEYEKALEIYDR  272 (491)
T ss_pred             HHHHHhhccCCCcchHHHHHHHHHHHhcchhhhHHHHHHhcccchhhhhHHHhhhhHHHHHhhhcccchhHHHHHHHH
Confidence            87777665433   333344455555677777777766543221   0000112222333344455777888877775

>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=93.40  E-value=2.5  Score=40.82  Aligned_cols=131  Identities=14%  Similarity=0.169  Sum_probs=71.3

Q ss_pred             HHcCChHHHHHHHH-HHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHH
Q 040371          118 AIHGLAADASAIFT-KMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEE  196 (410)
Q Consensus       118 ~~~g~~~~A~~l~~-~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~  196 (410)
                      .-.|+++++.++.. .-.-..++  ..-.+.++.-+.+.|..+.|+++-..-..             --+...++|+++.
T Consensus       272 v~~~d~~~v~~~i~~~~ll~~i~--~~~~~~i~~fL~~~G~~e~AL~~~~D~~~-------------rFeLAl~lg~L~~  336 (443)
T PF04053_consen  272 VLRGDFEEVLRMIAASNLLPNIP--KDQGQSIARFLEKKGYPELALQFVTDPDH-------------RFELALQLGNLDI  336 (443)
T ss_dssp             HHTT-HHH-----HHHHTGGG----HHHHHHHHHHHHHTT-HHHHHHHSS-HHH-------------HHHHHHHCT-HHH
T ss_pred             HHcCChhhhhhhhhhhhhcccCC--hhHHHHHHHHHHHCCCHHHHHhhcCChHH-------------HhHHHHhcCCHHH
Confidence            34566666655554 11111111  33356666666777777777765433221             2334566777777


Q ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          197 AYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       197 A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      |.++.++..   +...|..|-..+...|+++.|++.+.+.     .-+..|+-.|.-.|+.+.-.++.+....+|
T Consensus       337 A~~~a~~~~---~~~~W~~Lg~~AL~~g~~~lAe~c~~k~-----~d~~~L~lLy~~~g~~~~L~kl~~~a~~~~  403 (443)
T PF04053_consen  337 ALEIAKELD---DPEKWKQLGDEALRQGNIELAEECYQKA-----KDFSGLLLLYSSTGDREKLSKLAKIAEERG  403 (443)
T ss_dssp             HHHHCCCCS---THHHHHHHHHHHHHTTBHHHHHHHHHHC-----T-HHHHHHHHHHCT-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHhcC---cHHHHHHHHHHHHHcCCHHHHHHHHHhh-----cCccccHHHHHHhCCHHHHHHHHHHHHHcc
Confidence            777666553   6667777777777777777777776554     245566667777777766666666655554

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.

>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=93.39  E-value=3  Score=32.51  Aligned_cols=64  Identities=8%  Similarity=0.118  Sum_probs=43.5

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCC
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSI  174 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~  174 (410)
                      -.+..+......|+-+.-.+++.++... -+|++.....+..||.+.|+..++.+++.+.-++ |+
T Consensus        88 ~vD~ALd~lv~~~kkDqLdki~~~l~kn-~~~~p~~L~kia~Ay~klg~~r~~~ell~~ACek-G~  151 (161)
T PF09205_consen   88 YVDLALDILVKQGKKDQLDKIYNELKKN-EEINPEFLVKIANAYKKLGNTREANELLKEACEK-GL  151 (161)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHH------S-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHT-T-
T ss_pred             HHHHHHHHHHHhccHHHHHHHHHHHhhc-cCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHh-ch
Confidence            3455667778888888888888887653 4677777888888888999888888888888765 64

Their exact function has not, as yet, been determined. ; PDB: 1WY6_A.

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=93.35  E-value=3.4  Score=37.59  Aligned_cols=126  Identities=14%  Similarity=0.182  Sum_probs=84.2

Q ss_pred             HHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh--cC----CHHHHHHHHHhcccC-------ChhhHHHHHHHHHHcCC-
Q 040371           57 LNHAYWVHNLIIEKKIELNFILSAALIDMYSK--CG----KIQMAKEVFDTVQRN-------DVSVWNAMISGVAIHGL-  122 (410)
Q Consensus        57 ~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~--~g----~~~~A~~~f~~m~~~-------~~~~~~~li~~~~~~g~-  122 (410)
                      ++....+++.+.+.|+..+..++-+..-....  ..    ....|..+|+.|++.       +-.++.+|+..  ..++ 
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            45677899999999999888777664443333  22    256789999999853       44567777665  2232 


Q ss_pred             ---hHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHc-cCC--HHHHHHHHHHhhhhcCCCCChhHHHHHH
Q 040371          123 ---AADASAIFTKMEMFNVLPD-SITFLGLLTACSH-CGL--VEEGRKYFDHMRSRYSIQPQLEHYGAMV  185 (410)
Q Consensus       123 ---~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~-~g~--~~~a~~~~~~m~~~~~~~~~~~~~~~li  185 (410)
                         .+.+...|+.+...|...+ ..-+.+-+-++.. ...  +..+.++++.+.+. |+++...+|..+.
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~-~~kik~~~yp~lG  224 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKN-GVKIKYMHYPTLG  224 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHc-CCccccccccHHH
Confidence               4567788888888887664 3333333333332 222  45788889999876 9998888876554

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=93.33  E-value=1.4  Score=40.97  Aligned_cols=118  Identities=14%  Similarity=0.113  Sum_probs=82.7

Q ss_pred             HHHHHhcCCHHHHHHHHHhccc------------------CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHH
Q 040371           83 IDMYSKCGKIQMAKEVFDTVQR------------------NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSIT  144 (410)
Q Consensus        83 i~~y~~~g~~~~A~~~f~~m~~------------------~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t  144 (410)
                      .+.|.|.|++..|..-|++...                  .-+.+++.+..+|.+.+++.+|++.-.+.+..+ .+|...
T Consensus       215 Gn~~fK~gk~~~A~~~Yerav~~l~~~~~~~~ee~~~~~~~k~~~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KA  293 (397)
T KOG0543|consen  215 GNVLFKEGKFKLAKKRYERAVSFLEYRRSFDEEEQKKAEALKLACHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKA  293 (397)
T ss_pred             hhHHHhhchHHHHHHHHHHHHHHhhccccCCHHHHHHHHHHHHHHhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhH
Confidence            3567888888888887776321                  123467788888999999999999999888764 446666


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChh-HHHHHHHHHHhcCCHHH-HHHHHHhC
Q 040371          145 FLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLE-HYGAMVDLLGRAGHIEE-AYGLITSM  204 (410)
Q Consensus       145 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~-~~~~li~~~~~~g~~~~-A~~~~~~m  204 (410)
                      .--=..||...|+++.|+..|+.+.+   +.|+.. .-+.++.+--+.....+ ..++|..|
T Consensus       294 LyRrG~A~l~~~e~~~A~~df~ka~k---~~P~Nka~~~el~~l~~k~~~~~~kekk~y~~m  352 (397)
T KOG0543|consen  294 LYRRGQALLALGEYDLARDDFQKALK---LEPSNKAARAELIKLKQKIREYEEKEKKMYANM  352 (397)
T ss_pred             HHHHHHHHHhhccHHHHHHHHHHHHH---hCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66667888889999999999999884   366544 34444444444444433 35677776

>PF13281 DUF4071: Domain of unknown function (DUF4071)

Probab=93.12  E-value=7.6  Score=36.38  Aligned_cols=158  Identities=11%  Similarity=-0.012  Sum_probs=98.8

Q ss_pred             HHHHHHHcCChHHHHHHHHHHHHCCC--CC-CHHHHHHHHHHHHc---cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHH
Q 040371          113 MISGVAIHGLAADASAIFTKMEMFNV--LP-DSITFLGLLTACSH---CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVD  186 (410)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~g~--~p-~~~t~~~ll~a~~~---~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~  186 (410)
                      ++-.|-...+++..+++.+.|...-.  .+ ....--....|+.+   .|+.++|++++..+... .-.+++.+|..+..
T Consensus       147 lllSyRdiqdydamI~Lve~l~~~p~~~~~~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~-~~~~~~d~~gL~GR  225 (374)
T PF13281_consen  147 LLLSYRDIQDYDAMIKLVETLEALPTCDVANQHNIKFQYAFALNRRNKPGDREKALQILLPVLES-DENPDPDTLGLLGR  225 (374)
T ss_pred             HHHHhhhhhhHHHHHHHHHHhhccCccchhcchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhc-cCCCChHHHHHHHH
Confidence            44458888999999999999986411  11 11111233445566   89999999999995543 55667778877776


Q ss_pred             HHHh----c-----CCHHHHHHHHHhC-CCCCCHHH---HHHHHHHHHhcC-chhHHHHH-------HHhhc----cCCC
Q 040371          187 LLGR----A-----GHIEEAYGLITSM-TMEPDVVV---WRALLSACRTFK-RLELGEVA-------IVNIS----RLMG  241 (410)
Q Consensus       187 ~~~~----~-----g~~~~A~~~~~~m-~~~p~~~~---~~~li~~~~~~g-~~~~a~~~-------~~~~~----~~~~  241 (410)
                      .|-.    .     ..+++|...|.+. .++||..+   +.+|+....... .-.+..++       +.+..    ..+.
T Consensus       226 IyKD~~~~s~~~d~~~ldkAi~~Y~kgFe~~~~~Y~GIN~AtLL~~~g~~~~~~~el~~i~~~l~~llg~kg~~~~~~dY  305 (374)
T PF13281_consen  226 IYKDLFLESNFTDRESLDKAIEWYRKGFEIEPDYYSGINAATLLMLAGHDFETSEELRKIGVKLSSLLGRKGSLEKMQDY  305 (374)
T ss_pred             HHHHHHHHcCccchHHHHHHHHHHHHHHcCCccccchHHHHHHHHHcCCcccchHHHHHHHHHHHHHHHhhccccccccH
Confidence            5532    2     2477888888876 55666543   233333322211 11122222       11111    1233


Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          242 GDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       242 ~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      ..+.++..++.-.|+.++|.+..+.|....
T Consensus       306 Wd~ATl~Ea~vL~~d~~ka~~a~e~~~~l~  335 (374)
T PF13281_consen  306 WDVATLLEASVLAGDYEKAIQAAEKAFKLK  335 (374)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHhhcC
Confidence            456789999999999999999999998663

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=93.09  E-value=0.074  Score=30.69  Aligned_cols=28  Identities=18%  Similarity=0.283  Sum_probs=24.8

Q ss_pred             HhhccCCCchHHHHHHHHHhcCChhHHH
Q 040371          234 VNISRLMGGDYVLLSNMYCYLKRWDTAE  261 (410)
Q Consensus       234 ~~~~~~~~~~~~~l~~~~~~~g~~~~a~  261 (410)
                      .++.|.++.+|..|..+|...|++++|+
T Consensus         6 ie~~P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen    6 IELNPNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             HHHCCCCHHHHHHHHHHHHHCcCHHhhc
Confidence            4578999999999999999999999886

>PF13512 TPR_18: Tetratricopeptide repeat

Probab=92.86  E-value=2.4  Score=33.58  Aligned_cols=50  Identities=10%  Similarity=0.082  Sum_probs=26.9

Q ss_pred             HhcCCHHHHHHHHHhcccC------ChhhHHHHHHHHHHcCChHHHHHHHHHHHHC
Q 040371           87 SKCGKIQMAKEVFDTVQRN------DVSVWNAMISGVAIHGLAADASAIFTKMEMF  136 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~~------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  136 (410)
                      .+.|++++|.+.|+.+..+      ...+.-.++.+|.+.|++++|...+++..+.
T Consensus        21 l~~~~Y~~A~~~le~L~~ryP~g~ya~qAqL~l~yayy~~~~y~~A~a~~~rFirL   76 (142)
T PF13512_consen   21 LQKGNYEEAIKQLEALDTRYPFGEYAEQAQLDLAYAYYKQGDYEEAIAAYDRFIRL   76 (142)
T ss_pred             HHhCCHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence            3455566666666555532      1223344555566666666666666665553

>PF13170 DUF4003: Protein of unknown function (DUF4003)

Probab=92.85  E-value=7.3  Score=35.45  Aligned_cols=126  Identities=10%  Similarity=0.134  Sum_probs=81.9

Q ss_pred             HhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh--hC----CHHHHHHHHHHHHHcCC---CccHHHHHHHHHHHHhcCCH
Q 040371           22 FDEALRFFREMLSSKVEPDKFTFASVIYGCAR--LG----ALNHAYWVHNLIIEKKI---ELNFILSAALIDMYSKCGKI   92 (410)
Q Consensus        22 ~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~--~~----~~~~a~~~~~~~~~~g~---~~~~~~~~~li~~y~~~g~~   92 (410)
                      +++.+.+++.|.+.|.+-+.++|.+.......  ..    ....+..+|+.|.+.-.   .++..++.+|+.+  ...+.
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            45677888999999999998888876655544  22    35678999999988632   2455666666554  34443


Q ss_pred             ----HHHHHHHHhccc-----CCh-hhHHHHHHHHHHcCC--hHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040371           93 ----QMAKEVFDTVQR-----NDV-SVWNAMISGVAIHGL--AADASAIFTKMEMFNVLPDSITFLGLL  149 (410)
Q Consensus        93 ----~~A~~~f~~m~~-----~~~-~~~~~li~~~~~~g~--~~~A~~l~~~m~~~g~~p~~~t~~~ll  149 (410)
                          +.++.+|+.+.+     .|. ...+.++........  ...+.++++.+.+.|+++....|..+.
T Consensus       156 e~l~~~~E~~Y~~L~~~~f~kgn~LQ~LS~iLaL~~~~~~~~v~r~~~l~~~l~~~~~kik~~~yp~lG  224 (297)
T PF13170_consen  156 EELAERMEQCYQKLADAGFKKGNDLQFLSHILALSEGDDQEKVARVIELYNALKKNGVKIKYMHYPTLG  224 (297)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCccccccccHHH
Confidence                456667766654     233 333333333222222  457899999999999998877766543

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=92.84  E-value=5.9  Score=40.45  Aligned_cols=219  Identities=11%  Similarity=0.024  Sum_probs=124.4

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHH----CC----------C--CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLS----SK----------V--EPDKFTFASVIYGCARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~----~g----------~--~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~   70 (410)
                      .+.|.++.+|...+++-.-.-++....+    .+          +  ....-+...-+....+...++.|..+-   ...
T Consensus       284 ss~~~i~~~~d~~n~~v~ys~vl~~l~d~l~~w~~~~~vltsdg~~~~L~ek~le~kL~iL~kK~ly~~Ai~LA---k~~  360 (933)
T KOG2114|consen  284 SSSNRIFKAYDLRNRYVLYSSVLEDLSDNLIEWSFDCLVLTSDGVVHELIEKDLETKLDILFKKNLYKVAINLA---KSQ  360 (933)
T ss_pred             cchhheeehhhhcCcccchHHhHHHHHHHHHhcCCcEEEEecCCceeeeeeccHHHHHHHHHHhhhHHHHHHHH---Hhc
Confidence            4567788888887775433333333211    11          0  111223444555556666666665442   333


Q ss_pred             CCCccH--HHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHH
Q 040371           71 KIELNF--ILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGL  148 (410)
Q Consensus        71 g~~~~~--~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~l  148 (410)
                      +.+++.  .+.....+-+.+.|++++|...|-+-..-  .-=..+|.-|.......+-..+++.+.+.|+. +...-..|
T Consensus       361 ~~d~d~~~~i~~kYgd~Ly~Kgdf~~A~~qYI~tI~~--le~s~Vi~kfLdaq~IknLt~YLe~L~~~gla-~~dhttlL  437 (933)
T KOG2114|consen  361 HLDEDTLAEIHRKYGDYLYGKGDFDEATDQYIETIGF--LEPSEVIKKFLDAQRIKNLTSYLEALHKKGLA-NSDHTTLL  437 (933)
T ss_pred             CCCHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHccc--CChHHHHHHhcCHHHHHHHHHHHHHHHHcccc-cchhHHHH
Confidence            433332  23334445556778888887766543311  11123556666666677777778888887764 33334457


Q ss_pred             HHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhH
Q 040371          149 LTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLEL  228 (410)
Q Consensus       149 l~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~  228 (410)
                      +.+|.+.++.+.-.++.+.-. + |.-  ..-....+..+.+.+-+++|..+-.+.+.  +......++   -..+++++
T Consensus       438 LncYiKlkd~~kL~efI~~~~-~-g~~--~fd~e~al~Ilr~snyl~~a~~LA~k~~~--he~vl~ill---e~~~ny~e  508 (933)
T KOG2114|consen  438 LNCYIKLKDVEKLTEFISKCD-K-GEW--FFDVETALEILRKSNYLDEAELLATKFKK--HEWVLDILL---EDLHNYEE  508 (933)
T ss_pred             HHHHHHhcchHHHHHHHhcCC-C-cce--eeeHHHHHHHHHHhChHHHHHHHHHHhcc--CHHHHHHHH---HHhcCHHH
Confidence            888888888888777765544 2 211  11234566677777888888777766543  333333333   34677888


Q ss_pred             HHHHHHhhccCC
Q 040371          229 GEVAIVNISRLM  240 (410)
Q Consensus       229 a~~~~~~~~~~~  240 (410)
                      |.+.+..+.++.
T Consensus       509 Al~yi~slp~~e  520 (933)
T KOG2114|consen  509 ALRYISSLPISE  520 (933)
T ss_pred             HHHHHhcCCHHH
Confidence            888877665543

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=92.83  E-value=1.1  Score=40.03  Aligned_cols=78  Identities=13%  Similarity=0.195  Sum_probs=36.8

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhh----hcCCCCChhHHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRS----RYSIQPQLEHYGAM  184 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~----~~~~~~~~~~~~~l  184 (410)
                      ++..++..+...|+.+.+...++++.... +-|...|..++.+|.+.|....|+..|+++.+    ..|+.|...+....
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l~~~~~edlgi~P~~~~~~~y  233 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQLKKTLAEELGIDPAPELRALY  233 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHHHHHhhhhcCCCccHHHHHHH
Confidence            44444444444555555555555444431 22444455555555555555555544444332    23555555555444


Q ss_pred             HHH
Q 040371          185 VDL  187 (410)
Q Consensus       185 i~~  187 (410)
                      ...
T Consensus       234 ~~~  236 (280)
T COG3629         234 EEI  236 (280)
T ss_pred             HHH
Confidence            444

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=92.68  E-value=5.4  Score=33.46  Aligned_cols=213  Identities=17%  Similarity=0.067  Sum_probs=149.7

Q ss_pred             cCCHhHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc-CCCccHHHHHHHHHHHHhcCCHHHHH
Q 040371           19 NARFDEALRFFREMLSSKVE-PDKFTFASVIYGCARLGALNHAYWVHNLIIEK-KIELNFILSAALIDMYSKCGKIQMAK   96 (410)
Q Consensus        19 ~g~~~~a~~l~~~m~~~g~~-pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~-g~~~~~~~~~~li~~y~~~g~~~~A~   96 (410)
                      .+....+...+......... .....+......+...+.+..+...+...... ........+..+...+...+++..+.
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (291)
T COG0457          36 LGELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEAL  115 (291)
T ss_pred             HhhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHH
Confidence            46677777777777664322 13677888888888899999888888877763 34556677778888888889999999


Q ss_pred             HHHHhcccC--C-hhhHHHHHH-HHHHcCChHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHccCCHHHHHHHHHHhhh
Q 040371           97 EVFDTVQRN--D-VSVWNAMIS-GVAIHGLAADASAIFTKMEMFNV--LPDSITFLGLLTACSHCGLVEEGRKYFDHMRS  170 (410)
Q Consensus        97 ~~f~~m~~~--~-~~~~~~li~-~~~~~g~~~~A~~l~~~m~~~g~--~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~  170 (410)
                      +.+......  + ...+..... .+...|+.+.|...|.+......  ......+......+...++.+.+...+....+
T Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~  195 (291)
T COG0457         116 ELLEKALALDPDPDLAEALLALGALYELGDYEEALELYEKALELDPELNELAEALLALGALLEALGRYEEALELLEKALK  195 (291)
T ss_pred             HHHHHHHcCCCCcchHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHHHh
Confidence            999877652  2 123333333 68889999999999999855221  12334444555557788999999999999885


Q ss_pred             hcCCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCchhHHHHHH
Q 040371          171 RYSIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRALLSACRTFKRLELGEVAI  233 (410)
Q Consensus       171 ~~~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~li~~~~~~g~~~~a~~~~  233 (410)
                      .  ... ....+..+...+...+.+++|...+... ...|+ ...+..+...+...+..+.+...+
T Consensus       196 ~--~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  259 (291)
T COG0457         196 L--NPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEAL  259 (291)
T ss_pred             h--CcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHHHHHHH
Confidence            3  233 3677888888899999999999888877 44454 444555555555666677777763

>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=92.54  E-value=5.1  Score=32.86  Aligned_cols=136  Identities=6%  Similarity=0.021  Sum_probs=76.7

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcC--CHHHHHHHHHhC
Q 040371          127 SAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAG--HIEEAYGLITSM  204 (410)
Q Consensus       127 ~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g--~~~~A~~~~~~m  204 (410)
                      ++.++.+.+.+++|+...+..++..+.+.|.+..-.++++     +++-+|.....+.+-.+....  -..-|++.+.++
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~qllq-----~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL   88 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQLLQ-----YHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRL   88 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHHHHh-----hcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHh
Confidence            3455555666777777777777777777777666555443     344455544444443333221  133345555555


Q ss_pred             CCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 040371          205 TMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       205 ~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  272 (410)
                      +..     +..++..+...|++-+|.+++.+....+......++.+-.+.++...-..+++-..+++.
T Consensus        89 ~~~-----~~~iievLL~~g~vl~ALr~ar~~~~~~~~~~~~fLeAA~~~~D~~lf~~V~~ff~~~n~  151 (167)
T PF07035_consen   89 GTA-----YEEIIEVLLSKGQVLEALRYARQYHKVDSVPARKFLEAAANSNDDQLFYAVFRFFEERNL  151 (167)
T ss_pred             hhh-----HHHHHHHHHhCCCHHHHHHHHHHcCCcccCCHHHHHHHHHHcCCHHHHHHHHHHHHHhhH
Confidence            322     334445556677777777776554444434445566666666666666666666655543

>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=92.42  E-value=2.7  Score=35.04  Aligned_cols=59  Identities=17%  Similarity=0.213  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhcccCC------hhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQRND------VSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~~~~------~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      ..+..+.+.|.+.|+.+.|.+.|.++.+..      +..+-.+|......+++..+.....+...
T Consensus        37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~  101 (177)
T PF10602_consen   37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAES  101 (177)
T ss_pred             HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            456677788888888888888888876542      23455666777777777777777766654

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.

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=92.18  E-value=0.39  Score=27.97  Aligned_cols=26  Identities=12%  Similarity=0.432  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREML   33 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~   33 (410)
                      +|+.|-..|.+.|++++|+++|++.+
T Consensus         1 al~~Lg~~~~~~g~~~~Ai~~y~~aL   26 (36)
T PF13176_consen    1 ALNNLGRIYRQQGDYEKAIEYYEQAL   26 (36)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            46777778888888888888887744

>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.98  E-value=2  Score=37.81  Aligned_cols=94  Identities=21%  Similarity=0.290  Sum_probs=73.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhcccC------ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCC-CCCC-HHHHHHHH
Q 040371           78 LSAALIDMYSKCGKIQMAKEVFDTVQRN------DVSVWNAMISGVAIHGLAADASAIFTKMEMFN-VLPD-SITFLGLL  149 (410)
Q Consensus        78 ~~~~li~~y~~~g~~~~A~~~f~~m~~~------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~-~~t~~~ll  149 (410)
                      .|+.-++.| +.|++..|...|..-.+.      ...++.-|...+...|++++|..+|..+.+.- -.|- ...+.-|.
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 LYNAALDLY-KSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLYAQGDYEDAAYIFARVVKDYPKSPKAPDALLKLG  222 (262)
T ss_pred             HHHHHHHHH-HcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHHhcccchHHHHHHHHHHHhCCCCCCChHHHHHHH
Confidence            677777654 578899999999887642      22355558899999999999999999998752 2222 35677788


Q ss_pred             HHHHccCCHHHHHHHHHHhhhhc
Q 040371          150 TACSHCGLVEEGRKYFDHMRSRY  172 (410)
Q Consensus       150 ~a~~~~g~~~~a~~~~~~m~~~~  172 (410)
                      ....+.|+.++|...|+++.++|
T Consensus       223 ~~~~~l~~~d~A~atl~qv~k~Y  245 (262)
T COG1729         223 VSLGRLGNTDEACATLQQVIKRY  245 (262)
T ss_pred             HHHHHhcCHHHHHHHHHHHHHHC
Confidence            88889999999999999999874

>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]

Probab=91.77  E-value=13  Score=35.95  Aligned_cols=156  Identities=13%  Similarity=0.134  Sum_probs=117.2

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYS   87 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~   87 (410)
                      ..-+++..+.++....-+..+-.+|+.-|  -+...|..++..|... .-+.--.+++++.+..+. |++...-|.+.|-
T Consensus        68 ~l~~~~~~f~~n~k~~~veh~c~~~l~~~--e~kmal~el~q~y~en-~n~~l~~lWer~ve~dfn-Dvv~~ReLa~~yE  143 (711)
T COG1747          68 CLVTLLTIFGDNHKNQIVEHLCTRVLEYG--ESKMALLELLQCYKEN-GNEQLYSLWERLVEYDFN-DVVIGRELADKYE  143 (711)
T ss_pred             HHHHHHHHhccchHHHHHHHHHHHHHHhc--chHHHHHHHHHHHHhc-CchhhHHHHHHHHHhcch-hHHHHHHHHHHHH
Confidence            34567888888888888888888998754  4677889999999888 556777889999888754 6666777777777


Q ss_pred             hcCCHHHHHHHHHhcccCCh---------hhHHHHHHHHHHcCChHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHccCC
Q 040371           88 KCGKIQMAKEVFDTVQRNDV---------SVWNAMISGVAIHGLAADASAIFTKMEMF-NVLPDSITFLGLLTACSHCGL  157 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~~~~~---------~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~~t~~~ll~a~~~~g~  157 (410)
                      + ++.+++..+|.+...+-+         ..|.-++..-  ..+.+..+.+..+.+.. |..--.+.+.-+-.-|....+
T Consensus       144 k-ik~sk~a~~f~Ka~yrfI~~~q~~~i~evWeKL~~~i--~dD~D~fl~l~~kiqt~lg~~~~~Vl~qdv~~~Ys~~eN  220 (711)
T COG1747         144 K-IKKSKAAEFFGKALYRFIPRRQNAAIKEVWEKLPELI--GDDKDFFLRLQKKIQTKLGEGRGSVLMQDVYKKYSENEN  220 (711)
T ss_pred             H-hchhhHHHHHHHHHHHhcchhhhhhHHHHHHHHHHhc--cccHHHHHHHHHHHHHhhccchHHHHHHHHHHHhccccC
Confidence            7 888999999887753311         2677776532  35667777777777653 555556777777788899999


Q ss_pred             HHHHHHHHHHhhh
Q 040371          158 VEEGRKYFDHMRS  170 (410)
Q Consensus       158 ~~~a~~~~~~m~~  170 (410)
                      +++|.+++..+.+
T Consensus       221 ~~eai~Ilk~il~  233 (711)
T COG1747         221 WTEAIRILKHILE  233 (711)
T ss_pred             HHHHHHHHHHHhh
Confidence            9999999997764

>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=91.63  E-value=5.1  Score=33.36  Aligned_cols=60  Identities=13%  Similarity=0.142  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCH--HHHHHHHHHHHhhCCHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDK--FTFASVIYGCARLGALNHAYWVHNLI   67 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~--~t~~~ll~a~~~~~~~~~a~~~~~~~   67 (410)
                      .|..+..-|.+.|+.++|++.|.++......|..  ..+-.++..+...+++..+.....++
T Consensus        38 ~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka   99 (177)
T PF10602_consen   38 ALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKA   99 (177)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            3445555555555555555555555544333322  23444455555555555555444444

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.

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=91.41  E-value=0.75  Score=28.14  Aligned_cols=28  Identities=29%  Similarity=0.500  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHC
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSS   35 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~   35 (410)
                      .|..+...|.+.|++++|.++|++.++.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            4666777777777777777777777764

>COG4649 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.20  E-value=6  Score=32.50  Aligned_cols=117  Identities=14%  Similarity=0.118  Sum_probs=72.1

Q ss_pred             HhcCCHHHHHHHHHhcccCChhhHHHHH-----HHHHHcCChHHHHHHHHHHHHCCCCCCHH-HHHHH--HHHHHccCCH
Q 040371           87 SKCGKIQMAKEVFDTVQRNDVSVWNAMI-----SGVAIHGLAADASAIFTKMEMFNVLPDSI-TFLGL--LTACSHCGLV  158 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~~~~~~~~~li-----~~~~~~g~~~~A~~l~~~m~~~g~~p~~~-t~~~l--l~a~~~~g~~  158 (410)
                      ++.|..++|...|..+.+.+--.|-.|.     ...++.|+..+|...|++.-...-.|-.. -..-|  .-.+...|.+
T Consensus        69 A~~~k~d~Alaaf~~lektg~g~YpvLA~mr~at~~a~kgdta~AV~aFdeia~dt~~P~~~rd~ARlraa~lLvD~gsy  148 (221)
T COG4649          69 AQENKTDDALAAFTDLEKTGYGSYPVLARMRAATLLAQKGDTAAAVAAFDEIAADTSIPQIGRDLARLRAAYLLVDNGSY  148 (221)
T ss_pred             HHcCCchHHHHHHHHHHhcCCCcchHHHHHHHHHHHhhcccHHHHHHHHHHHhccCCCcchhhHHHHHHHHHHHhccccH
Confidence            5567778888888888776655555443     34566788888888888876654444322 11111  1233466777


Q ss_pred             HHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          159 EEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       159 ~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      ++...-.+.+..+ +-+.....-.+|--+-.+.|++..|..+|..+
T Consensus       149 ~dV~srvepLa~d-~n~mR~sArEALglAa~kagd~a~A~~~F~qi  193 (221)
T COG4649         149 DDVSSRVEPLAGD-GNPMRHSAREALGLAAYKAGDFAKAKSWFVQI  193 (221)
T ss_pred             HHHHHHhhhccCC-CChhHHHHHHHHhHHHHhccchHHHHHHHHHH
Confidence            7777666665533 33333344456666666778888888888776

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=91.00  E-value=10  Score=33.25  Aligned_cols=146  Identities=15%  Similarity=0.134  Sum_probs=77.4

Q ss_pred             HHHHHcCChHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhc-
Q 040371          115 SGVAIHGLAADASAIFTKMEMFNV--LPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRA-  191 (410)
Q Consensus       115 ~~~~~~g~~~~A~~l~~~m~~~g~--~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-  191 (410)
                      ..-.+.|++++|.+.|+.+.....  +-...+...++-++-+.+++++|...+++....++-.|+. -|..-|.+++.- 
T Consensus        42 ~~~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~-dY~~YlkgLs~~~  120 (254)
T COG4105          42 LTELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNA-DYAYYLKGLSYFF  120 (254)
T ss_pred             HHHHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCCh-hHHHHHHHHHHhc
Confidence            334567888888888888775421  1134556666777777888888888888877666666654 344444444321 


Q ss_pred             ------CCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHH
Q 040371          192 ------GHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVRE  265 (410)
Q Consensus       192 ------g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  265 (410)
                            .+...+.+-|..+         ..+|.-|-.+.-...|..-+......-...=..+.+-|.+.|.+..|..-++
T Consensus       121 ~i~~~~rDq~~~~~A~~~f---------~~~i~ryPnS~Ya~dA~~~i~~~~d~LA~~Em~IaryY~kr~~~~AA~nR~~  191 (254)
T COG4105         121 QIDDVTRDQSAARAAFAAF---------KELVQRYPNSRYAPDAKARIVKLNDALAGHEMAIARYYLKRGAYVAAINRFE  191 (254)
T ss_pred             cCCccccCHHHHHHHHHHH---------HHHHHHCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHH
Confidence                  1111222222221         1122222222222222222111111011112346678899999999999999


Q ss_pred             HHHhC
Q 040371          266 IMKKK  270 (410)
Q Consensus       266 ~m~~~  270 (410)
                      +|.+.
T Consensus       192 ~v~e~  196 (254)
T COG4105         192 EVLEN  196 (254)
T ss_pred             HHHhc
Confidence            98876

>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A

Probab=90.46  E-value=0.67  Score=26.94  Aligned_cols=24  Identities=13%  Similarity=0.011  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHH
Q 040371          110 WNAMISGVAIHGLAADASAIFTKM  133 (410)
Q Consensus       110 ~~~li~~~~~~g~~~~A~~l~~~m  133 (410)
                      |+.|...|.+.|++++|+++|++.
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            455555566666666666666553

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=90.07  E-value=12  Score=34.58  Aligned_cols=43  Identities=9%  Similarity=0.244  Sum_probs=20.2

Q ss_pred             HcCCHhHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHhhCCHHHH
Q 040371           18 RNARFDEALRFFREMLSS--KVEPDKFTFASVIYGCARLGALNHA   60 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~--g~~pd~~t~~~ll~a~~~~~~~~~a   60 (410)
                      ++.+.++|+..+.+-+..  ...---.+|..+..+.++.|.++++
T Consensus        18 ~s~~~~~al~~w~~~L~~l~~~~~Rf~~lG~l~~a~s~~g~y~~m   62 (518)
T KOG1941|consen   18 QSNQTEKALQVWTKVLEKLSDLMGRFRVLGCLVTAHSEMGRYKEM   62 (518)
T ss_pred             cCchHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhhhhHHHHHH
Confidence            455566666666554432  0111122445555555555555444

>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=89.93  E-value=14  Score=33.22  Aligned_cols=135  Identities=10%  Similarity=0.112  Sum_probs=68.1

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHC--------CCCCCH-----HHHHHHHHHHHhhCCHH---HHHHHHHHHHHc
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSS--------KVEPDK-----FTFASVIYGCARLGALN---HAYWVHNLIIEK   70 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~--------g~~pd~-----~t~~~ll~a~~~~~~~~---~a~~~~~~~~~~   70 (410)
                      +.||.-...+.+..++++|...+++..+.        ...|+.     .++..+..++...+..+   .|..+.+.+...
T Consensus        37 ~~yn~G~~l~~~~~~~~~a~~wL~~a~~~l~~~~~~~~~~~~~~elr~~iL~~La~~~l~~~~~~~~~ka~~~l~~l~~e  116 (278)
T PF08631_consen   37 VCYNIGKSLLSKKDKYEEAVKWLQRAYDILEKPGKMDKLSPDGSELRLSILRLLANAYLEWDTYESVEKALNALRLLESE  116 (278)
T ss_pred             HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhhhccccCCcHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHh
Confidence            34666666655554776666665554321        123332     34445555555555443   344455555332


Q ss_pred             CCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccC---ChhhHHHHHHHHHH--cCChHHHHHHHHHHHHCCCCCCH
Q 040371           71 KIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRN---DVSVWNAMISGVAI--HGLAADASAIFTKMEMFNVLPDS  142 (410)
Q Consensus        71 g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~~--~g~~~~A~~l~~~m~~~g~~p~~  142 (410)
                       .+..+.++-.-+..+.+.++.+.+.+++.+|...   ....+..++..+-+  ......|...+..+....+.|..
T Consensus       117 -~~~~~~~~~L~l~il~~~~~~~~~~~~L~~mi~~~~~~e~~~~~~l~~i~~l~~~~~~~a~~~ld~~l~~r~~~~~  192 (278)
T PF08631_consen  117 -YGNKPEVFLLKLEILLKSFDEEEYEEILMRMIRSVDHSESNFDSILHHIKQLAEKSPELAAFCLDYLLLNRFKSSE  192 (278)
T ss_pred             -CCCCcHHHHHHHHHHhccCChhHHHHHHHHHHHhcccccchHHHHHHHHHHHHhhCcHHHHHHHHHHHHHHhCCCh
Confidence             2223444444455555677777777777776532   22345555544421  23344555666655555444443

It is also involved in sporulation [].

>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A

Probab=89.89  E-value=11  Score=32.00  Aligned_cols=168  Identities=14%  Similarity=0.111  Sum_probs=77.4

Q ss_pred             HHHHHHhhCCHHHHHHHHHHHHHcCC--CccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--CC--hhhHHHHHHHHHHc
Q 040371           47 VIYGCARLGALNHAYWVHNLIIEKKI--ELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--ND--VSVWNAMISGVAIH  120 (410)
Q Consensus        47 ll~a~~~~~~~~~a~~~~~~~~~~g~--~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~--~~~~~~li~~~~~~  120 (410)
                      ........|+++.|.+.|+.+.....  +--....-.++.+|.+.|++++|...|++..+  |+  ...+-..+.+.+.-
T Consensus        11 ~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~~~   90 (203)
T PF13525_consen   11 KALEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLSYY   90 (203)
T ss_dssp             HHHHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHH
Confidence            33445567778888888887776521  11233445566677777888887777777653  21  11222222222111


Q ss_pred             CChHHHHHHHHHHHHCCCCCC-------HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCC
Q 040371          121 GLAADASAIFTKMEMFNVLPD-------SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGH  193 (410)
Q Consensus       121 g~~~~A~~l~~~m~~~g~~p~-------~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~  193 (410)
                      .......       .  ...|       ..+|..++.-|=.+....+|...+..+...     =..+--.+.+.|.+.|.
T Consensus        91 ~~~~~~~-------~--~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l~~l~~~-----la~~e~~ia~~Y~~~~~  156 (203)
T PF13525_consen   91 KQIPGIL-------R--SDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRLAELRNR-----LAEHELYIARFYYKRGK  156 (203)
T ss_dssp             HHHHHHH----------TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHHH-----HHHHHHHHHHHHHCTT-
T ss_pred             HhCccch-------h--cccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHccc
Confidence            1000000       0  0011       123334444444555555555555554432     11223345566777777


Q ss_pred             HHHHHHHHHhC----CCCC-CHHHHHHHHHHHHhcCchhH
Q 040371          194 IEEAYGLITSM----TMEP-DVVVWRALLSACRTFKRLEL  228 (410)
Q Consensus       194 ~~~A~~~~~~m----~~~p-~~~~~~~li~~~~~~g~~~~  228 (410)
                      +..|..-++.+    |-.| .......++.++...|..+.
T Consensus       157 y~aA~~r~~~v~~~yp~t~~~~~al~~l~~~y~~l~~~~~  196 (203)
T PF13525_consen  157 YKAAIIRFQYVIENYPDTPAAEEALARLAEAYYKLGLKQA  196 (203)
T ss_dssp             HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-HHH
T ss_pred             HHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHhCChHH
Confidence            77776666655    2111 12334455555555555553

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=89.79  E-value=2.9  Score=30.88  Aligned_cols=62  Identities=10%  Similarity=0.213  Sum_probs=43.6

Q ss_pred             hHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHH
Q 040371          123 AADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVD  186 (410)
Q Consensus       123 ~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~  186 (410)
                      .-+..+-++.+....+.|+.....+.|.||.+..++..|.++|+.++.+.|-.  ...|..++.
T Consensus        26 ~we~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~--~~~Y~~~lq   87 (108)
T PF02284_consen   26 GWELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNK--KEIYPYILQ   87 (108)
T ss_dssp             HHHHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT---TTHHHHHHH
T ss_pred             HHHHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCh--HHHHHHHHH
Confidence            33555666666667788999999999999999999999999999988764433  336777664

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 ....

>PF13428 TPR_14: Tetratricopeptide repeat

Probab=89.66  E-value=1.6  Score=26.66  Aligned_cols=28  Identities=14%  Similarity=0.170  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHc
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~   70 (410)
                      ++..+..++...|++++|+++++++++.
T Consensus         3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~   30 (44)
T PF13428_consen    3 AWLALARAYRRLGQPDEAERLLRRALAL   30 (44)
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            3444555555555555555555555554

>TIGR02508 type_III_yscG type III secretion protein, YscG family

Probab=89.61  E-value=6.2  Score=29.09  Aligned_cols=87  Identities=15%  Similarity=0.134  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHC
Q 040371           57 LNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMF  136 (410)
Q Consensus        57 ~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  136 (410)
                      -++|..|-+.+...+-. ...+--.-+..+...|++++|..+.+.+..||+..|-++-.  .+.|..+++..-+.+|...
T Consensus        21 HqEA~tIAdwL~~~~~~-~E~v~lIRlsSLmNrG~Yq~Al~l~~~~~~pdlepw~ALce--~rlGl~s~l~~rl~rla~s   97 (115)
T TIGR02508        21 HQEANTIADWLHLKGES-EEAVQLIRLSSLMNRGDYQSALQLGNKLCYPDLEPWLALCE--WRLGLGSALESRLNRLAAS   97 (115)
T ss_pred             HHHHHHHHHHHhcCCch-HHHHHHHHHHHHHccchHHHHHHhcCCCCCchHHHHHHHHH--HhhccHHHHHHHHHHHHhC
Confidence            45666666666554422 33333344556678899999999999999999999988765  4678888888888888777


Q ss_pred             CCCCCHHHHHH
Q 040371          137 NVLPDSITFLG  147 (410)
Q Consensus       137 g~~p~~~t~~~  147 (410)
                      | .|...+|..
T Consensus        98 g-~p~lq~Faa  107 (115)
T TIGR02508        98 G-DPRLQTFVA  107 (115)
T ss_pred             C-CHHHHHHHH
Confidence            6 455555543

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.

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=89.44  E-value=3.1  Score=30.38  Aligned_cols=63  Identities=10%  Similarity=0.204  Sum_probs=48.4

Q ss_pred             ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHH
Q 040371          122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVD  186 (410)
Q Consensus       122 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~  186 (410)
                      +.-++.+-++.+....+.|+.....+.|.||.+.+++..|.++|+..+.+.|.  +...|..++.
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~--~~~~y~~~lq   84 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGA--HKEIYPYILQ   84 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccC--chhhHHHHHH
Confidence            45566667777777788999999999999999999999999999988755332  4446666554

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.

>KOG4555 consensus TPR repeat-containing protein [Function unknown]

Probab=89.37  E-value=3.7  Score=31.99  Aligned_cols=85  Identities=15%  Similarity=0.151  Sum_probs=64.7

Q ss_pred             HHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHC-CCCCCH---HHHHHHHHHHHccCC
Q 040371           85 MYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMF-NVLPDS---ITFLGLLTACSHCGL  157 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~---~t~~~ll~a~~~~g~  157 (410)
                      +.+..|+++.|++.|.+...   .....||.-..+|.-.|+.++|++=+++..+. |-+ +.   ..|.--...|...|+
T Consensus        52 alaE~g~Ld~AlE~F~qal~l~P~raSayNNRAQa~RLq~~~e~ALdDLn~AleLag~~-trtacqa~vQRg~lyRl~g~  130 (175)
T KOG4555|consen   52 ALAEAGDLDGALELFGQALCLAPERASAYNNRAQALRLQGDDEEALDDLNKALELAGDQ-TRTACQAFVQRGLLYRLLGN  130 (175)
T ss_pred             HHHhccchHHHHHHHHHHHHhcccchHhhccHHHHHHHcCChHHHHHHHHHHHHhcCcc-chHHHHHHHHHHHHHHHhCc
Confidence            56788999999999987653   47789999999999999999999988887764 322 22   234444455677888


Q ss_pred             HHHHHHHHHHhhh
Q 040371          158 VEEGRKYFDHMRS  170 (410)
Q Consensus       158 ~~~a~~~~~~m~~  170 (410)
                      .+.|..=|+...+
T Consensus       131 dd~AR~DFe~AA~  143 (175)
T KOG4555|consen  131 DDAARADFEAAAQ  143 (175)
T ss_pred             hHHHHHhHHHHHH
Confidence            8888888887664

>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=89.32  E-value=5.6  Score=37.14  Aligned_cols=60  Identities=13%  Similarity=0.056  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      .+..+.-++.+++.+..|++.-...+..+ ++|+-..---..+|...|+++.|+..|+++.
T Consensus       259 ~~lNlA~c~lKl~~~~~Ai~~c~kvLe~~-~~N~KALyRrG~A~l~~~e~~~A~~df~ka~  318 (397)
T KOG0543|consen  259 CHLNLAACYLKLKEYKEAIESCNKVLELD-PNNVKALYRRGQALLALGEYDLARDDFQKAL  318 (397)
T ss_pred             HhhHHHHHHHhhhhHHHHHHHHHHHHhcC-CCchhHHHHHHHHHHhhccHHHHHHHHHHHH
Confidence            44555555556666666666555555554 3344444444555555666666666666554

>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]

Probab=89.16  E-value=13  Score=38.25  Aligned_cols=136  Identities=17%  Similarity=0.178  Sum_probs=71.9

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      +.|++++|..-|-+-... +.|.     .++.-+-.......-..+++.+.+.|+. +...-+.|+++|.|.++.++-.+
T Consensus       380 ~Kgdf~~A~~qYI~tI~~-le~s-----~Vi~kfLdaq~IknLt~YLe~L~~~gla-~~dhttlLLncYiKlkd~~kL~e  452 (933)
T KOG2114|consen  380 GKGDFDEATDQYIETIGF-LEPS-----EVIKKFLDAQRIKNLTSYLEALHKKGLA-NSDHTTLLLNCYIKLKDVEKLTE  452 (933)
T ss_pred             hcCCHHHHHHHHHHHccc-CChH-----HHHHHhcCHHHHHHHHHHHHHHHHcccc-cchhHHHHHHHHHHhcchHHHHH
Confidence            456667766666554432 2321     2333333444444455566677777765 55566788999999999888888


Q ss_pred             HHHhcccCChh-hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040371           98 VFDTVQRNDVS-VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHM  168 (410)
Q Consensus        98 ~f~~m~~~~~~-~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  168 (410)
                      +.+.-..-... -....+..+.+.+-.++|.-+-.+...     +......++   -..+++++|.++++.+
T Consensus       453 fI~~~~~g~~~fd~e~al~Ilr~snyl~~a~~LA~k~~~-----he~vl~ill---e~~~ny~eAl~yi~sl  516 (933)
T KOG2114|consen  453 FISKCDKGEWFFDVETALEILRKSNYLDEAELLATKFKK-----HEWVLDILL---EDLHNYEEALRYISSL  516 (933)
T ss_pred             HHhcCCCcceeeeHHHHHHHHHHhChHHHHHHHHHHhcc-----CHHHHHHHH---HHhcCHHHHHHHHhcC
Confidence            77766521110 123344444455555555544433321     122222222   2345566666555544

>PF13431 TPR_17: Tetratricopeptide repeat

Probab=89.11  E-value=0.74  Score=26.44  Aligned_cols=24  Identities=21%  Similarity=0.145  Sum_probs=16.5

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHH
Q 040371           73 ELNFILSAALIDMYSKCGKIQMAK   96 (410)
Q Consensus        73 ~~~~~~~~~li~~y~~~g~~~~A~   96 (410)
                      +-+..+|+.|...|...|++++|+
T Consensus        10 P~n~~a~~nla~~~~~~g~~~~A~   33 (34)
T PF13431_consen   10 PNNAEAYNNLANLYLNQGDYEEAI   33 (34)
T ss_pred             CCCHHHHHHHHHHHHHCcCHHhhc
Confidence            445667777777777777777764

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=88.76  E-value=1.1  Score=25.31  Aligned_cols=28  Identities=14%  Similarity=0.474  Sum_probs=21.0

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLS   34 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~   34 (410)
                      .+|..+...|...|++++|+..|++.++
T Consensus         2 ~~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    2 EAYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            4677778888888888888888887765

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 ....

>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK

Probab=88.62  E-value=11  Score=30.13  Aligned_cols=89  Identities=6%  Similarity=-0.010  Sum_probs=44.0

Q ss_pred             hhCCHHHHHHHHHHHHHcCC-CccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCCh-hhHHHHHHHHHHcCChHHHHHHH
Q 040371           53 RLGALNHAYWVHNLIIEKKI-ELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDV-SVWNAMISGVAIHGLAADASAIF  130 (410)
Q Consensus        53 ~~~~~~~a~~~~~~~~~~g~-~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~-~~~~~li~~~~~~g~~~~A~~l~  130 (410)
                      ..++.+.+..+++.|.-.-. .+...++-  .-.+...|++++|.++|+++.+... ..|..-+.+++..-..+..+..+
T Consensus        22 ~~~d~~D~e~lLdALrvLrP~~~e~d~~d--g~l~i~rg~w~eA~rvlr~l~~~~~~~p~~kAL~A~CL~al~Dp~Wr~~   99 (153)
T TIGR02561        22 RSADPYDAQAMLDALRVLRPNLKELDMFD--GWLLIARGNYDEAARILRELLSSAGAPPYGKALLALCLNAKGDAEWHVH   99 (153)
T ss_pred             hcCCHHHHHHHHHHHHHhCCCccccchhH--HHHHHHcCCHHHHHHHHHhhhccCCCchHHHHHHHHHHHhcCChHHHHH
Confidence            45666666666666644310 11222222  3345667777777777777765442 25555555554443333333333


Q ss_pred             -HHHHHCCCCCCHH
Q 040371          131 -TKMEMFNVLPDSI  143 (410)
Q Consensus       131 -~~m~~~g~~p~~~  143 (410)
                       .++.+.|-.|+..
T Consensus       100 A~~~le~~~~~~a~  113 (153)
T TIGR02561       100 ADEVLARDADADAV  113 (153)
T ss_pred             HHHHHHhCCCHhHH
Confidence             2333444444433

This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.

>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.59  E-value=30  Score=35.16  Aligned_cols=103  Identities=17%  Similarity=0.074  Sum_probs=79.9

Q ss_pred             HHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCC
Q 040371          162 RKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMG  241 (410)
Q Consensus       162 ~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~  241 (410)
                      +.+++.+..++|..-..-+.+--+.-+...|+..+|.++-.+..+ ||-..|-.=+.+++..+++++-+++.....+  |
T Consensus       668 l~lQ~~Le~q~~~~f~dlSl~dTv~~li~~g~~k~a~ql~~~Fki-pdKr~~wLk~~aLa~~~kweeLekfAkskks--P  744 (829)
T KOG2280|consen  668 LKLQRTLEDQFGGSFVDLSLHDTVTTLILIGQNKRAEQLKSDFKI-PDKRLWWLKLTALADIKKWEELEKFAKSKKS--P  744 (829)
T ss_pred             HHHHHHHHHHhccccccCcHHHHHHHHHHccchHHHHHHHHhcCC-cchhhHHHHHHHHHhhhhHHHHHHHHhccCC--C
Confidence            334555555556554555666667778888999999999888753 6888888889999999999998888766654  5


Q ss_pred             chHHHHHHHHHhcCChhHHHHHHHHH
Q 040371          242 GDYVLLSNMYCYLKRWDTAENVREIM  267 (410)
Q Consensus       242 ~~~~~l~~~~~~~g~~~~a~~~~~~m  267 (410)
                      .-|.-.+.+|.+.|+.++|.+++-+.
T Consensus       745 IGy~PFVe~c~~~~n~~EA~KYiprv  770 (829)
T KOG2280|consen  745 IGYLPFVEACLKQGNKDEAKKYIPRV  770 (829)
T ss_pred             CCchhHHHHHHhcccHHHHhhhhhcc
Confidence            67888889999999999999887554

>COG0457 NrfG FOG: TPR repeat [General function prediction only]

Probab=88.52  E-value=13  Score=30.93  Aligned_cols=215  Identities=19%  Similarity=0.085  Sum_probs=148.8

Q ss_pred             hCCHHHHHHHHHHHHHcCCC-ccHHHHHHHHHHHHhcCCHHHHHHHHHhccc-----CChhhHHHHHHHHHHcCChHHHH
Q 040371           54 LGALNHAYWVHNLIIEKKIE-LNFILSAALIDMYSKCGKIQMAKEVFDTVQR-----NDVSVWNAMISGVAIHGLAADAS  127 (410)
Q Consensus        54 ~~~~~~a~~~~~~~~~~g~~-~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~~~~~~~~li~~~~~~g~~~~A~  127 (410)
                      .+....+...+......... ............+...+++..+...+.....     .....+......+...+...++.
T Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  115 (291)
T COG0457          36 LGELAEALELLEEALELLPNSDLAGLLLLLALALLKLGRLEEALELLEKALELELLPNLAEALLNLGLLLEALGKYEEAL  115 (291)
T ss_pred             HhhHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHcccHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHHHhhHHHHH
Confidence            35556666666666555322 1467788888899999999999988887642     34556777777888888999999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHH-HHHccCCHHHHHHHHHHhhhhcCC--CCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          128 AIFTKMEMFNVLPDSITFLGLLT-ACSHCGLVEEGRKYFDHMRSRYSI--QPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       128 ~l~~~m~~~g~~p~~~t~~~ll~-a~~~~g~~~~a~~~~~~m~~~~~~--~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      +.+.........+. ........ .+...|+++.+...+...... ..  ......+......+...++.+++...+.+.
T Consensus       116 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~  193 (291)
T COG0457         116 ELLEKALALDPDPD-LAEALLALGALYELGDYEEALELYEKALEL-DPELNELAEALLALGALLEALGRYEEALELLEKA  193 (291)
T ss_pred             HHHHHHHcCCCCcc-hHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-CCCccchHHHHHHhhhHHHHhcCHHHHHHHHHHH
Confidence            99999887544432 22222223 788999999999999998531 21  123344455555577889999999998887


Q ss_pred             -CCCCC--HHHHHHHHHHHHhcCchhHHHHHHH---hhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          205 -TMEPD--VVVWRALLSACRTFKRLELGEVAIV---NISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       205 -~~~p~--~~~~~~li~~~~~~g~~~~a~~~~~---~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                       ...++  ...+..+-..+...++.+.+...+.   ...|.....+..+...+...+.++++...+......
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  265 (291)
T COG0457         194 LKLNPDDDAEALLNLGLLYLKLGKYEEALEYYEKALELDPDNAEALYNLALLLLELGRYEEALEALEKALEL  265 (291)
T ss_pred             HhhCcccchHHHHHhhHHHHHcccHHHHHHHHHHHHhhCcccHHHHhhHHHHHHHcCCHHHHHHHHHHHHHh
Confidence             33444  5777788888888888888888833   333332334555666666777889998888776654

>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]

Probab=88.43  E-value=7  Score=35.02  Aligned_cols=59  Identities=12%  Similarity=0.103  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTV  102 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m  102 (410)
                      ++..++.++...++++.+...++.+.... +-+...|..+|.+|.+.|+...|+..|+++
T Consensus       155 ~l~~lae~~~~~~~~~~~~~~l~~Li~~d-p~~E~~~~~lm~~y~~~g~~~~ai~~y~~l  213 (280)
T COG3629         155 ALTKLAEALIACGRADAVIEHLERLIELD-PYDEPAYLRLMEAYLVNGRQSAAIRAYRQL  213 (280)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCchHHHHHHHHH
Confidence            33344444444444444444444444432 224444444445555555544444444444

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=88.33  E-value=26  Score=34.00  Aligned_cols=138  Identities=11%  Similarity=0.039  Sum_probs=72.8

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      +..+++.-+++-++.++  +.||-.+.-. +.+--....+.++++++++.++.|-.       .    |.+....+..-.
T Consensus       180 RERnp~aRIkaA~eALe--i~pdCAdAYI-LLAEEeA~Ti~Eae~l~rqAvkAgE~-------~----lg~s~~~~~~g~  245 (539)
T PF04184_consen  180 RERNPQARIKAAKEALE--INPDCADAYI-LLAEEEASTIVEAEELLRQAVKAGEA-------S----LGKSQFLQHHGH  245 (539)
T ss_pred             hcCCHHHHHHHHHHHHH--hhhhhhHHHh-hcccccccCHHHHHHHHHHHHHHHHH-------h----hchhhhhhcccc
Confidence            45555555555555554  3454432222 22222345578888888888776411       0    011000000001


Q ss_pred             HHHhcccCCh----hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371           98 VFDTVQRNDV----SVWNAMISGVAIHGLAADASAIFTKMEMFNVL-PDSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus        98 ~f~~m~~~~~----~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      .++....++.    ..-.-+..+.-+.|+.+||++.|++|.+.... -+....-.|+.++...+.+.++..++..-.
T Consensus       246 ~~e~~~~Rdt~~~~y~KrRLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYd  322 (539)
T PF04184_consen  246 FWEAWHRRDTNVLVYAKRRLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYD  322 (539)
T ss_pred             hhhhhhccccchhhhhHHHHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhc
Confidence            1122222222    12223445555678888888888888764311 123355668888888888888888887764

The molecular function of this protein is uncertain.

>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]

Probab=88.03  E-value=17  Score=31.70  Aligned_cols=83  Identities=12%  Similarity=0.003  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCC--hhhHHHHHHHHHHc
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRND--VSVWNAMISGVAIH  120 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~--~~~~~~li~~~~~~  120 (410)
                      .|.-...+|-...+++++..-+....+. ...+...|.+       ...++.|.-+..+|..-+  +..|+--...|..+
T Consensus        33 ~yekAAvafRnAk~feKakdcLlkA~~~-yEnnrslfhA-------AKayEqaamLake~~klsEvvdl~eKAs~lY~E~  104 (308)
T KOG1585|consen   33 LYEKAAVAFRNAKKFEKAKDCLLKASKG-YENNRSLFHA-------AKAYEQAAMLAKELSKLSEVVDLYEKASELYVEC  104 (308)
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHH-HHhcccHHHH-------HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHh
Confidence            3444455666666777776655544421 1222222211       111233333333333221  22344455666666


Q ss_pred             CChHHHHHHHHHH
Q 040371          121 GLAADASAIFTKM  133 (410)
Q Consensus       121 g~~~~A~~l~~~m  133 (410)
                      |.++-|-..+++.
T Consensus       105 GspdtAAmaleKA  117 (308)
T KOG1585|consen  105 GSPDTAAMALEKA  117 (308)
T ss_pred             CCcchHHHHHHHH
Confidence            6666655555543

>COG3118 Thioredoxin domain-containing protein [Posttranslational modification, protein turnover, chaperones]

Probab=87.88  E-value=20  Score=32.23  Aligned_cols=137  Identities=12%  Similarity=0.082  Sum_probs=81.1

Q ss_pred             HHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCCh-hhH---HHHHHHHHHcCChH
Q 040371           49 YGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDV-SVW---NAMISGVAIHGLAA  124 (410)
Q Consensus        49 ~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~-~~~---~~li~~~~~~g~~~  124 (410)
                      ......|++..+..+++...... +-+..+--.|..+|...|+.+.|..+++.++.... ..|   .+-|..+.+.....
T Consensus       142 ~~~~~~e~~~~a~~~~~~al~~~-~~~~~~~~~la~~~l~~g~~e~A~~iL~~lP~~~~~~~~~~l~a~i~ll~qaa~~~  220 (304)
T COG3118         142 KELIEAEDFGEAAPLLKQALQAA-PENSEAKLLLAECLLAAGDVEAAQAILAALPLQAQDKAAHGLQAQIELLEQAAATP  220 (304)
T ss_pred             hhhhhccchhhHHHHHHHHHHhC-cccchHHHHHHHHHHHcCChHHHHHHHHhCcccchhhHHHHHHHHHHHHHHHhcCC
Confidence            34567788888888888887764 33456667788889999999999999998874321 122   22344444444444


Q ss_pred             HHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhh-cCCCCChhHHHHHHHHHHh
Q 040371          125 DASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSR-YSIQPQLEHYGAMVDLLGR  190 (410)
Q Consensus       125 ~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~-~~~~~~~~~~~~li~~~~~  190 (410)
                      +..++-.+.-.   .| |...-..+...+...|+.+.|.+.+-.+.++ .|.. |...-..|++.+.-
T Consensus       221 ~~~~l~~~~aa---dPdd~~aa~~lA~~~~~~g~~e~Ale~Ll~~l~~d~~~~-d~~~Rk~lle~f~~  284 (304)
T COG3118         221 EIQDLQRRLAA---DPDDVEAALALADQLHLVGRNEAALEHLLALLRRDRGFE-DGEARKTLLELFEA  284 (304)
T ss_pred             CHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccc-CcHHHHHHHHHHHh
Confidence            44444444432   34 4444555666777777777777655554433 2222 33344444444433

>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]

Probab=87.86  E-value=43  Score=36.05  Aligned_cols=81  Identities=17%  Similarity=0.175  Sum_probs=48.2

Q ss_pred             HHHHHHhcCCHHHHHHHHHhCCCCCCHHH--HHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHH
Q 040371          184 MVDLLGRAGHIEEAYGLITSMTMEPDVVV--WRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAE  261 (410)
Q Consensus       184 li~~~~~~g~~~~A~~~~~~m~~~p~~~~--~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  261 (410)
                      -+.+|..+|++.+|+.+-.++....|...  -..|.+-+...++.-+|-+++.+...+    +.-.+..|++...|++|.
T Consensus       971 Al~a~~~~~dWr~~l~~a~ql~~~~de~~~~a~~L~s~L~e~~kh~eAa~il~e~~sd----~~~av~ll~ka~~~~eAl 1046 (1265)
T KOG1920|consen  971 ALKAYKECGDWREALSLAAQLSEGKDELVILAEELVSRLVEQRKHYEAAKILLEYLSD----PEEAVALLCKAKEWEEAL 1046 (1265)
T ss_pred             HHHHHHHhccHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHcccchhHHHHHHHHhcC----HHHHHHHHhhHhHHHHHH
Confidence            34556666666666666666533333322  356777777777777777764443322    223445567777888888


Q ss_pred             HHHHHHH
Q 040371          262 NVREIMK  268 (410)
Q Consensus       262 ~~~~~m~  268 (410)
                      ++-..-.
T Consensus      1047 rva~~~~ 1053 (1265)
T KOG1920|consen 1047 RVASKAK 1053 (1265)
T ss_pred             HHHHhcc
Confidence            8765544

>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=87.78  E-value=6.3  Score=33.27  Aligned_cols=67  Identities=10%  Similarity=-0.080  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc-------cCChhhHHHHHHHHHHcCChHHH
Q 040371           59 HAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ-------RNDVSVWNAMISGVAIHGLAADA  126 (410)
Q Consensus        59 ~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~-------~~~~~~~~~li~~~~~~g~~~~A  126 (410)
                      .|.+.|-.+...+.--++....+|...|. ..+.++|..++.+..       +.|+..+.+|++.|-+.|+.+.|
T Consensus       124 ~A~~~fL~~E~~~~l~t~elq~aLAtyY~-krD~~Kt~~ll~~~L~l~~~~~~~n~eil~sLas~~~~~~~~e~A  197 (203)
T PF11207_consen  124 EALRRFLQLEGTPELETAELQYALATYYT-KRDPEKTIQLLLRALELSNPDDNFNPEILKSLASIYQKLKNYEQA  197 (203)
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHHHHHHH-ccCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhcchhhh
Confidence            34444444444444445555555555554 334455555444332       22445555555555555555554

>KOG4570 consensus Uncharacterized conserved protein [Function unknown]

Probab=87.59  E-value=5.5  Score=35.94  Aligned_cols=98  Identities=12%  Similarity=0.204  Sum_probs=72.5

Q ss_pred             cCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc-C--------ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC
Q 040371           70 KKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR-N--------DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP  140 (410)
Q Consensus        70 ~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-~--------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  140 (410)
                      .|.+....+...++..-....+++++...+-++.. +        ...+|--++    ..=++++++.++..=.+-|+-|
T Consensus        58 ~g~~~s~~~Vd~~V~v~~~~~~idd~~~~LyKlRhs~~a~~~~~~~~~~~irll----lky~pq~~i~~l~npIqYGiF~  133 (418)
T KOG4570|consen   58 RGLPVSSLTVDRLVDVISSREEIDDAEYYLYKLRHSPNAWYLRNWTIHTWIRLL----LKYDPQKAIYTLVNPIQYGIFP  133 (418)
T ss_pred             cCCCcceeehhhhhhccccccchhHHHHHHHHHhcCcchhhhccccHHHHHHHH----HccChHHHHHHHhCcchhcccc
Confidence            34555555666677666777888999888877653 2        222333322    2346778999888888889999


Q ss_pred             CHHHHHHHHHHHHccCCHHHHHHHHHHhhhh
Q 040371          141 DSITFLGLLTACSHCGLVEEGRKYFDHMRSR  171 (410)
Q Consensus       141 ~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~  171 (410)
                      |.+|++.++..+.+.+++.+|.++...|...
T Consensus       134 dqf~~c~l~D~flk~~n~~~aa~vvt~~~~q  164 (418)
T KOG4570|consen  134 DQFTFCLLMDSFLKKENYKDAASVVTEVMMQ  164 (418)
T ss_pred             chhhHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence            9999999999999999999999988887654

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=87.42  E-value=1.5  Score=25.92  Aligned_cols=29  Identities=24%  Similarity=0.520  Sum_probs=21.3

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLS   34 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~   34 (410)
                      ..+++.|...|...|++++|+.++++...
T Consensus         2 a~~~~~la~~~~~~g~~~~A~~~~~~al~   30 (42)
T PF13374_consen    2 ASALNNLANAYRAQGRYEEALELLEEALE   30 (42)
T ss_dssp             HHHHHHHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhhhcchhhHHHHHHHH
Confidence            35677888888888888888888877653

>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va

Probab=86.72  E-value=6.7  Score=28.72  Aligned_cols=48  Identities=15%  Similarity=0.181  Sum_probs=35.4

Q ss_pred             CHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q 040371           21 RFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLII   68 (410)
Q Consensus        21 ~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~   68 (410)
                      +.-++.+-++.+....+.|++....+.|.||-+.+++..|.++++-+.
T Consensus        22 D~we~rr~mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK   69 (103)
T cd00923          22 DGWELRRGLNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIK   69 (103)
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            334455556666666778888888888888888888888888888665

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.

>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=86.57  E-value=1.7  Score=24.58  Aligned_cols=27  Identities=7%  Similarity=0.003  Sum_probs=15.1

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      +|..+...|...|++++|+..|++.++
T Consensus         3 ~~~~~g~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF00515_consen    3 AYYNLGNAYFQLGDYEEALEYYQRALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHH
Confidence            455555556666666666666655554

It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....

>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases

Probab=86.46  E-value=27  Score=32.32  Aligned_cols=90  Identities=11%  Similarity=0.132  Sum_probs=60.9

Q ss_pred             CCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCC-CCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccC-------CCchH
Q 040371          173 SIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMT-MEPDVVVWRALLSACRTFKRLELGEVAIVNISRL-------MGGDY  244 (410)
Q Consensus       173 ~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~-------~~~~~  244 (410)
                      ...++..+|..++..-.-         ++..+. ......+|..+...+++.|+++.|...+......       .+...
T Consensus       117 ~~~~~~~~~~~il~~R~~---------~l~~~~~~~~~~~~~l~~a~~aRk~g~~~~A~~~l~~~~~~~~~~~~~~~~v~  187 (352)
T PF02259_consen  117 NMQDDFSVWEPILSLRRL---------VLSLILLPEELAETWLKFAKLARKAGNFQLALSALNRLFQLNPSSESLLPRVF  187 (352)
T ss_pred             HhccchHHHHHHHHHHHH---------HHhcccchhHHHHHHHHHHHHHHHCCCcHHHHHHHHHHhccCCcccCCCcchH
Confidence            345566677666643211         222121 2235678999999999999999999985554432       35566


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          245 VLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       245 ~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      ..-+...-..|+..+|...++...+..
T Consensus       188 ~e~akllw~~g~~~~Ai~~L~~~~~~~  214 (352)
T PF02259_consen  188 LEYAKLLWAQGEQEEAIQKLRELLKCR  214 (352)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence            666788888999999999988877633

Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding

>PRK11906 transcriptional regulator; Provisional

Probab=85.78  E-value=35  Score=32.88  Aligned_cols=43  Identities=9%  Similarity=0.126  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040371           59 HAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTV  102 (410)
Q Consensus        59 ~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m  102 (410)
                      +|.++-++.++.+ +.|......+.....-.|+++.|...|++.
T Consensus       322 ~a~~~A~rAveld-~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA  364 (458)
T PRK11906        322 KALELLDYVSDIT-TVDGKILAIMGLITGLSGQAKVSHILFEQA  364 (458)
T ss_pred             HHHHHHHHHHhcC-CCCHHHHHHHHHHHHhhcchhhHHHHHHHH
Confidence            3444444444443 234444444444444444455555555443

>PF04184 ST7: ST7 protein; InterPro: IPR007311 The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene

Probab=85.64  E-value=37  Score=33.01  Aligned_cols=79  Identities=15%  Similarity=0.238  Sum_probs=54.6

Q ss_pred             HHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCC-C-CCC--HHHHHHHHHHHHh
Q 040371          147 GLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMT-M-EPD--VVVWRALLSACRT  222 (410)
Q Consensus       147 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~-~-~p~--~~~~~~li~~~~~  222 (410)
                      .+...+.+.|+.++|.+.|.+|.+.............|+.+|...+.+.++..++.+-. + -|.  ...|++.+--++.
T Consensus       264 RLAmCarklGr~~EAIk~~rdLlke~p~~~~l~IrenLie~LLelq~Yad~q~lL~kYdDi~lpkSAti~YTaALLkaRa  343 (539)
T PF04184_consen  264 RLAMCARKLGRLREAIKMFRDLLKEFPNLDNLNIRENLIEALLELQAYADVQALLAKYDDISLPKSATICYTAALLKARA  343 (539)
T ss_pred             HHHHHHHHhCChHHHHHHHHHHHhhCCccchhhHHHHHHHHHHhcCCHHHHHHHHHHhccccCCchHHHHHHHHHHHHHh
Confidence            35556668899999999999998653332345577789999999999999999988873 2 233  3456665544444


Q ss_pred             cCc
Q 040371          223 FKR  225 (410)
Q Consensus       223 ~g~  225 (410)
                      .++
T Consensus       344 v~d  346 (539)
T PF04184_consen  344 VGD  346 (539)
T ss_pred             hcc
Confidence            443

The molecular function of this protein is uncertain.

>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=85.12  E-value=0.28  Score=39.22  Aligned_cols=53  Identities=15%  Similarity=0.126  Sum_probs=26.7

Q ss_pred             HHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040371           48 IYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFD  100 (410)
Q Consensus        48 l~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~  100 (410)
                      +..+.+.+.+....++++.+.+.+...+....+.|+.+|++.++.++..++++
T Consensus        14 i~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~   66 (143)
T PF00637_consen   14 ISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK   66 (143)
T ss_dssp             HHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT
T ss_pred             HHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc
Confidence            33344444455555555555554444455556666666666655455554444

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.

>PRK11906 transcriptional regulator; Provisional

Probab=85.05  E-value=38  Score=32.65  Aligned_cols=82  Identities=16%  Similarity=0.100  Sum_probs=47.0

Q ss_pred             hHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHH
Q 040371          123 AADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLI  201 (410)
Q Consensus       123 ~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~  201 (410)
                      ..+|.++-++..+.+ .-|......+..+....++++.|...|++..   .+.|| ...|........-+|+.++|.+.+
T Consensus       320 ~~~a~~~A~rAveld-~~Da~a~~~~g~~~~~~~~~~~a~~~f~rA~---~L~Pn~A~~~~~~~~~~~~~G~~~~a~~~i  395 (458)
T PRK11906        320 AQKALELLDYVSDIT-TVDGKILAIMGLITGLSGQAKVSHILFEQAK---IHSTDIASLYYYRALVHFHNEKIEEARICI  395 (458)
T ss_pred             HHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHhhcchhhHHHHHHHHh---hcCCccHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            345555555555533 2255555555555566666777777777765   34454 344444444455677777777777


Q ss_pred             Hh-CCCCC
Q 040371          202 TS-MTMEP  208 (410)
Q Consensus       202 ~~-m~~~p  208 (410)
                      ++ +...|
T Consensus       396 ~~alrLsP  403 (458)
T PRK11906        396 DKSLQLEP  403 (458)
T ss_pred             HHHhccCc
Confidence            66 34444

>PF13929 mRNA_stabil: mRNA stabilisation

Probab=84.77  E-value=12  Score=33.42  Aligned_cols=114  Identities=10%  Similarity=0.084  Sum_probs=0.0

Q ss_pred             HcCChHHHHHHHHHHHH-CCCCCCHHHHHHHHHHHHc--cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHH
Q 040371          119 IHGLAADASAIFTKMEM-FNVLPDSITFLGLLTACSH--CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIE  195 (410)
Q Consensus       119 ~~g~~~~A~~l~~~m~~-~g~~p~~~t~~~ll~a~~~--~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~  195 (410)
                      ++....+|+.+|+.... +.+--|..+...+++....  ......--++.+.+...++-.++..+....+..+++.+++.
T Consensus       140 ~N~~Vv~aL~L~~~~~~~~~Ii~d~evislLL~sMv~~~~~~l~alYEvV~~l~~t~~~~l~~~vi~~Il~~L~~~~dW~  219 (292)
T PF13929_consen  140 RNKIVVEALKLYDGLNPDESIIFDEEVISLLLKSMVIDENTKLNALYEVVDFLVSTFSKSLTRNVIISILEILAESRDWN  219 (292)
T ss_pred             hhHHHHHHHHHhhccCcccceeeChHHHHHHHHHHHhccccchhhHHHHHHHHHhccccCCChhHHHHHHHHHHhcccHH


Q ss_pred             HHHHHHHhC----CCCCCHHHHHHHHHHHHhcCchhHHHHH
Q 040371          196 EAYGLITSM----TMEPDVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       196 ~A~~~~~~m----~~~p~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      +-.++++..    ....|...|..+|..-..+|+.....++
T Consensus       220 kl~~fW~~~~~~~~~~~D~rpW~~FI~li~~sgD~~~~~ki  260 (292)
T PF13929_consen  220 KLFQFWEQCIPNSVPGNDPRPWAEFIKLIVESGDQEVMRKI  260 (292)
T ss_pred             HHHHHHHHhcccCCCCCCCchHHHHHHHHHHcCCHHHHHHH

>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=84.52  E-value=20  Score=29.10  Aligned_cols=19  Identities=11%  Similarity=0.060  Sum_probs=10.2

Q ss_pred             HHhcCCHHHHHHHHHhccc
Q 040371           86 YSKCGKIQMAKEVFDTVQR  104 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~  104 (410)
                      +.+.|++++|+.+|+++..
T Consensus        54 ~i~r~~w~dA~rlLr~l~~   72 (160)
T PF09613_consen   54 HIVRGDWDDALRLLRELEE   72 (160)
T ss_pred             HHHhCCHHHHHHHHHHHhc
Confidence            4455555555555555543

>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=84.45  E-value=0.44  Score=38.00  Aligned_cols=86  Identities=9%  Similarity=0.117  Sum_probs=60.2

Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC
Q 040371           11 SMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG   90 (410)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g   90 (410)
                      .+|..+.+.+.++.....++.+...+...+....+.++..|++.+..+....+++   ..    +.+-...++..+-+.|
T Consensus        12 ~vi~~~~~~~~~~~l~~yLe~~~~~~~~~~~~~~~~L~~ly~~~~~~~~l~~~L~---~~----~~yd~~~~~~~c~~~~   84 (143)
T PF00637_consen   12 EVISAFEERNQPEELIEYLEALVKENKENNPDLHTLLLELYIKYDPYEKLLEFLK---TS----NNYDLDKALRLCEKHG   84 (143)
T ss_dssp             CCHHHCTTTT-GGGCTCCHHHHHHTSTC-SHHHHHHHHHHHHCTTTCCHHHHTTT---SS----SSS-CTHHHHHHHTTT
T ss_pred             HHHHHHHhCCCHHHHHHHHHHHHhcccccCHHHHHHHHHHHHhcCCchHHHHHcc---cc----cccCHHHHHHHHHhcc
Confidence            4577788889999999999999877666678888999999999987777776665   11    1122345566666677


Q ss_pred             CHHHHHHHHHhcc
Q 040371           91 KIQMAKEVFDTVQ  103 (410)
Q Consensus        91 ~~~~A~~~f~~m~  103 (410)
                      .+++|.-++.++.
T Consensus        85 l~~~a~~Ly~~~~   97 (143)
T PF00637_consen   85 LYEEAVYLYSKLG   97 (143)
T ss_dssp             SHHHHHHHHHCCT
T ss_pred             hHHHHHHHHHHcc
Confidence            7777766666554

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.

>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A

Probab=83.95  E-value=2.7  Score=24.83  Aligned_cols=26  Identities=12%  Similarity=0.164  Sum_probs=14.5

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKME  134 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~  134 (410)
                      +++.|...|...|++++|+.++++..
T Consensus         4 ~~~~la~~~~~~g~~~~A~~~~~~al   29 (42)
T PF13374_consen    4 ALNNLANAYRAQGRYEEALELLEEAL   29 (42)
T ss_dssp             HHHHHHHHHHHCT-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcchhhHHHHHHH
Confidence            45555556666666666666665543

>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]

Probab=82.82  E-value=3.1  Score=23.23  Aligned_cols=27  Identities=19%  Similarity=0.584  Sum_probs=20.9

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLS   34 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~   34 (410)
                      .|..+-..|.+.|++++|++.|++..+
T Consensus         3 ~~~~lg~~~~~~~~~~~A~~~~~~al~   29 (34)
T PF07719_consen    3 AWYYLGQAYYQLGNYEEAIEYFEKALE   29 (34)
T ss_dssp             HHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            567777888888888888888888765

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 ....

>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]

Probab=82.50  E-value=38  Score=30.69  Aligned_cols=46  Identities=11%  Similarity=0.100  Sum_probs=21.0

Q ss_pred             CChhHHHHHHHHHHHc--CCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRN--ARFDEALRFFREMLSSKVEPDKFTFASVIYGC   51 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~--g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~   51 (410)
                      |.++.+|-+|+-|.-.  +--++...++.-+  .|..++...=.+++.+.
T Consensus       109 ~~~qvf~KliRRykyLeK~fE~e~~k~Llfl--k~F~e~Er~KLA~~Tal  156 (412)
T KOG2297|consen  109 NSVQVFQKLIRRYKYLEKNFENEMRKFLLFL--KLFEENERKKLAMLTAL  156 (412)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HccCHHHHHHHHHHHHH
Confidence            3456677777665421  2112222222222  24556655555555444

>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=82.41  E-value=26  Score=28.78  Aligned_cols=133  Identities=12%  Similarity=0.105  Sum_probs=75.5

Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccH-HHHHHHHHHHHhcCCHHHHHHHHHhccc
Q 040371           26 LRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNF-ILSAALIDMYSKCGKIQMAKEVFDTVQR  104 (410)
Q Consensus        26 ~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~-~~~~~li~~y~~~g~~~~A~~~f~~m~~  104 (410)
                      ++..+.+.+.+++|+...+..+++.+.+.|.+..-.+    +++.++-+|. .+...|++.-.   ....+.++=-.|..
T Consensus        14 lEYirSl~~~~i~~~~~L~~lli~lLi~~~~~~~L~q----llq~~Vi~DSk~lA~~LLs~~~---~~~~~~Ql~lDMLk   86 (167)
T PF07035_consen   14 LEYIRSLNQHNIPVQHELYELLIDLLIRNGQFSQLHQ----LLQYHVIPDSKPLACQLLSLGN---QYPPAYQLGLDMLK   86 (167)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHHHHcCCHHHHHH----HHhhcccCCcHHHHHHHHHhHc---cChHHHHHHHHHHH
Confidence            4455566667888888888888998888888765444    3344444443 33333333222   22333333333433


Q ss_pred             CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          105 NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       105 ~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      +=-..+..++..+...|++-+|+.+.+.....    +...-..++.+-.+.++...=..+|....
T Consensus        87 RL~~~~~~iievLL~~g~vl~ALr~ar~~~~~----~~~~~~~fLeAA~~~~D~~lf~~V~~ff~  147 (167)
T PF07035_consen   87 RLGTAYEEIIEVLLSKGQVLEALRYARQYHKV----DSVPARKFLEAAANSNDDQLFYAVFRFFE  147 (167)
T ss_pred             HhhhhHHHHHHHHHhCCCHHHHHHHHHHcCCc----ccCCHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            32335666777788888888888888765322    11222345666666666554444444433

>COG4785 NlpI Lipoprotein NlpI, contains TPR repeats [General function prediction only]

Probab=82.15  E-value=32  Score=29.60  Aligned_cols=180  Identities=15%  Similarity=0.035  Sum_probs=94.7

Q ss_pred             hcCCHHHHHHHHHhcc--cCC-hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHH
Q 040371           88 KCGKIQMAKEVFDTVQ--RND-VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKY  164 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~--~~~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~  164 (410)
                      ..|-++-|+-=|.+..  .|+ ...||-+---+...|+++.|.+.|+...+.... ...++..-.-++.-.|++..|.+=
T Consensus        77 SlGL~~LAR~DftQaLai~P~m~~vfNyLG~Yl~~a~~fdaa~eaFds~~ELDp~-y~Ya~lNRgi~~YY~gR~~LAq~d  155 (297)
T COG4785          77 SLGLRALARNDFSQALAIRPDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELDPT-YNYAHLNRGIALYYGGRYKLAQDD  155 (297)
T ss_pred             hhhHHHHHhhhhhhhhhcCCCcHHHHHHHHHHHHhcccchHHHHHhhhHhccCCc-chHHHhccceeeeecCchHhhHHH
Confidence            3444555555554433  333 356777777777888888888888887764322 122222222233345777777665


Q ss_pred             HHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHH-HHHhCCCCCCHHHHHHHHHHHHhcCchhHH-HHHHHhhccCC--
Q 040371          165 FDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYG-LITSMTMEPDVVVWRALLSACRTFKRLELG-EVAIVNISRLM--  240 (410)
Q Consensus       165 ~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~-~~~~m~~~p~~~~~~~li~~~~~~g~~~~a-~~~~~~~~~~~--  240 (410)
                      |...-..-.-.|-...|--++   -+.-++.+|.. +.++. ...|..-|...|-.+---.-.+++ .+-+.....++  
T Consensus       156 ~~~fYQ~D~~DPfR~LWLYl~---E~k~dP~~A~tnL~qR~-~~~d~e~WG~~iV~~yLgkiS~e~l~~~~~a~a~~n~~  231 (297)
T COG4785         156 LLAFYQDDPNDPFRSLWLYLN---EQKLDPKQAKTNLKQRA-EKSDKEQWGWNIVEFYLGKISEETLMERLKADATDNTS  231 (297)
T ss_pred             HHHHHhcCCCChHHHHHHHHH---HhhCCHHHHHHHHHHHH-HhccHhhhhHHHHHHHHhhccHHHHHHHHHhhccchHH
Confidence            554432212222223333222   22334555543 33333 234555666555443222111111 11111111111  


Q ss_pred             -----CchHHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 040371          241 -----GGDYVLLSNMYCYLKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       241 -----~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  272 (410)
                           ..+|.-|..-|...|..++|..+|+.....++
T Consensus       232 ~Ae~LTEtyFYL~K~~l~~G~~~~A~~LfKLaiannV  268 (297)
T COG4785         232 LAEHLTETYFYLGKYYLSLGDLDEATALFKLAVANNV  268 (297)
T ss_pred             HHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhH
Confidence                 35788899999999999999999998776654

>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]

Probab=81.35  E-value=44  Score=31.10  Aligned_cols=124  Identities=12%  Similarity=0.040  Sum_probs=59.7

Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHHHHcC-----CCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc-------cCChh----
Q 040371           45 ASVIYGCARLGALNHAYWVHNLIIEKK-----IELNFILSAALIDMYSKCGKIQMAKEVFDTVQ-------RNDVS----  108 (410)
Q Consensus        45 ~~ll~a~~~~~~~~~a~~~~~~~~~~g-----~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~-------~~~~~----  108 (410)
                      .++-.|+...+.++++.+.|+...+..     -.....++-+|-+.|.+..++++|.-+..+..       -.|..    
T Consensus       126 l~~~~Ahlgls~fq~~Lesfe~A~~~A~~~~D~~LElqvcv~Lgslf~~l~D~~Kal~f~~kA~~lv~s~~l~d~~~kyr  205 (518)
T KOG1941|consen  126 LSMGNAHLGLSVFQKALESFEKALRYAHNNDDAMLELQVCVSLGSLFAQLKDYEKALFFPCKAAELVNSYGLKDWSLKYR  205 (518)
T ss_pred             hhHHHHhhhHHHHHHHHHHHHHHHHHhhccCCceeeeehhhhHHHHHHHHHhhhHHhhhhHhHHHHHHhcCcCchhHHHH
Confidence            334455555666666666666554431     11234566666666666666666654333221       11221    


Q ss_pred             --hHHHHHHHHHHcCChHHHHHHHHHHHH----CCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040371          109 --VWNAMISGVAIHGLAADASAIFTKMEM----FNVLPD-SITFLGLLTACSHCGLVEEGRKYFDHM  168 (410)
Q Consensus       109 --~~~~li~~~~~~g~~~~A~~l~~~m~~----~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m  168 (410)
                        +..-|.-++-..|....|.+.-++..+    .|-.|. ......+...|...|+.+.|+.-+++.
T Consensus       206 ~~~lyhmaValR~~G~LgdA~e~C~Ea~klal~~Gdra~~arc~~~~aDIyR~~gd~e~af~rYe~A  272 (518)
T KOG1941|consen  206 AMSLYHMAVALRLLGRLGDAMECCEEAMKLALQHGDRALQARCLLCFADIYRSRGDLERAFRRYEQA  272 (518)
T ss_pred             HHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHhcccHhHHHHHHHHH
Confidence              112233445555555555555544322    232221 122334455566666666666555543

>KOG1130 consensus Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms]

Probab=80.77  E-value=3.3  Score=38.70  Aligned_cols=128  Identities=12%  Similarity=0.046  Sum_probs=92.0

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHc----CC-CccHHHHHHHHHHHHhcCCHHHHHHHHHhcc-------cCCh--
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEK----KI-ELNFILSAALIDMYSKCGKIQMAKEVFDTVQ-------RNDV--  107 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~-~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~-------~~~~--  107 (410)
                      ..|..+-+.|.-+|+++.|...|+.-+..    |- ......+..|.++|+-.|+++.|.+.|....       ++.+  
T Consensus       196 Ra~GnLGNTyYlLGdf~~ai~~H~~RL~ia~efGDrAaeRRA~sNlgN~hiflg~fe~A~ehYK~tl~LAielg~r~vEA  275 (639)
T KOG1130|consen  196 RAYGNLGNTYYLLGDFDQAIHFHKLRLEIAQEFGDRAAERRAHSNLGNCHIFLGNFELAIEHYKLTLNLAIELGNRTVEA  275 (639)
T ss_pred             chhcccCceeeeeccHHHHHHHHHHHHHHHHHhhhHHHHHHhhcccchhhhhhcccHhHHHHHHHHHHHHHHhcchhHHH
Confidence            45666777777788999999988765432    21 1234567889999999999999998886532       3433  


Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHHHHC-----CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          108 SVWNAMISGVAIHGLAADASAIFTKMEMF-----NVLPDSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      .+..++.+.|.-...+++|+..+.+-+.-     ...-....+-+|..++...|..++|+.+...-.
T Consensus       276 QscYSLgNtytll~e~~kAI~Yh~rHLaIAqeL~DriGe~RacwSLgna~~alg~h~kAl~fae~hl  342 (639)
T KOG1130|consen  276 QSCYSLGNTYTLLKEVQKAITYHQRHLAIAQELEDRIGELRACWSLGNAFNALGEHRKALYFAELHL  342 (639)
T ss_pred             HHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence            35566788888888899999888764331     112234678889999999999999988776544

>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1

Probab=80.45  E-value=15  Score=27.30  Aligned_cols=46  Identities=15%  Similarity=0.258  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q 040371           24 EALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIE   69 (410)
Q Consensus        24 ~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~   69 (410)
                      +...-++.+....+.|++....+.|.||-+.+++..|.++++-+..
T Consensus        28 e~rrglN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~   73 (108)
T PF02284_consen   28 ELRRGLNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKD   73 (108)
T ss_dssp             HHHHHHHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            3444444555556677777777777777777777777777776653

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 ....

>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length

Probab=80.33  E-value=57  Score=31.35  Aligned_cols=248  Identities=13%  Similarity=0.070  Sum_probs=132.2

Q ss_pred             HHHcCCHhHHHHHHHHHHHCCCCCCHHH------HHHHHHHHHhhCCHHHHHHHHHHHHHc-CCCccHHHHHHHHHHHHh
Q 040371           16 FVRNARFDEALRFFREMLSSKVEPDKFT------FASVIYGCARLGALNHAYWVHNLIIEK-KIELNFILSAALIDMYSK   88 (410)
Q Consensus        16 ~~~~g~~~~a~~l~~~m~~~g~~pd~~t------~~~ll~a~~~~~~~~~a~~~~~~~~~~-g~~~~~~~~~~li~~y~~   88 (410)
                      +.+++++.+|..+|.+..++ ...+++.      -+.+++|+. ..+++..........+. |-.+-...+-+|+  .-+
T Consensus        16 Lqkq~~~~esEkifskI~~e-~~~~~f~lkeEvl~grilnAff-l~nld~Me~~l~~l~~~~~~s~~l~LF~~L~--~Y~   91 (549)
T PF07079_consen   16 LQKQKKFQESEKIFSKIYDE-KESSPFLLKEEVLGGRILNAFF-LNNLDLMEKQLMELRQQFGKSAYLPLFKALV--AYK   91 (549)
T ss_pred             HHHHhhhhHHHHHHHHHHHH-hhcchHHHHHHHHhhHHHHHHH-HhhHHHHHHHHHHHHHhcCCchHHHHHHHHH--HHH
Confidence            34678899999999998764 2333222      344666664 45666666666666554 3333333444433  357


Q ss_pred             cCCHHHHHHHHHhcccC------------------ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCC----CCHHHHH
Q 040371           89 CGKIQMAKEVFDTVQRN------------------DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVL----PDSITFL  146 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~~------------------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~----p~~~t~~  146 (410)
                      .+.+++|.+.|..-.+.                  |..-=+..+..+...|.+.++..++++|...=.+    -+..+|+
T Consensus        92 ~k~~~kal~~ls~w~~~~~~~~~~~Ld~ni~~l~~df~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd  171 (549)
T PF07079_consen   92 QKEYRKALQALSVWKEQIKGTESPWLDTNIQQLFSDFFLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYD  171 (549)
T ss_pred             hhhHHHHHHHHHHHHhhhcccccchhhhhHHHHhhHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHH
Confidence            78888888877654321                  1122245566777889999999998888765333    5778888


Q ss_pred             HHHHHHHccCCHH---------------HHHHHHHHhhhhc-----CCCCChhHHHHHHHHHHhc-----CCHHHHHHHH
Q 040371          147 GLLTACSHCGLVE---------------EGRKYFDHMRSRY-----SIQPQLEHYGAMVDLLGRA-----GHIEEAYGLI  201 (410)
Q Consensus       147 ~ll~a~~~~g~~~---------------~a~~~~~~m~~~~-----~~~~~~~~~~~li~~~~~~-----g~~~~A~~~~  201 (410)
                      .++-.++++=.++               .+.-+..+|...-     .+.|.......++....-.     --+-.+.+.+
T Consensus       172 ~~vlmlsrSYfLEl~e~~s~dl~pdyYemilfY~kki~~~d~~~Y~k~~peeeL~s~imqhlfi~p~e~l~~~mq~l~~W  251 (549)
T PF07079_consen  172 RAVLMLSRSYFLELKESMSSDLYPDYYEMILFYLKKIHAFDQRPYEKFIPEEELFSTIMQHLFIVPKERLPPLMQILENW  251 (549)
T ss_pred             HHHHHHhHHHHHHHHHhcccccChHHHHHHHHHHHHHHHHhhchHHhhCcHHHHHHHHHHHHHhCCHhhccHHHHHHHHH
Confidence            7665555431111               1111111111000     1112222222222211110     1112233333


Q ss_pred             HhCCCCCCHH-HHHHHHHHHHhcCchhHHHHH--------HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040371          202 TSMTMEPDVV-VWRALLSACRTFKRLELGEVA--------IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       202 ~~m~~~p~~~-~~~~li~~~~~~g~~~~a~~~--------~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                      ++--+.|+.. ....|+..+..  +.+.+..+        +.++...-..++..++....+.++...|.+.+..+.-
T Consensus       252 e~~yv~p~~~LVi~~L~~~f~~--~~e~~~~~ce~ia~~~i~~Lke~li~~F~~~Ls~~Vk~~~T~~a~q~l~lL~~  326 (549)
T PF07079_consen  252 ENFYVHPNYDLVIEPLKQQFMS--DPEQVGHFCEAIASSKIEKLKEELIDRFGNLLSFKVKQVQTEEAKQYLALLKI  326 (549)
T ss_pred             HhhccCCchhHHHHHHHHHHhc--ChHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHh
Confidence            3333456533 34455555444  44444444        2222223345677888888889999999888877764

Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.

>COG4105 ComL DNA uptake lipoprotein [General function prediction only]

Probab=80.21  E-value=41  Score=29.63  Aligned_cols=61  Identities=15%  Similarity=0.250  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCC-C-CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSK-V-EPDKFTFASVIYGCARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g-~-~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~   70 (410)
                      |+.-+. -.+.|++++|.+-|+.+.... . +-..-+...++.++-+.++++.|....++.++.
T Consensus        38 Y~~g~~-~L~~gn~~~A~~~fe~l~~~~p~s~~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~l  100 (254)
T COG4105          38 YNEGLT-ELQKGNYEEAIKYFEALDSRHPFSPYSEQAQLDLAYAYYKNGEYDLALAYIDRFIRL  100 (254)
T ss_pred             HHHHHH-HHhcCCHHHHHHHHHHHHHcCCCCcccHHHHHHHHHHHHhcccHHHHHHHHHHHHHh
Confidence            443333 346788888888888877542 1 112345555666677777888888777777665

---

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	410
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	3e-08
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	6e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 55.2 bits (131), Expect = 3e-08
 Identities = 30/309 (9%), Positives = 85/309 (27%), Gaps = 17/309 (5%)

Query: 32  MLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK 91
              +   P +   A ++       +L+          + ++        A         +
Sbjct: 83  TRQAPESPWEEQLARLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQ 142

Query: 92  IQMAKEVFDTVQRN-------DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSIT 144
           + +A  +               + ++NA++ G A  G   +   +   ++   + PD ++
Sbjct: 143 LPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLS 202

Query: 145 FLGLLTACSHCGLVEEG-RKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITS 203
           +   L              +  + M         L     ++    RA  ++  + +  +
Sbjct: 203 YAAALQCMGRQDQDAGTIERCLEQMSQEGLKLQALF-TAVLLSEEDRATVLKAVHKVKPT 261

Query: 204 MTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENV 263
            ++ P     +       +    ++           +      L  ++      + A  V
Sbjct: 262 FSLPP-----QLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFEKQLHMELASRV 316

Query: 264 REIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPAT 323
             +  +K    S+            + +         +A+ +    L +      F    
Sbjct: 317 CVVSVEKPTLPSKEVKHARKTLKTLRDQW---EKALCRALRETKNRLEREVYEGRFSLYP 373

Query: 324 ELVLMDVSE 332
            L L+D  E
Sbjct: 374 FLCLLDERE 382

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens} Length = 1134

 Score = 51.0 bits (120), Expect = 6e-07
 Identities = 14/100 (14%), Positives = 40/100 (40%), Gaps = 1/100 (1%)

Query: 5   DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYW-V 63
            +  +N+++ G+ R   F E +     +  + + PD  ++A+ +    R           
Sbjct: 164 TLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERC 223

Query: 64  HNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ 103
              + ++ ++L  + +A L+    +   ++   +V  T  
Sbjct: 224 LEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFS 263

>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 = 45.6 bits (107), Expect = 3e-05
 Identities = 65/450 (14%), Positives = 143/450 (31%), Gaps = 119/450 (26%)

Query: 1   MPDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD-----------KFTFASVIY 49
           M  K  + W ++     +N    E +    + L  +++P+           K    S+  
Sbjct: 180 MDFK--IFWLNL-----KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232

Query: 50  GCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYS-KCGKIQMAKEVFDTVQRNDVS 108
              RL  L    + + L++     L  + +A   + ++  C KI     +  T       
Sbjct: 233 ELRRL--LKSKPYENCLLV-----LLNVQNAKAWNAFNLSC-KI-----LLTT---RFKQ 276

Query: 109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLT------ACS----HCGLV 158
           V + + +    H      S   T  E+ ++L   + +L            +       ++
Sbjct: 277 VTDFLSAATTTHISLDHHSMTLTPDEVKSLL---LKYLDCRPQDLPREVLTTNPRRLSII 333

Query: 159 EEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLS 218
            E         + +      +H     D L     IE +        +EP     R +  
Sbjct: 334 AE---SIRDGLATWD---NWKHVN--CDKLTTI--IESSLN-----VLEPAEY--RKM-- 374

Query: 219 ACRTFKRLELGEVAI----VNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRK 274
               F RL     ++     +I        +LLS ++  + + D    V ++ K   V K
Sbjct: 375 ----FDRL-----SVFPPSAHIP------TILLSLIWFDVIKSDVMVVVNKLHKYSLVEK 419

Query: 275 SQGKSWLELAGVIHQFKAGDRSHPE--AQAIDKILGSLIQRTKSEGFLPATELVLMDVSE 332
              +S + +  +  + K    +        +D    ++ +   S+  +P           
Sbjct: 420 QPKESTISIPSIYLELKVKLENEYALHRSIVDHY--NIPKTFDSDDLIPPYL-------- 469

Query: 333 EEKEGNLYHHSEKLALAYGILKTSPGTEI----RISKNLR-----ICHDCHSWIKMISRL 383
              +   Y H     + + +        +     +  + R     I HD  +W    S L
Sbjct: 470 ---DQYFYSH-----IGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSIL 521

Query: 384 --LRRVIIVRDRIRFH--RFEGGLCSCGDY 409
             L+++   +  I  +  ++E  + +  D+
Sbjct: 522 NTLQQLKFYKPYICDNDPKYERLVNAILDF 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 = 45.2 bits (106), Expect = 4e-05
 Identities = 58/469 (12%), Positives = 125/469 (26%), Gaps = 133/469 (28%)

Query: 4   KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKV------EPDKFTFASVIYGCARL--- 54
           KD++S       FV N    +     + +LS +         D  +    ++        
Sbjct: 19  KDILSVF--EDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQE 76

Query: 55  --------GALNHAY-WVHNLIIEKKIELNFILSAALIDMYSKC-GKIQMAKEVFD--TV 102
                     L   Y +     +   I+      + +  MY +   ++    +VF    V
Sbjct: 77  EMVQKFVEEVLRINYKF-----LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131

Query: 103 QRND--VSVWNAMIS-----GVAIHG--------LAADASAIFTKMEMFNVLPDSITFLG 147
            R    + +  A++       V I G        +A D    +            I +L 
Sbjct: 132 SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKM---DFKIFWLN 188

Query: 148 LLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTME 207
           L    S   ++E  +K    +   ++       + + + L      I      +  +   
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWT---SRSDHSSNIKL-----RIHSIQAELRRLLKS 240

Query: 208 P----------DV---VVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYL 254
                      +V     W A   +C+           ++  +R       L +    + 
Sbjct: 241 KPYENCLLVLLNVQNAKAWNAFNLSCKI----------LL-TTRFKQVTDFLSAATTTH- 288

Query: 255 KRWDTAENVREIMKKKGVRKSQGKS----WLELAGVIHQFKAGDRSHPEAQAIDKILGSL 310
                   +        +   + KS    +L+        +  D    E    +    S+
Sbjct: 289 --------ISLDHHSMTLTPDEVKSLLLKYLDC-------RPQDLP-REVLTTNPRRLSI 332

Query: 311 IQRTKSEGFLPATELVLMDVSEEEKEGNLYHHSEKLALAYGILKTSPGTEIR-------- 362
           I  +  +G   AT        +  K  N    +  +  +  +L+ +   E R        
Sbjct: 333 IAESIRDG--LAT-------WDNWKHVNCDKLTTIIESSLNVLEPA---EYRKMFDRLSV 380

Query: 363 ISKNLRICHD--CHSWIKMISR--------LLRRVIIVRD----RIRFH 397
              +  I        W  +I          L +  ++ +      I   
Sbjct: 381 FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIP 429

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	410
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	100.0
4g26_A	501	Pentatricopeptide repeat-containing protein AT2G3	99.98
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.95
2xpi_A	597	Anaphase-promoting complex subunit CUT9; cell cycl	99.95
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.86
1w3b_A	388	UDP-N-acetylglucosamine--peptide N-acetylglucosami	99.84
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.84
2y4t_A	450	DNAJ homolog subfamily C member 3; chaperone, endo	99.83
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.79
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.79
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.78
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.77
3spa_A	1134	Mtrpol, DNA-directed RNA polymerase, mitochondrial	99.77
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.75
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.74
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.74
3ieg_A	359	DNAJ homolog subfamily C member 3; TPR motif, chap	99.74
2gw1_A	514	Mitochondrial precursor proteins import receptor;	99.73
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.7
3hym_B	330	Cell division cycle protein 16 homolog; APC, anaph	99.7
1fch_A	368	Peroxisomal targeting signal 1 receptor; protein-p	99.7
1b89_A	449	Protein (clathrin heavy chain); triskelion, coated	99.69
4eqf_A	365	PEX5-related protein; accessory protein, tetratric	99.69
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.69
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.68
3mkr_A	291	Coatomer subunit epsilon; tetratricopeptide repeat	99.67
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.6
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.6
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.59
3fp2_A	537	TPR repeat-containing protein YHR117W; TOM71, mito	99.59
3uq3_A	258	Heat shock protein STI1; HSP90, peptide binding, c	99.59
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.58
3cv0_A	327	Peroxisome targeting signal 1 receptor PEX5; TPR m	99.58
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.58
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.54
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.51
2pl2_A	217	Hypothetical conserved protein TTC0263; TPR, prote	99.51
2ho1_A	252	Type 4 fimbrial biogenesis protein PILF; type IV p	99.5
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.49
2vq2_A	225	PILW, putative fimbrial biogenesis and twitching m	99.49
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.49
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.49
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.48
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.47
1xnf_A	275	Lipoprotein NLPI; TPR, tetratricopeptide, structur	99.46
2q7f_A	243	YRRB protein; TPR, protein binding; 2.49A {Bacillu	99.45
1ouv_A	273	Conserved hypothetical secreted protein; TPR repea	99.45
3u4t_A	272	TPR repeat-containing protein; structural genomics	99.44
2h6f_A	382	Protein farnesyltransferase/geranylgeranyltransfer	99.4
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.39
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.39
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.38
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.36
2xm6_A	490	Protein corresponding to locus C5321 from CFT073 s	99.36
3nf1_A	311	KLC 1, kinesin light chain 1; TPR, structural geno	99.34
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.34
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.32
3vtx_A	184	MAMA; tetratricopeptide repeats (TPR) containing p	99.31
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.31
2ond_A	308	Cleavage stimulation factor 77 kDa subunit; HAT do	99.28
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	99.28
4abn_A	474	Tetratricopeptide repeat protein 5; P53 cofactor,	99.26
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.26
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.26
1xi4_A	1630	Clathrin heavy chain; alpha-ZIG-ZAG, beta-propelle	99.23
4g1t_A	472	Interferon-induced protein with tetratricopeptide	99.22
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.2
3sf4_A	406	G-protein-signaling modulator 2; tetratricopeptide	99.19
3ulq_A	383	Response regulator aspartate phosphatase F; tetrat	99.17
4a1s_A	411	PINS, partner of inscuteable; cell cycle, LGN, mit	99.16
3ro2_A	338	PINS homolog, G-protein-signaling modulator 2; TPR	99.16
3as5_A	186	MAMA; tetratricopeptide repeats (TPR) containing p	99.16
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.14
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.14
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.12
2ooe_A	530	Cleavage stimulation factor 77 kDa subunit; HAT do	99.12
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.12
3edt_B	283	KLC 2, kinesin light chain 2; superhelical, struct	99.1
4gyw_A	723	UDP-N-acetylglucosamine--peptide N- acetylglucosam	99.1
1qqe_A	292	Vesicular transport protein SEC17; helix-turn-heli	99.08
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	99.08
4i17_A	228	Hypothetical protein; TPR repeats protein, structu	99.06
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.04
3q15_A	378	PSP28, response regulator aspartate phosphatase H;	99.01
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.96
1hz4_A	373	MALT regulatory protein; two-helix bundles, helix	98.95
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.91
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.91
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.91
2fo7_A	136	Synthetic consensus TPR protein; tetratricopeptide	98.89
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.88
3mv2_B	310	Coatomer subunit epsilon; vesicular membrane coat	98.87
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.86
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.78
3urz_A	208	Uncharacterized protein; tetratricopeptide repeats	98.77
2pzi_A	681	Probable serine/threonine-protein kinase PKNG; ATP	98.77
3e4b_A	452	ALGK; tetratricopeptide repeat, superhelix, algina	98.76
3qky_A	261	Outer membrane assembly lipoprotein YFIO; membrane	98.75
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.71
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.71
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.69
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.68
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.68
3rjv_A	212	Putative SEL1 repeat protein; alpha-alpha superhel	98.68
1hh8_A	213	P67PHOX, NCF-2, neutrophil cytosol factor 2; cell	98.67
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.67
3qou_A	287	Protein YBBN; thioredoxin-like fold, tetratricopep	98.66
2ifu_A	307	Gamma-SNAP; membrane fusion, snare complex disasse	98.65
2yhc_A	225	BAMD, UPF0169 lipoprotein YFIO; essential BAM comp	98.63
2r5s_A	176	Uncharacterized protein VP0806; APC090868.1, vibri	98.62
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.61
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.57
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.56
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.56
2vsy_A	568	XCC0866; transferase, glycosyl transferase, GT-B,	98.56
4ga2_A	150	E3 SUMO-protein ligase ranbp2; TPR motif, nuclear	98.56
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.54
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.5
3dra_A	306	Protein farnesyltransferase/geranylgeranyltransfer	98.5
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.48
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.47
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.47
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.47
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.45
3gw4_A	203	Uncharacterized protein; structural genomics, PSI-	98.44
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	98.42
1a17_A	166	Serine/threonine protein phosphatase 5; hydrolase,	98.39
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	98.39
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.39
1na0_A	125	Designed protein CTPR3; de novo protein; HET: IPT;	98.38
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.38
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.37
4gco_A	126	Protein STI-1; structural genomics, PSI-biology, m	98.37
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.36
4e6h_A	679	MRNA 3'-END-processing protein RNA14; HAT domain,	98.36
3gyz_A	151	Chaperone protein IPGC; asymmetric homodimer, tetr	98.3
2c2l_A	281	CHIP, carboxy terminus of HSP70-interacting protei	98.3
2vyi_A	131	SGTA protein; chaperone, TPR repeat, phosphoprotei	98.27
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.25
2vgx_A	148	Chaperone SYCD; alternative dimer assembly, tetrat	98.24
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.24
2e2e_A	177	Formate-dependent nitrite reductase complex NRFG;	98.24
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.23
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.22
2lni_A	133	Stress-induced-phosphoprotein 1; structural genomi	98.21
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.2
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.2
1p5q_A	336	FKBP52, FK506-binding protein 4; isomerase; 2.80A	98.19
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.18
3upv_A	126	Heat shock protein STI1; TPR-fold, adaptor protein	98.17
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.17
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.17
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	98.16
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.15
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.14
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.14
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	98.12
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	98.11
3q7a_A	349	Farnesyltransferase alpha subunit; protein prenylt	98.11
3q49_B	137	STIP1 homology and U box-containing protein 1; E3	98.07
1elw_A	118	TPR1-domain of HOP; HOP, TPR-domain, peptide-compl	98.06
3sz7_A	164	HSC70 cochaperone (SGT); TPR domain, GET4, GET5, G	98.06
4gcn_A	127	Protein STI-1; structural genomics, PSI-biology, m	98.06
2xcb_A	142	PCRH, regulatory protein PCRH; protein transport,	98.05
1elr_A	131	TPR2A-domain of HOP; HOP, TPR-domain, peptide-comp	98.04
4f3v_A	282	ESX-1 secretion system protein ECCA1; tetratricope	98.04
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	98.04
2fbn_A	198	70 kDa peptidylprolyl isomerase, putative; sulfur	98.02
2kck_A	112	TPR repeat; tetratricopeptide repeat, structural g	98.01
3ro3_A	164	PINS homolog, G-protein-signaling modulator 2; asy	97.96
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.9
2dba_A	148	Smooth muscle cell associated protein-1, isoform 2	97.88
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.85
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	97.85
1hxi_A	121	PEX5, peroxisome targeting signal 1 receptor PEX5;	97.84
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	97.82
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.79
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.77
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.71
2xev_A	129	YBGF; tetratricopeptide, alpha-helical, metal bind	97.71
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.71
1kt0_A	457	FKBP51, 51 kDa FK506-binding protein; FKBP-like pp	97.71
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.71
3dss_A	331	Geranylgeranyl transferase type-2 subunit alpha; p	97.7
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.7
2uy1_A	493	Cleavage stimulation factor 77; RNA-binding protei	97.69
3rkv_A	162	Putative peptidylprolyl isomerase; structural geno	97.68
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.68
1wao_1	477	Serine/threonine protein phosphatase 5; hydrolase,	97.67
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.67
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	97.64
3k9i_A	117	BH0479 protein; putative protein binding protein,	97.63
3n71_A	490	Histone lysine methyltransferase SMYD1; heart deve	97.63
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	97.53
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.52
2if4_A	338	ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha,	97.4
2l6j_A	111	TPR repeat-containing protein associated with HSP;	97.37
2hr2_A	159	Hypothetical protein; alpha-alpha superhelix fold,	97.34
2kat_A	115	Uncharacterized protein; NESG, structure, structur	97.34
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.25
1dce_A	567	Protein (RAB geranylgeranyltransferase alpha subun	97.23
1klx_A	138	Cysteine rich protein B; structural genomics, heli	97.03
2kat_A	115	Uncharacterized protein; NESG, structure, structur	96.97
1na3_A	91	Designed protein CTPR2; de novo protein; HET: IPT;	96.97
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.96
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.93
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.88
3ma5_A	100	Tetratricopeptide repeat domain protein; NESG, str	96.87
3mkq_A	814	Coatomer beta'-subunit; beta-propeller, alpha-sole	96.76
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.7
1zu2_A	158	Mitochondrial import receptor subunit TOM20-3; TPR	96.69
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.56
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.53
3qww_A	433	SET and MYND domain-containing protein 2; methyltr	96.5
3qwp_A	429	SET and MYND domain-containing protein 3; SMYD3,SE	96.44
3ly7_A	372	Transcriptional activator CADC; alpha/beta domain,	96.35
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	96.32
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	96.03
2kc7_A	99	BFR218_protein; tetratricopeptide repeat, all-alph	95.86
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	94.85
1pc2_A	152	Mitochondria fission protein; unknown function; NM	94.25
3bee_A	93	Putative YFRE protein; putaive YFRE protein, struc	94.2
1pc2_A	152	Mitochondria fission protein; unknown function; NM	94.17
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	94.03
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	93.99
3u64_A	301	Protein TP_0956; tetratrico peptide repeat, protei	93.63
1wy6_A	172	Hypothetical protein ST1625; helical repeat protei	93.51
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	93.18
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	92.79
2v5f_A	104	Prolyl 4-hydroxylase subunit alpha-1; endoplasmic	92.44
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	92.13
3mkq_B	177	Coatomer subunit alpha; beta-propeller, alpha-sole	92.12
2p58_C	116	Putative type III secretion protein YSCG; type III	91.61
2uwj_G	115	Type III export protein PSCG; virulence, chaperone	90.83
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	90.5
3lvg_A	624	Clathrin heavy chain 1; SELF assembly, coated PIT,	89.76
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	88.31
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	87.78
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	86.63
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	86.62
2ff4_A	388	Probable regulatory protein EMBR; winged-helix, te	86.51
1nzn_A	126	CGI-135 protein, fission protein FIS1P; TPR, unkno	86.21
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	86.19
4fhn_B	1139	Nucleoporin NUP120; protein complex,structural pro	86.16
1v54_E	109	Cytochrome C oxidase polypeptide VA; oxidoreductas	85.73
2y69_E	152	Cytochrome C oxidase subunit 5A; electron transpor	85.71
4gns_B	754	Protein CSD3, chitin biosynthesis protein CHS6; FN	84.69
4h7y_A	161	Dual specificity protein kinase TTK; mitotic check	83.99
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	82.92
3ffl_A	167	Anaphase-promoting complex subunit 7; tetratricope	80.86

>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=100.00  E-value=5.4e-32  Score=262.77  Aligned_cols=185  Identities=15%  Similarity=0.186  Sum_probs=166.6

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCC---------HHHHHHHHHHHHHcCCCccH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGA---------LNHAYWVHNLIIEKKIELNF   76 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~---------~~~a~~~~~~~~~~g~~~~~   76 (410)
                      ...++.+|.+|++.|++++|+++|++|.+.|++||..||+++|.+|++.+.         ++.|.++|+.|.+.|+.||.
T Consensus        26 e~~l~~~id~c~k~G~~~~A~~lf~~M~~~Gv~pd~~tyn~Li~~c~~~~~~~~~~~~~~l~~A~~lf~~M~~~G~~Pd~  105 (501)
T 4g26_A           26 EALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNE  105 (501)
T ss_dssp             HHHHHHHHHHTTTSCCHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHHTTCCCCH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCHhHHHHHHHHHHhCCchhhhhhcchHHHHHHHHHHHHHhCCCCCH
Confidence            346888899999999999999999999999999999999999999987654         78899999999999999999


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhccc----CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQR----NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTAC  152 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~~----~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~  152 (410)
                      .+||+||++|++.|++++|.++|++|.+    ||+.+||+||.+|++.|+.++|.++|++|.+.|+.||..||++||.+|
T Consensus       106 ~tyn~lI~~~~~~g~~~~A~~l~~~M~~~g~~Pd~~tyn~lI~~~~~~g~~~~A~~l~~~M~~~G~~Pd~~ty~~Li~~~  185 (501)
T 4g26_A          106 ATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALLKVS  185 (501)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHcCCCCccceehHHHHHHHHCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence            9999999999999999999999999873    688999999999999999999999999999999999999999999999


Q ss_pred             HccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhc
Q 040371          153 SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRA  191 (410)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~  191 (410)
                      ++.|++++|.++|++|.+. |..|+..||+.++..|+..
T Consensus       186 ~~~g~~d~A~~ll~~Mr~~-g~~ps~~T~~~l~~~F~s~  223 (501)
T 4g26_A          186 MDTKNADKVYKTLQRLRDL-VRQVSKSTFDMIEEWFKSE  223 (501)
T ss_dssp             HHTTCHHHHHHHHHHHHHH-TSSBCHHHHHHHHHHHHSH
T ss_pred             hhCCCHHHHHHHHHHHHHh-CCCcCHHHHHHHHHHHhcC
Confidence            9999999999999999875 9999999999999988764

>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=99.98  E-value=3.3e-31  Score=257.19  Aligned_cols=201  Identities=9%  Similarity=0.112  Sum_probs=174.5

Q ss_pred             hHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCC---------H
Q 040371           23 DEALRFFREMLSSKVEPDK-FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK---------I   92 (410)
Q Consensus        23 ~~a~~l~~~m~~~g~~pd~-~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~---------~   92 (410)
                      ..+..+++++.+.++.+.+ ..++.+|.+|++.|++++|.++|+.|.+.|+.||..+||+||++|++.+.         +
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            3455677788777766544 46889999999999999999999999999999999999999999998765         7


Q ss_pred             HHHHHHHHhcc----cCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040371           93 QMAKEVFDTVQ----RNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHM  168 (410)
Q Consensus        93 ~~A~~~f~~m~----~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  168 (410)
                      ++|.++|++|.    .||..+||+||.+|++.|++++|.++|++|.+.|+.||..||+++|.+|++.|++++|.++|++|
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            89999999997    47999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC---CCCCCHHHHHHHHHHHHhcC
Q 040371          169 RSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM---TMEPDVVVWRALLSACRTFK  224 (410)
Q Consensus       169 ~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m---~~~p~~~~~~~li~~~~~~g  224 (410)
                      .+. |+.||..+|++||++|++.|++++|.+++++|   +..|+..||+.++..++..+
T Consensus       167 ~~~-G~~Pd~~ty~~Li~~~~~~g~~d~A~~ll~~Mr~~g~~ps~~T~~~l~~~F~s~~  224 (501)
T 4g26_A          167 VES-EVVPEEPELAALLKVSMDTKNADKVYKTLQRLRDLVRQVSKSTFDMIEEWFKSEV  224 (501)
T ss_dssp             HHT-TCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTSSBCHHHHHHHHHHHHSHH
T ss_pred             Hhc-CCCCCHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHhcCc
Confidence            975 99999999999999999999999999999999   78999999999999987643

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.95  E-value=4e-27  Score=234.93  Aligned_cols=309  Identities=9%  Similarity=-0.120  Sum_probs=246.0

Q ss_pred             CCCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHH
Q 040371            2 PDKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAA   81 (410)
Q Consensus         2 ~~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~   81 (410)
                      |.+++.+|+.++..|.+.|++++|+.+|++|..  ..||..++..++.+|.+.|++++|.++|+.+...  +++..+++.
T Consensus        80 ~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~--~~p~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~  155 (597)
T 2xpi_A           80 SLSREDYLRLWRHDALMQQQYKCAAFVGEKVLD--ITGNPNDAFWLAQVYCCTGDYARAKCLLTKEDLY--NRSSACRYL  155 (597)
T ss_dssp             --CHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HHCCHHHHHHHHHHHHHTTCHHHHHHHHHHTCGG--GTCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHccCchHHHHHHHHHHh--hCCCchHHHHHHHHHHHcCcHHHHHHHHHHHhcc--ccchhHHHH
Confidence            457889999999999999999999999999985  5788899999999999999999999999988654  678999999


Q ss_pred             HHHHHHhcCCHHHHHHHHHhcccC-------------------ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCC----
Q 040371           82 LIDMYSKCGKIQMAKEVFDTVQRN-------------------DVSVWNAMISGVAIHGLAADASAIFTKMEMFNV----  138 (410)
Q Consensus        82 li~~y~~~g~~~~A~~~f~~m~~~-------------------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~----  138 (410)
                      ++.+|.++|++++|.++|+++...                   ++.+|+.++.+|.+.|++++|+++|++|.+.+.    
T Consensus       156 l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~  235 (597)
T 2xpi_A          156 AAFCLVKLYDWQGALNLLGETNPFRKDEKNANKLLMQDGGIKLEASMCYLRGQVYTNLSNFDRAKECYKEALMVDAKCYE  235 (597)
T ss_dssp             HHHHHHHTTCHHHHHHHHCSSCTTC----------CCCSSCCHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHH
T ss_pred             HHHHHHHHhhHHHHHHHHhccCCccccccccccccccccccchhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCchhhH
Confidence            999999999999999999954433                   478999999999999999999999999975431    


Q ss_pred             ------------------------------------------------------------------CCCHHHHHHHHHHH
Q 040371          139 ------------------------------------------------------------------LPDSITFLGLLTAC  152 (410)
Q Consensus       139 ------------------------------------------------------------------~p~~~t~~~ll~a~  152 (410)
                                                                                        .++..++..++.+|
T Consensus       236 ~~~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~l~~~~  315 (597)
T 2xpi_A          236 AFDQLVSNHLLTADEEWDLVLKLNYSTYSKEDAAFLRSLYMLKLNKTSHEDELRRAEDYLSSINGLEKSSDLLLCKADTL  315 (597)
T ss_dssp             HHHHHHHTTCSCHHHHHHHHHHSCTHHHHGGGHHHHHHHHHTTSCTTTTHHHHHHHHHHHHTSTTGGGCHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccchhHHHHHHhcCCcccccchHHHHHHHHHHHHHHHcCcchHHHHHHHHHHhhcCCchHHHHHHHHHHH
Confidence                                                                              15677788888888


Q ss_pred             HccCCHHHHHHHHHHhhhhcC--------------------------------CCCChhHHHHHHHHHHhcCCHHHHHHH
Q 040371          153 SHCGLVEEGRKYFDHMRSRYS--------------------------------IQPQLEHYGAMVDLLGRAGHIEEAYGL  200 (410)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~~~--------------------------------~~~~~~~~~~li~~~~~~g~~~~A~~~  200 (410)
                      .+.|++++|..+|+.+.+...                                .+.+..+|+.++.+|.+.|++++|.++
T Consensus       316 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  395 (597)
T 2xpi_A          316 FVRSRFIDVLAITTKILEIDPYNLDVYPLHLASLHESGEKNKLYLISNDLVDRHPEKAVTWLAVGIYYLCVNKISEARRY  395 (597)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHhccHHHHHHH
Confidence            899999999999988874311                                122456777788888888888888888


Q ss_pred             HHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHHH---HhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCC
Q 040371          201 ITSM-TMEP-DVVVWRALLSACRTFKRLELGEVAI---VNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKS  275 (410)
Q Consensus       201 ~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~~---~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~  275 (410)
                      |+++ ...| +..+|+.++.++.+.|++++|..++   .+..|.+..++..++.+|.+.|++++|.++|+++.+..  |+
T Consensus       396 ~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~--~~  473 (597)
T 2xpi_A          396 FSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLFQGTHLPYLFLGMQHMQLGNILLANEYLQSSYALF--QY  473 (597)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CC
T ss_pred             HHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CC
Confidence            8876 3334 5778888888888888888888883   44567777788888888888888888888888887643  22


Q ss_pred             CceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHHHCCcccCC
Q 040371          276 QGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGFLPAT  323 (410)
Q Consensus       276 ~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~~pd~  323 (410)
                      ....|..       +...+...|+.++|.+.++++.+...+.|..|+.
T Consensus       474 ~~~~~~~-------l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~  514 (597)
T 2xpi_A          474 DPLLLNE-------LGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKP  514 (597)
T ss_dssp             CHHHHHH-------HHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGG
T ss_pred             ChHHHHH-------HHHHHHHhCCHHHHHHHHHHHHHhhhccccchhh
Confidence            2222321       2344556789999999999777766666777874

>2xpi_A Anaphase-promoting complex subunit CUT9; cell cycle, TPR, ubiquitin ligase; 2.60A {Schizosaccharomyces pombe}

Probab=99.95  E-value=4.8e-25  Score=219.85  Aligned_cols=262  Identities=14%  Similarity=0.077  Sum_probs=238.2

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      +|+.+|+.++.+|.+.|++++|+++|++|.+.+ +.+..++..++.++.+.|++++|.++++.+.+.. +.+..+++.++
T Consensus       303 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~  380 (597)
T 2xpi_A          303 KSSDLLLCKADTLFVRSRFIDVLAITTKILEID-PYNLDVYPLHLASLHESGEKNKLYLISNDLVDRH-PEKAVTWLAVG  380 (597)
T ss_dssp             GCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCCTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHhcCHHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHhCCHHHHHHHHHHHHhhC-cccHHHHHHHH
Confidence            788999999999999999999999999999764 4477899999999999999999999999999764 56899999999


Q ss_pred             HHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      .+|.++|++++|.++|+++.+   .+..+|+.++.+|.+.|++++|+++|++|...+ +++..++..++.+|.+.|++++
T Consensus       381 ~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~g~~~~  459 (597)
T 2xpi_A          381 IYYLCVNKISEARRYFSKSSTMDPQFGPAWIGFAHSFAIEGEHDQAISAYTTAARLF-QGTHLPYLFLGMQHMQLGNILL  459 (597)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT-TTCSHHHHHHHHHHHHHTCHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCCHHH
Confidence            999999999999999998863   467899999999999999999999999998864 4478899999999999999999


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-------CCCCC--HHHHHHHHHHHHhcCchhHHHH
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-------TMEPD--VVVWRALLSACRTFKRLELGEV  231 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-------~~~p~--~~~~~~li~~~~~~g~~~~a~~  231 (410)
                      |.++|+.+.+.  .+.+..+|+.++..|.+.|++++|.++|+++       +..|+  ..+|..+..+|...|++++|..
T Consensus       460 A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~p~~~~~~~~~l~~~~~~~g~~~~A~~  537 (597)
T 2xpi_A          460 ANEYLQSSYAL--FQYDPLLLNELGVVAFNKSDMQTAINHFQNALLLVKKTQSNEKPWAATWANLGHAYRKLKMYDAAID  537 (597)
T ss_dssp             HHHHHHHHHHH--CCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCSGGGHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHh--CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHHHHHHhcCHHHHHH
Confidence            99999999864  2346889999999999999999999999988       45787  7899999999999999999999


Q ss_pred             H---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          232 A---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       232 ~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      .   ..+..|.++.+|..++.+|.+.|++++|.+.++++.+.
T Consensus       538 ~~~~~~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~l~~  579 (597)
T 2xpi_A          538 ALNQGLLLSTNDANVHTAIALVYLHKKIPGLAITHLHESLAI  579 (597)
T ss_dssp             HHHHHHHHSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHhc
Confidence            9   45567888899999999999999999999999998874

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.86  E-value=9.1e-20  Score=171.91  Aligned_cols=291  Identities=11%  Similarity=0.045  Sum_probs=226.9

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +..+|+.+...|.+.|++++|++.|+++.+.. +.+..+|..+..++...|++++|.+.+..+++.. +.+..++..+..
T Consensus        66 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  143 (388)
T 1w3b_A           66 LAEAYSNLGNVYKERGQLQEAIEHYRHALRLK-PDFIDGYINLAAALVAAGDMEGAVQAYVSALQYN-PDLYCVRSDLGN  143 (388)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHC-TTCTHHHHHHHH
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHcC-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHH
Confidence            55678888888888888888888888887642 3345578888888888888888888888888764 335667777888


Q ss_pred             HHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a  161 (410)
                      .|.+.|++++|.+.|+++.+  | +..+|+.+...|.+.|++++|+..|+++.... +.+...+..+...+...|++++|
T Consensus       144 ~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A  222 (388)
T 1w3b_A          144 LLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTLD-PNFLDAYINLGNVLKEARIFDRA  222 (388)
T ss_dssp             HHHTTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCTTHH
T ss_pred             HHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHH
Confidence            88888888888888887753  3 46788888888888888999999888888743 22456677888888888999999


Q ss_pred             HHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHh
Q 040371          162 RKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVN  235 (410)
Q Consensus       162 ~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~  235 (410)
                      ...|....+.   .| +..++..+...|.+.|++++|.+.|+++ ...| +..+|..+...+...|++++|...   ..+
T Consensus       223 ~~~~~~al~~---~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~  299 (388)
T 1w3b_A          223 VAAYLRALSL---SPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALR  299 (388)
T ss_dssp             HHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhh---CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            9888887743   34 4678889999999999999999999987 4455 467899999999999999999998   456


Q ss_pred             hccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHH
Q 040371          236 ISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSL  310 (410)
Q Consensus       236 ~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l  310 (410)
                      ..|.++.++..+..+|.+.|++++|.+.++++.+..  |+....|..       +...+...|+.++|...+++.
T Consensus       300 ~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~~-------l~~~~~~~g~~~~A~~~~~~a  365 (388)
T 1w3b_A          300 LCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVF--PEFAAAHSN-------LASVLQQQGKLQEALMHYKEA  365 (388)
T ss_dssp             HCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSC--TTCHHHHHH-------HHHHHHTTTCCHHHHHHHHHH
T ss_pred             hCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC--CCcHHHHHH-------HHHHHHHcCCHHHHHHHHHHH
Confidence            678888889999999999999999999999987642  332222221       223455678889999888743

>1w3b_A UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110; OGT, glcnac, nucleoporin, O-linked glycosylation, TPR repeat, protein binding; 2.85A {Homo sapiens} SCOP: a.118.8.1

Probab=99.84  E-value=2.3e-18  Score=162.26  Aligned_cols=259  Identities=12%  Similarity=0.059  Sum_probs=226.0

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      +..+|+.+..+|.+.|++++|++.|+++.+.  .| +...+..+...+...|++++|.+.++.+++.. +.+..+++.+.
T Consensus       100 ~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~  176 (388)
T 1w3b_A          100 FIDGYINLAAALVAAGDMEGAVQAYVSALQY--NPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQ-PNFAVAWSNLG  176 (388)
T ss_dssp             CHHHHHHHHHHHHHHSCSSHHHHHHHHHHHH--CTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            4567999999999999999999999999875  44 45577788888999999999999999999874 45688999999


Q ss_pred             HHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVE  159 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~  159 (410)
                      ..|.+.|++++|...|+++.+  | +...|..+...+...|++++|+..|++....  .| +..++..+...+...|+++
T Consensus       177 ~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~  254 (388)
T 1w3b_A          177 CVFNAQGEIWLAIHHFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSL--SPNHAVVHGNLACVYYEQGLID  254 (388)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh--CcCCHHHHHHHHHHHHHcCCHH
Confidence            999999999999999998863  3 5678999999999999999999999998874  45 5788899999999999999


Q ss_pred             HHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCchhHHHHHH---H
Q 040371          160 EGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TME-PDVVVWRALLSACRTFKRLELGEVAI---V  234 (410)
Q Consensus       160 ~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~-p~~~~~~~li~~~~~~g~~~~a~~~~---~  234 (410)
                      +|...|+.+.+.  -+.+..+|..+...|.+.|++++|.+.|+++ ... .+..+|..+...+...|++++|...+   .
T Consensus       255 ~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al  332 (388)
T 1w3b_A          255 LAIDTYRRAIEL--QPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKAL  332 (388)
T ss_dssp             HHHHHHHHHHHT--CSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            999999999853  2335778999999999999999999999988 333 47889999999999999999999994   4


Q ss_pred             hhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          235 NISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       235 ~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      +..|.+..++..+..+|.+.|++++|.+.++++.+.
T Consensus       333 ~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~  368 (388)
T 1w3b_A          333 EVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             TSCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             hcCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            556777788999999999999999999999998764

>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=99.84  E-value=5.1e-19  Score=169.89  Aligned_cols=292  Identities=10%  Similarity=-0.010  Sum_probs=234.3

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      ++..|..+...|.+.|++++|+.+|+++.+. .+.+..+|..+..++...|++++|...++.+++.+ +.+..++..+..
T Consensus        25 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~-~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~  102 (450)
T 2y4t_A           25 DVEKHLELGKKLLAAGQLADALSQFHAAVDG-DPDNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGH  102 (450)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHH
Confidence            4568999999999999999999999999875 25578899999999999999999999999999886 456889999999


Q ss_pred             HHHhcCCHHHHHHHHHhcccCC---h---hhHHHHHH------------HHHHcCChHHHHHHHHHHHHCCCCCCHHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQRND---V---SVWNAMIS------------GVAIHGLAADASAIFTKMEMFNVLPDSITFL  146 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~~~---~---~~~~~li~------------~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~  146 (410)
                      +|.+.|++++|.+.|+++.+.+   .   ..|..++.            .|.+.|++++|+..|+++.... +.+..++.
T Consensus       103 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  181 (450)
T 2y4t_A          103 LLLKQGKLDEAEDDFKKVLKSNPSENEEKEAQSQLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVC-VWDAELRE  181 (450)
T ss_dssp             HHHHTTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCChHHHH
Confidence            9999999999999999987532   3   56666644            4888999999999999998753 34677888


Q ss_pred             HHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHH--------
Q 040371          147 GLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRAL--------  216 (410)
Q Consensus       147 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~l--------  216 (410)
                      .+..++...|++++|..+|+.+.+.  .+.+..+|..+...|.+.|++++|...|+++ ...|+ ...+..+        
T Consensus       182 ~l~~~~~~~g~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~  259 (450)
T 2y4t_A          182 LRAECFIKEGEPRKAISDLKAASKL--KNDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQVKKLNK  259 (450)
T ss_dssp             HHHHHHHHTTCGGGGHHHHHHHHHH--HCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHH
Confidence            9999999999999999999998853  2346789999999999999999999999988 44454 4445444        


Q ss_pred             ----HHHHHhcCchhHHHHH---HHhhccCCC----chHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECC
Q 040371          217 ----LSACRTFKRLELGEVA---IVNISRLMG----GDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAG  285 (410)
Q Consensus       217 ----i~~~~~~g~~~~a~~~---~~~~~~~~~----~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~  285 (410)
                          ...+...|++++|...   ..+..|.++    ..+..+..+|.+.|++++|...++++.+..  |+....|..   
T Consensus       260 ~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~--p~~~~~~~~---  334 (450)
T 2y4t_A          260 LIESAEELIRDGRYTDATSKYESVMKTEPSIAEYTVRSKERICHCFSKDEKPVEAIRVCSEVLQME--PDNVNALKD---  334 (450)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC--TTCHHHHHH---
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC--cccHHHHHH---
Confidence                7788999999999998   344556553    267788999999999999999999887642  322223321   


Q ss_pred             EEEEEEeCCCCCccHHHHHHHHHHH
Q 040371          286 VIHQFKAGDRSHPEAQAIDKILGSL  310 (410)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~l~~l  310 (410)
                          +...+...|+.++|...+++.
T Consensus       335 ----l~~~~~~~~~~~~A~~~~~~a  355 (450)
T 2y4t_A          335 ----RAEAYLIEEMYDEAIQDYETA  355 (450)
T ss_dssp             ----HHHHHHHTTCHHHHHHHHHHH
T ss_pred             ----HHHHHHHhcCHHHHHHHHHHH
Confidence                223345678888888888743

>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=99.83  E-value=5.7e-18  Score=162.54  Aligned_cols=261  Identities=12%  Similarity=0.024  Sum_probs=222.5

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccH---HHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNF---ILSA   80 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~---~~~~   80 (410)
                      .+..+|..+...|.+.|++++|+..|+++.+.+ +.+..++..+..++...|++++|.+.++.+.+.. +.+.   ..+.
T Consensus        58 ~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~~~  135 (450)
T 2y4t_A           58 DNYIAYYRRATVFLAMGKSKAALPDLTKVIQLK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSN-PSENEEKEAQS  135 (450)
T ss_dssp             TCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSC-CCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCChhhHHHHH
Confidence            467899999999999999999999999999864 4467899999999999999999999999999864 3344   5666


Q ss_pred             HHH------------HHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHH
Q 040371           81 ALI------------DMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITF  145 (410)
Q Consensus        81 ~li------------~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~  145 (410)
                      .+.            ..|.+.|++++|...|+++.+   .+..+|..+...|.+.|++++|++.|+++.... +.+..++
T Consensus       136 ~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~  214 (450)
T 2y4t_A          136 QLIKSDEMQRLRSQALNAFGSGDYTAAIAFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLK-NDNTEAF  214 (450)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHH-CSCHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHH
Confidence            554            449999999999999998763   467899999999999999999999999998753 3467889


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-hhHHHHH------------HHHHHhcCCHHHHHHHHHhC-CCCCC--
Q 040371          146 LGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAM------------VDLLGRAGHIEEAYGLITSM-TMEPD--  209 (410)
Q Consensus       146 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~l------------i~~~~~~g~~~~A~~~~~~m-~~~p~--  209 (410)
                      ..+...+...|++++|...|+.+.+.   .|+ ...+..+            ...|.+.|++++|...|+++ ...|+  
T Consensus       215 ~~l~~~~~~~g~~~~A~~~~~~~~~~---~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~p~~~  291 (450)
T 2y4t_A          215 YKISTLYYQLGDHELSLSEVRECLKL---DQDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSIA  291 (450)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCCSSH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHh---CCChHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcch
Confidence            99999999999999999999999853   343 4445444            78899999999999999988 34454  


Q ss_pred             ---HHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          210 ---VVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       210 ---~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                         ...|..+...+...|++++|...   ..+..|.++..+..+..+|...|++++|.+.+++..+.
T Consensus       292 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~  358 (450)
T 2y4t_A          292 EYTVRSKERICHCFSKDEKPVEAIRVCSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYETAQEH  358 (450)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence               45788888999999999999999   44567888889999999999999999999999998874

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.79  E-value=1.2e-19  Score=181.88  Aligned_cols=131  Identities=11%  Similarity=0.122  Sum_probs=115.0

Q ss_pred             CccHHHHHHHHHHHHhcCCHHHHHHHHHhcc-------cCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHH
Q 040371           73 ELNFILSAALIDMYSKCGKIQMAKEVFDTVQ-------RNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITF  145 (410)
Q Consensus        73 ~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~-------~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~  145 (410)
                      ..-..+||+||++|+++|++++|.++|++|.       .||++|||+||.+|++.|+.++|.++|++|.+.|+.||.+||
T Consensus       124 ~~~~~TynaLIdglcK~G~leeA~~Lf~eM~~m~~kG~~PdvvTYNtLI~Glck~G~~~eA~~Lf~eM~~~G~~PDvvTY  203 (1134)
T 3spa_A          124 SGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSY  203 (1134)
T ss_dssp             CHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHSHHHHTTCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTTCCCCHHHH
T ss_pred             HhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhcCCCCCHhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCcHHHH
Confidence            3345789999999999999999999998764       479999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHccCC-HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          146 LGLLTACSHCGL-VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       146 ~~ll~a~~~~g~-~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      +++|.++++.|. .++|.++|++|.++ |+.||..+|++++....+.+-++.+.++...+
T Consensus       204 ntLI~glcK~G~~~e~A~~Ll~EM~~k-G~~PD~vtY~~ll~~~eR~~vL~~Vrkv~P~f  262 (1134)
T 3spa_A          204 AAALQCMGRQDQDAGTIERCLEQMSQE-GLKLQALFTAVLLSEEDRATVLKAVHKVKPTF  262 (1134)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHHHHHHH-TCCSHHHHHHSCCCHHHHHHHHHHHGGGCCCC
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHHHc-CCCCChhhcccccChhhHHHHHHHHHHhCccc
Confidence            999999999998 47899999999987 99999999999998887775555554444333

>3hym_B Cell division cycle protein 16 homolog; APC, anaphase promoting complex, cell cycle, mitosis, cyclosome, TPR, ubiquitin, ubiquitin ligase, twinning; 2.80A {Homo sapiens}

Probab=99.79  E-value=1e-16  Score=146.86  Aligned_cols=261  Identities=11%  Similarity=0.049  Sum_probs=222.9

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      |...+..+...+...|++++|+++|+++.+.. +.+...+..++.++...|++++|..+++.+++.. +.+..++..+..
T Consensus        21 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~   98 (330)
T 3hym_B           21 NLDVVVSLAERHYYNCDFKMCYKLTSVVMEKD-PFHASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGC   98 (330)
T ss_dssp             CCTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHH
Confidence            45567788899999999999999999998753 4455677778888999999999999999999875 456788999999


Q ss_pred             HHHhcC-CHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           85 MYSKCG-KIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        85 ~y~~~g-~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      .|...| ++++|.+.|++..+   .+...|..+...|...|++++|++.|++..... +.+...+..+...+...|++++
T Consensus        99 ~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~  177 (330)
T 3hym_B           99 YYLMVGHKNEHARRYLSKATTLEKTYGPAWIAYGHSFAVESEHDQAMAAYFTAAQLM-KGCHLPMLYIGLEYGLTNNSKL  177 (330)
T ss_dssp             HHHHSCSCHHHHHHHHHHHHTTCTTCTHHHHHHHHHHHHHTCHHHHHHHHHHHHHHT-TTCSHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhc-cccHHHHHHHHHHHHHHhhHHH
Confidence            999999 99999999998764   356789999999999999999999999998753 2245667778899999999999


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CC----------CCCHHHHHHHHHHHHhcCchhHH
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TM----------EPDVVVWRALLSACRTFKRLELG  229 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~----------~p~~~~~~~li~~~~~~g~~~~a  229 (410)
                      |...|+.+.+.  .+.+...+..+...|.+.|++++|...+++. ..          ..+..+|..+...+...|++++|
T Consensus       178 A~~~~~~al~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A  255 (330)
T 3hym_B          178 AERFFSQALSI--APEDPFVMHEVGVVAFQNGEWKTAEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEA  255 (330)
T ss_dssp             HHHHHHHHHTT--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHHHHHHHh--CCCChHHHHHHHHHHHHcccHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHH
Confidence            99999999853  3445788999999999999999999999877 11          23467899999999999999999


Q ss_pred             HHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          230 EVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       230 ~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      ...   ..+..|.++..+..+..+|.+.|++++|.+.+++..+.
T Consensus       256 ~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  299 (330)
T 3hym_B          256 LDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVDYFHTALGL  299 (330)
T ss_dssp             HHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHHHHHHHHcc
Confidence            999   55667888899999999999999999999999876543

>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=99.78  E-value=8.1e-17  Score=150.13  Aligned_cols=257  Identities=13%  Similarity=0.027  Sum_probs=215.1

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +...|..+...|.+.|++++|+..|+++.+.. +.+..++..+..++...|+++.|...++.+++.. +.+..++..+..
T Consensus        63 ~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~l~~  140 (368)
T 1fch_A           63 DHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAV  140 (368)
T ss_dssp             TCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHhcC-CCCHHHHHHHHH
Confidence            45678899999999999999999999999863 4577899999999999999999999999999885 557889999999


Q ss_pred             HHHhcCCHHHHHHHHHhcccC---ChhhHHH---------------HHHHHHHcCChHHHHHHHHHHHHCCCC-CCHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQRN---DVSVWNA---------------MISGVAIHGLAADASAIFTKMEMFNVL-PDSITF  145 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~~---~~~~~~~---------------li~~~~~~g~~~~A~~l~~~m~~~g~~-p~~~t~  145 (410)
                      .|.+.|++++|.+.|+++...   +...+..               .+..+...|++++|+..|+++...... ++..++
T Consensus       141 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~  220 (368)
T 1fch_A          141 SFTNESLQRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQ  220 (368)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCcCcHHHHHHHHHHhhhhcccHHHHHHHHHhhcccHHHHHHHHHHHHHhCcCcccHHHH
Confidence            999999999999999987642   2223321               233444889999999999999875322 147888


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhc
Q 040371          146 LGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTF  223 (410)
Q Consensus       146 ~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~  223 (410)
                      ..+...+...|++++|...|+.+.+.  .+.+...|..+...|.+.|++++|...|++. ...| +...|..+...+...
T Consensus       221 ~~l~~~~~~~g~~~~A~~~~~~al~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~  298 (368)
T 1fch_A          221 CGLGVLFNLSGEYDKAVDCFTAALSV--RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINL  298 (368)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHh--CcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHC
Confidence            99999999999999999999998854  2335788999999999999999999999987 3444 578899999999999


Q ss_pred             CchhHHHHH---HHhhccCC-----------CchHHHHHHHHHhcCChhHHHHHHH
Q 040371          224 KRLELGEVA---IVNISRLM-----------GGDYVLLSNMYCYLKRWDTAENVRE  265 (410)
Q Consensus       224 g~~~~a~~~---~~~~~~~~-----------~~~~~~l~~~~~~~g~~~~a~~~~~  265 (410)
                      |++++|...   ..+..|.+           ..+|..+..+|...|++++|..+++
T Consensus       299 g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  354 (368)
T 1fch_A          299 GAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADA  354 (368)
T ss_dssp             TCHHHHHHHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhCCCCCCccccccchhhHHHHHHHHHHHHhCChHhHHHhHH
Confidence            999999998   44555655           5678899999999999999998875

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.77  E-value=4.9e-17  Score=151.79  Aligned_cols=258  Identities=12%  Similarity=0.025  Sum_probs=211.0

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +...|..+...+.+.|++++|+..|+++.+.. +.+..+|..+..++...|++++|...++++++.. +.+..++..+..
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            55679999999999999999999999998753 4578899999999999999999999999999875 456889999999


Q ss_pred             HHHhcCCHHHHHHHHHhcccCC-------------hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCC-CCHHHHHHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQRND-------------VSVWNAMISGVAIHGLAADASAIFTKMEMFNVL-PDSITFLGLLT  150 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~~~-------------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~-p~~~t~~~ll~  150 (410)
                      .|.+.|++++|...|+++.+.+             ...++.+...|...|++++|++.|+++...... ++..++..+..
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            9999999999999999886421             123344578899999999999999999886322 15788999999


Q ss_pred             HHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhH
Q 040371          151 ACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLEL  228 (410)
Q Consensus       151 a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~  228 (410)
                      .+...|++++|...|+.+.+.  .+.+..+|..+...|.+.|++++|...|++. ...| +..+|..+...+...|++++
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            999999999999999999864  2345789999999999999999999999987 4445 47889999999999999999


Q ss_pred             HHHH---HHhhccC------------CCchHHHHHHHHHhcCChhHHHHHHHH
Q 040371          229 GEVA---IVNISRL------------MGGDYVLLSNMYCYLKRWDTAENVREI  266 (410)
Q Consensus       229 a~~~---~~~~~~~------------~~~~~~~l~~~~~~~g~~~~a~~~~~~  266 (410)
                      |...   ..++.|.            +...+..+..++...|+.+.+.++.++
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            9999   3444444            256788899999999999988877643

>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}

Probab=99.77  E-value=3.2e-19  Score=178.92  Aligned_cols=146  Identities=11%  Similarity=0.114  Sum_probs=122.6

Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHH---HcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc----cCChhhHHHH
Q 040371           41 KFTFASVIYGCARLGALNHAYWVHNLII---EKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ----RNDVSVWNAM  113 (410)
Q Consensus        41 ~~t~~~ll~a~~~~~~~~~a~~~~~~~~---~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~----~~~~~~~~~l  113 (410)
                      ..||+++|++|++.|++++|.++|..|.   +.|+.||+.+||+||++|++.|++++|.++|++|.    .||++|||+|
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            4689999999999999999999998876   45899999999999999999999999999999997    5899999999


Q ss_pred             HHHHHHcCCh-HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC------hhHHHHHHH
Q 040371          114 ISGVAIHGLA-ADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ------LEHYGAMVD  186 (410)
Q Consensus       114 i~~~~~~g~~-~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~------~~~~~~li~  186 (410)
                      |.++++.|+. ++|.++|++|...|+.||.+||++++.++.+.+-++..    +.+..  ++.|+      ..+...|.+
T Consensus       207 I~glcK~G~~~e~A~~Ll~EM~~kG~~PD~vtY~~ll~~~eR~~vL~~V----rkv~P--~f~p~~~~~~~~~t~~LL~d  280 (1134)
T 3spa_A          207 LQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAV----HKVKP--TFSLPPQLPPPVNTSKLLRD  280 (1134)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTCCSHHHHHHSCCCHHHHHHHHHHH----GGGCC--CCCCCCCCCCCCCCCTTTHH
T ss_pred             HHHHHhCCCcHHHHHHHHHHHHHcCCCCChhhcccccChhhHHHHHHHH----HHhCc--ccCCCCCCcccccchHHHHH
Confidence            9999999985 78999999999999999999999999887765444444    44432  33333      455566778


Q ss_pred             HHHhcC
Q 040371          187 LLGRAG  192 (410)
Q Consensus       187 ~~~~~g  192 (410)
                      .|.+.+
T Consensus       281 l~s~d~  286 (1134)
T 3spa_A          281 VYAKDG  286 (1134)
T ss_dssp             HHCCCS
T ss_pred             HHccCC
Confidence            887765

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.75  E-value=8.5e-17  Score=156.74  Aligned_cols=294  Identities=12%  Similarity=0.023  Sum_probs=231.5

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +...|-.....|.+.|++++|+..|+++....  ||..+|..+..++...|+++.|.+.++.+++.+ +.+..++..+..
T Consensus         5 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~--p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~   81 (514)
T 2gw1_A            5 YALALKDKGNQFFRNKKYDDAIKYYNWALELK--EDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRAS   81 (514)
T ss_dssp             HHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC--ccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHH
Confidence            34567888899999999999999999999854  799999999999999999999999999999875 557889999999


Q ss_pred             HHHhcCCHHHHHHHHHhcccCC----------------------------------------------------------
Q 040371           85 MYSKCGKIQMAKEVFDTVQRND----------------------------------------------------------  106 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~~~----------------------------------------------------------  106 (410)
                      +|.+.|++++|...|+++...+                                                          
T Consensus        82 ~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (514)
T 2gw1_A           82 ANEGLGKFADAMFDLSVLSLNGDFNDASIEPMLERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSV  161 (514)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHHHHHHHHHHHHHHTTC---------------------------CCCCH
T ss_pred             HHHHHhhHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchh
Confidence            9999999999999998774321                                                          


Q ss_pred             ------------------------hhhHHHHHHHHHH---cCChHHHHHHHHHHHH-----CCCCC--------CHHHHH
Q 040371          107 ------------------------VSVWNAMISGVAI---HGLAADASAIFTKMEM-----FNVLP--------DSITFL  146 (410)
Q Consensus       107 ------------------------~~~~~~li~~~~~---~g~~~~A~~l~~~m~~-----~g~~p--------~~~t~~  146 (410)
                                              ...|......+..   .|++++|+..|+++..     ....|        +..++.
T Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  241 (514)
T 2gw1_A          162 TSMASFFGIFKPELTFANYDESNEADKELMNGLSNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLE  241 (514)
T ss_dssp             HHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHHHHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHH
Confidence                                    1222223333333   7999999999999987     32122        345677


Q ss_pred             HHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcC
Q 040371          147 GLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFK  224 (410)
Q Consensus       147 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g  224 (410)
                      .+...+...|++++|..+|+.+.+.   .|+...+..+...|...|++++|...+++. ...| +...|..+...+...|
T Consensus       242 ~~~~~~~~~~~~~~A~~~~~~~l~~---~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  318 (514)
T 2gw1_A          242 HTGIFKFLKNDPLGAHEDIKKAIEL---FPRVNSYIYMALIMADRNDSTEYYNYFDKALKLDSNNSSVYYHRGQMNFILQ  318 (514)
T ss_dssp             HHHHHHHHSSCHHHHHHHHHHHHHH---CCCHHHHHHHHHHHHTSSCCTTGGGHHHHHHTTCTTCTHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhh---CccHHHHHHHHHHHHHCCCHHHHHHHHHHHhhcCcCCHHHHHHHHHHHHHhC
Confidence            8888899999999999999998864   344788899999999999999999999887 4444 5678888999999999


Q ss_pred             chhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHH
Q 040371          225 RLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQ  301 (410)
Q Consensus       225 ~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~  301 (410)
                      ++++|...   ..+..|.+...+..+...|...|++++|...++++.+..  |+....|..       +...+...|+.+
T Consensus       319 ~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~-------la~~~~~~~~~~  389 (514)
T 2gw1_A          319 NYDQAGKDFDKAKELDPENIFPYIQLACLAYRENKFDDCETLFSEAKRKF--PEAPEVPNF-------FAEILTDKNDFD  389 (514)
T ss_dssp             CTTHHHHHHHHHHHTCSSCSHHHHHHHHHTTTTTCHHHHHHHHHHHHHHS--TTCSHHHHH-------HHHHHHHTTCHH
T ss_pred             CHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHc--ccCHHHHHH-------HHHHHHHCCCHH
Confidence            99999998   455678888889999999999999999999999987643  222122211       112234567888


Q ss_pred             HHHHHHHHHHHH
Q 040371          302 AIDKILGSLIQR  313 (410)
Q Consensus       302 ~~~~~l~~l~~~  313 (410)
                      +|...+++....
T Consensus       390 ~A~~~~~~a~~~  401 (514)
T 2gw1_A          390 KALKQYDLAIEL  401 (514)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            998888865543

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.74  E-value=3.5e-15  Score=137.98  Aligned_cols=261  Identities=11%  Similarity=-0.004  Sum_probs=143.8

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCC--ccHHHHHHH-
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIE--LNFILSAAL-   82 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~--~~~~~~~~l-   82 (410)
                      ..+|..+...|...|++++|+..|+++.+.. +.+...+..+..++...|++++|...++.+.+....  .+...+..+ 
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~  115 (359)
T 3ieg_A           37 YIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGHLLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLV  115 (359)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHHHHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHH
Confidence            4455555555555555555555555555431 223445555555555555555555555555554210  233333333 


Q ss_pred             -----------HHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHH
Q 040371           83 -----------IDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGL  148 (410)
Q Consensus        83 -----------i~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~l  148 (410)
                                 ...|...|++++|.+.|+++.+   .+...|..+...|...|++++|+..|++..... +.+..++..+
T Consensus       116 ~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l  194 (359)
T 3ieg_A          116 KADEMQRLRSQALDAFDGADYTAAITFLDKILEVCVWDAELRELRAECFIKEGEPRKAISDLKAASKLK-SDNTEAFYKI  194 (359)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-SCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHH
Confidence                       3455555666666665555432   244455566666666666666666666665532 2245555666


Q ss_pred             HHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHH------------HHHHHHHhcCCHHHHHHHHHhC-CCCCC-H----
Q 040371          149 LTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYG------------AMVDLLGRAGHIEEAYGLITSM-TMEPD-V----  210 (410)
Q Consensus       149 l~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~------------~li~~~~~~g~~~~A~~~~~~m-~~~p~-~----  210 (410)
                      ...+...|++++|...|+...+..  +.+...+.            .+...+.+.|++++|...+++. ...|+ .    
T Consensus       195 a~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~  272 (359)
T 3ieg_A          195 STLYYQLGDHELSLSEVRECLKLD--QDHKRCFAHYKQVKKLNKLIESAEELIRDGRYTDATSKYESVMKTEPSVAEYTV  272 (359)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhhC--ccchHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHH
Confidence            666666666666666666665421  11222222            2244466666666666666665 22232 2    


Q ss_pred             HHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          211 VVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       211 ~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      ..+..+...+...|++++|...   ..+..|.++..+..+..+|...|++++|.+.+++..+.
T Consensus       273 ~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~  335 (359)
T 3ieg_A          273 RSKERICHCFSKDEKPVEAIRICSEVLQMEPDNVNALKDRAEAYLIEEMYDEAIQDYEAAQEH  335 (359)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc
Confidence            1233455566677777777776   34455666667777777777777777777777776653

>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=99.74  E-value=2.6e-16  Score=143.93  Aligned_cols=257  Identities=10%  Similarity=-0.028  Sum_probs=213.5

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +...|..+...+.+.|++++|+.+|+++.+.. +.+..++..+..++...|+++.|.+.++.+.+.. +.+..++..+..
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~   97 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAV   97 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cCCHHHHHHHHH
Confidence            44567788899999999999999999998753 4477889999999999999999999999999875 557889999999


Q ss_pred             HHHhcCCHHHHHHHHHhcccC---ChhhHHHH--------------HH-HHHHcCChHHHHHHHHHHHHCCCCCCHHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQRN---DVSVWNAM--------------IS-GVAIHGLAADASAIFTKMEMFNVLPDSITFL  146 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~~---~~~~~~~l--------------i~-~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~  146 (410)
                      .|.+.|++++|.+.|++....   +...+..+              .. .+...|++++|.+.|+++.... +.+..++.
T Consensus        98 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  176 (327)
T 3cv0_A           98 SHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMN-PNDAQLHA  176 (327)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHTSTTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHHS-TTCHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhhC-CCCHHHHH
Confidence            999999999999999987643   23334333              22 3777899999999999998753 33678888


Q ss_pred             HHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcC
Q 040371          147 GLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFK  224 (410)
Q Consensus       147 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g  224 (410)
                      .+...+...|++++|...++.+.+.  .+.+...+..+...|.+.|++++|...+++. ...| +..+|..+...+...|
T Consensus       177 ~la~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g  254 (327)
T 3cv0_A          177 SLGVLYNLSNNYDSAAANLRRAVEL--RPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMS  254 (327)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhc
Confidence            9999999999999999999998864  2335788999999999999999999999987 3334 5788999999999999


Q ss_pred             chhHHHHH---HHhhccC------------CCchHHHHHHHHHhcCChhHHHHHHHH
Q 040371          225 RLELGEVA---IVNISRL------------MGGDYVLLSNMYCYLKRWDTAENVREI  266 (410)
Q Consensus       225 ~~~~a~~~---~~~~~~~------------~~~~~~~l~~~~~~~g~~~~a~~~~~~  266 (410)
                      ++++|...   .....|.            +...+..+..+|.+.|++++|..++++
T Consensus       255 ~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~  311 (327)
T 3cv0_A          255 QYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQ  311 (327)
T ss_dssp             CHHHHHHHHHHHHHHHTTSCC-----CCTHHHHHHHHHHHHHHHTTCHHHHHHHTTC
T ss_pred             cHHHHHHHHHHHHHhCCccccccccchhhcCHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence            99999998   4455666            566788899999999999999998864

>3ieg_A DNAJ homolog subfamily C member 3; TPR motif, chaperone, endoplasmic reticulum, TPR repeat, UNF protein response; 2.51A {Mus musculus}

Probab=99.74  E-value=8.9e-15  Score=135.22  Aligned_cols=291  Identities=9%  Similarity=-0.030  Sum_probs=231.3

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      |+..|..+...+.+.|++++|+..|+++.+.. +.+..++..+..++...|+++.|...++.+++.. +.+...+..+..
T Consensus         2 ~~~~~~~~~~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~   79 (359)
T 3ieg_A            2 DVEKHLELGKKLLAAGQLADALSQFHAAVDGD-PDNYIAYYRRATVFLAMGKSKAALPDLTKVIALK-MDFTAARLQRGH   79 (359)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCcchHHHHHHH
Confidence            56788899999999999999999999998753 4467899999999999999999999999999875 447789999999


Q ss_pred             HHHhcCCHHHHHHHHHhcccC------ChhhHHHH------------HHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQRN------DVSVWNAM------------ISGVAIHGLAADASAIFTKMEMFNVLPDSITFL  146 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~~------~~~~~~~l------------i~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~  146 (410)
                      .|.+.|++++|...|++..+.      +...|..+            ...+...|++++|++.|+++.... +.+...+.
T Consensus        80 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  158 (359)
T 3ieg_A           80 LLLKQGKLDEAEDDFKKVLKSNPSEQEEKEAESQLVKADEMQRLRSQALDAFDGADYTAAITFLDKILEVC-VWDAELRE  158 (359)
T ss_dssp             HHHHHTCHHHHHHHHHHHHTSCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHH
T ss_pred             HHHHcCChHHHHHHHHHHHhcCCcccChHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCchHHHH
Confidence            999999999999999988643      23344444            578889999999999999998753 34677888


Q ss_pred             HHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHH---------
Q 040371          147 GLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRA---------  215 (410)
Q Consensus       147 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~---------  215 (410)
                      .+...+...|++++|...++.+.+.  .+.+...+..+...|...|++++|...+++. ...|+ ...|..         
T Consensus       159 ~~~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~  236 (359)
T 3ieg_A          159 LRAECFIKEGEPRKAISDLKAASKL--KSDNTEAFYKISTLYYQLGDHELSLSEVRECLKLDQDHKRCFAHYKQVKKLNK  236 (359)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHTT--CSCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHHH
Confidence            8999999999999999999999853  3446789999999999999999999999887 33343 333332         


Q ss_pred             ---HHHHHHhcCchhHHHHH---HHhhccCCCc----hHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECC
Q 040371          216 ---LLSACRTFKRLELGEVA---IVNISRLMGG----DYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAG  285 (410)
Q Consensus       216 ---li~~~~~~g~~~~a~~~---~~~~~~~~~~----~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~  285 (410)
                         +...+...|++++|...   ..+..|.++.    .+..+..+|.+.|++++|.+.+++..+..  |+....|..   
T Consensus       237 ~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~~---  311 (359)
T 3ieg_A          237 LIESAEELIRDGRYTDATSKYESVMKTEPSVAEYTVRSKERICHCFSKDEKPVEAIRICSEVLQME--PDNVNALKD---  311 (359)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCCSSHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTCHHHHHH---
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC--cccHHHHHH---
Confidence               25568899999999999   4455566543    35568899999999999999999987752  332222321   


Q ss_pred             EEEEEEeCCCCCccHHHHHHHHHH
Q 040371          286 VIHQFKAGDRSHPEAQAIDKILGS  309 (410)
Q Consensus       286 ~~~~~~~~~~~~~~~~~~~~~l~~  309 (410)
                          +...+...|+.++|...+++
T Consensus       312 ----~~~~~~~~g~~~~A~~~~~~  331 (359)
T 3ieg_A          312 ----RAEAYLIEEMYDEAIQDYEA  331 (359)
T ss_dssp             ----HHHHHHHTTCHHHHHHHHHH
T ss_pred             ----HHHHHHHcCCHHHHHHHHHH
Confidence                12223456788888888874

>2gw1_A Mitochondrial precursor proteins import receptor; TPR, protein transport; 3.00A {Saccharomyces cerevisiae}

Probab=99.73  E-value=1.2e-15  Score=148.59  Aligned_cols=297  Identities=9%  Similarity=-0.047  Sum_probs=236.8

Q ss_pred             CCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCC---------
Q 040371            3 DKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIE---------   73 (410)
Q Consensus         3 ~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~---------   73 (410)
                      .||..+|..+..+|.+.|++++|+..|+++.+.+ +.+..+|..+..++...|++++|...++.+.+.+..         
T Consensus        36 ~p~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~  114 (514)
T 2gw1_A           36 KEDPVFYSNLSACYVSVGDLKKVVEMSTKALELK-PDYSKVLLRRASANEGLGKFADAMFDLSVLSLNGDFNDASIEPML  114 (514)
T ss_dssp             CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSCCGGGTHHHH
T ss_pred             CccHHHHHhHHHHHHHHhhHHHHHHHHHHHhccC-hHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCccchHHHHH
Confidence            3788999999999999999999999999998853 446679999999999999999999999999876521         


Q ss_pred             ---------------------------------------------------------------------ccHHHHHHHHH
Q 040371           74 ---------------------------------------------------------------------LNFILSAALID   84 (410)
Q Consensus        74 ---------------------------------------------------------------------~~~~~~~~li~   84 (410)
                                                                                           .+...+..+..
T Consensus       115 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  194 (514)
T 2gw1_A          115 ERNLNKQAMSKLKEKFGDIDTATATPTELSTQPAKERKDKQENLPSVTSMASFFGIFKPELTFANYDESNEADKELMNGL  194 (514)
T ss_dssp             HHHHHHHHHHHHTTC---------------------------CCCCHHHHHHHHTTSCCCCCCSSCCSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhhccCChhhHHHhhccCCchhHHHHHHHhhcCHHHHHHHhcCCcHHHHHHHHHH
Confidence                                                                                 11333344444


Q ss_pred             HHHh---cCCHHHHHHHHHhccc----------------C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHH
Q 040371           85 MYSK---CGKIQMAKEVFDTVQR----------------N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSIT  144 (410)
Q Consensus        85 ~y~~---~g~~~~A~~~f~~m~~----------------~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t  144 (410)
                      .+..   .|++++|...|+++.+                + +..+|..+...|...|++++|+..|+++....  |+..+
T Consensus       195 ~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~--~~~~~  272 (514)
T 2gw1_A          195 SNLYKRSPESYDKADESFTKAARLFEEQLDKNNEDEKLKEKLAISLEHTGIFKFLKNDPLGAHEDIKKAIELF--PRVNS  272 (514)
T ss_dssp             HHHSSCCTTHHHHHHHHHHHHHHHHHHHTTTSTTCHHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHC--CCHHH
T ss_pred             HHHHhhhhccHHHHHHHHHHHHHHhhhhhccCccccccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--ccHHH
Confidence            4443   8999999999998765                2 35688899999999999999999999998864  44778


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHh
Q 040371          145 FLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRT  222 (410)
Q Consensus       145 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~  222 (410)
                      +..+...+...|++++|...++.+.+.  .+.+...+..+...|...|++++|...+++. ...| +...|..+...+..
T Consensus       273 ~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~  350 (514)
T 2gw1_A          273 YIYMALIMADRNDSTEYYNYFDKALKL--DSNNSSVYYHRGQMNFILQNYDQAGKDFDKAKELDPENIFPYIQLACLAYR  350 (514)
T ss_dssp             HHHHHHHHHTSSCCTTGGGHHHHHHTT--CTTCTHHHHHHHHHHHHTTCTTHHHHHHHHHHHTCSSCSHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHhhc--CcCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhChhhHHHHHHHHHHHHH
Confidence            888999999999999999999998853  3346778999999999999999999999987 3344 56788899999999


Q ss_pred             cCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCC----ceeEEEECCEEEEEEeCCC
Q 040371          223 FKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQ----GKSWLELAGVIHQFKAGDR  295 (410)
Q Consensus       223 ~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~----~~s~~~~~~~~~~~~~~~~  295 (410)
                      .|++++|...   ..+..|.++..+..+...|.+.|++++|...++++.+..-....    ...|..       +...+.
T Consensus       351 ~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~-------l~~~~~  423 (514)
T 2gw1_A          351 ENKFDDCETLFSEAKRKFPEAPEVPNFFAEILTDKNDFDKALKQYDLAIELENKLDGIYVGIAPLVG-------KATLLT  423 (514)
T ss_dssp             TTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSSSCSSCSHHHHH-------HHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhhhccchHHHHHHHHHH-------HHHHHh
Confidence            9999999999   45667888889999999999999999999999988664211100    001211       112234


Q ss_pred             C---CccHHHHHHHHHHHH
Q 040371          296 S---HPEAQAIDKILGSLI  311 (410)
Q Consensus       296 ~---~~~~~~~~~~l~~l~  311 (410)
                      .   .|+.++|...+++..
T Consensus       424 ~~~~~~~~~~A~~~~~~a~  442 (514)
T 2gw1_A          424 RNPTVENFIEATNLLEKAS  442 (514)
T ss_dssp             TSCCTTHHHHHHHHHHHHH
T ss_pred             hhhhcCCHHHHHHHHHHHH
Confidence            4   788899998888543

>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=99.70  E-value=2.8e-17  Score=153.38  Aligned_cols=263  Identities=11%  Similarity=0.088  Sum_probs=124.1

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      ..+|+.|..++.+.|++++|++.|.+      .+|..+|..++.++...|++++|+..++...+.  .+++.+.+.|+.+
T Consensus        32 ~~vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~yl~~ark~--~~~~~i~~~Li~~  103 (449)
T 1b89_A           32 PAVWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFA  103 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hHHHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHHh--CccchhHHHHHHH
Confidence            35999999999999999999999965      357889999999999999999999988888774  4568889999999


Q ss_pred             HHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040371           86 YSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYF  165 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  165 (410)
                      |.|+|+++++.++|+.   |+..+|+.+...|...|++++|...|..+         ..|..+..++.+.|++++|.+.+
T Consensus       104 Y~Klg~l~e~e~f~~~---pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a---------~n~~~LA~~L~~Lg~yq~AVea~  171 (449)
T 1b89_A          104 LAKTNRLAELEEFING---PNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDGA  171 (449)
T ss_dssp             -----CHHHHTTTTTC---C----------------CTTTHHHHHHHT---------TCHHHHHHHHHTTTCHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHcC---CcHHHHHHHHHHHHHcCCHHHHHHHHHHh---------hhHHHHHHHHHHhccHHHHHHHH
Confidence            9999999999988864   77789999999999999999999999977         37899999999999999999999


Q ss_pred             HHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHH---HhhccCCCc
Q 040371          166 DHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAI---VNISRLMGG  242 (410)
Q Consensus       166 ~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~---~~~~~~~~~  242 (410)
                      ..+.       ++.+|..++.+|...|+++.|......+...|+.  ...++..|.+.|.+++|..++   ..+++....
T Consensus       172 ~KA~-------~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~~~ad~--l~~lv~~Yek~G~~eEai~lLe~aL~le~ah~~  242 (449)
T 1b89_A          172 RKAN-------STRTWKEVCFACVDGKEFRLAQMCGLHIVVHADE--LEELINYYQDRGYFEELITMLEAALGLERAHMG  242 (449)
T ss_dssp             HHHT-------CHHHHHHHHHHHHHTTCHHHHHHTTTTTTTCHHH--HHHHHHHHHHTTCHHHHHHHHHHHTTSTTCCHH
T ss_pred             HHcC-------CchhHHHHHHHHHHcCcHHHHHHHHHHHHhCHhh--HHHHHHHHHHCCCHHHHHHHHHHHhCCcHHHHH
Confidence            9872       6889999999999999999998777766555544  446888999999999998883   344444556


Q ss_pred             hHHHHHHHHHhc--CChhHHHHHHHHHHhCCCcC-----CCceeEEEECCEEEEEEeCCCCCccHHHHHHH
Q 040371          243 DYVLLSNMYCYL--KRWDTAENVREIMKKKGVRK-----SQGKSWLELAGVIHQFKAGDRSHPEAQAIDKI  306 (410)
Q Consensus       243 ~~~~l~~~~~~~--g~~~~a~~~~~~m~~~g~~~-----~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~  306 (410)
                      .|.-|.-+|++-  ++..+..+.|.  .+-+++|     +...-|.++       +.-|...++.+.|...
T Consensus       243 ~ftel~il~~ky~p~k~~ehl~~~~--~~ini~k~~~~~~~~~~w~e~-------~~ly~~~~e~d~A~~t  304 (449)
T 1b89_A          243 MFTELAILYSKFKPQKMREHLELFW--SRVNIPKVLRAAEQAHLWAEL-------VFLYDKYEEYDNAIIT  304 (449)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHS--TTSCHHHHHHHHHTTTCHHHH-------HHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHH--HHhcCcHHHHHHHHHHHHHHH-------HHHHHhhchHHHHHHH
Confidence            778888888765  34444444443  2334544     333445431       1223445666666554

>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=99.70  E-value=1.4e-14  Score=132.42  Aligned_cols=250  Identities=10%  Similarity=0.015  Sum_probs=209.3

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLG-ALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~-~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      +...+..++..+.+.|++++|+.+|+++.+.. +.+...+..+...+...| ++++|.+.++.+.+.. +.+..++..+.
T Consensus        55 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~  132 (330)
T 3hym_B           55 HASCLPVHIGTLVELNKANELFYLSHKLVDLY-PSNPVSWFAVGCYYLMVGHKNEHARRYLSKATTLE-KTYGPAWIAYG  132 (330)
T ss_dssp             CTTTHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTSTHHHHHHHHHHHHSCSCHHHHHHHHHHHHTTC-TTCTHHHHHHH
T ss_pred             ChhhHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CccHHHHHHHH
Confidence            44567778899999999999999999998753 446778999999999999 9999999999999875 44678899999


Q ss_pred             HHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      ..|...|++++|...|++..+   .+..+|..+...|...|++++|.+.|++..... +.+..++..+...+...|++++
T Consensus       133 ~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~  211 (330)
T 3hym_B          133 HSFAVESEHDQAMAAYFTAAQLMKGCHLPMLYIGLEYGLTNNSKLAERFFSQALSIA-PEDPFVMHEVGVVAFQNGEWKT  211 (330)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHHTTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHccCHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcccHHH
Confidence            999999999999999998763   346788889999999999999999999998753 3457788899999999999999


Q ss_pred             HHHHHHHhhhhcC-------CCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHH
Q 040371          161 GRKYFDHMRSRYS-------IQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEV  231 (410)
Q Consensus       161 a~~~~~~m~~~~~-------~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~  231 (410)
                      |...|+.+.+...       .+.....+..+...|.+.|++++|...+++. ...| +...|..+...+...|++++|..
T Consensus       212 A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~la~~~~~~g~~~~A~~  291 (330)
T 3hym_B          212 AEKWFLDALEKIKAIGNEVTVDKWEPLLNNLGHVCRKLKKYAEALDYHRQALVLIPQNASTYSAIGYIHSLMGNFENAVD  291 (330)
T ss_dssp             HHHHHHHHHHHHTTTSCSCTTTTCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhccHHHHHH
Confidence            9999999875321       1334678999999999999999999999987 3334 56788999999999999999999


Q ss_pred             H---HHhhccCCCchHHHHHHHH-HhcCCh
Q 040371          232 A---IVNISRLMGGDYVLLSNMY-CYLKRW  257 (410)
Q Consensus       232 ~---~~~~~~~~~~~~~~l~~~~-~~~g~~  257 (410)
                      .   ..+..|.++..+..+..++ ...|+.
T Consensus       292 ~~~~al~~~p~~~~~~~~l~~~~~~~~g~~  321 (330)
T 3hym_B          292 YFHTALGLRRDDTFSVTMLGHCIEMYIGDS  321 (330)
T ss_dssp             HHHTTTTTCSCCHHHHHHHHHHHHTTTTC-
T ss_pred             HHHHHHccCCCchHHHHHHHHHHHHHhCch
Confidence            9   4456677777788888877 455554

>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=99.70  E-value=2.2e-15  Score=140.35  Aligned_cols=254  Identities=11%  Similarity=0.028  Sum_probs=197.9

Q ss_pred             HHHHcCCHhHHHH-HHHHHHHCCC-CC--CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC
Q 040371           15 GFVRNARFDEALR-FFREMLSSKV-EP--DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG   90 (410)
Q Consensus        15 ~~~~~g~~~~a~~-l~~~m~~~g~-~p--d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g   90 (410)
                      +|...|++++|++ .|++...... .|  +...+..+...+...|++++|...++.+++.. +.+..++..+...|.+.|
T Consensus        34 ~~~~~~~~~~a~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g  112 (368)
T 1fch_A           34 AHPWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENE  112 (368)
T ss_dssp             ------------CHHHHCCCCCCSSCTTTTCSSHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHhhhhhHHHhcCCCCcccchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCc
Confidence            3445678888888 7776554211 11  34567888999999999999999999999875 557889999999999999


Q ss_pred             CHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHH---------------HHHHH
Q 040371           91 KIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLG---------------LLTAC  152 (410)
Q Consensus        91 ~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~---------------ll~a~  152 (410)
                      ++++|...|++..+   .+..+|..+...|...|++++|++.|+++...... +...+..               .+..+
T Consensus       113 ~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  191 (368)
T 1fch_A          113 QELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPA-YAHLVTPAEEGAGGAGLGPSKRILGSL  191 (368)
T ss_dssp             CHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSTT-TGGGCC---------------CTTHHH
T ss_pred             CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcC-cHHHHHHHHHHhhhhcccHHHHHHHHH
Confidence            99999999998763   46789999999999999999999999999885422 2222211               23444


Q ss_pred             HccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHH
Q 040371          153 SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGE  230 (410)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~  230 (410)
                      ...|++++|..+|+.+.+...-.++..++..+...|.+.|++++|...+++. ...| +..+|..+...+...|++++|.
T Consensus       192 ~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~  271 (368)
T 1fch_A          192 LSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAV  271 (368)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             hhcccHHHHHHHHHHHHHhCcCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHcCCHHHHH
Confidence            4889999999999999865222225788999999999999999999999987 3345 5788999999999999999999


Q ss_pred             HH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          231 VA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       231 ~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      ..   ..+..|.++..+..+..+|.+.|++++|...+++..+.
T Consensus       272 ~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  314 (368)
T 1fch_A          272 AAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNM  314 (368)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            99   45667888889999999999999999999999988764

>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=99.69  E-value=2e-17  Score=154.26  Aligned_cols=218  Identities=12%  Similarity=0.156  Sum_probs=95.4

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      +.|+.++|.++++++      +++.+|..+..++.+.|++++|.+.|.+      .+|...|..++..+...|++++|++
T Consensus        15 ~~~~ld~A~~fae~~------~~~~vWs~La~A~l~~g~~~eAIdsfik------a~D~~~y~~V~~~ae~~g~~EeAi~   82 (449)
T 1b89_A           15 HIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKGMVKEAIDSYIK------ADDPSSYMEVVQAANTSGNWEELVK   82 (449)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HccCHHHHHHHHHhC------CChHHHHHHHHHHHHcCCHHHHHHHHHc------CCCHHHHHHHHHHHHhCCCHHHHHH
Confidence            568899999999987      2345999999999999999999999964      3578899999999999999999999


Q ss_pred             HHHhccc--CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCC
Q 040371           98 VFDTVQR--NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQ  175 (410)
Q Consensus        98 ~f~~m~~--~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~  175 (410)
                      .++...+  +++.+.+.++.+|.+.|+++++.++++       .|+..+|..+...|...|++++|..+|..+       
T Consensus        83 yl~~ark~~~~~~i~~~Li~~Y~Klg~l~e~e~f~~-------~pn~~a~~~IGd~~~~~g~yeeA~~~Y~~a-------  148 (449)
T 1b89_A           83 YLQMARKKARESYVETELIFALAKTNRLAELEEFIN-------GPNNAHIQQVGDRCYDEKMYDAAKLLYNNV-------  148 (449)
T ss_dssp             --------------------------CHHHHTTTTT-------CC----------------CTTTHHHHHHHT-------
T ss_pred             HHHHHHHhCccchhHHHHHHHHHHhCCHHHHHHHHc-------CCcHHHHHHHHHHHHHcCCHHHHHHHHHHh-------
Confidence            7776553  456789999999999999999998885       478889999999999999999999999977       


Q ss_pred             CChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcC
Q 040371          176 PQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLK  255 (410)
Q Consensus       176 ~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g  255 (410)
                         ..|..|++++.+.|++++|.+.+++++   +..+|..++.+|...|+++.|......+. ..+.....++..|.+.|
T Consensus       149 ---~n~~~LA~~L~~Lg~yq~AVea~~KA~---~~~~Wk~v~~aCv~~~ef~lA~~~~l~L~-~~ad~l~~lv~~Yek~G  221 (449)
T 1b89_A          149 ---SNFGRLASTLVHLGEYQAAVDGARKAN---STRTWKEVCFACVDGKEFRLAQMCGLHIV-VHADELEELINYYQDRG  221 (449)
T ss_dssp             ---TCHHHHHHHHHTTTCHHHHHHHHHHHT---CHHHHHHHHHHHHHTTCHHHHHHTTTTTT-TCHHHHHHHHHHHHHTT
T ss_pred             ---hhHHHHHHHHHHhccHHHHHHHHHHcC---CchhHHHHHHHHHHcCcHHHHHHHHHHHH-hCHhhHHHHHHHHHHCC
Confidence               369999999999999999999999983   89999999999999999999988844443 33334557899999999


Q ss_pred             ChhHHHHHHHHHH
Q 040371          256 RWDTAENVREIMK  268 (410)
Q Consensus       256 ~~~~a~~~~~~m~  268 (410)
                      ++++|..+++...
T Consensus       222 ~~eEai~lLe~aL  234 (449)
T 1b89_A          222 YFEELITMLEAAL  234 (449)
T ss_dssp             CHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHh
Confidence            9999999998764

>4eqf_A PEX5-related protein; accessory protein, tetratricopeptide repeat, TPR; 3.00A {Mus musculus}

Probab=99.69  E-value=4.2e-15  Score=138.59  Aligned_cols=228  Identities=12%  Similarity=-0.024  Sum_probs=189.9

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISG  116 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~  116 (410)
                      +...+..+...+.+.|++++|...++.+++.. +.+..++..+...|.+.|++++|...|++..+   .+..+|..+...
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            34458889999999999999999999999875 55789999999999999999999999998763   357899999999


Q ss_pred             HHHcCChHHHHHHHHHHHHCCCCCCH-----------HHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHH
Q 040371          117 VAIHGLAADASAIFTKMEMFNVLPDS-----------ITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMV  185 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p~~-----------~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li  185 (410)
                      |...|++++|+..|+++...  .|+.           ..+..+...+...|++++|..+|+.+.+...-.++..++..+.
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            99999999999999999874  3332           2233457788999999999999999987532223688999999


Q ss_pred             HHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHH
Q 040371          186 DLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTA  260 (410)
Q Consensus       186 ~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a  260 (410)
                      ..|.+.|++++|.+.|++. ...| +..+|..+...+...|++++|...   ..+..|.++.++..+..+|.+.|++++|
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            9999999999999999987 3344 678999999999999999999999   5566788888999999999999999999


Q ss_pred             HHHHHHHHhC
Q 040371          261 ENVREIMKKK  270 (410)
Q Consensus       261 ~~~~~~m~~~  270 (410)
                      ...+++..+.
T Consensus       301 ~~~~~~al~~  310 (365)
T 4eqf_A          301 VSNFLTALSL  310 (365)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999988764

>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=99.69  E-value=2.1e-14  Score=140.77  Aligned_cols=259  Identities=11%  Similarity=0.028  Sum_probs=201.2

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      ..|..+...|.+.|++++|+..|+++.+.. +.+..+|..+..++...|++++|.+.++.+++.+ +.+..++..+...|
T Consensus        26 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~  103 (537)
T 3fp2_A           26 VQLKNRGNHFFTAKNFNEAIKYYQYAIELD-PNEPVFYSNISACYISTGDLEKVIEFTTKALEIK-PDHSKALLRRASAN  103 (537)
T ss_dssp             HHHHHHHHHHHHTTCCC-CHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhhC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CchHHHHHHHHHHH
Confidence            456677777777778888888777777643 3466677777777777778888877777777764 44667777777777


Q ss_pred             HhcCCHHHHHHHHHhc----------------------------------------------------------------
Q 040371           87 SKCGKIQMAKEVFDTV----------------------------------------------------------------  102 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m----------------------------------------------------------------  102 (410)
                      .+.|++++|...|+.+                                                                
T Consensus       104 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  183 (537)
T 3fp2_A          104 ESLGNFTDAMFDLSVLSLNGDFDGASIEPMLERNLNKQAMKVLNENLSKDEGRGSQVLPSNTSLASFFGIFDSHLEVSSV  183 (537)
T ss_dssp             HHHTCHHHHHHHHHHHC-----------CHHHHHHHHHHHHHHHHHCC-------CCCCCHHHHHHHHHTSCHHHHHHTS
T ss_pred             HHcCCHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHhCccccccccchHhHHHHHHHhcChHHHHHHH
Confidence            7777777777666322                                                                


Q ss_pred             ---------------------------------------------cc--CC--------hhhHHHHHHHHHHcCChHHHH
Q 040371          103 ---------------------------------------------QR--ND--------VSVWNAMISGVAIHGLAADAS  127 (410)
Q Consensus       103 ---------------------------------------------~~--~~--------~~~~~~li~~~~~~g~~~~A~  127 (410)
                                                                   .+  |+        ..+|..+...+...|++++|+
T Consensus       184 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~~~A~~~~~~~l~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~  263 (537)
T 3fp2_A          184 NTSSNYDTAYALLSDALQRLYSATDEGYLVANDLLTKSTDMYHSLLSANTVDDPLRENAALALCYTGIFHFLKNNLLDAQ  263 (537)
T ss_dssp             CCCCSSCSSHHHHHHHHHHHHTCSHHHHHHHHHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             hhccccccHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHCCCcchhhHHHHHHHHHHHHHHHhcccHHHHH
Confidence                                                         11  11        124555667788889999999


Q ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CC
Q 040371          128 AIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TM  206 (410)
Q Consensus       128 ~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~  206 (410)
                      ..|++....  .|+..++..+...+...|++++|...|+.+.+.  .+.+..+|..+...|...|++++|...+++. ..
T Consensus       264 ~~~~~~~~~--~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~  339 (537)
T 3fp2_A          264 VLLQESINL--HPTPNSYIFLALTLADKENSQEFFKFFQKAVDL--NPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSL  339 (537)
T ss_dssp             HHHHHHHHH--CCCHHHHHHHHHHTCCSSCCHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhc--CCCchHHHHHHHHHHHhcCHHHHHHHHHHHhcc--CCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence            999999874  566778888888999999999999999998864  2335778999999999999999999999987 33


Q ss_pred             CC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          207 EP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       207 ~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      .| +...|..+...+...|++++|...   ..+..|.++..+..+...|...|++++|.+.+++..+..
T Consensus       340 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~  408 (537)
T 3fp2_A          340 NPENVYPYIQLACLLYKQGKFTESEAFFNETKLKFPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLE  408 (537)
T ss_dssp             CTTCSHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcC
Confidence            34 467888899999999999999999   556678888899999999999999999999999887643

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.68  E-value=6.3e-15  Score=133.26  Aligned_cols=243  Identities=8%  Similarity=-0.004  Sum_probs=172.5

Q ss_pred             HHHHHHcCCHhHHHHHHHHHHHCCCCCCH--HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC
Q 040371           13 IGGFVRNARFDEALRFFREMLSSKVEPDK--FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG   90 (410)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~g~~pd~--~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g   90 (410)
                      |.-....|++.+|+..+++...  ..|+.  .....+..++...|+++.|...++.    .-+|+...+..+...|.+.|
T Consensus         6 ~~~~~~~g~y~~ai~~~~~~~~--~~p~~~~e~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~   79 (291)
T 3mkr_A            6 VKNAFYIGSYQQCINEAQRVKP--SSPERDVERDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHS   79 (291)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCC--CSHHHHHHHHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCST
T ss_pred             HHHHHHHHHHHHHHHHHHhccc--CCchhhHHHHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCC
Confidence            3445567888888888776543  34443  3445667788888888888765543    23566777788888888888


Q ss_pred             CHHHHHHHHHhccc----C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040371           91 KIQMAKEVFDTVQR----N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYF  165 (410)
Q Consensus        91 ~~~~A~~~f~~m~~----~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  165 (410)
                      +.++|.+.|+++..    | +...+..+...|.+.|++++|++.|++      +.+...+..+...+.+.|++++|...|
T Consensus        80 ~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~~~~g~~~~Al~~l~~------~~~~~~~~~l~~~~~~~g~~~~A~~~l  153 (291)
T 3mkr_A           80 RRDAIVAELDREMSRSVDVTNTTFLLMAASIYFYDQNPDAALRTLHQ------GDSLECMAMTVQILLKLDRLDLARKEL  153 (291)
T ss_dssp             THHHHHHHHHHHHHSCCCCSCHHHHHHHHHHHHHTTCHHHHHHHHTT------CCSHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCHHHHHHHHhC------CCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            88888888887642    3 455666677788888888888888876      356677777888888888888888888


Q ss_pred             HHhhhhcCCCCChhH---HHHHHHHHHhcCCHHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCchhHHHHH---HHhhc
Q 040371          166 DHMRSRYSIQPQLEH---YGAMVDLLGRAGHIEEAYGLITSM-TME-PDVVVWRALLSACRTFKRLELGEVA---IVNIS  237 (410)
Q Consensus       166 ~~m~~~~~~~~~~~~---~~~li~~~~~~g~~~~A~~~~~~m-~~~-p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~  237 (410)
                      +.+.+.   .|+...   ..+++..+...|++++|..+|+++ ... .+...|+.+..++...|++++|+..   ..+..
T Consensus       154 ~~~~~~---~p~~~~~~l~~a~~~l~~~~~~~~eA~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~  230 (291)
T 3mkr_A          154 KKMQDQ---DEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADKCSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKD  230 (291)
T ss_dssp             HHHHHH---CTTCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHhh---CcCcHHHHHHHHHHHHHhCchHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence            888754   344321   123334444557888888888887 222 3677788888888888888888888   45667


Q ss_pred             cCCCchHHHHHHHHHhcCChhH-HHHHHHHHHhC
Q 040371          238 RLMGGDYVLLSNMYCYLKRWDT-AENVREIMKKK  270 (410)
Q Consensus       238 ~~~~~~~~~l~~~~~~~g~~~~-a~~~~~~m~~~  270 (410)
                      |.++.++..++..+...|+.++ +.++++++.+.
T Consensus       231 p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~  264 (291)
T 3mkr_A          231 SGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDA  264 (291)
T ss_dssp             TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence            8888888888888888888865 56777776654

>3mkr_A Coatomer subunit epsilon; tetratricopeptide repeats (TPR), beta-hairpin, alpha-solenoi transport protein; 2.60A {Bos taurus}

Probab=99.67  E-value=2.2e-14  Score=129.67  Aligned_cols=241  Identities=9%  Similarity=0.011  Sum_probs=193.8

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCC-CccHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKI-ELNFILSAALIDMY   86 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~-~~~~~~~~~li~~y   86 (410)
                      ..-.+..+|...|++++|+..++.    .-+|+..++..+...+...++.+.|.+.++.++..+. +.+..++..+...|
T Consensus        36 ~~~~l~r~yi~~g~~~~al~~~~~----~~~~~~~a~~~la~~~~~~~~~~~A~~~l~~ll~~~~~P~~~~~~~~la~~~  111 (291)
T 3mkr_A           36 RDVFLYRAYLAQRKYGVVLDEIKP----SSAPELQAVRMFAEYLASHSRRDAIVAELDREMSRSVDVTNTTFLLMAASIY  111 (291)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHSCT----TSCHHHHHHHHHHHHHHCSTTHHHHHHHHHHHHHSCCCCSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHhcc----cCChhHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcccCCCCHHHHHHHHHHH
Confidence            445678999999999999987754    2466778889999999999999999999999998774 44677888888999


Q ss_pred             HhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHH---HHHHHHHHccCCHHHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITF---LGLLTACSHCGLVEEGRK  163 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~---~~ll~a~~~~g~~~~a~~  163 (410)
                      .+.|++++|.+.|++  ..+...+..+...|.+.|++++|.+.|+++.+.  .|+....   ...+..+...|++++|..
T Consensus       112 ~~~g~~~~Al~~l~~--~~~~~~~~~l~~~~~~~g~~~~A~~~l~~~~~~--~p~~~~~~l~~a~~~l~~~~~~~~eA~~  187 (291)
T 3mkr_A          112 FYDQNPDAALRTLHQ--GDSLECMAMTVQILLKLDRLDLARKELKKMQDQ--DEDATLTQLATAWVSLAAGGEKLQDAYY  187 (291)
T ss_dssp             HHTTCHHHHHHHHTT--CCSHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCTTHHHHHHH
T ss_pred             HHCCCHHHHHHHHhC--CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh--CcCcHHHHHHHHHHHHHhCchHHHHHHH
Confidence            999999999999999  467889999999999999999999999999886  3654321   123344455699999999


Q ss_pred             HHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhH-HHHH---HHhhc
Q 040371          164 YFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLEL-GEVA---IVNIS  237 (410)
Q Consensus       164 ~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~-a~~~---~~~~~  237 (410)
                      +|+++.+.  .+.+...++.+..+|.+.|++++|...|++. ...| +..++..++..+...|+.++ +.++   +.+..
T Consensus       188 ~~~~~l~~--~p~~~~~~~~la~~~~~~g~~~eA~~~l~~al~~~p~~~~~l~~l~~~~~~~g~~~eaa~~~~~~~~~~~  265 (291)
T 3mkr_A          188 IFQEMADK--CSPTLLLLNGQAACHMAQGRWEAAEGVLQEALDKDSGHPETLINLVVLSQHLGKPPEVTNRYLSQLKDAH  265 (291)
T ss_dssp             HHHHHHHH--SCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHh--CCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence            99999975  3557889999999999999999999999996 4456 67789999999999999876 4555   55667


Q ss_pred             cCCCchHHHHHHHHHhcCChhHHHH
Q 040371          238 RLMGGDYVLLSNMYCYLKRWDTAEN  262 (410)
Q Consensus       238 ~~~~~~~~~l~~~~~~~g~~~~a~~  262 (410)
                      |.++.    +.+...+.+.++++..
T Consensus       266 P~~~~----~~d~~~~~~~fd~~~~  286 (291)
T 3mkr_A          266 RSHPF----IKEYRAKENDFDRLVL  286 (291)
T ss_dssp             TTCHH----HHHHHHHHHHHHHHHH
T ss_pred             CCChH----HHHHHHHHHHHHHHHH
Confidence            77653    3345555555655544

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.60  E-value=1.5e-13  Score=118.62  Aligned_cols=195  Identities=15%  Similarity=0.072  Sum_probs=155.6

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      ++...|..+...+.+.|++++|+..|++..+.. +.+...+..+..++.+.|++++|...+++.++.. +.+...+..+.
T Consensus         3 ~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg   80 (217)
T 2pl2_A            3 TAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVART-PRYLGGYMVLS   80 (217)
T ss_dssp             -CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHH
Confidence            356788999999999999999999999998753 4467889999999999999999999999999875 55788899999


Q ss_pred             HHHHhc-----------CCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHH
Q 040371           84 DMYSKC-----------GKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLL  149 (410)
Q Consensus        84 ~~y~~~-----------g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll  149 (410)
                      ..|.+.           |++++|...|++..+  | +...|..+...|...|++++|+..|++..+..  .+...+..+.
T Consensus        81 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~--~~~~~~~~la  158 (217)
T 2pl2_A           81 EAYVALYRQAEDRERGKGYLEQALSVLKDAERVNPRYAPLHLQRGLVYALLGERDKAEASLKQALALE--DTPEIRSALA  158 (217)
T ss_dssp             HHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHH
T ss_pred             HHHHHhhhhhhhhcccccCHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhcc--cchHHHHHHH
Confidence            999999           999999999988763  3 56788889999999999999999999998876  6778888899


Q ss_pred             HHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          150 TACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       150 ~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      .++...|++++|...|+...+.  -+.+...+..+...+.+.|++++|...|++.
T Consensus       159 ~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~  211 (217)
T 2pl2_A          159 ELYLSMGRLDEALAQYAKALEQ--APKDLDLRVRYASALLLKGKAEEAARAAALE  211 (217)
T ss_dssp             HHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTC--------------
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            9999999999999999998853  2335678888889999999999999888765

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.60  E-value=1.3e-13  Score=121.28  Aligned_cols=216  Identities=13%  Similarity=0.026  Sum_probs=165.8

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCC--cc----HHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIE--LN----FILS   79 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~--~~----~~~~   79 (410)
                      ...|..+...|.+.|++++|+..|++..+..  ++..++..+..++...|++++|...+..+++....  ++    ..++
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~   82 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSF   82 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHH
Confidence            4578889999999999999999999998776  77888999999999999999999999988775311  11    5788


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCH
Q 040371           80 AALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLV  158 (410)
Q Consensus        80 ~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~  158 (410)
                      ..+...|.+.|++++|...|++....+..     ...+...|++++|...++++...  .| +...+..+...+...|++
T Consensus        83 ~~l~~~~~~~~~~~~A~~~~~~a~~~~~~-----~~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~  155 (258)
T 3uq3_A           83 ARIGNAYHKLGDLKKTIEYYQKSLTEHRT-----ADILTKLRNAEKELKKAEAEAYV--NPEKAEEARLEGKEYFTKSDW  155 (258)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHCCC-----HHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhcCch-----hHHHHHHhHHHHHHHHHHHHHHc--CcchHHHHHHHHHHHHHhcCH
Confidence            88889999999999999999887642111     23466678888888888888774  33 455677777888888888


Q ss_pred             HHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH
Q 040371          159 EEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       159 ~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      ++|...|+.+.+.  .+.+...|..+...|.+.|++++|...+++. ...| +...|..+...+...|++++|...
T Consensus       156 ~~A~~~~~~a~~~--~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~  229 (258)
T 3uq3_A          156 PNAVKAYTEMIKR--APEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVKEYASALET  229 (258)
T ss_dssp             HHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHhc--CcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence            8888888888753  2335677888888888888888888888776 3333 456677777777777777777766

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.59  E-value=1.6e-13  Score=122.06  Aligned_cols=242  Identities=10%  Similarity=-0.087  Sum_probs=190.5

Q ss_pred             HHcCCHhHHHHHHHHHHHCCC--CC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHH
Q 040371           17 VRNARFDEALRFFREMLSSKV--EP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQ   93 (410)
Q Consensus        17 ~~~g~~~~a~~l~~~m~~~g~--~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~   93 (410)
                      ...|++++|+..|+++.+...  +| +..++..+..++...|++++|...++.+++.. +.+..++..+...|.+.|+++
T Consensus        16 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~   94 (275)
T 1xnf_A           16 QPTLQQEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFD   94 (275)
T ss_dssp             CCCHHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHH
T ss_pred             CccchHHHHHHHHHHHHhcccccCchhHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHH
Confidence            346889999999999987632  12 45688889999999999999999999999875 457889999999999999999


Q ss_pred             HHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhh
Q 040371           94 MAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRS  170 (410)
Q Consensus        94 ~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~  170 (410)
                      +|.+.|++..+   .+..+|..+...|.+.|++++|...|+++.+.  .|+.......+..+...|++++|...+.....
T Consensus        95 ~A~~~~~~al~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~  172 (275)
T 1xnf_A           95 AAYEAFDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQD--DPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFE  172 (275)
T ss_dssp             HHHHHHHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCccccHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCCChHHHHHHHHHHHhcCHHHHHHHHHHHHh
Confidence            99999998764   36789999999999999999999999999874  45555555556666778999999999988875


Q ss_pred             hcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-----HHHHHHHHHHHHhcCchhHHHHHHHhhccCCCchH
Q 040371          171 RYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-----VVVWRALLSACRTFKRLELGEVAIVNISRLMGGDY  244 (410)
Q Consensus       171 ~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-----~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~  244 (410)
                      .  .+++...+. ++..+...+..++|...+++. ...|+     ..+|..+...+...|++++|...+.+....++..+
T Consensus       173 ~--~~~~~~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~  249 (275)
T 1xnf_A          173 K--SDKEQWGWN-IVEFYLGNISEQTLMERLKADATDNTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHNF  249 (275)
T ss_dssp             H--SCCCSTHHH-HHHHHTTSSCHHHHHHHHHHHCCSHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTTC
T ss_pred             c--CCcchHHHH-HHHHHHHhcCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCchhH
Confidence            4  234444444 777788888899999999887 33332     57788888999999999999999554444444445


Q ss_pred             HHHHHHHHhcCChhHHHHHH
Q 040371          245 VLLSNMYCYLKRWDTAENVR  264 (410)
Q Consensus       245 ~~l~~~~~~~g~~~~a~~~~  264 (410)
                      .....++...|++++|.+.+
T Consensus       250 ~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          250 VEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHHHHHHHHHhhHHHH
Confidence            55567788888888887765

>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=99.59  E-value=5.4e-13  Score=130.67  Aligned_cols=245  Identities=10%  Similarity=0.006  Sum_probs=202.4

Q ss_pred             CCHhHHHHHHHHHHHCCCCCC--------HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCC
Q 040371           20 ARFDEALRFFREMLSSKVEPD--------KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK   91 (410)
Q Consensus        20 g~~~~a~~l~~~m~~~g~~pd--------~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~   91 (410)
                      |++++|+.+|+++.+.  .|+        ..++..+...+...|+++.|...+..+.+..  |+..++..+...|.+.|+
T Consensus       216 ~~~~~A~~~~~~~l~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~--~~~~~~~~l~~~~~~~~~  291 (537)
T 3fp2_A          216 DLLTKSTDMYHSLLSA--NTVDDPLRENAALALCYTGIFHFLKNNLLDAQVLLQESINLH--PTPNSYIFLALTLADKEN  291 (537)
T ss_dssp             HHHHHHHHHHHHHHC----CCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHTCCSSC
T ss_pred             HHHHHHHHHHHHHHHH--CCCcchhhHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHhcC--CCchHHHHHHHHHHHhcC
Confidence            5899999999999874  343        2356667778888999999999999999874  558889999999999999


Q ss_pred             HHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040371           92 IQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHM  168 (410)
Q Consensus        92 ~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  168 (410)
                      +++|...|++..+   .+..+|..+...|...|++++|++.|++..... +.+..++..+...+...|++++|..+|+.+
T Consensus       292 ~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~g~~~~A~~~~~~~  370 (537)
T 3fp2_A          292 SQEFFKFFQKAVDLNPEYPPTYYHRGQMYFILQDYKNAKEDFQKAQSLN-PENVYPYIQLACLLYKQGKFTESEAFFNET  370 (537)
T ss_dssp             CHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCSHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            9999999998763   367789999999999999999999999998753 224677888999999999999999999999


Q ss_pred             hhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC----C----CCCCHHHHHHHHHHHHhc----------CchhHHH
Q 040371          169 RSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM----T----MEPDVVVWRALLSACRTF----------KRLELGE  230 (410)
Q Consensus       169 ~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m----~----~~p~~~~~~~li~~~~~~----------g~~~~a~  230 (410)
                      .+.  .+.+...+..+...|.+.|++++|...|++.    +    .......+..+...+...          |++++|.
T Consensus       371 ~~~--~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~A~  448 (537)
T 3fp2_A          371 KLK--FPTLPEVPTFFAEILTDRGDFDTAIKQYDIAKRLEEVQEKIHVGIGPLIGKATILARQSSQDPTQLDEEKFNAAI  448 (537)
T ss_dssp             HHH--CTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHCSSCSSTTHHHHHHHHHHHHHHTC----CCHHHHHHHH
T ss_pred             HHh--CCCChHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCcchhhHHHHHHHHHHHHHHHHHhhccchhhhHhHHHHHH
Confidence            864  2345678999999999999999999999886    1    111223344445566777          9999999


Q ss_pred             HH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          231 VA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       231 ~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      ..   ..+..|.++..+..+..+|.+.|++++|.+.+++..+..
T Consensus       449 ~~~~~a~~~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~  492 (537)
T 3fp2_A          449 KLLTKACELDPRSEQAKIGLAQLKLQMEKIDEAIELFEDSAILA  492 (537)
T ss_dssp             HHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC
Confidence            99   556678888899999999999999999999999987653

>3uq3_A Heat shock protein STI1; HSP90, peptide binding, chaperone; 2.60A {Saccharomyces cerevisiae}

Probab=99.59  E-value=2.2e-13  Score=119.77  Aligned_cols=217  Identities=9%  Similarity=-0.053  Sum_probs=186.7

Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-C-------hhhH
Q 040371           41 KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-D-------VSVW  110 (410)
Q Consensus        41 ~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~-------~~~~  110 (410)
                      ...|..+...+...|++++|...+..+++..  .+..++..+...|.+.|++++|...|++..+  | +       ..+|
T Consensus         5 a~~~~~~g~~~~~~~~~~~A~~~~~~a~~~~--~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~   82 (258)
T 3uq3_A            5 ADKEKAEGNKFYKARQFDEAIEHYNKAWELH--KDITYLNNRAAAEYEKGEYETAISTLNDAVEQGREMRADYKVISKSF   82 (258)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS--CCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhh--ccHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccccchHHHHHHH
Confidence            4578888899999999999999999999987  7889999999999999999999999998763  2 1       5789


Q ss_pred             HHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHh
Q 040371          111 NAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGR  190 (410)
Q Consensus       111 ~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~  190 (410)
                      ..+...|...|++++|+..|++....  .|+.       ..+...|++++|...++.+...  .+.+...+..+...|..
T Consensus        83 ~~l~~~~~~~~~~~~A~~~~~~a~~~--~~~~-------~~~~~~~~~~~a~~~~~~~~~~--~~~~~~~~~~~~~~~~~  151 (258)
T 3uq3_A           83 ARIGNAYHKLGDLKKTIEYYQKSLTE--HRTA-------DILTKLRNAEKELKKAEAEAYV--NPEKAEEARLEGKEYFT  151 (258)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHH--CCCH-------HHHHHHHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcccHHHHHHHHHHHHhc--Cchh-------HHHHHHhHHHHHHHHHHHHHHc--CcchHHHHHHHHHHHHH
Confidence            99999999999999999999999884  4553       3456678899999999998852  22346788899999999


Q ss_pred             cCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHH
Q 040371          191 AGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVRE  265 (410)
Q Consensus       191 ~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  265 (410)
                      .|++++|...+++. ...| +..+|..+...+...|++++|...   ..+..|.++..+..+..+|.+.|++++|.+.++
T Consensus       152 ~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~  231 (258)
T 3uq3_A          152 KSDWPNAVKAYTEMIKRAPEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQIAVKEYASALETLD  231 (258)
T ss_dssp             TTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence            99999999999987 3334 678899999999999999999999   556678888889999999999999999999999


Q ss_pred             HHHhC
Q 040371          266 IMKKK  270 (410)
Q Consensus       266 ~m~~~  270 (410)
                      +..+.
T Consensus       232 ~a~~~  236 (258)
T 3uq3_A          232 AARTK  236 (258)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            87654

>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=99.58  E-value=6.8e-13  Score=116.63  Aligned_cols=194  Identities=10%  Similarity=-0.034  Sum_probs=141.9

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      ...|..+...|...|++++|++.|+++.+.. +.+...+..+..++...|++++|.+.++.+.+.. +.+..++..+...
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~  114 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASD-SRNARVLNNYGGF  114 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHH
Confidence            4567777888888888888888888877642 3356677777788888888888888888877764 3466777778888


Q ss_pred             HHhcCCHHHHHHHHHhccc----C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           86 YSKCGKIQMAKEVFDTVQR----N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~----~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      |.+.|++++|.+.|+++..    | +...|..+...|.+.|++++|.+.|++..... +.+...+..+...+...|++++
T Consensus       115 ~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~g~~~~  193 (252)
T 2ho1_A          115 LYEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRLN-RNQPSVALEMADLLYKEREYVP  193 (252)
T ss_dssp             HHHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHcCCHHH
Confidence            8888888888888877654    2 34567777777788888888888888777643 2245667777777778888888


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      |..+++.+.+  ..+.+...+..+...|.+.|++++|.+.++++
T Consensus       194 A~~~~~~~~~--~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~~  235 (252)
T 2ho1_A          194 ARQYYDLFAQ--GGGQNARSLLLGIRLAKVFEDRDTAASYGLQL  235 (252)
T ss_dssp             HHHHHHHHHT--TSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHH--hCcCcHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            8888877764  22345566777777777888888887777776

>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=99.58  E-value=4e-13  Score=122.53  Aligned_cols=226  Identities=12%  Similarity=-0.019  Sum_probs=187.8

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISG  116 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~  116 (410)
                      +...+......+...|++++|..+++.+++.. +.+..++..+...|.+.|++++|.+.|++..+   .+..+|..+...
T Consensus        20 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~   98 (327)
T 3cv0_A           20 YHENPMEEGLSMLKLANLAEAALAFEAVCQAA-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVS   98 (327)
T ss_dssp             GSSCHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCcCCHHHHHHHHHH
Confidence            34456777888999999999999999999875 45788999999999999999999999998763   367789999999


Q ss_pred             HHHcCChHHHHHHHHHHHHCCCCCCH-HHHHHH--------------HH-HHHccCCHHHHHHHHHHhhhhcCCCCChhH
Q 040371          117 VAIHGLAADASAIFTKMEMFNVLPDS-ITFLGL--------------LT-ACSHCGLVEEGRKYFDHMRSRYSIQPQLEH  180 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p~~-~t~~~l--------------l~-a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~  180 (410)
                      |...|++++|++.|+++...  .|+. ..+..+              .. .+...|++++|..+++.+.+.  .+.+...
T Consensus        99 ~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~  174 (327)
T 3cv0_A           99 HTNEHNANAALASLRAWLLS--QPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEM--NPNDAQL  174 (327)
T ss_dssp             HHHTTCHHHHHHHHHHHHHT--STTTTTC--------------------CCTTSHHHHHHHHHHHHHHHHH--STTCHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHh--CCccHHHHHHHhHHHHHHHHHHHHHHhHHHHHcccHHHHHHHHHHHHhh--CCCCHHH
Confidence            99999999999999999875  3332 223222              22 377889999999999999864  2336788


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcC
Q 040371          181 YGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLK  255 (410)
Q Consensus       181 ~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g  255 (410)
                      +..+...|.+.|++++|.+.+++. ...| +..+|..+...+...|++++|...   ..+..|.+...+..+...|.+.|
T Consensus       175 ~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~g  254 (327)
T 3cv0_A          175 HASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMS  254 (327)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhccHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhc
Confidence            999999999999999999999987 3344 578899999999999999999999   45567778888999999999999


Q ss_pred             ChhHHHHHHHHHHhC
Q 040371          256 RWDTAENVREIMKKK  270 (410)
Q Consensus       256 ~~~~a~~~~~~m~~~  270 (410)
                      ++++|.+.+++..+.
T Consensus       255 ~~~~A~~~~~~a~~~  269 (327)
T 3cv0_A          255 QYDLAAKQLVRAIYM  269 (327)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHh
Confidence            999999999988764

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.58  E-value=6.3e-13  Score=114.27  Aligned_cols=208  Identities=12%  Similarity=0.006  Sum_probs=164.3

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +...|..+...|...|++++|+..|+++.+.. +.+...+..+..++...|+++.|.+.++.+.+.. +.+..++..+..
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~   84 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIK-PDSAEINNNYGW   84 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCChHHHHHHHH
Confidence            46678899999999999999999999988753 4467788888899999999999999999998874 446778888999


Q ss_pred             HHHhc-CCHHHHHHHHHhccc--CC---hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCH
Q 040371           85 MYSKC-GKIQMAKEVFDTVQR--ND---VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLV  158 (410)
Q Consensus        85 ~y~~~-g~~~~A~~~f~~m~~--~~---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~  158 (410)
                      .|... |++++|...|+++.+  .+   ...|..+...|...|++++|+..|+++.+.. +.+...+..+...+...|++
T Consensus        85 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~  163 (225)
T 2vq2_A           85 FLCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAAQ-PQFPPAFKELARTKMLAGQL  163 (225)
T ss_dssp             HHHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCchHHHHHHHHHHHcCCH
Confidence            99999 999999999988765  22   4678888888899999999999998887753 23467778888888889999


Q ss_pred             HHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHH
Q 040371          159 EEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRAL  216 (410)
Q Consensus       159 ~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~l  216 (410)
                      ++|..+++.+.+. .-..+...+..+...+...|+.++|..+++.+ ...|+......+
T Consensus       164 ~~A~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~  221 (225)
T 2vq2_A          164 GDADYYFKKYQSR-VEVLQADDLLLGWKIAKALGNAQAAYEYEAQLQANFPYSEELQTV  221 (225)
T ss_dssp             HHHHHHHHHHHHH-HCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHHHHHHHHHHHh-CCCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            9999999888753 11145667777778888888888888888876 345654444333

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.54  E-value=3.7e-13  Score=117.41  Aligned_cols=196  Identities=10%  Similarity=0.084  Sum_probs=142.2

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      .+..+|..+...+.+.|++++|+..|+++.+.. +.+...+..+..++...|++++|...++.+.+.. +.+..++..+.
T Consensus        21 ~~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la   98 (243)
T 2q7f_A           21 MASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELD-SSAATAYYGAG   98 (243)
T ss_dssp             ---------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CcchHHHHHHH
Confidence            345678888888999999999999999988753 4467788888889999999999999999988874 44678888889


Q ss_pred             HHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      ..|.+.|++++|.+.|++..+   .+...|..+...|.+.|++++|+..|+++.... +.+...+..+...+...|++++
T Consensus        99 ~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~  177 (243)
T 2q7f_A           99 NVYVVKEMYKEAKDMFEKALRAGMENGDLFYMLGTVLVKLEQPKLALPYLQRAVELN-ENDTEARFQFGMCLANEGMLDE  177 (243)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHcCCHHH
Confidence            999999999999999987653   366788888888889999999999998887652 3356777788888888899999


Q ss_pred             HHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          161 GRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       161 a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      |...|+.+.+.  .+.+...+..+...|.+.|++++|.+.+++.
T Consensus       178 A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~  219 (243)
T 2q7f_A          178 ALSQFAAVTEQ--DPGHADAFYNAGVTYAYKENREKALEMLDKA  219 (243)
T ss_dssp             HHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CcccHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            99998888753  2334677888888888888888888888876

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.51  E-value=3.5e-12  Score=113.28  Aligned_cols=232  Identities=10%  Similarity=-0.043  Sum_probs=162.1

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc--HHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN--FILSAALIDM   85 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~--~~~~~~li~~   85 (410)
                      .+......+.+.|++++|+..|++..+.. +.+...+..+..++...|++++|.+.++.+++.+-.++  ...+..+...
T Consensus         5 ~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~~   83 (272)
T 3u4t_A            5 VEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGKI   83 (272)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHHH
Confidence            44556778888999999999999998753 33455788888899999999999999999988432222  3457888889


Q ss_pred             HHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHH
Q 040371           86 YSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a  161 (410)
                      |.+.|++++|.+.|++..+   .+..+|..+...|...|++++|++.|++..+.  .| +...+..+...+...+++++|
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            9999999999999987753   35678888888899999999999999888765  34 445555555244455689999


Q ss_pred             HHHHHHhhhhcCCCCChhHHHHHHHHHHhcCC---HHHHHHHHHhC----CCCCC------HHHHHHHHHHHHhcCchhH
Q 040371          162 RKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGH---IEEAYGLITSM----TMEPD------VVVWRALLSACRTFKRLEL  228 (410)
Q Consensus       162 ~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~---~~~A~~~~~~m----~~~p~------~~~~~~li~~~~~~g~~~~  228 (410)
                      ...|+.+.+.  .+.+...+..+...+...|+   +++|...+++.    ...|+      ...|..+-..+...|++++
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            9999888753  12235667777777777776   66666666554    11122      1344555555566666666


Q ss_pred             HHHH---HHhhccCCCchH
Q 040371          229 GEVA---IVNISRLMGGDY  244 (410)
Q Consensus       229 a~~~---~~~~~~~~~~~~  244 (410)
                      |...   ..++.|.++...
T Consensus       240 A~~~~~~al~~~p~~~~a~  258 (272)
T 3u4t_A          240 ADAAWKNILALDPTNKKAI  258 (272)
T ss_dssp             HHHHHHHHHHHCTTCHHHH
T ss_pred             HHHHHHHHHhcCccHHHHH
Confidence            6665   334445444333

>2pl2_A Hypothetical conserved protein TTC0263; TPR, protein binding; 2.50A {Thermus thermophilus}

Probab=99.51  E-value=1.1e-12  Score=113.19  Aligned_cols=194  Identities=12%  Similarity=0.017  Sum_probs=113.7

Q ss_pred             CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHH
Q 040371           38 EPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMI  114 (410)
Q Consensus        38 ~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li  114 (410)
                      +++...+..+..++...|++++|...++..++.. +.+...+..+...|.+.|++++|...|++..+  | +...|..+.
T Consensus         2 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~P~~~~a~~~lg   80 (217)
T 2pl2_A            2 QTAEQNPLRLGVQLYALGRYDAALTLFERALKEN-PQDPEALYWLARTQLKLGLVNPALENGKTLVARTPRYLGGYMVLS   80 (217)
T ss_dssp             --CCHHHHHHHHHHHHTTCHHHHHHHHHHHHTTS-SSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHH
Confidence            4456667777777777777777777777777654 44566777777777777777777777776542  2 455666677


Q ss_pred             HHHHHc-----------CChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHH
Q 040371          115 SGVAIH-----------GLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYG  182 (410)
Q Consensus       115 ~~~~~~-----------g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  182 (410)
                      ..|.+.           |++++|+..|++..+.  .| +...+..+..++...|++++|...|+...+. .  .+...+.
T Consensus        81 ~~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~--~P~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~-~--~~~~~~~  155 (217)
T 2pl2_A           81 EAYVALYRQAEDRERGKGYLEQALSVLKDAERV--NPRYAPLHLQRGLVYALLGERDKAEASLKQALAL-E--DTPEIRS  155 (217)
T ss_dssp             HHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-C--CCHHHHH
T ss_pred             HHHHHhhhhhhhhcccccCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcCChHHHHHHHHHHHhc-c--cchHHHH
Confidence            777766           6666666666666553  33 3445555666666666666666666666643 3  4555666


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHH
Q 040371          183 AMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAEN  262 (410)
Q Consensus       183 ~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~  262 (410)
                      .+...|...|++++|...|++.                             .+..|.++..+..+..+|.+.|++++|..
T Consensus       156 ~la~~~~~~g~~~~A~~~~~~a-----------------------------l~~~P~~~~~~~~la~~~~~~g~~~~A~~  206 (217)
T 2pl2_A          156 ALAELYLSMGRLDEALAQYAKA-----------------------------LEQAPKDLDLRVRYASALLLKGKAEEAAR  206 (217)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHH-----------------------------HHHSTTCHHHHHHHHHHHTC---------
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH-----------------------------HHhCCCChHHHHHHHHHHHHccCHHHHHH
Confidence            6666666666666666666554                             23345555555566666666666666666


Q ss_pred             HHHH
Q 040371          263 VREI  266 (410)
Q Consensus       263 ~~~~  266 (410)
                      .+++
T Consensus       207 ~~~~  210 (217)
T 2pl2_A          207 AAAL  210 (217)
T ss_dssp             ----
T ss_pred             HHHH
Confidence            5554

>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=99.50  E-value=8e-12  Score=109.70  Aligned_cols=189  Identities=13%  Similarity=0.046  Sum_probs=123.5

Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHH
Q 040371           41 KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGV  117 (410)
Q Consensus        41 ~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~  117 (410)
                      ...+..+...+...|++++|.+.++.+++.. +.+..++..+...|.+.|++++|.+.|++..+   .+...|..+...|
T Consensus        37 ~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~la~~~  115 (252)
T 2ho1_A           37 RDAYIQLGLGYLQRGNTEQAKVPLRKALEID-PSSADAHAALAVVFQTEMEPKLADEEYRKALASDSRNARVLNNYGGFL  115 (252)
T ss_dssp             HHHHHHHHHHHHHTTCTGGGHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCChHHHHHHHHHHHhcC-CChHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCcHHHHHHHHHHH
Confidence            3456666677777777777777777777654 34566777777777777777777777776542   2556677777777


Q ss_pred             HHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHH
Q 040371          118 AIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEE  196 (410)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~  196 (410)
                      ...|++++|++.|+++...+..| +...+..+...+...|++++|...|+.+.+. . +.+...+..+...|.+.|++++
T Consensus       116 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~~~~-~-~~~~~~~~~la~~~~~~g~~~~  193 (252)
T 2ho1_A          116 YEQKRYEEAYQRLLEASQDTLYPERSRVFENLGLVSLQMKKPAQAKEYFEKSLRL-N-RNQPSVALEMADLLYKEREYVP  193 (252)
T ss_dssp             HHTTCHHHHHHHHHHHTTCTTCTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH-C-SCCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHhHHHHHHHHHHHHHhCccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc-C-cccHHHHHHHHHHHHHcCCHHH
Confidence            77777777777777776633344 3455666666777777777777777776643 1 2245666677777777777777


Q ss_pred             HHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH
Q 040371          197 AYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       197 A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      |...+++. ...| +...+..+...+...|+.++|...
T Consensus       194 A~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~  231 (252)
T 2ho1_A          194 ARQYYDLFAQGGGQNARSLLLGIRLAKVFEDRDTAASY  231 (252)
T ss_dssp             HHHHHHHHHTTSCCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHhCcCcHHHHHHHHHHHHHccCHHHHHHH
Confidence            77777665 3333 344555555556666666666655

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.49  E-value=2.8e-12  Score=120.66  Aligned_cols=266  Identities=13%  Similarity=0.032  Sum_probs=205.5

Q ss_pred             CCChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHhhCCHHHHHHHHHHHHHc----CCCc
Q 040371            3 DKDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD----KFTFASVIYGCARLGALNHAYWVHNLIIEK----KIEL   74 (410)
Q Consensus         3 ~~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd----~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~~~   74 (410)
                      ++....|......+.+.|++++|+..|++..+.. +.+    ...+..+..++...|+++.|...++++++.    +..|
T Consensus         6 ~~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~   84 (406)
T 3sf4_A            6 EASCLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQL   84 (406)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccH
Confidence            3456678888899999999999999999998753 223    356788889999999999999999987654    2222


Q ss_pred             -cHHHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----hhhHHHHHHHHHHcCC--------------------hH
Q 040371           75 -NFILSAALIDMYSKCGKIQMAKEVFDTVQR-----ND----VSVWNAMISGVAIHGL--------------------AA  124 (410)
Q Consensus        75 -~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~~----~~~~~~li~~~~~~g~--------------------~~  124 (410)
                       ...++..+...|...|++++|...|++..+     ++    ..+|..+...|...|+                    ++
T Consensus        85 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~  164 (406)
T 3sf4_A           85 GEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQ  164 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHH
Confidence             356788899999999999999999987653     22    3488889999999999                    99


Q ss_pred             HHHHHHHHHHHC----CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC----hhHHHHHHHHHHhcCCHH
Q 040371          125 DASAIFTKMEMF----NVLPD-SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ----LEHYGAMVDLLGRAGHIE  195 (410)
Q Consensus       125 ~A~~l~~~m~~~----g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~----~~~~~~li~~~~~~g~~~  195 (410)
                      +|++.|++....    +..|. ..++..+...+...|++++|...++...+...-.++    ...+..+...|...|+++
T Consensus       165 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  244 (406)
T 3sf4_A          165 AAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFE  244 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChH
Confidence            999999877542    21222 346778888999999999999999988753211222    337888999999999999


Q ss_pred             HHHHHHHhC-C---CCCC----HHHHHHHHHHHHhcCchhHHHHHHH---hhccCC------CchHHHHHHHHHhcCChh
Q 040371          196 EAYGLITSM-T---MEPD----VVVWRALLSACRTFKRLELGEVAIV---NISRLM------GGDYVLLSNMYCYLKRWD  258 (410)
Q Consensus       196 ~A~~~~~~m-~---~~p~----~~~~~~li~~~~~~g~~~~a~~~~~---~~~~~~------~~~~~~l~~~~~~~g~~~  258 (410)
                      +|...+++. .   ..++    ..++..+...+...|++++|...+.   ...+..      ..++..+...|...|+++
T Consensus       245 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  324 (406)
T 3sf4_A          245 TASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWSLGNAYTALGNHD  324 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHH
T ss_pred             HHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCCHH
Confidence            999998876 1   1112    4577888888999999999999832   222221      346778999999999999


Q ss_pred             HHHHHHHHHHh
Q 040371          259 TAENVREIMKK  269 (410)
Q Consensus       259 ~a~~~~~~m~~  269 (410)
                      +|.+.+++..+
T Consensus       325 ~A~~~~~~al~  335 (406)
T 3sf4_A          325 QAMHFAEKHLE  335 (406)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999998654

>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein; secretin, TPR repeat, type IV pilus, bacterail virulence; 1.54A {Neisseria meningitidis}

Probab=99.49  E-value=9.8e-12  Score=106.72  Aligned_cols=190  Identities=11%  Similarity=-0.026  Sum_probs=134.5

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISG  116 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~  116 (410)
                      +...+..+...+...|++++|.+.++.+++.. +.+..++..+...|...|++++|.+.|++..+   .+..+|..+...
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~l~~~   85 (225)
T 2vq2_A            7 VSNIKTQLAMEYMRGQDYRQATASIEDALKSD-PKNELAWLVRAEIYQYLKVNDKAQESFRQALSIKPDSAEINNNYGWF   85 (225)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhhHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHH
Confidence            45567777778888888888888888887764 44577777888888888888888888877653   356677777788


Q ss_pred             HHHc-CChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCH
Q 040371          117 VAIH-GLAADASAIFTKMEMFNVLPD-SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHI  194 (410)
Q Consensus       117 ~~~~-g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~  194 (410)
                      |... |++++|+..|+++...+..|+ ...+..+...+...|++++|...|+.+.+.  .+.+...+..+...|.+.|++
T Consensus        86 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~  163 (225)
T 2vq2_A           86 LCGRLNRPAESMAYFDKALADPTYPTPYIANLNKGICSAKQGQFGLAEAYLKRSLAA--QPQFPPAFKELARTKMLAGQL  163 (225)
T ss_dssp             HHTTTCCHHHHHHHHHHHHTSTTCSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHTCH
T ss_pred             HHHhcCcHHHHHHHHHHHHcCcCCcchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCchHHHHHHHHHHHcCCH
Confidence            8888 888888888888776333343 456667777777888888888888877753  122466777777778888888


Q ss_pred             HHHHHHHHhC-CCCC--CHHHHHHHHHHHHhcCchhHHHHH
Q 040371          195 EEAYGLITSM-TMEP--DVVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       195 ~~A~~~~~~m-~~~p--~~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      ++|...+++. ...|  +...+..+...+...|+.+.+..+
T Consensus       164 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~  204 (225)
T 2vq2_A          164 GDADYYFKKYQSRVEVLQADDLLLGWKIAKALGNAQAAYEY  204 (225)
T ss_dssp             HHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCcHHHHHHH
Confidence            8887777765 2222  445555555556666766666666

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.49  E-value=1.8e-12  Score=122.52  Aligned_cols=263  Identities=10%  Similarity=-0.035  Sum_probs=202.7

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCH----HHHHHHHHHHHhhCCHHHHHHHHHHHHHc----C-CCccHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDK----FTFASVIYGCARLGALNHAYWVHNLIIEK----K-IELNFI   77 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~----~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g-~~~~~~   77 (410)
                      ..+..+...+.+.|++++|+..|++..+.. +.+.    ..+..+..++...|+++.|...+++.++.    + .+....
T Consensus        49 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  127 (411)
T 4a1s_A           49 LELALEGERLCNAGDCRAGVAFFQAAIQAG-TEDLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAK  127 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHhc-ccChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHH
Confidence            345667788899999999999999998853 2233    46888889999999999999999988764    2 123467


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhcccC---------ChhhHHHHHHHHHHcCC-----------------hHHHHHHHH
Q 040371           78 LSAALIDMYSKCGKIQMAKEVFDTVQRN---------DVSVWNAMISGVAIHGL-----------------AADASAIFT  131 (410)
Q Consensus        78 ~~~~li~~y~~~g~~~~A~~~f~~m~~~---------~~~~~~~li~~~~~~g~-----------------~~~A~~l~~  131 (410)
                      ++..+...|...|++++|...|++..+.         ...+|+.+...|...|+                 +++|++.|+
T Consensus       128 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~  207 (411)
T 4a1s_A          128 SSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQ  207 (411)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHH
Confidence            7889999999999999999999876531         24578889999999999                 999999998


Q ss_pred             HHHHC----CCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC----hhHHHHHHHHHHhcCCHHHHHHHHH
Q 040371          132 KMEMF----NVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ----LEHYGAMVDLLGRAGHIEEAYGLIT  202 (410)
Q Consensus       132 ~m~~~----g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~----~~~~~~li~~~~~~g~~~~A~~~~~  202 (410)
                      +....    +..| ...++..+...+...|++++|...|+...+...-.++    ...+..+...|...|++++|...++
T Consensus       208 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  287 (411)
T 4a1s_A          208 ENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYK  287 (411)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHH
Confidence            87542    2122 2346778888999999999999999988753111112    2378889999999999999999998


Q ss_pred             hC-CCC---C----CHHHHHHHHHHHHhcCchhHHHHHHH---hhccC------CCchHHHHHHHHHhcCChhHHHHHHH
Q 040371          203 SM-TME---P----DVVVWRALLSACRTFKRLELGEVAIV---NISRL------MGGDYVLLSNMYCYLKRWDTAENVRE  265 (410)
Q Consensus       203 ~m-~~~---p----~~~~~~~li~~~~~~g~~~~a~~~~~---~~~~~------~~~~~~~l~~~~~~~g~~~~a~~~~~  265 (410)
                      +. ...   .    ...++..+...+...|++++|...+.   ...+.      ...++..+..+|.+.|++++|.+.++
T Consensus       288 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  367 (411)
T 4a1s_A          288 RTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLAIAQELGDRIGEARACWSLGNAHSAIGGHERALKYAE  367 (411)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccHHHHHHHHH
Confidence            76 111   1    24677888888999999999999832   22221      12367889999999999999999999


Q ss_pred             HHHhC
Q 040371          266 IMKKK  270 (410)
Q Consensus       266 ~m~~~  270 (410)
                      +..+.
T Consensus       368 ~al~~  372 (411)
T 4a1s_A          368 QHLQL  372 (411)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87653

>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=99.49  E-value=5e-12  Score=118.36  Aligned_cols=241  Identities=9%  Similarity=0.053  Sum_probs=193.6

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCC-HHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGA-LNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~-~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      ...|+.+...+.+.|++++|+..|++.+... +-+...|..+..++...|+ +++|...++++++.. +.+..+|+.+..
T Consensus        97 ~~a~~~lg~~~~~~g~~~~Al~~~~~al~l~-P~~~~a~~~~g~~l~~~g~d~~eAl~~~~~al~l~-P~~~~a~~~~g~  174 (382)
T 2h6f_A           97 RDVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRV  174 (382)
T ss_dssp             HHHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHC-CCCHHHHHHHHH
Confidence            4578889999999999999999999998753 3367789999999999996 999999999999975 457889999999


Q ss_pred             HHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc-cCCHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSH-CGLVEE  160 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~-~g~~~~  160 (410)
                      +|.+.|++++|+..|++..+   .+..+|+.+..++.+.|++++|+..|+++.+.. +-+...|+.+..++.. .|..++
T Consensus       175 ~~~~~g~~~eAl~~~~kal~ldP~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l~-P~~~~a~~~lg~~l~~l~~~~~e  253 (382)
T 2h6f_A          175 LVEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKED-VRNNSVWNQRYFVISNTTGYNDR  253 (382)
T ss_dssp             HHHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCSCSH
T ss_pred             HHHHccCHHHHHHHHHHHHHhCccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcCcchH
Confidence            99999999999999998864   467899999999999999999999999998853 2256788888888888 666577


Q ss_pred             H-----HHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcC--CHHHHHHHHHhCCCCC-CHHHHHHHHHHHHhcC-------
Q 040371          161 G-----RKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAG--HIEEAYGLITSMTMEP-DVVVWRALLSACRTFK-------  224 (410)
Q Consensus       161 a-----~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g--~~~~A~~~~~~m~~~p-~~~~~~~li~~~~~~g-------  224 (410)
                      |     ...|+...+.   .| +...|+.+...|.+.|  ++++|++.+.++...| +...+..+...+...|       
T Consensus       254 A~~~~el~~~~~Al~l---~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~~~~p~~~~al~~La~~~~~~~~~~~~~~  330 (382)
T 2h6f_A          254 AVLEREVQYTLEMIKL---VPHNESAWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNK  330 (382)
T ss_dssp             HHHHHHHHHHHHHHHH---STTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHTTCSSH
T ss_pred             HHHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHccCccchHHHHHHHHHhccCCCCHHHHHHHHHHHHHHhcccccch
Confidence            7     4778887743   34 4678888888899888  6899999888875555 4567788888887764       


Q ss_pred             --chhHHHHH---H-HhhccCCCchHHHHHHHHH
Q 040371          225 --RLELGEVA---I-VNISRLMGGDYVLLSNMYC  252 (410)
Q Consensus       225 --~~~~a~~~---~-~~~~~~~~~~~~~l~~~~~  252 (410)
                        .+++|..+   + .+.+|.....|..+...+.
T Consensus       331 ~~~~~~A~~~~~~l~~~~DP~r~~~w~~~~~~l~  364 (382)
T 2h6f_A          331 EDILNKALELCEILAKEKDTIRKEYWRYIGRSLQ  364 (382)
T ss_dssp             HHHHHHHHHHHHHHHHTTCGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCchhHHHHHHHHHHHH
Confidence              25778877   3 4556666666666655544

>1ouv_A Conserved hypothetical secreted protein; TPR repeat, HCP repeat, cysteine rich protein, loop-helix-TU repeat protein, hydrolase; 2.00A {Helicobacter pylori} SCOP: a.118.18.1

Probab=99.48  E-value=5.8e-11  Score=105.79  Aligned_cols=215  Identities=10%  Similarity=-0.059  Sum_probs=165.8

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh----hCCHHHHHHHHHHHHHcCCCccHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCAR----LGALNHAYWVHNLIIEKKIELNFILS   79 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~----~~~~~~a~~~~~~~~~~g~~~~~~~~   79 (410)
                      .+..++..+-..|.+.|++++|+..|++..+.+   +...+..+...+..    .+++++|...+++..+.+   +...+
T Consensus         4 ~~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~   77 (273)
T 1ouv_A            4 QDPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGC   77 (273)
T ss_dssp             -CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHH
T ss_pred             CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCC---CHHHH
Confidence            356788888899999999999999999988733   55677888888888    999999999999998876   67788


Q ss_pred             HHHHHHHHh----cCCHHHHHHHHHhcccC-ChhhHHHHHHHHHH----cCChHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040371           80 AALIDMYSK----CGKIQMAKEVFDTVQRN-DVSVWNAMISGVAI----HGLAADASAIFTKMEMFNVLPDSITFLGLLT  150 (410)
Q Consensus        80 ~~li~~y~~----~g~~~~A~~~f~~m~~~-~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  150 (410)
                      ..+..+|..    .|++++|.+.|++..+. +..++..+...|..    .+++++|++.|++..+.+   +...+..+..
T Consensus        78 ~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~  154 (273)
T 1ouv_A           78 HLLGNLYYSGQGVSQNTNKALQYYSKACDLKYAEGCASLGGIYHDGKVVTRDFKKAVEYFTKACDLN---DGDGCTILGS  154 (273)
T ss_dssp             HHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHH
T ss_pred             HHHHHHHhCCCCcccCHHHHHHHHHHHHHcCCccHHHHHHHHHHcCCCcccCHHHHHHHHHHHHhcC---cHHHHHHHHH
Confidence            888889998    99999999999877643 66788888888888    899999999999888865   4556666777


Q ss_pred             HHHc----cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHh----cCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHH
Q 040371          151 ACSH----CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGR----AGHIEEAYGLITSM-TMEPDVVVWRALLSACR  221 (410)
Q Consensus       151 a~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~  221 (410)
                      .+..    .+++++|...|+...+. +   +...+..+...|..    .+++++|...|++. ... +...+..+-..+.
T Consensus       155 ~~~~~~~~~~~~~~A~~~~~~a~~~-~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~-~~~a~~~l~~~~~  229 (273)
T 1ouv_A          155 LYDAGRGTPKDLKKALASYDKACDL-K---DSPGCFNAGNMYHHGEGATKNFKEALARYSKACELE-NGGGCFNLGAMQY  229 (273)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTT-CHHHHHHHHHHHH
T ss_pred             HHHcCCCCCCCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCC-CHHHHHHHHHHHH
Confidence            7777    88999999999888753 2   45677788888888    88888888888775 222 2444444444444


Q ss_pred             h----cCchhHHHHH
Q 040371          222 T----FKRLELGEVA  232 (410)
Q Consensus       222 ~----~g~~~~a~~~  232 (410)
                      .    .+++++|...
T Consensus       230 ~g~~~~~~~~~A~~~  244 (273)
T 1ouv_A          230 NGEGVTRNEKQAIEN  244 (273)
T ss_dssp             TTSSSSCCSTTHHHH
T ss_pred             cCCCcccCHHHHHHH
Confidence            4    4455555444

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.47  E-value=4.1e-12  Score=115.83  Aligned_cols=264  Identities=13%  Similarity=0.019  Sum_probs=202.2

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHhhCCHHHHHHHHHHHHHc----CCC-ccH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD----KFTFASVIYGCARLGALNHAYWVHNLIIEK----KIE-LNF   76 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd----~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~~-~~~   76 (410)
                      ...+......+.+.|++++|+..|++..+.. +.+    ...+..+...+...|+++.|.+.++...+.    +.. ...
T Consensus         5 ~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~   83 (338)
T 3ro2_A            5 CLELALEGERLCKSGDCRAGVSFFEAAVQVG-TEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEA   83 (338)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHhhC-cccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHH
Confidence            3456677788999999999999999998753 223    357788889999999999999999887654    222 236


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----hhhHHHHHHHHHHcCC--------------------hHHHH
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQR-----ND----VSVWNAMISGVAIHGL--------------------AADAS  127 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~~----~~~~~~li~~~~~~g~--------------------~~~A~  127 (410)
                      .++..+...|...|++++|...|++..+     ++    ..+|..+...|...|+                    +++|.
T Consensus        84 ~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~  163 (338)
T 3ro2_A           84 KASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAV  163 (338)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHH
Confidence            6788999999999999999999987642     22    3478888999999999                    99999


Q ss_pred             HHHHHHHHC----CCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC----hhHHHHHHHHHHhcCCHHHHH
Q 040371          128 AIFTKMEMF----NVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ----LEHYGAMVDLLGRAGHIEEAY  198 (410)
Q Consensus       128 ~l~~~m~~~----g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~----~~~~~~li~~~~~~g~~~~A~  198 (410)
                      +.+++....    +..| ...++..+...+...|++++|...++...+...-.++    ...+..+...|...|++++|.
T Consensus       164 ~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~  243 (338)
T 3ro2_A          164 DLYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETAS  243 (338)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHH
Confidence            999887542    2122 2346777888899999999999999987643111112    337888899999999999999


Q ss_pred             HHHHhC-C---CCCC----HHHHHHHHHHHHhcCchhHHHHHHH---hhccCC------CchHHHHHHHHHhcCChhHHH
Q 040371          199 GLITSM-T---MEPD----VVVWRALLSACRTFKRLELGEVAIV---NISRLM------GGDYVLLSNMYCYLKRWDTAE  261 (410)
Q Consensus       199 ~~~~~m-~---~~p~----~~~~~~li~~~~~~g~~~~a~~~~~---~~~~~~------~~~~~~l~~~~~~~g~~~~a~  261 (410)
                      ..+++. .   ..++    ..++..+...+...|++++|...+.   ...+..      ..++..+...|.+.|++++|.
T Consensus       244 ~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~  323 (338)
T 3ro2_A          244 EYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELKDRIGEGRACWSLGNAYTALGNHDQAM  323 (338)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChHHHH
Confidence            998876 1   1112    4567778888999999999999832   222221      236778999999999999999


Q ss_pred             HHHHHHHhC
Q 040371          262 NVREIMKKK  270 (410)
Q Consensus       262 ~~~~~m~~~  270 (410)
                      +.+++..+.
T Consensus       324 ~~~~~a~~~  332 (338)
T 3ro2_A          324 HFAEKHLEI  332 (338)
T ss_dssp             HHHHHHHHC
T ss_pred             HHHHHHHHH
Confidence            999988764

>1xnf_A Lipoprotein NLPI; TPR, tetratricopeptide, structural genomi unknown function; 1.98A {Escherichia coli} SCOP: a.118.8.1

Probab=99.46  E-value=5.4e-12  Score=112.13  Aligned_cols=220  Identities=8%  Similarity=-0.090  Sum_probs=173.0

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +..+|..+...|...|++++|+..|++..+.. +.+..+|..+..++...|++++|...++.+++.. +.+..++..+..
T Consensus        42 ~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~  119 (275)
T 1xnf_A           42 RAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGI  119 (275)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-ccccHHHHHHHH
Confidence            45689999999999999999999999998753 4468899999999999999999999999999874 446889999999


Q ss_pred             HHHhcCCHHHHHHHHHhccc--CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQR--NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGR  162 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~--~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  162 (410)
                      .|.+.|++++|...|+++.+  |+...+...+..+...|++++|+..|++..... +++...+ .++..+...+..++|.
T Consensus       120 ~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~a~  197 (275)
T 1xnf_A          120 ALYYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKS-DKEQWGW-NIVEFYLGNISEQTLM  197 (275)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHS-CCCSTHH-HHHHHHTTSSCHHHHH
T ss_pred             HHHHhccHHHHHHHHHHHHHhCCCChHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CcchHHH-HHHHHHHHhcCHHHHH
Confidence            99999999999999998863  444444555555677799999999998877652 3444444 4777788888999999


Q ss_pred             HHHHHhhhhcCCCCC-----hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHHH
Q 040371          163 KYFDHMRSRYSIQPQ-----LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVAI  233 (410)
Q Consensus       163 ~~~~~m~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~~  233 (410)
                      ..+....+.   .|+     ...+..+...|.+.|++++|...|++. ...|+.  +.....++...|++++|...+
T Consensus       198 ~~~~~~~~~---~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~--~~~~~~~~~~l~~~~~a~~~~  269 (275)
T 1xnf_A          198 ERLKADATD---NTSLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHN--FVEHRYALLELSLLGQDQDDL  269 (275)
T ss_dssp             HHHHHHCCS---HHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTT--CHHHHHHHHHHHHHHHC----
T ss_pred             HHHHHHhcc---cccccccccHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCchh--HHHHHHHHHHHHHHHhhHHHH
Confidence            999887642   221     578889999999999999999999987 556643  222344566677777776553

>2q7f_A YRRB protein; TPR, protein binding; 2.49A {Bacillus subtilis} SCOP: k.38.1.1

Probab=99.45  E-value=3.5e-12  Score=111.16  Aligned_cols=202  Identities=12%  Similarity=0.058  Sum_probs=129.8

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISG  116 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~  116 (410)
                      ...+|..+...+...|+++.|...++.+++.. +.+..++..+...|.+.|++++|...|++..+   .+..+|..+...
T Consensus        22 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~  100 (243)
T 2q7f_A           22 ASMTGGQQMGRGSEFGDYEKAAEAFTKAIEEN-KEDAIPYINFANLLSSVNELERALAFYDKALELDSSAATAYYGAGNV  100 (243)
T ss_dssp             --------------------CCTTHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcchHHHHHHHHH
Confidence            44566777777788888888888888887754 44677788888888888888888888887653   356677888888


Q ss_pred             HHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHH
Q 040371          117 VAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEE  196 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~  196 (410)
                      |...|++++|++.|+++.+.. +.+...+..+...+...|++++|..+++.+.+.  .+.+...+..+...|.+.|++++
T Consensus       101 ~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~l~~~~~~~~~~~~  177 (243)
T 2q7f_A          101 YVVKEMYKEAKDMFEKALRAG-MENGDLFYMLGTVLVKLEQPKLALPYLQRAVEL--NENDTEARFQFGMCLANEGMLDE  177 (243)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHT-CCSHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHhccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccHHHHHHHHHHHHHh--CCccHHHHHHHHHHHHHcCCHHH
Confidence            888888888888888877653 335666777777888888888888888887753  23356677777888888888888


Q ss_pred             HHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHH
Q 040371          197 AYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYV  245 (410)
Q Consensus       197 A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~  245 (410)
                      |.+.+++. ...| +..+|..+...+...|++++|...   ..+..|.++..+.
T Consensus       178 A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~  231 (243)
T 2q7f_A          178 ALSQFAAVTEQDPGHADAFYNAGVTYAYKENREKALEMLDKAIDIQPDHMLALH  231 (243)
T ss_dssp             HHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTHHHHHHHHHHHHCTTCHHHHH
T ss_pred             HHHHHHHHHHhCcccHHHHHHHHHHHHHccCHHHHHHHHHHHHccCcchHHHHH
Confidence            88877776 2223 456666666677777777777766   3344454444333

>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=99.45  E-value=7.8e-11  Score=104.91  Aligned_cols=223  Identities=10%  Similarity=-0.061  Sum_probs=188.7

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh----cCCHHHHHHHHHhcccC-ChhhHHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK----CGKIQMAKEVFDTVQRN-DVSVWNAMI  114 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~----~g~~~~A~~~f~~m~~~-~~~~~~~li  114 (410)
                      +..++..+...+...|++++|.+.+++..+.+   +...+..+..+|..    .|++++|...|++..+. +..++..+.
T Consensus         5 ~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~~---~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg   81 (273)
T 1ouv_A            5 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLG   81 (273)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence            56678888889999999999999999999843   56788889999999    99999999999987643 678899999


Q ss_pred             HHHHH----cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc----cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHH
Q 040371          115 SGVAI----HGLAADASAIFTKMEMFNVLPDSITFLGLLTACSH----CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVD  186 (410)
Q Consensus       115 ~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~  186 (410)
                      ..|..    .+++++|+..|++..+.+   +...+..+...+..    .+++++|...|+...+. +   +...+..+..
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            99999    999999999999998875   67788888889998    99999999999999864 4   5677888888


Q ss_pred             HHHh----cCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCchhHHHHHHHhh-ccCCCchHHHHHHHHHh----
Q 040371          187 LLGR----AGHIEEAYGLITSMTMEPDVVVWRALLSACRT----FKRLELGEVAIVNI-SRLMGGDYVLLSNMYCY----  253 (410)
Q Consensus       187 ~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~-~~~~~~~~~~l~~~~~~----  253 (410)
                      .|..    .+++++|...|++.-...+...+..+-..+..    .+++++|...+.+. ...++..+..+..+|.+    
T Consensus       155 ~~~~~~~~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~~~~g~~~~~~~~~A~~~~~~a~~~~~~~a~~~l~~~~~~g~~~  234 (273)
T 1ouv_A          155 LYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELENGGGCFNLGAMQYNGEGV  234 (273)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSS
T ss_pred             HHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCc
Confidence            9998    99999999999987222366778888888888    99999999994332 22335678889999999    


Q ss_pred             cCChhHHHHHHHHHHhCCC
Q 040371          254 LKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       254 ~g~~~~a~~~~~~m~~~g~  272 (410)
                      .+++++|.+.+++..+.|-
T Consensus       235 ~~~~~~A~~~~~~a~~~~~  253 (273)
T 1ouv_A          235 TRNEKQAIENFKKGCKLGA  253 (273)
T ss_dssp             SCCSTTHHHHHHHHHHHTC
T ss_pred             ccCHHHHHHHHHHHHHcCC
Confidence            9999999999999887653

>3u4t_A TPR repeat-containing protein; structural genomics, PSI- protein structure initiative, northeast structural genomics consortium, NESG; 2.28A {Cytophaga hutchinsonii}

Probab=99.44  E-value=2.8e-11  Score=107.36  Aligned_cols=225  Identities=9%  Similarity=-0.050  Sum_probs=176.6

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--CCh----hhHHHHHH
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--NDV----SVWNAMIS  115 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~~----~~~~~li~  115 (410)
                      ..+......+...|+++.|...++.+++.. +.+..++..+...|.+.|++++|...|++..+  ++.    .+|..+..
T Consensus         4 ~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~-p~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~lg~   82 (272)
T 3u4t_A            4 DVEFRYADFLFKNNNYAEAIEVFNKLEAKK-YNSPYIYNRRAVCYYELAKYDLAQKDIETYFSKVNATKAKSADFEYYGK   82 (272)
T ss_dssp             -CHHHHHHHHHTTTCHHHHHHHHHHHHHTT-CCCSTTHHHHHHHHHHTTCHHHHHHHHHHHHTTSCTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHHhhHHHHHHHHHHHHhccCchhHHHHHHHHHHH
Confidence            345566778889999999999999999874 34566888999999999999999999998765  222    24889999


Q ss_pred             HHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHH
Q 040371          116 GVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIE  195 (410)
Q Consensus       116 ~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~  195 (410)
                      .|...|++++|++.|++..+.. +.+..++..+...+...|++++|...|+...+.  .+.+...|..+...+...++++
T Consensus        83 ~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~~~~~~~~~~l~~~~~~~~~~~  159 (272)
T 3u4t_A           83 ILMKKGQDSLAIQQYQAAVDRD-TTRLDMYGQIGSYFYNKGNFPLAIQYMEKQIRP--TTTDPKVFYELGQAYYYNKEYV  159 (272)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHGGGCCS--SCCCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHcccHHHHHHHHHHHHhcC-cccHHHHHHHHHHHHHccCHHHHHHHHHHHhhc--CCCcHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999998853 235578889999999999999999999998853  2334667777773444455999


Q ss_pred             HHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCc---hhHHHHH---HHhhc---cCC-----CchHHHHHHHHHhcCChhH
Q 040371          196 EAYGLITSM-TMEPD-VVVWRALLSACRTFKR---LELGEVA---IVNIS---RLM-----GGDYVLLSNMYCYLKRWDT  259 (410)
Q Consensus       196 ~A~~~~~~m-~~~p~-~~~~~~li~~~~~~g~---~~~a~~~---~~~~~---~~~-----~~~~~~l~~~~~~~g~~~~  259 (410)
                      +|.+.|++. ...|+ ...+..+...+...|+   .++|...   ..+..   |..     ...|..+...|.+.|++++
T Consensus       160 ~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  239 (272)
T 3u4t_A          160 KADSSFVKVLELKPNIYIGYLWRARANAAQDPDTKQGLAKPYYEKLIEVCAPGGAKYKDELIEANEYIAYYYTINRDKVK  239 (272)
T ss_dssp             HHHHHHHHHHHHSTTCHHHHHHHHHHHHHHSTTCSSCTTHHHHHHHHHHHGGGGGGGHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHHHHHHHhCccchHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHHcCCHHH
Confidence            999999987 44454 6777777788887787   7777776   22221   221     1467789999999999999


Q ss_pred             HHHHHHHHHhC
Q 040371          260 AENVREIMKKK  270 (410)
Q Consensus       260 a~~~~~~m~~~  270 (410)
                      |.+.+++..+.
T Consensus       240 A~~~~~~al~~  250 (272)
T 3u4t_A          240 ADAAWKNILAL  250 (272)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhc
Confidence            99999998764

>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=99.40  E-value=1.8e-11  Score=114.54  Aligned_cols=226  Identities=12%  Similarity=0.062  Sum_probs=186.8

Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCC-HHHHHHHHHhccc---CChhhHHHHHHH
Q 040371           41 KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK-IQMAKEVFDTVQR---NDVSVWNAMISG  116 (410)
Q Consensus        41 ~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~-~~~A~~~f~~m~~---~~~~~~~~li~~  116 (410)
                      ...|..+..++...|++++|.+.++++++.. +.+..+|+.+...|.+.|+ +++|+..|++...   .+...|+.+...
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            3577888888999999999999999999975 5578999999999999997 9999999998874   367899999999


Q ss_pred             HHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHh-cCCHH
Q 040371          117 VAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGR-AGHIE  195 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~-~g~~~  195 (410)
                      |...|++++|+..|+++.+.. +-+...|..+..++.+.|++++|...|+.+.+.  -+-+...|+.+..+|.+ .|..+
T Consensus       176 ~~~~g~~~eAl~~~~kal~ld-P~~~~a~~~lg~~~~~~g~~~eAl~~~~~al~l--~P~~~~a~~~lg~~l~~l~~~~~  252 (382)
T 2h6f_A          176 VEWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE--DVRNNSVWNQRYFVISNTTGYND  252 (382)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCSCS
T ss_pred             HHHccCHHHHHHHHHHHHHhC-ccCHHHHHHHHHHHHHcCChHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCcch
Confidence            999999999999999999853 226788999999999999999999999999864  12357889999999999 67667


Q ss_pred             HH-----HHHHHhC-CCCC-CHHHHHHHHHHHHhcC--chhHHHHHHH--hhccCCCchHHHHHHHHHhcC---------
Q 040371          196 EA-----YGLITSM-TMEP-DVVVWRALLSACRTFK--RLELGEVAIV--NISRLMGGDYVLLSNMYCYLK---------  255 (410)
Q Consensus       196 ~A-----~~~~~~m-~~~p-~~~~~~~li~~~~~~g--~~~~a~~~~~--~~~~~~~~~~~~l~~~~~~~g---------  255 (410)
                      +|     +..|++. .+.| +...|..+...+...|  ++++|...+.  +..|.++..+..|..+|.+.|         
T Consensus       253 eA~~~~el~~~~~Al~l~P~~~~a~~~l~~ll~~~g~~~~~~a~~~~~~~~~~p~~~~al~~La~~~~~~~~~~~~~~~~  332 (382)
T 2h6f_A          253 RAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKED  332 (382)
T ss_dssp             HHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTTCGGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHHHHHTTCSSHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHccCccchHHHHHHHHHhccCCCCHHHHHHHHHHHHHHhcccccchHH
Confidence            77     4667665 4556 5678988888888888  6888888744  445666667888999998874         


Q ss_pred             ChhHHHHHHHHH-HhC
Q 040371          256 RWDTAENVREIM-KKK  270 (410)
Q Consensus       256 ~~~~a~~~~~~m-~~~  270 (410)
                      ..++|.++++++ .+.
T Consensus       333 ~~~~A~~~~~~l~~~~  348 (382)
T 2h6f_A          333 ILNKALELCEILAKEK  348 (382)
T ss_dssp             HHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHh
Confidence            358999999998 443

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.39  E-value=2.7e-10  Score=103.58  Aligned_cols=232  Identities=14%  Similarity=0.060  Sum_probs=173.8

Q ss_pred             hhHHHHHHHHHHHc----CCH----hHHHHHHHHHHHCCCCCCHHHHHHHHHHHH-------hhCCH-------HHHHHH
Q 040371            6 VVSWNSMIGGFVRN----ARF----DEALRFFREMLSSKVEPDKFTFASVIYGCA-------RLGAL-------NHAYWV   63 (410)
Q Consensus         6 ~~~~n~li~~~~~~----g~~----~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~-------~~~~~-------~~a~~~   63 (410)
                      ...|...+.--.++    ++.    ++|+.+|++.+... +-+...|..+...+.       ..|++       ++|..+
T Consensus         8 ~~~W~~yi~~E~~~~~~~~~~~~~~~~a~~~~~~al~~~-p~~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~   86 (308)
T 2ond_A            8 VDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLVL-GHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANI   86 (308)
T ss_dssp             HHHHHHHHHHHHTCTTCCCCHHHHHHHHHHHHHHHHHHH-TTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCcccCCchHHHHHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHH
Confidence            45688887766554    233    68889999998752 446678887777765       35775       899999


Q ss_pred             HHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-Chh-hHHHHHHHHHHcCChHHHHHHHHHHHHCCCC
Q 040371           64 HNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVS-VWNAMISGVAIHGLAADASAIFTKMEMFNVL  139 (410)
Q Consensus        64 ~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~-~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  139 (410)
                      +++.++.-.+.+...|..++..+.+.|++++|+++|++..+  | +.. .|..+...+.+.|+.++|..+|++..+.. +
T Consensus        87 ~~rAl~~~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-p  165 (308)
T 2ond_A           87 YERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDA-R  165 (308)
T ss_dssp             HHHHHTTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTST-T
T ss_pred             HHHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHhccccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-C
Confidence            99999842244677899999999999999999999998764  3 343 89999999999999999999999998753 2


Q ss_pred             CCHHHHHHHHHHHH-ccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-C---CCC--CHHH
Q 040371          140 PDSITFLGLLTACS-HCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-T---MEP--DVVV  212 (410)
Q Consensus       140 p~~~t~~~ll~a~~-~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~---~~p--~~~~  212 (410)
                      ++...|........ ..|+.++|..+|+...+..  +.+...|..++..+.+.|++++|..+|++. .   ..|  ....
T Consensus       166 ~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~--p~~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l  243 (308)
T 2ond_A          166 TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEI  243 (308)
T ss_dssp             CCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH--TTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHH
T ss_pred             CCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC--CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHH
Confidence            34444543333322 3699999999999988642  235788899999999999999999999887 2   344  3667


Q ss_pred             HHHHHHHHHhcCchhHHHHH---HHhhccCCC
Q 040371          213 WRALLSACRTFKRLELGEVA---IVNISRLMG  241 (410)
Q Consensus       213 ~~~li~~~~~~g~~~~a~~~---~~~~~~~~~  241 (410)
                      |..++......|+.+.|..+   ..+..|.+.
T Consensus       244 ~~~~~~~~~~~g~~~~a~~~~~~a~~~~p~~~  275 (308)
T 2ond_A          244 WARFLAFESNIGDLASILKVEKRRFTAFREEY  275 (308)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHTTTTT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHccccc
Confidence            88888888888888888887   444555543

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.39  E-value=2.1e-09  Score=104.26  Aligned_cols=254  Identities=9%  Similarity=-0.082  Sum_probs=174.1

Q ss_pred             ChhHHHHHHHHHHH----cCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh----hCCHHHHHHHHHHHHHcCCCccH
Q 040371            5 DVVSWNSMIGGFVR----NARFDEALRFFREMLSSKVEPDKFTFASVIYGCAR----LGALNHAYWVHNLIIEKKIELNF   76 (410)
Q Consensus         5 ~~~~~n~li~~~~~----~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~----~~~~~~a~~~~~~~~~~g~~~~~   76 (410)
                      |..++..+-..|..    .+++++|+..|++..+.|   +...+..+...+..    .++.++|.+.|++..+.|   +.
T Consensus        38 ~~~a~~~lg~~y~~g~~~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~  111 (490)
T 2xm6_A           38 EAKAQLELGYRYFQGNETTKDLTQAMDWFRRAAEQG---YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LP  111 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             CHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CH
Confidence            45566667777777    788888888888877654   55666777777777    778888888888887765   55


Q ss_pred             HHHHHHHHHHHh----cCCHHHHHHHHHhcccC-ChhhHHHHHHHHHH----cCChHHHHHHHHHHHHCCCCCCHHHHHH
Q 040371           77 ILSAALIDMYSK----CGKIQMAKEVFDTVQRN-DVSVWNAMISGVAI----HGLAADASAIFTKMEMFNVLPDSITFLG  147 (410)
Q Consensus        77 ~~~~~li~~y~~----~g~~~~A~~~f~~m~~~-~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~  147 (410)
                      ..+..|..+|..    .+++++|.+.|++..+. +..++..+...|..    .++.++|++.|++..+.|   +...+..
T Consensus       112 ~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~---~~~a~~~  188 (490)
T 2xm6_A          112 QAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQGRDSGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQG---NVWSCNQ  188 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHH
Confidence            666777777777    67888888888776543 55677777777776    677888888888777654   4556666


Q ss_pred             HHHHHHc----cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHh----cCCHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 040371          148 LLTACSH----CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGR----AGHIEEAYGLITSMTMEPDVVVWRALLSA  219 (410)
Q Consensus       148 ll~a~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~li~~  219 (410)
                      +...+..    .++.++|...|+...+. +   +...+..+...|..    .+++++|..+|++.-...+...+..+-..
T Consensus       189 Lg~~y~~g~g~~~~~~~A~~~~~~a~~~-~---~~~a~~~lg~~y~~g~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~  264 (490)
T 2xm6_A          189 LGYMYSRGLGVERNDAISAQWYRKSATS-G---DELGQLHLADMYYFGIGVTQDYTQSRVLFSQSAEQGNSIAQFRLGYI  264 (490)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHhcCCCCCcCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            6666666    67788888888777643 2   45566667777765    67777777777776222345555555555


Q ss_pred             HHh----cCchhHHHHHHHh-hccCCCchHHHHHHHHHhc-----CChhHHHHHHHHHHhCC
Q 040371          220 CRT----FKRLELGEVAIVN-ISRLMGGDYVLLSNMYCYL-----KRWDTAENVREIMKKKG  271 (410)
Q Consensus       220 ~~~----~g~~~~a~~~~~~-~~~~~~~~~~~l~~~~~~~-----g~~~~a~~~~~~m~~~g  271 (410)
                      +..    .++.++|...+.+ ....++..+..|..+|...     ++.++|...+++..+.|
T Consensus       265 y~~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~~~~g~~~~~~~A~~~~~~a~~~~  326 (490)
T 2xm6_A          265 LEQGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHLYDKGAEGVAKNREQAISWYTKSAEQG  326 (490)
T ss_dssp             HHHTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHCBTTBCCCHHHHHHHHHHHHHTT
T ss_pred             HHCCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCCcCCHHHHHHHHHHHHhcC
Confidence            555    6777777776332 2234445566677777666     67777777777766654

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.38  E-value=4e-10  Score=108.46  Aligned_cols=264  Identities=11%  Similarity=0.033  Sum_probs=191.4

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHC-----C--CCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC------
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSS-----K--VEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKK------   71 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~-----g--~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g------   71 (410)
                      +..||.|-..|...|++++|++.|++..+.     +  ..| ...+|..+..++...|++++|...++++.+..      
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            457999999999999999999999887541     1  123 45689999999999999999999999887531      


Q ss_pred             C-CccHHHHHHHHHHHHhcC--CHHHHHHHHHhccc--C-ChhhHHHHHHH---HHHcCChHHHHHHHHHHHHCCCCCCH
Q 040371           72 I-ELNFILSAALIDMYSKCG--KIQMAKEVFDTVQR--N-DVSVWNAMISG---VAIHGLAADASAIFTKMEMFNVLPDS  142 (410)
Q Consensus        72 ~-~~~~~~~~~li~~y~~~g--~~~~A~~~f~~m~~--~-~~~~~~~li~~---~~~~g~~~~A~~l~~~m~~~g~~p~~  142 (410)
                      . .....+++.+..++.+.|  ++++|...|++..+  | +...+..+...   +...++.++|++.|++..+.. +.+.
T Consensus       131 ~~~~~~~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p~~~  209 (472)
T 4g1t_A          131 YRIESPELDCEEGWTRLKCGGNQNERAKVCFEKALEKKPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-PDNQ  209 (472)
T ss_dssp             SCCCCHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-SSCH
T ss_pred             cchhhHHHHHHHHHHHHHHccccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-Ccch
Confidence            1 123566666666666654  69999999998763  4 45556555544   345678889999999887742 2245


Q ss_pred             HHHHHHHHHHHc----cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHH
Q 040371          143 ITFLGLLTACSH----CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRAL  216 (410)
Q Consensus       143 ~t~~~ll~a~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~l  216 (410)
                      .++..+...+..    .|..++|.++++.....  .+.+...+..+...|.+.|++++|...+++. ...|+ ..++..+
T Consensus       210 ~~~~~l~~~~~~~~~~~~~~~~a~~~~~~al~~--~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l  287 (472)
T 4g1t_A          210 YLKVLLALKLHKMREEGEEEGEGEKLVEEALEK--APGVTDVLRSAAKFYRRKDEPDKAIELLKKALEYIPNNAYLHCQI  287 (472)
T ss_dssp             HHHHHHHHHHHHCC------CHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHh--CccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHhCCChHHHHHHH
Confidence            555555545444    46788999999988753  2345778899999999999999999999987 44564 5556555


Q ss_pred             HHHHHhc-------------------CchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 040371          217 LSACRTF-------------------KRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       217 i~~~~~~-------------------g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  272 (410)
                      -..+...                   +..+.|...   ..+..|.+...+..+..+|...|++++|.+.|++..+...
T Consensus       288 g~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~  365 (472)
T 4g1t_A          288 GCCYRAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEANDNLFRVCSILASLHALADQYEEAEYYFQKEFSKEL  365 (472)
T ss_dssp             HHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHCTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCC
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhcCCchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCC
Confidence            4444321                   224445544   4566788889999999999999999999999999877654

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.36  E-value=5.4e-12  Score=114.07  Aligned_cols=165  Identities=11%  Similarity=0.086  Sum_probs=103.8

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHC-------CCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc------CC
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSS-------KVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK------KI   72 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~-------g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~------g~   72 (410)
                      ..+|..+...|...|++++|+.+|+++.+.       ..+....++..+...+...|++++|...++.+++.      +-
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            456777888888888888888888877652       12223456667777777778888887777777654      21


Q ss_pred             -CccHHHHHHHHHHHHhcCCHHHHHHHHHhccc-------C----ChhhHHHHHHHHHHcCChHHHHHHHHHHHHC----
Q 040371           73 -ELNFILSAALIDMYSKCGKIQMAKEVFDTVQR-------N----DVSVWNAMISGVAIHGLAADASAIFTKMEMF----  136 (410)
Q Consensus        73 -~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-------~----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----  136 (410)
                       +....++..+...|...|++++|...|++..+       +    ...+|..+...|...|++++|++.|++....    
T Consensus       107 ~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~  186 (311)
T 3nf1_A          107 HPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTK  186 (311)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence             22355667777777777777777777765542       1    2235566666666666666666666666543    


Q ss_pred             --CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhhh
Q 040371          137 --NVLPD-SITFLGLLTACSHCGLVEEGRKYFDHMRS  170 (410)
Q Consensus       137 --g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~  170 (410)
                        +..|+ ..++..+...+...|++++|..+|+.+.+
T Consensus       187 ~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  223 (311)
T 3nf1_A          187 LGPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILT  223 (311)
T ss_dssp             SCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             hCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence              11222 23455555666666666666666666553

>2xm6_A Protein corresponding to locus C5321 from CFT073 strain; unknown function, SEL1-like repeats; 1.68A {Escherichia coli}

Probab=99.36  E-value=2.9e-09  Score=103.27  Aligned_cols=254  Identities=11%  Similarity=-0.034  Sum_probs=157.4

Q ss_pred             ChhHHHHHHHHHHH----cCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh----hCCHHHHHHHHHHHHHcCCCccH
Q 040371            5 DVVSWNSMIGGFVR----NARFDEALRFFREMLSSKVEPDKFTFASVIYGCAR----LGALNHAYWVHNLIIEKKIELNF   76 (410)
Q Consensus         5 ~~~~~n~li~~~~~----~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~----~~~~~~a~~~~~~~~~~g~~~~~   76 (410)
                      +...+..|-..|..    .+++++|++.|++..+.|   +...+..+...+..    .+++++|...+++..+.|   +.
T Consensus        74 ~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~  147 (490)
T 2xm6_A           74 YTPAEYVLGLRYMNGEGVPQDYAQAVIWYKKAALKG---LPQAQQNLGVMYHEGNGVKVDKAESVKWFRLAAEQG---RD  147 (490)
T ss_dssp             CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CH
T ss_pred             CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCC---CH
Confidence            44566667777777    777888888887777654   45566666666666    667788888887777765   45


Q ss_pred             HHHHHHHHHHHh----cCCHHHHHHHHHhccc-CChhhHHHHHHHHHH----cCChHHHHHHHHHHHHCCCCCCHHHHHH
Q 040371           77 ILSAALIDMYSK----CGKIQMAKEVFDTVQR-NDVSVWNAMISGVAI----HGLAADASAIFTKMEMFNVLPDSITFLG  147 (410)
Q Consensus        77 ~~~~~li~~y~~----~g~~~~A~~~f~~m~~-~~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~  147 (410)
                      ..+..|..+|..    .++.++|.+.|++..+ .+..++..+...|..    .++.++|++.|++..+.|   +...+..
T Consensus       148 ~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~y~~g~g~~~~~~~A~~~~~~a~~~~---~~~a~~~  224 (490)
T 2xm6_A          148 SGQQSMGDAYFEGDGVTRDYVMAREWYSKAAEQGNVWSCNQLGYMYSRGLGVERNDAISAQWYRKSATSG---DELGQLH  224 (490)
T ss_dssp             HHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHCC---CHHHHHH
Confidence            666677777776    6777777777776543 356667777777766    677777777777776654   3445555


Q ss_pred             HHHHHHc----cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHh----cCCHHHHHHHHHhCCCCCCHHHHHHHHHH
Q 040371          148 LLTACSH----CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGR----AGHIEEAYGLITSMTMEPDVVVWRALLSA  219 (410)
Q Consensus       148 ll~a~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~li~~  219 (410)
                      +...+..    .++.++|..+|+...+. +   +...+..+..+|..    .+++++|..+|++.-..-+...+..+-..
T Consensus       225 lg~~y~~g~g~~~~~~~A~~~~~~a~~~-~---~~~a~~~lg~~y~~g~~~~~d~~~A~~~~~~a~~~~~~~a~~~Lg~~  300 (490)
T 2xm6_A          225 LADMYYFGIGVTQDYTQSRVLFSQSAEQ-G---NSIAQFRLGYILEQGLAGAKEPLKALEWYRKSAEQGNSDGQYYLAHL  300 (490)
T ss_dssp             HHHHHHHTSSSCCCHHHHHHHHHHHHTT-T---CHHHHHHHHHHHHHTTTSSCCHHHHHHHHHHHHTTTCHHHHHHHHHH
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence            5555554    56777777777766542 2   34455556666665    66677777766665212244455555555


Q ss_pred             HHhc-----CchhHHHHHHHh-hccCCCchHHHHHHHHHhcC---ChhHHHHHHHHHHhCC
Q 040371          220 CRTF-----KRLELGEVAIVN-ISRLMGGDYVLLSNMYCYLK---RWDTAENVREIMKKKG  271 (410)
Q Consensus       220 ~~~~-----g~~~~a~~~~~~-~~~~~~~~~~~l~~~~~~~g---~~~~a~~~~~~m~~~g  271 (410)
                      +...     +++++|...+.+ ....++..+..|..+|...|   +.++|.+.+++..+.|
T Consensus       301 y~~~~~g~~~~~~~A~~~~~~a~~~~~~~a~~~lg~~y~~~g~~~~~~~A~~~~~~a~~~~  361 (490)
T 2xm6_A          301 YDKGAEGVAKNREQAISWYTKSAEQGDATAQANLGAIYFRLGSEEEHKKAVEWFRKAAAKG  361 (490)
T ss_dssp             HHHCBTTBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSCCHHHHHHHHHHHHHHHHTT
T ss_pred             HHcCCCCCcCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHCC
Confidence            5544     566666666221 22233344555555555544   4556666666555543

>3nf1_A KLC 1, kinesin light chain 1; TPR, structural genomics consortium (SGC), motor PR transport protein; 2.80A {Homo sapiens}

Probab=99.34  E-value=2.7e-11  Score=109.43  Aligned_cols=192  Identities=15%  Similarity=0.137  Sum_probs=145.4

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHc-------CCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc-------C--
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEK-------KIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR-------N--  105 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~-------g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-------~--  105 (410)
                      .++..+...+...|++++|..+++.+.+.       ..+....++..+...|...|++++|...|++...       +  
T Consensus        28 ~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~  107 (311)
T 3nf1_A           28 RTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAANLLNDALAIREKTLGKDH  107 (311)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCC
Confidence            45677778888899999999999888774       3344567788888999999999999988887642       1  


Q ss_pred             --ChhhHHHHHHHHHHcCChHHHHHHHHHHHHC------CCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhc----
Q 040371          106 --DVSVWNAMISGVAIHGLAADASAIFTKMEMF------NVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRY----  172 (410)
Q Consensus       106 --~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~------g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~----  172 (410)
                        ...+|..+...|...|++++|...|++....      +..| ....+..+...+...|++++|..+|+.+.+..    
T Consensus       108 ~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~~~~~  187 (311)
T 3nf1_A          108 PAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKDHPDVAKQLNNLALLCQNQGKYEEVEYYYQRALEIYQTKL  187 (311)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHTS
T ss_pred             hHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHh
Confidence              2457888888899999999999999888764      2223 34567778888889999999999998876531    


Q ss_pred             -CCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhCC---------------------------------------------
Q 040371          173 -SIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSMT---------------------------------------------  205 (410)
Q Consensus       173 -~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m~---------------------------------------------  205 (410)
                       +..| ....+..+...|.+.|++++|.+.+++.-                                             
T Consensus       188 ~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~  267 (311)
T 3nf1_A          188 GPDDPNVAKTKNNLASCYLKQGKFKQAETLYKEILTRAHEREFGSVDDENKPIWMHAEEREECKGKQKDGTSFGEYGGWY  267 (311)
T ss_dssp             CTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHC------CCHHHHHHHHHHC-------CCSCCCC---
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHhcCchhhHHHHHHHHHHH
Confidence             1122 24578888888999999999988887651                                             


Q ss_pred             -----CCC-CHHHHHHHHHHHHhcCchhHHHHHH
Q 040371          206 -----MEP-DVVVWRALLSACRTFKRLELGEVAI  233 (410)
Q Consensus       206 -----~~p-~~~~~~~li~~~~~~g~~~~a~~~~  233 (410)
                           ..| +..+|..+...|...|++++|...+
T Consensus       268 ~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~  301 (311)
T 3nf1_A          268 KACKVDSPTVTTTLKNLGALYRRQGKFEAAETLE  301 (311)
T ss_dssp             ------CHHHHHHHHHHHHHHHHHTCHHHHHHHH
T ss_pred             hhcCCCCchHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence                 123 3456888888899999999999883

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.34  E-value=3.4e-10  Score=94.28  Aligned_cols=163  Identities=13%  Similarity=0.043  Sum_probs=113.6

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +...|..+-..|.+.|++++|++.|++.++.. +-+..++..+..++...|+++.|...+....... +.+..++..+..
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~-~~~~~~~~~~~~   81 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLD-TTSAEAYYILGS   81 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcC-chhHHHHHHHHH
Confidence            45667778888888888888888888777642 2355677777777777788888877777777664 345666667777


Q ss_pred             HHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a  161 (410)
                      .+...++++.|...+++...   .+..+|..+...|.+.|++++|++.|++..+.. +.+..++..+..++.+.|++++|
T Consensus        82 ~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~~lg~~~~~~g~~~~A  160 (184)
T 3vtx_A           82 ANFMIDEKQAAIDALQRAIALNTVYADAYYKLGLVYDSMGEHDKAIEAYEKTISIK-PGFIRAYQSIGLAYEGKGLRDEA  160 (184)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHhCccchHHHHHHHHHHHHhCCchhHHHHHHHHHHhc-chhhhHHHHHHHHHHHCCCHHHH
Confidence            77777777777777776542   345667777777777777777777777776642 22455666677777777777777


Q ss_pred             HHHHHHhhh
Q 040371          162 RKYFDHMRS  170 (410)
Q Consensus       162 ~~~~~~m~~  170 (410)
                      ...|+...+
T Consensus       161 ~~~~~~al~  169 (184)
T 3vtx_A          161 VKYFKKALE  169 (184)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHh
Confidence            777777653

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.32  E-value=5.7e-10  Score=109.42  Aligned_cols=144  Identities=16%  Similarity=0.116  Sum_probs=94.0

Q ss_pred             cCCHH-------HHHHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-H-HHHHHHHHHHHhc
Q 040371          155 CGLVE-------EGRKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-V-VVWRALLSACRTF  223 (410)
Q Consensus       155 ~g~~~-------~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~-~~~~~li~~~~~~  223 (410)
                      .|+++       +|..+|+...+  .+.| +...|..++..+.+.|++++|..+|++. ...|+ . ..|..+...+.+.
T Consensus       292 ~g~~~~a~~~~~~A~~~~~~Al~--~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~  369 (530)
T 2ooe_A          292 KGDMNNAKLFSDEAANIYERAIS--TLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRA  369 (530)
T ss_dssp             TTCCHHHHHHHHHHHHHHHHHTT--TTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHH
T ss_pred             ccchhhhhhhhHHHHHHHHHHHH--HhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHh
Confidence            57766       78888888774  2334 4678888888888888888888888876 44554 2 4788888888888


Q ss_pred             CchhHHHHHHHh---hccCCCchHHHHHHH-HHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCcc
Q 040371          224 KRLELGEVAIVN---ISRLMGGDYVLLSNM-YCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPE  299 (410)
Q Consensus       224 g~~~~a~~~~~~---~~~~~~~~~~~l~~~-~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~  299 (410)
                      |+++.|..++.+   ..|.+...|...+.+ +...|+.++|..+|+...+..  |+....|..       ++.-....|+
T Consensus       370 ~~~~~A~~~~~~Al~~~~~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~--p~~~~~~~~-------~~~~~~~~g~  440 (530)
T 2ooe_A          370 EGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLA-------YIDYLSHLNE  440 (530)
T ss_dssp             HHHHHHHHHHHHHHTCTTCCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH--TTCHHHHHH-------HHHHHTTTTC
T ss_pred             cCHHHHHHHHHHHHhccCCchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHC--CCCHHHHHH-------HHHHHHhCCC
Confidence            888888888332   233333334333323 335788888888888776542  333233421       1222345788


Q ss_pred             HHHHHHHHHH
Q 040371          300 AQAIDKILGS  309 (410)
Q Consensus       300 ~~~~~~~l~~  309 (410)
                      .++|...+++
T Consensus       441 ~~~Ar~~~~~  450 (530)
T 2ooe_A          441 DNNTRVLFER  450 (530)
T ss_dssp             HHHHHHHHHH
T ss_pred             HhhHHHHHHH
Confidence            8888888874

>3vtx_A MAMA; tetratricopeptide repeats (TPR) containing protein, peptide protein, protein binding; 1.75A {Candidatus magnetobacterium bavaricum} PDB: 3vty_A

Probab=99.31  E-value=3.7e-10  Score=94.05  Aligned_cols=167  Identities=11%  Similarity=0.028  Sum_probs=132.8

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISG  116 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~  116 (410)
                      +...|..+..++...|++++|.+.|++.++.. +.+..++..+...|.+.|++++|...+.....   .+...|..+...
T Consensus         4 ~~~iy~~lG~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~   82 (184)
T 3vtx_A            4 TTTIYMDIGDKKRTKGDFDGAIRAYKKVLKAD-PNNVETLLKLGKTYMDIGLPNDAIESLKKFVVLDTTSAEAYYILGSA   82 (184)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCchhHHHHHHHHHH
Confidence            56788888899999999999999999988875 45788888889999999999999988887653   356677778888


Q ss_pred             HHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHH
Q 040371          117 VAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEE  196 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~  196 (410)
                      +...++++.|.+.+.+..... +-+...+..+...+.+.|++++|.+.|+...+.  -+.+...|..+...|.+.|++++
T Consensus        83 ~~~~~~~~~a~~~~~~a~~~~-~~~~~~~~~lg~~~~~~g~~~~A~~~~~~~l~~--~p~~~~~~~~lg~~~~~~g~~~~  159 (184)
T 3vtx_A           83 NFMIDEKQAAIDALQRAIALN-TVYADAYYKLGLVYDSMGEHDKAIEAYEKTISI--KPGFIRAYQSIGLAYEGKGLRDE  159 (184)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHHHHHHHhCCchhHHHHHHHHHHh--cchhhhHHHHHHHHHHHCCCHHH
Confidence            888899999999988887642 235667778888888899999999999888753  13356788888888999999999


Q ss_pred             HHHHHHhC-CCCCCH
Q 040371          197 AYGLITSM-TMEPDV  210 (410)
Q Consensus       197 A~~~~~~m-~~~p~~  210 (410)
                      |.+.|++. ...|+.
T Consensus       160 A~~~~~~al~~~p~~  174 (184)
T 3vtx_A          160 AVKYFKKALEKEEKK  174 (184)
T ss_dssp             HHHHHHHHHHTTHHH
T ss_pred             HHHHHHHHHhCCccC
Confidence            98888876 445543

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.31  E-value=2.9e-11  Score=116.88  Aligned_cols=205  Identities=6%  Similarity=-0.043  Sum_probs=167.8

Q ss_pred             HHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCH-HHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHH
Q 040371           57 LNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKI-QMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTK  132 (410)
Q Consensus        57 ~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~-~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~  132 (410)
                      ++.+.+.++...+.. +.+...+..+...|...|++ ++|.+.|++..+  | +..+|..+...|.+.|++++|++.|++
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            455566666555432 45788899999999999999 999999988753  3 577899999999999999999999999


Q ss_pred             HHHCCCCCCHHHHHHHHHHHHcc---------CCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhc--------CCHH
Q 040371          133 MEMFNVLPDSITFLGLLTACSHC---------GLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRA--------GHIE  195 (410)
Q Consensus       133 m~~~g~~p~~~t~~~ll~a~~~~---------g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~--------g~~~  195 (410)
                      ..+.  .|+...+..+...+...         |++++|...|+...+.  -+.+...|..+..+|...        |+++
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            8874  57778888888888888         9999999999998853  233477888899999888        8999


Q ss_pred             HHHHHHHhC-CCCC----CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHH
Q 040371          196 EAYGLITSM-TMEP----DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREI  266 (410)
Q Consensus       196 ~A~~~~~~m-~~~p----~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  266 (410)
                      +|.+.|++. ...|    +...|..+-..+...|++++|...   ..++.|.+...+..+..++...|++++|.+.+.+
T Consensus       239 ~A~~~~~~al~~~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~a~~~l~~~~~~lg~~~eAi~~~~~  317 (474)
T 4abn_A          239 QALSAYAQAEKVDRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAWPEPQQREQQLLEFLSRLTSLLESKGK  317 (474)
T ss_dssp             HHHHHHHHHHHHCGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHhCCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            999999887 4455    678899999999999999999998   5567788888888999999999999988875543

>2ond_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 2.80A {Mus musculus} SCOP: a.118.8.7

Probab=99.28  E-value=9.1e-10  Score=100.03  Aligned_cols=197  Identities=11%  Similarity=0.079  Sum_probs=157.5

Q ss_pred             ChhHHHHHHHHHHH-------cCCH-------hHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVR-------NARF-------DEALRFFREMLSSKVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIE   69 (410)
Q Consensus         5 ~~~~~n~li~~~~~-------~g~~-------~~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~   69 (410)
                      +...|..+...+.+       .|++       ++|..+|++..+. +.| +...|..+...+...|+++.|.++|+++++
T Consensus        49 ~~~~w~~~~~~~~~~~~~l~~~g~~~~~~~~~~~A~~~~~rAl~~-~~p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~  127 (308)
T 2ond_A           49 HPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIST-LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLA  127 (308)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTT-TTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHhchhhhhccchhhcccchHHHHHHHHHHHHH-hCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHHh
Confidence            45678888887764       5886       8999999999873 345 556899999999999999999999999998


Q ss_pred             cCCCccHH-HHHHHHHHHHhcCCHHHHHHHHHhcccC---ChhhHHHHHHHHH-HcCChHHHHHHHHHHHHCCCCCCHHH
Q 040371           70 KKIELNFI-LSAALIDMYSKCGKIQMAKEVFDTVQRN---DVSVWNAMISGVA-IHGLAADASAIFTKMEMFNVLPDSIT  144 (410)
Q Consensus        70 ~g~~~~~~-~~~~li~~y~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~-~~g~~~~A~~l~~~m~~~g~~p~~~t  144 (410)
                      .. +.+.. +|..++..+.+.|++++|+.+|++..+.   +...|........ ..|+.++|..+|++..+.. +-+...
T Consensus       128 ~~-p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~a~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~  205 (308)
T 2ond_A          128 IE-DIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY-GDIPEY  205 (308)
T ss_dssp             SS-SSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHH-TTCHHH
T ss_pred             cc-ccCccHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHH
Confidence            53 22343 8999999999999999999999988753   3344443333222 2699999999999998752 225677


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhhhhcCCCC--ChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          145 FLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP--QLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       145 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~--~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      +..++..+.+.|++++|..+|+...+...+.|  ....|..++..+.+.|+.++|..+++++
T Consensus       206 ~~~~~~~~~~~g~~~~A~~~~~~al~~~~l~p~~~~~l~~~~~~~~~~~g~~~~a~~~~~~a  267 (308)
T 2ond_A          206 VLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKVEKRR  267 (308)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            88889999999999999999999986423455  3678999999999999999999999887

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=99.28  E-value=9.3e-09  Score=95.73  Aligned_cols=261  Identities=13%  Similarity=0.019  Sum_probs=185.5

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHH----HHHHHHHHHHhhCCHHHHHHHHHHHHHc----CCC-ccHHHH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKF----TFASVIYGCARLGALNHAYWVHNLIIEK----KIE-LNFILS   79 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~----t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~~-~~~~~~   79 (410)
                      +......+...|++++|...+++.....-..+..    ++..+...+...|+++.|.+.+++..+.    |.. ....+.
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            3444556778999999999999988753222222    4566667788999999999999988764    211 112346


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhccc----------C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCC--C--CHHH
Q 040371           80 AALIDMYSKCGKIQMAKEVFDTVQR----------N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVL--P--DSIT  144 (410)
Q Consensus        80 ~~li~~y~~~g~~~~A~~~f~~m~~----------~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~--p--~~~t  144 (410)
                      +.+...|...|++++|...|++...          + ...++..+...|...|++++|...+++.......  |  ...+
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            7788899999999999999987642          1 1235667788899999999999999988764221  1  2345


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHH-----HHHHHHHhcCCHHHHHHHHHhC-CCCCC-----HHHH
Q 040371          145 FLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYG-----AMVDLLGRAGHIEEAYGLITSM-TMEPD-----VVVW  213 (410)
Q Consensus       145 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~-----~li~~~~~~g~~~~A~~~~~~m-~~~p~-----~~~~  213 (410)
                      +..+...+...|++++|...++.......-......+.     ..+..+...|++++|...+++. ...|.     ...+
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            77788888999999999999998874311111111222     2334578999999999999987 22221     3356


Q ss_pred             HHHHHHHHhcCchhHHHHHHHhh---ccC-----C-CchHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040371          214 RALLSACRTFKRLELGEVAIVNI---SRL-----M-GGDYVLLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       214 ~~li~~~~~~g~~~~a~~~~~~~---~~~-----~-~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                      ..+...+...|++++|...+.+.   .+.     . ...+..+..+|...|+.++|...+++...
T Consensus       257 ~~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~al~  321 (373)
T 1hz4_A          257 RNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  321 (373)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            67778889999999999883322   111     1 12566678889999999999999988754

>4abn_A Tetratricopeptide repeat protein 5; P53 cofactor, stress-response, DNA repair, gene regulation; 2.05A {Mus musculus}

Probab=99.26  E-value=1.8e-10  Score=111.27  Aligned_cols=209  Identities=10%  Similarity=-0.021  Sum_probs=172.3

Q ss_pred             CCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCH-HHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHH
Q 040371           20 ARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGAL-NHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEV   98 (410)
Q Consensus        20 g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~-~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~   98 (410)
                      ..+++++..+++.... .+.+...+..+..++...|++ ++|.+.++++++.. +.+...+..+...|.+.|++++|.+.
T Consensus        82 ~~~~~al~~l~~~~~~-~~~~a~~~~~lg~~~~~~g~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~  159 (474)
T 4abn_A           82 EEMEKTLQQMEEVLGS-AQVEAQALMLKGKALNVTPDYSPEAEVLLSKAVKLE-PELVEAWNQLGEVYWKKGDVTSAHTC  159 (474)
T ss_dssp             HHHHHHHHHHHHHHTT-CCCCHHHHHHHHHHHTSSSSCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcc-CchhHHHHHHHHHHHHhccccHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence            4477888888877654 244777888888999999999 99999999998875 44688999999999999999999999


Q ss_pred             HHhcc--cCChhhHHHHHHHHHHc---------CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc--------CCHH
Q 040371           99 FDTVQ--RNDVSVWNAMISGVAIH---------GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHC--------GLVE  159 (410)
Q Consensus        99 f~~m~--~~~~~~~~~li~~~~~~---------g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~--------g~~~  159 (410)
                      |++..  .|+...|..+...|...         |++++|++.|++..+.. +-+...+..+..++...        |+++
T Consensus       160 ~~~al~~~p~~~~~~~lg~~~~~~~~~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~~~~g~~~  238 (474)
T 4abn_A          160 FSGALTHCKNKVSLQNLSMVLRQLQTDSGDEHSRHVMDSVRQAKLAVQMD-VLDGRSWYILGNAYLSLYFNTGQNPKISQ  238 (474)
T ss_dssp             HHHHHTTCCCHHHHHHHHHHHTTCCCSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHhhCCCHHHHHHHHHHHHHhccCChhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHHHHhhccccchHH
Confidence            99876  46677888888889888         99999999999988753 23567788888888888        8999


Q ss_pred             HHHHHHHHhhhhcCCCC----ChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHHH
Q 040371          160 EGRKYFDHMRSRYSIQP----QLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVAI  233 (410)
Q Consensus       160 ~a~~~~~~m~~~~~~~~----~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~~  233 (410)
                      +|...|+...+.   .|    +...|..+...|.+.|++++|.+.|++. ...| +...|..+...+...|++++|....
T Consensus       239 ~A~~~~~~al~~---~p~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~p~~~~a~~~l~~~~~~lg~~~eAi~~~  315 (474)
T 4abn_A          239 QALSAYAQAEKV---DRKASSNPDLHLNRATLHKYEESYGEALEGFSQAAALDPAWPEPQQREQQLLEFLSRLTSLLESK  315 (474)
T ss_dssp             HHHHHHHHHHHH---CGGGGGCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHh---CCCcccCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            999999998853   33    6788999999999999999999999887 4445 4667888888888899998888763


Q ss_pred             H
Q 040371          234 V  234 (410)
Q Consensus       234 ~  234 (410)
                      .
T Consensus       316 ~  316 (474)
T 4abn_A          316 G  316 (474)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.26  E-value=2.1e-09  Score=111.98  Aligned_cols=227  Identities=14%  Similarity=0.192  Sum_probs=137.3

Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC
Q 040371           11 SMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG   90 (410)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g   90 (410)
                      -+...+...|.+++|..+|++..    . .....+.++.   ..+++++|.++.++.      .+..+|..+..++.+.|
T Consensus      1054 eIA~Iai~lglyEEAf~IYkKa~----~-~~~A~~VLie---~i~nldrAiE~Aerv------n~p~vWsqLAKAql~~G 1119 (1630)
T 1xi4_A         1054 DIANIAISNELFEEAFAIFRKFD----V-NTSAVQVLIE---HIGNLDRAYEFAERC------NEPAVWSQLAKAQLQKG 1119 (1630)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHcC----C-HHHHHHHHHH---HHhhHHHHHHHHHhc------CCHHHHHHHHHHHHhCC
Confidence            34556666777777777776631    0 1111111211   344455554444433      12444445555555555


Q ss_pred             CHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCC--------------------------CCCCHHH
Q 040371           91 KIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFN--------------------------VLPDSIT  144 (410)
Q Consensus        91 ~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g--------------------------~~p~~~t  144 (410)
                      ++++|...|.+.  .|...|.-++..+.+.|++++|++.|...++..                          -.|+...
T Consensus      1120 ~~kEAIdsYiKA--dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~~e~~Idt~LafaYAKl~rleele~fI~~~n~ad 1197 (1630)
T 1xi4_A         1120 MVKEAIDSYIKA--DDPSSYMEVVQAANTSGNWEELVKYLQMARKKARESYVETELIFALAKTNRLAELEEFINGPNNAH 1197 (1630)
T ss_pred             CHHHHHHHHHhc--CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhcccccccHHHHHHHHhhcCHHHHHHHHhCCCHHH
Confidence            555555555332  344444445555555555555555543322211                          1234445


Q ss_pred             HHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcC
Q 040371          145 FLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFK  224 (410)
Q Consensus       145 ~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g  224 (410)
                      +..+...|...|++++|..+|...          ..|..+...|.+.|++++|.+.+++.   .+..+|..+-.+|...|
T Consensus      1198 ~~~iGd~le~eg~YeeA~~~Y~kA----------~ny~rLA~tLvkLge~q~AIEaarKA---~n~~aWkev~~acve~~ 1264 (1630)
T 1xi4_A         1198 IQQVGDRCYDEKMYDAAKLLYNNV----------SNFGRLASTLVHLGEYQAAVDGARKA---NSTRTWKEVCFACVDGK 1264 (1630)
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHhh----------hHHHHHHHHHHHhCCHHHHHHHHHHh---CCHHHHHHHHHHHhhhh
Confidence            556666667777777777777664          26888888888888888888888876   36788888888888888


Q ss_pred             chhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHH
Q 040371          225 RLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIM  267 (410)
Q Consensus       225 ~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m  267 (410)
                      ++..|...... ...++..+..++..|.+.|.+++|..+++.-
T Consensus      1265 Ef~LA~~cgl~-Iiv~~deLeeli~yYe~~G~feEAI~LlE~a 1306 (1630)
T 1xi4_A         1265 EFRLAQMCGLH-IVVHADELEELINYYQDRGYFEELITMLEAA 1306 (1630)
T ss_pred             HHHHHHHHHHh-hhcCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            88888888443 2334556778888999999999999988654

>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=99.26  E-value=6.5e-10  Score=91.91  Aligned_cols=161  Identities=12%  Similarity=0.084  Sum_probs=123.4

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      ..|..+...|...|++++|+..|+++.+.. +.+...+..+..++...|+++.|...++.+.+.. +.+..++..+...|
T Consensus         9 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~   86 (186)
T 3as5_A            9 VYYRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADA-PDNVKVATVLGLTY   86 (186)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHH
Confidence            467788888889999999999998887542 3467778888888888899999998888888764 44677788888888


Q ss_pred             HhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRK  163 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~  163 (410)
                      .+.|++++|.+.|++...   .+...|..+...|...|++++|.+.|++..... +.+...+..+...+...|++++|..
T Consensus        87 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~  165 (186)
T 3as5_A           87 VQVQKYDLAVPLLIKVAEANPINFNVRFRLGVALDNLGRFDEAIDSFKIALGLR-PNEGKVHRAIAFSYEQMGRHEEALP  165 (186)
T ss_dssp             HHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHhcCcHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhcC-ccchHHHHHHHHHHHHcCCHHHHHH
Confidence            888888888888887653   355677777777888888888888888777653 2345667777777777888888888


Q ss_pred             HHHHhhh
Q 040371          164 YFDHMRS  170 (410)
Q Consensus       164 ~~~~m~~  170 (410)
                      .++.+.+
T Consensus       166 ~~~~~~~  172 (186)
T 3as5_A          166 HFKKANE  172 (186)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7777664

>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=99.23  E-value=2.8e-09  Score=111.11  Aligned_cols=232  Identities=10%  Similarity=0.067  Sum_probs=184.2

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +..+|..+-.++.+.|++++|++.|.+.      -|...|..++.+|.+.|+++++.+.+....+..  +++.+.+.++.
T Consensus      1104 ~p~vWsqLAKAql~~G~~kEAIdsYiKA------dD~say~eVa~~~~~lGkyEEAIeyL~mArk~~--~e~~Idt~Laf 1175 (1630)
T 1xi4_A         1104 EPAVWSQLAKAQLQKGMVKEAIDSYIKA------DDPSSYMEVVQAANTSGNWEELVKYLQMARKKA--RESYVETELIF 1175 (1630)
T ss_pred             CHHHHHHHHHHHHhCCCHHHHHHHHHhc------CChHHHHHHHHHHHHcCCHHHHHHHHHHHHhhc--ccccccHHHHH
Confidence            3568999999999999999999999663      377889999999999999999999999888764  45555556999


Q ss_pred             HHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKY  164 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~  164 (410)
                      +|+|.+++++...+.   ..++...|..+...|...|++++|..+|...         ..|..+...+.+.|++++|.+.
T Consensus      1176 aYAKl~rleele~fI---~~~n~ad~~~iGd~le~eg~YeeA~~~Y~kA---------~ny~rLA~tLvkLge~q~AIEa 1243 (1630)
T 1xi4_A         1176 ALAKTNRLAELEEFI---NGPNNAHIQQVGDRCYDEKMYDAAKLLYNNV---------SNFGRLASTLVHLGEYQAAVDG 1243 (1630)
T ss_pred             HHHhhcCHHHHHHHH---hCCCHHHHHHHHHHHHhcCCHHHHHHHHHhh---------hHHHHHHHHHHHhCCHHHHHHH
Confidence            999999999644443   4567778888999999999999999999984         4799999999999999999999


Q ss_pred             HHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHH---HhhccCCC
Q 040371          165 FDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAI---VNISRLMG  241 (410)
Q Consensus       165 ~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~---~~~~~~~~  241 (410)
                      ++...       +..+|..+-.++...|++..|......+  ..+...+..++..|...|.+++|..++   ..+++...
T Consensus      1244 arKA~-------n~~aWkev~~acve~~Ef~LA~~cgl~I--iv~~deLeeli~yYe~~G~feEAI~LlE~aL~LeraH~ 1314 (1630)
T 1xi4_A         1244 ARKAN-------STRTWKEVCFACVDGKEFRLAQMCGLHI--VVHADELEELINYYQDRGYFEELITMLEAALGLERAHM 1314 (1630)
T ss_pred             HHHhC-------CHHHHHHHHHHHhhhhHHHHHHHHHHhh--hcCHHHHHHHHHHHHHcCCHHHHHHHHHHHhccChhHh
Confidence            98764       5678888888888899999888776643  335555668888899999999999883   34455555


Q ss_pred             chHHHHHHHHHhc--CChhHHHHHHH
Q 040371          242 GDYVLLSNMYCYL--KRWDTAENVRE  265 (410)
Q Consensus       242 ~~~~~l~~~~~~~--g~~~~a~~~~~  265 (410)
                      ..|.-|...|++.  ++..++.+.|.
T Consensus      1315 gmftELaiLyaKy~peklmEhlk~f~ 1340 (1630)
T 1xi4_A         1315 GMFTELAILYSKFKPQKMREHLELFW 1340 (1630)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            6676677777654  33444444443

>4g1t_A Interferon-induced protein with tetratricopeptide 2; ISG, all alpha helix, antivirus, antiviral protein; 2.80A {Homo sapiens}

Probab=99.22  E-value=1.3e-09  Score=104.76  Aligned_cols=259  Identities=10%  Similarity=-0.019  Sum_probs=167.1

Q ss_pred             hHHHHHHHHHHHc--CCHhHHHHHHHHHHHCCCCCC-HHHHHHHHHHH---HhhCCHHHHHHHHHHHHHcCCCccHHHHH
Q 040371            7 VSWNSMIGGFVRN--ARFDEALRFFREMLSSKVEPD-KFTFASVIYGC---ARLGALNHAYWVHNLIIEKKIELNFILSA   80 (410)
Q Consensus         7 ~~~n~li~~~~~~--g~~~~a~~l~~~m~~~g~~pd-~~t~~~ll~a~---~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (410)
                      .+|+.+-.++...  +++++|++.|++..+.  .|+ ...+..+..++   ...++.+.|.+.+++.++.. +.+..++.
T Consensus       137 ~~~~~~g~~~~~~~~~~y~~A~~~~~kal~~--~p~~~~~~~~~~~~~~~l~~~~~~~~al~~~~~al~l~-p~~~~~~~  213 (472)
T 4g1t_A          137 ELDCEEGWTRLKCGGNQNERAKVCFEKALEK--KPKNPEFTSGLAIASYRLDNWPPSQNAIDPLRQAIRLN-PDNQYLKV  213 (472)
T ss_dssp             HHHHHHHHHHHHHCTTHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHSCCCCCTHHHHHHHHHHC-SSCHHHHH
T ss_pred             HHHHHHHHHHHHHccccHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhcCchHHHHHHHHHHHHhhcC-CcchHHHH
Confidence            4566555556554  4689999999999874  444 44555544443   45567788888888888875 44666676


Q ss_pred             HHHHHHHhc----CCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHH
Q 040371           81 ALIDMYSKC----GKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD-SITFLGLLTAC  152 (410)
Q Consensus        81 ~li~~y~~~----g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~  152 (410)
                      .+...+.+.    |++++|.+.|++...   .+..+|+.+...|...|++++|++.|++..+.  .|+ ..++..+...+
T Consensus       214 ~l~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~y  291 (472)
T 4g1t_A          214 LLALKLHKMREEGEEEGEGEKLVEEALEKAPGVTDVLRSAAKFYRRKDEPDKAIELLKKALEY--IPNNAYLHCQIGCCY  291 (472)
T ss_dssp             HHHHHHHHCC------CHHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHcCchHHHHHHHHHHHHh--CCChHHHHHHHHHHH
Confidence            666555554    567889999987653   35678899999999999999999999998874  443 45555554444


Q ss_pred             Hc-------------------cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHH
Q 040371          153 SH-------------------CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVV  212 (410)
Q Consensus       153 ~~-------------------~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~  212 (410)
                      ..                   .+..++|...|+...+.  -+.+...+..+...|.+.|++++|...|++. ...|+...
T Consensus       292 ~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~lg~~~~~~~~~~~A~~~~~kaL~~~~~~~~  369 (472)
T 4g1t_A          292 RAKVFQVMNLRENGMYGKRKLLELIGHAVAHLKKADEA--NDNLFRVCSILASLHALADQYEEAEYYFQKEFSKELTPVA  369 (472)
T ss_dssp             HHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHH--CTTTCCCHHHHHHHHHHTTCHHHHHHHHHHHHHSCCCHHH
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHhhHHHHHHHHHHHhhc--CCchhhhhhhHHHHHHHhccHHHHHHHHHHHHhcCCCChH
Confidence            32                   12356777777777643  1234567888899999999999999999876 44444332


Q ss_pred             ----HHHHHH-HHHhcCchhHHHHHH---------------------------HhhccCCCchHHHHHHHHHhcCChhHH
Q 040371          213 ----WRALLS-ACRTFKRLELGEVAI---------------------------VNISRLMGGDYVLLSNMYCYLKRWDTA  260 (410)
Q Consensus       213 ----~~~li~-~~~~~g~~~~a~~~~---------------------------~~~~~~~~~~~~~l~~~~~~~g~~~~a  260 (410)
                          +..+.. .....|+.++|...+                           .+..|.++.+|..|..+|...|++++|
T Consensus       370 ~~~~~~~~~~~~~~~~~~~~~Ai~~y~kal~i~~~~~~~~~~~~~l~~~~~~~l~~~p~~~~~~~~LG~~~~~~g~~~~A  449 (472)
T 4g1t_A          370 KQLLHLRYGNFQLYQMKCEDKAIHHFIEGVKINQKSREKEKMKDKLQKIAKMRLSKNGADSEALHVLAFLQELNEKMQQA  449 (472)
T ss_dssp             HHHHHHHHHHHHHHTSSCHHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHHHHHCC-CTTHHHHHHHHHHHHHHCC--
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHH
Confidence                222222 234567777776651                           133577888999999999999999999


Q ss_pred             HHHHHHHHhCCC
Q 040371          261 ENVREIMKKKGV  272 (410)
Q Consensus       261 ~~~~~~m~~~g~  272 (410)
                      .+.|++..+.|-
T Consensus       450 ~~~y~kALe~~~  461 (472)
T 4g1t_A          450 DEDSERGLESGS  461 (472)
T ss_dssp             ------------
T ss_pred             HHHHHHHHhcCC
Confidence            999999887654

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.20  E-value=1.1e-09  Score=102.50  Aligned_cols=223  Identities=10%  Similarity=-0.045  Sum_probs=167.0

Q ss_pred             HHHHHHhhCCHHHHHHHHHHHHHc----CCCc-cHHHHHHHHHHHHhcCCHHHHHHHHHhccc-----C-----ChhhHH
Q 040371           47 VIYGCARLGALNHAYWVHNLIIEK----KIEL-NFILSAALIDMYSKCGKIQMAKEVFDTVQR-----N-----DVSVWN  111 (410)
Q Consensus        47 ll~a~~~~~~~~~a~~~~~~~~~~----g~~~-~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~-----~~~~~~  111 (410)
                      ....+...|+++.|...+....+.    +-++ ...++..+...|...|++++|...|++..+     +     ...+++
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            556677899999999999999874    2222 356788999999999999999998887642     1     135788


Q ss_pred             HHHHHHHHcCChHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhh---cCC-CCChhHHH
Q 040371          112 AMISGVAIHGLAADASAIFTKMEMF----NVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSR---YSI-QPQLEHYG  182 (410)
Q Consensus       112 ~li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~---~~~-~~~~~~~~  182 (410)
                      .+...|...|++++|++.|++....    +-.+ ...++..+...+...|++++|...|+...+-   .+. +....++.
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            8999999999999999999988653    1111 1246788889999999999999999988751   122 22356788


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhC-CC-----CCC-HHHHHHHHHHHHhcCc---hhHHHHHHHhhc--cCCCchHHHHHHH
Q 040371          183 AMVDLLGRAGHIEEAYGLITSM-TM-----EPD-VVVWRALLSACRTFKR---LELGEVAIVNIS--RLMGGDYVLLSNM  250 (410)
Q Consensus       183 ~li~~~~~~g~~~~A~~~~~~m-~~-----~p~-~~~~~~li~~~~~~g~---~~~a~~~~~~~~--~~~~~~~~~l~~~  250 (410)
                      .+...|.+.|++++|...+++. .+     .|. ...+..+-..+...|+   +++|..++.+..  +.....+..+...
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            8999999999999999998876 11     122 2334556666778888   666766655442  2223467789999


Q ss_pred             HHhcCChhHHHHHHHHHHh
Q 040371          251 YCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       251 ~~~~g~~~~a~~~~~~m~~  269 (410)
                      |.+.|++++|...+++..+
T Consensus       349 y~~~g~~~~A~~~~~~al~  367 (383)
T 3ulq_A          349 YHERKNFQKASAYFLKVEQ  367 (383)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHH
Confidence            9999999999999998754

>3sf4_A G-protein-signaling modulator 2; tetratricopeptide repeat, TPR, cell polarity, asymmetric CEL division, mitotic spindle orientation; 2.60A {Homo sapiens}

Probab=99.19  E-value=1.5e-09  Score=101.70  Aligned_cols=277  Identities=12%  Similarity=0.052  Sum_probs=201.1

Q ss_pred             CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc----HHHHHHHHHHHHhcCCHHHHHHHHHhccc-----C---
Q 040371           38 EPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN----FILSAALIDMYSKCGKIQMAKEVFDTVQR-----N---  105 (410)
Q Consensus        38 ~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~----~~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~---  105 (410)
                      .+....+......+...|++++|...++.+++.+.. +    ..++..+...|...|++++|...|++...     .   
T Consensus         6 ~~~~~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~   84 (406)
T 3sf4_A            6 EASCLELALEGERLCKSGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQL   84 (406)
T ss_dssp             CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCcc-cHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccH
Confidence            445667778888899999999999999999987432 3    46788999999999999999999987542     1   


Q ss_pred             -ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCC-CCC----HHHHHHHHHHHHccCC--------------------HH
Q 040371          106 -DVSVWNAMISGVAIHGLAADASAIFTKMEMFNV-LPD----SITFLGLLTACSHCGL--------------------VE  159 (410)
Q Consensus       106 -~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~----~~t~~~ll~a~~~~g~--------------------~~  159 (410)
                       ...+|..+...|...|++++|+..|++...... .++    ..++..+...+...|+                    ++
T Consensus        85 ~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~a~~~~~  164 (406)
T 3sf4_A           85 GEAKASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDVGEFPEEVRDALQ  164 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHTCC-------CCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHcCCcccccccchhhhhhhhHHHHHH
Confidence             245788899999999999999999998865311 112    3467788888999999                    99


Q ss_pred             HHHHHHHHhhhhc---CCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC----CCCCC----HHHHHHHHHHHHhcCchh
Q 040371          160 EGRKYFDHMRSRY---SIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSM----TMEPD----VVVWRALLSACRTFKRLE  227 (410)
Q Consensus       160 ~a~~~~~~m~~~~---~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~p~----~~~~~~li~~~~~~g~~~  227 (410)
                      +|...+....+..   +..| ....+..+...|...|++++|...+++.    +..++    ..++..+...+...|+++
T Consensus       165 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~  244 (406)
T 3sf4_A          165 AAVDFYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFE  244 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTBHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHcCChH
Confidence            9999998865421   1111 1357888889999999999999998876    11122    347788888899999999


Q ss_pred             HHHHHHH---hhccCC------CchHHHHHHHHHhcCChhHHHHHHHHHHhC----CCcCCCceeEEEECCEEEEEEeCC
Q 040371          228 LGEVAIV---NISRLM------GGDYVLLSNMYCYLKRWDTAENVREIMKKK----GVRKSQGKSWLELAGVIHQFKAGD  294 (410)
Q Consensus       228 ~a~~~~~---~~~~~~------~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~----g~~~~~~~s~~~~~~~~~~~~~~~  294 (410)
                      +|...+.   ...+..      ..++..+...|...|++++|.+.+++..+.    +-.+.....+..       +...+
T Consensus       245 ~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~-------la~~~  317 (406)
T 3sf4_A          245 TASEYYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLAIAQELNDRIGEGRACWS-------LGNAY  317 (406)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH-------HHHHH
T ss_pred             HHHHHHHHHHHHHHhCcCchHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHhcCCcHHHHHHHHH-------HHHHH
Confidence            9999832   222322      346778899999999999999999887543    111110111110       11223


Q ss_pred             CCCccHHHHHHHHHHHHHHHHHCCcccC
Q 040371          295 RSHPEAQAIDKILGSLIQRTKSEGFLPA  322 (410)
Q Consensus       295 ~~~~~~~~~~~~l~~l~~~m~~~g~~pd  322 (410)
                      ...|+.++|...+++..+...+.|..|.
T Consensus       318 ~~~g~~~~A~~~~~~al~~~~~~~~~~~  345 (406)
T 3sf4_A          318 TALGNHDQAMHFAEKHLEISREVGDKSG  345 (406)
T ss_dssp             HHHTCHHHHHHHHHHHHHHHHHTTCHHH
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHhcCCcc
Confidence            3467889999999887777666665443

>3ulq_A Response regulator aspartate phosphatase F; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis}

Probab=99.17  E-value=2.7e-09  Score=99.92  Aligned_cols=221  Identities=10%  Similarity=0.019  Sum_probs=172.3

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC--C----CccHHHHH
Q 040371           12 MIGGFVRNARFDEALRFFREMLSS----KVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKK--I----ELNFILSA   80 (410)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~----g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g--~----~~~~~~~~   80 (410)
                      ....+...|++++|+..|++..+.    +-.+ ...++..+..++...|+++.|...+.+.++..  .    +....+++
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            445677899999999999998763    1122 23578888999999999999999999887641  1    12246788


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhccc-----CC----hhhHHHHHHHHHHcCChHHHHHHHHHHHHC----CCCC-CHHHHH
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQR-----ND----VSVWNAMISGVAIHGLAADASAIFTKMEMF----NVLP-DSITFL  146 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~-----~~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~  146 (410)
                      .+...|...|++++|...|++..+     ++    ..+|+.+...|...|++++|++.|++....    +..| ...++.
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            999999999999999999987652     12    247888999999999999999999998762    3323 456788


Q ss_pred             HHHHHHHccCCHHHHHHHHHHhhhhc---CCCCChhHHHHHHHHHHhcCC---HHHHHHHHHhCCCCCCH-HHHHHHHHH
Q 040371          147 GLLTACSHCGLVEEGRKYFDHMRSRY---SIQPQLEHYGAMVDLLGRAGH---IEEAYGLITSMTMEPDV-VVWRALLSA  219 (410)
Q Consensus       147 ~ll~a~~~~g~~~~a~~~~~~m~~~~---~~~~~~~~~~~li~~~~~~g~---~~~A~~~~~~m~~~p~~-~~~~~li~~  219 (410)
                      .+...+.+.|++++|...++...+..   +-+.....+..+...|...|+   +++|+.++++.+..|+. ..+..+...
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            89999999999999999999876431   111122345677788888998   89999999998655543 466778888


Q ss_pred             HHhcCchhHHHHH
Q 040371          220 CRTFKRLELGEVA  232 (410)
Q Consensus       220 ~~~~g~~~~a~~~  232 (410)
                      |...|++++|...
T Consensus       349 y~~~g~~~~A~~~  361 (383)
T 3ulq_A          349 YHERKNFQKASAY  361 (383)
T ss_dssp             HHHTTCHHHHHHH
T ss_pred             HHHCCCHHHHHHH
Confidence            9999999999988

>4a1s_A PINS, partner of inscuteable; cell cycle, LGN, mitotic spindle orientation, asymmetric CEL divisions; 2.10A {Drosophila melanogaster}

Probab=99.16  E-value=1.1e-09  Score=103.40  Aligned_cols=227  Identities=11%  Similarity=0.035  Sum_probs=175.2

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccH----HHHHHHHHHHHhcCCHHHHHHHHHhcccC---------Chh
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNF----ILSAALIDMYSKCGKIQMAKEVFDTVQRN---------DVS  108 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~----~~~~~li~~y~~~g~~~~A~~~f~~m~~~---------~~~  108 (410)
                      ..+..+...+...|++++|...++.+++.... +.    .++..+...|...|++++|...|++..+.         ...
T Consensus        49 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~  127 (411)
T 4a1s_A           49 LELALEGERLCNAGDCRAGVAFFQAAIQAGTE-DLRTLSAIYSQLGNAYFYLGDYNKAMQYHKHDLTLAKSMNDRLGEAK  127 (411)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHHHhccc-ChhHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccCchHHHH
Confidence            45556677888999999999999999987532 33    57889999999999999999999876521         345


Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCC-----------------HHHHHHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMF----NVLP-DSITFLGLLTACSHCGL-----------------VEEGRKYFD  166 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~~ll~a~~~~g~-----------------~~~a~~~~~  166 (410)
                      +|..+...|...|++++|+..|++....    +-.| ...++..+...+...|+                 +++|...++
T Consensus       128 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~a~~~~~~A~~~~~  207 (411)
T 4a1s_A          128 SSGNLGNTLKVMGRFDEAAICCERHLTLARQLGDRLSEGRALYNLGNVYHAKGKHLGQRNPGKFGDDVKEALTRAVEFYQ  207 (411)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHHHHHHcCcccccccchhhhhhhhHHHHHHHHHHH
Confidence            7888999999999999999999987654    1122 24567788889999999                 999999988


Q ss_pred             Hhhhhc---CCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC-CC---CCC----HHHHHHHHHHHHhcCchhHHHHHHH
Q 040371          167 HMRSRY---SIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSM-TM---EPD----VVVWRALLSACRTFKRLELGEVAIV  234 (410)
Q Consensus       167 ~m~~~~---~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~---~p~----~~~~~~li~~~~~~g~~~~a~~~~~  234 (410)
                      ...+..   +..+ ....+..+...|...|++++|...+++. ..   .++    ..++..+...+...|++++|...+.
T Consensus       208 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~  287 (411)
T 4a1s_A          208 ENLKLMRDLGDRGAQGRACGNLGNTYYLLGDFQAAIEHHQERLRIAREFGDRAAERRANSNLGNSHIFLGQFEDAAEHYK  287 (411)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTCHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHCcCHHHHHHHHH
Confidence            865321   1111 2357888889999999999999999886 11   122    2377888888999999999999832


Q ss_pred             ---hhccCC------CchHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040371          235 ---NISRLM------GGDYVLLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       235 ---~~~~~~------~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                         ...+..      ..++..+..+|...|++++|...+++..+
T Consensus       288 ~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  331 (411)
T 4a1s_A          288 RTLALAVELGEREVEAQSCYSLGNTYTLLHEFNTAIEYHNRHLA  331 (411)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence               222322      34677889999999999999999998765

>3ro2_A PINS homolog, G-protein-signaling modulator 2; TPR repeat, protein-protein interaction, protein-binding, PR binding; 2.30A {Mus musculus}

Probab=99.16  E-value=1e-09  Score=99.80  Aligned_cols=227  Identities=12%  Similarity=0.046  Sum_probs=173.1

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc----HHHHHHHHHHHHhcCCHHHHHHHHHhccc-----C----Chh
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIELN----FILSAALIDMYSKCGKIQMAKEVFDTVQR-----N----DVS  108 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~----~~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~----~~~  108 (410)
                      ..+......+...|+++.|...++.+++.... +    ..++..+...|...|++++|.+.|++...     +    ...
T Consensus         6 ~~l~~~g~~~~~~g~~~~A~~~~~~al~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~   84 (338)
T 3ro2_A            6 LELALEGERLCKSGDCRAGVSFFEAAVQVGTE-DLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAK   84 (338)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCS-CHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHhhCcc-cHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhcccccHHHHH
Confidence            34555667788999999999999999987422 3    46788999999999999999999987642     1    245


Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCC-CCC----HHHHHHHHHHHHccCC--------------------HHHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNV-LPD----SITFLGLLTACSHCGL--------------------VEEGRK  163 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~----~~t~~~ll~a~~~~g~--------------------~~~a~~  163 (410)
                      +|..+...|...|++++|...|++...... .++    ..++..+...+...|+                    +++|..
T Consensus        85 ~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~A~~  164 (338)
T 3ro2_A           85 ASGNLGNTLKVLGNFDEAIVCCQRHLDISRELNDKVGEARALYNLGNVYHAKGKSFGCPGPQDTGEFPEDVRNALQAAVD  164 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSSSSSCC----CCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHcCcccccchhhhhhhhhhhHHHHHHHHHH
Confidence            788899999999999999999998765311 112    3367788888899999                    999999


Q ss_pred             HHHHhhhhc---CCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC----CCCCC----HHHHHHHHHHHHhcCchhHHHH
Q 040371          164 YFDHMRSRY---SIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSM----TMEPD----VVVWRALLSACRTFKRLELGEV  231 (410)
Q Consensus       164 ~~~~m~~~~---~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~p~----~~~~~~li~~~~~~g~~~~a~~  231 (410)
                      .++...+..   +..+ ....+..+...|...|++++|...+++.    +..++    ..++..+...+...|++++|..
T Consensus       165 ~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~  244 (338)
T 3ro2_A          165 LYEENLSLVTALGDRAAQGRAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERRAYSNLGNAYIFLGEFETASE  244 (338)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            998865321   1111 1347888889999999999999999876    11122    3477888888999999999999


Q ss_pred             HHH---hhccCC------CchHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040371          232 AIV---NISRLM------GGDYVLLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       232 ~~~---~~~~~~------~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                      .+.   ...+..      ..++..+...|...|++++|...+++..+
T Consensus       245 ~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a~~  291 (338)
T 3ro2_A          245 YYKKTLLLARQLKDRAVEAQSCYSLGNTYTLLQDYEKAIDYHLKHLA  291 (338)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhcchhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            832   222222      34677889999999999999999988754

>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=99.16  E-value=3.1e-09  Score=87.75  Aligned_cols=156  Identities=15%  Similarity=0.074  Sum_probs=72.2

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHc
Q 040371           44 FASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIH  120 (410)
Q Consensus        44 ~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~  120 (410)
                      +..+...+...|++++|...++.+.+.. +.+..++..+...|.+.|++++|...|++..+   .+...|..+...|...
T Consensus        11 ~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~   89 (186)
T 3as5_A           11 YRDKGISHAKAGRYSQAVMLLEQVYDAD-AFDVDVALHLGIAYVKTGAVDRGTELLERSLADAPDNVKVATVLGLTYVQV   89 (186)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHTTTCCTT-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCHHHHHHHHHHHHHhC-ccChHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHh
Confidence            3444444445555555555555444332 22344445555555555555555555544331   2334444444555555


Q ss_pred             CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHH
Q 040371          121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGL  200 (410)
Q Consensus       121 g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~  200 (410)
                      |++++|.+.|+++.... +.+...+..+...+...|++++|..+++.+.+.  .+.+...+..+...|.+.|++++|.+.
T Consensus        90 ~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~~la~~~~~~~~~~~A~~~  166 (186)
T 3as5_A           90 QKYDLAVPLLIKVAEAN-PINFNVRFRLGVALDNLGRFDEAIDSFKIALGL--RPNEGKVHRAIAFSYEQMGRHEEALPH  166 (186)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHhcC-cHhHHHHHHHHHHHHHcCcHHHHHHHHHHHHhc--CccchHHHHHHHHHHHHcCCHHHHHHH
Confidence            55555555555544431 223344444444445555555555555554432  112234444444445555555555444


Q ss_pred             HHh
Q 040371          201 ITS  203 (410)
Q Consensus       201 ~~~  203 (410)
                      +++
T Consensus       167 ~~~  169 (186)
T 3as5_A          167 FKK  169 (186)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=99.14  E-value=2.2e-09  Score=108.37  Aligned_cols=161  Identities=13%  Similarity=0.046  Sum_probs=142.5

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      +..+|+.|-..|.+.|++++|++.|++.++.  .| +..+|..+..++.+.|++++|.+.|++.++.. +.+...++.|.
T Consensus         8 ~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l--~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l~-P~~~~a~~nLg   84 (723)
T 4gyw_A            8 HADSLNNLANIKREQGNIEEAVRLYRKALEV--FPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRIS-PTFADAYSNMG   84 (723)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHH
Confidence            3568999999999999999999999999875  44 57799999999999999999999999999875 44688999999


Q ss_pred             HHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVE  159 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~  159 (410)
                      .+|.+.|++++|++.|++..+   .+..+|+.+...|.+.|++++|++.|++..+.  .| +...+..+..++...|+++
T Consensus        85 ~~l~~~g~~~~A~~~~~kAl~l~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l--~P~~~~a~~~L~~~l~~~g~~~  162 (723)
T 4gyw_A           85 NTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKL--KPDFPDAYCNLAHCLQIVCDWT  162 (723)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSCCHHHHHHHHHHHHHTTCCT
T ss_pred             HHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCChHHHhhhhhHHHhcccHH
Confidence            999999999999999998763   36789999999999999999999999999874  55 4677889999999999999


Q ss_pred             HHHHHHHHhhh
Q 040371          160 EGRKYFDHMRS  170 (410)
Q Consensus       160 ~a~~~~~~m~~  170 (410)
                      +|.+.+++..+
T Consensus       163 ~A~~~~~kal~  173 (723)
T 4gyw_A          163 DYDERMKKLVS  173 (723)
T ss_dssp             THHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99998887653

>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=99.14  E-value=4.4e-10  Score=99.72  Aligned_cols=153  Identities=12%  Similarity=0.038  Sum_probs=95.6

Q ss_pred             HcCCHhHHHHHHHHHHHC-------CCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc------CC-CccHHHHHHHH
Q 040371           18 RNARFDEALRFFREMLSS-------KVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK------KI-ELNFILSAALI   83 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~-------g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~------g~-~~~~~~~~~li   83 (410)
                      ..|++++|+..|++..+.       ..+....++..+..++...|++++|...+..+++.      +- +....++..+.
T Consensus        13 ~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~   92 (283)
T 3edt_B           13 GLVPRGSAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLA   92 (283)
T ss_dssp             CCSCSSSHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHH
Confidence            456666666666665441       11223456777777788888888888888777654      22 22355677777


Q ss_pred             HHHHhcCCHHHHHHHHHhccc-------C----ChhhHHHHHHHHHHcCChHHHHHHHHHHHHC------CCCC-CHHHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR-------N----DVSVWNAMISGVAIHGLAADASAIFTKMEMF------NVLP-DSITF  145 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~-------~----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~------g~~p-~~~t~  145 (410)
                      ..|...|++++|...|++...       +    ...+|..+...|...|++++|+..|++....      +..| ...++
T Consensus        93 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~  172 (283)
T 3edt_B           93 VLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTK  172 (283)
T ss_dssp             HHHHTTTCHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHH
T ss_pred             HHHHHhccHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence            777788888877777766542       1    2345666666677777777777777766553      1122 23445


Q ss_pred             HHHHHHHHccCCHHHHHHHHHHhhh
Q 040371          146 LGLLTACSHCGLVEEGRKYFDHMRS  170 (410)
Q Consensus       146 ~~ll~a~~~~g~~~~a~~~~~~m~~  170 (410)
                      ..+...+...|++++|..+|+.+.+
T Consensus       173 ~~la~~~~~~g~~~~A~~~~~~~l~  197 (283)
T 3edt_B          173 NNLASCYLKQGKYQDAETLYKEILT  197 (283)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            5666666666666666666666553

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.12  E-value=7.9e-09  Score=93.06  Aligned_cols=93  Identities=8%  Similarity=-0.046  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhcccC-----C----hhhHHHHHHHHHHc-CChHHHHHHHHHHHHCCC---CC-C-
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQRN-----D----VSVWNAMISGVAIH-GLAADASAIFTKMEMFNV---LP-D-  141 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~~~-----~----~~~~~~li~~~~~~-g~~~~A~~l~~~m~~~g~---~p-~-  141 (410)
                      .+++.+..+|.+.|++++|...|++..+-     +    ..+|+.+...|... |++++|+..|++..+...   .+ . 
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            34444444444444444444444433210     1    12444444444443 555555554444433100   00 0 


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          142 SITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       142 ~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      ..++..+...+...|++++|...|+...
T Consensus       158 ~~~~~~lg~~~~~~g~~~~A~~~~~~al  185 (292)
T 1qqe_A          158 NKCFIKCADLKALDGQYIEASDIYSKLI  185 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence            1234444444445555555555555444

>2ooe_A Cleavage stimulation factor 77 kDa subunit; HAT domain, structural protein; 3.00A {Mus musculus} SCOP: a.118.8.7

Probab=99.12  E-value=1.6e-08  Score=99.00  Aligned_cols=221  Identities=14%  Similarity=0.084  Sum_probs=153.2

Q ss_pred             hHHHHHHHHHHHcC----CH----hHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh-------hCCHH-------HHHHHH
Q 040371            7 VSWNSMIGGFVRNA----RF----DEALRFFREMLSSKVEPDKFTFASVIYGCAR-------LGALN-------HAYWVH   64 (410)
Q Consensus         7 ~~~n~li~~~~~~g----~~----~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~-------~~~~~-------~a~~~~   64 (410)
                      ..|...+.....++    +.    ++++.+|++.+.. .+-+...|......+.+       .|+++       .|+.++
T Consensus       231 ~~w~~~~~~e~~~~~~~~~~~~~~~~a~~~y~~al~~-~p~~~~~w~~~~~~~~~~~~~~~~~g~~~~a~~~~~~A~~~~  309 (530)
T 2ooe_A          231 DMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQCLLV-LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIY  309 (530)
T ss_dssp             HHHHHHHHHHHHCSSCCSCSHHHHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCccCCcchhHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhchhhhhccchhhhhhhhHHHHHHH
Confidence            46666664443322    22    3677888888764 23456677777777765       68876       788888


Q ss_pred             HHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-Ch-hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC
Q 040371           65 NLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DV-SVWNAMISGVAIHGLAADASAIFTKMEMFNVLP  140 (410)
Q Consensus        65 ~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~-~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p  140 (410)
                      ++.++.-.+.+..+|..++..+.+.|++++|+.+|++..+  | +. ..|...+..+.+.|+.++|.++|++..+.  .|
T Consensus       310 ~~Al~~~~p~~~~l~~~~~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~A~~~~~~Al~~--~~  387 (530)
T 2ooe_A          310 ERAISTLLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKARED--AR  387 (530)
T ss_dssp             HHHTTTTCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSSSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--TT
T ss_pred             HHHHHHhCcccHHHHHHHHHHHHhcCCHHHHHHHHHHHhCccccCchHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--cC
Confidence            8887632345688888888888888888888888887753  3 32 47888888888888888888888888764  23


Q ss_pred             C-HHHHHHHHHH-HHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC----CCCCC--HHH
Q 040371          141 D-SITFLGLLTA-CSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM----TMEPD--VVV  212 (410)
Q Consensus       141 ~-~~t~~~ll~a-~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~p~--~~~  212 (410)
                      + ...|...... +...|+.++|..+|+...+..  +.+...|..+++.+.+.|+.++|..+|++.    +..|+  ...
T Consensus       388 ~~~~~~~~~a~~~~~~~~~~~~A~~~~e~al~~~--p~~~~~~~~~~~~~~~~g~~~~Ar~~~~~al~~~~~~~~~~~~l  465 (530)
T 2ooe_A          388 TRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKY--GDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEI  465 (530)
T ss_dssp             CCTHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHH--TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHSCCSCGGGCHHH
T ss_pred             CchHHHHHHHHHHHHHcCChhHHHHHHHHHHHHC--CCCHHHHHHHHHHHHhCCCHhhHHHHHHHHHhccCCCHHHHHHH
Confidence            2 2233222222 235788888888888877542  234678888888888888888888888876    22332  457


Q ss_pred             HHHHHHHHHhcCchhHHHHH
Q 040371          213 WRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       213 ~~~li~~~~~~g~~~~a~~~  232 (410)
                      |...+.....+|+.+.+..+
T Consensus       466 w~~~~~~e~~~G~~~~~~~~  485 (530)
T 2ooe_A          466 WARFLAFESNIGDLASILKV  485 (530)
T ss_dssp             HHHHHHHHHHSSCHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHH
Confidence            77777777777887777776

>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=99.12  E-value=1.9e-08  Score=86.65  Aligned_cols=201  Identities=10%  Similarity=0.032  Sum_probs=152.9

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      .|...|......|.+.|++++|+..|++..+...+++...+..+..++...|++++|.+.++..++.. +.+..++..+.
T Consensus         5 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~   83 (228)
T 4i17_A            5 TDPNQLKNEGNDALNAKNYAVAFEKYSEYLKLTNNQDSVTAYNCGVCADNIKKYKEAADYFDIAIKKN-YNLANAYIGKS   83 (228)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT-CSHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHhhcHHHHHHHHHHHHHhC-cchHHHHHHHH
Confidence            45678889999999999999999999999886533788888889999999999999999999999875 44788899999


Q ss_pred             HHHHhcCCHHHHHHHHHhccc--C-Ch-------hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC---HHHHHHHHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR--N-DV-------SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD---SITFLGLLT  150 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~--~-~~-------~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~---~~t~~~ll~  150 (410)
                      ..|.+.|++++|...|++..+  | +.       ..|..+...+...|++++|++.|++..+.  .|+   ...+..+..
T Consensus        84 ~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~l~~  161 (228)
T 4i17_A           84 AAYRDMKNNQEYIATLTEGIKAVPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATDV--TSKKWKTDALYSLGV  161 (228)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS--SCHHHHHHHHHHHHH
T ss_pred             HHHHHcccHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHhc--CCCcccHHHHHHHHH
Confidence            999999999999999998763  3 34       45888888899999999999999999874  565   345666666


Q ss_pred             HHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHH
Q 040371          151 ACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRAL  216 (410)
Q Consensus       151 a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~l  216 (410)
                      .+..     .+..+++.+... + ..+...|....  ....+.+++|...+++. ...|+......+
T Consensus       162 ~~~~-----~~~~~~~~a~~~-~-~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~p~~~~~~~~  219 (228)
T 4i17_A          162 LFYN-----NGADVLRKATPL-A-SSNKEKYASEK--AKADAAFKKAVDYLGEAVTLSPNRTEIKQM  219 (228)
T ss_dssp             HHHH-----HHHHHHHHHGGG-T-TTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCTTCHHHHHH
T ss_pred             HHHH-----HHHHHHHHHHhc-c-cCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcCCCCHHHHHH
Confidence            6543     445556665532 2 22344444443  33456689999999887 455654433333

>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=99.10  E-value=2e-09  Score=95.35  Aligned_cols=197  Identities=14%  Similarity=0.086  Sum_probs=136.4

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHC------CCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc------C-
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSS------KVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEK------K-   71 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~------g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~------g-   71 (410)
                      ..+|+.+...|...|++++|+..|++..+.      +-.| ...++..+..++...|++++|.+.+.++++.      . 
T Consensus        43 ~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~  122 (283)
T 3edt_B           43 ATMLNILALVYRDQNKYKEAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKF  122 (283)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTCHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCC
Confidence            567999999999999999999999998753      2223 3557888999999999999999999998875      1 


Q ss_pred             CCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccC-----------ChhhHHHHHHHHHHcCChHHHHHHHHHHHHC----
Q 040371           72 IELNFILSAALIDMYSKCGKIQMAKEVFDTVQRN-----------DVSVWNAMISGVAIHGLAADASAIFTKMEMF----  136 (410)
Q Consensus        72 ~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~-----------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----  136 (410)
                      .+....++..+...|...|++++|...|++..+.           ...+|..+...|...|++++|...|++....    
T Consensus       123 ~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~~~~  202 (283)
T 3edt_B          123 HPDVAKQLNNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEK  202 (283)
T ss_dssp             CHHHHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh
Confidence            1334678899999999999999999999876532           2457888999999999999999999998763    


Q ss_pred             ---CCCCCHHH-HHHHHHHHHccC------CHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          137 ---NVLPDSIT-FLGLLTACSHCG------LVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       137 ---g~~p~~~t-~~~ll~a~~~~g------~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                         ...|.... +..+.......+      .+..+...+.....  ..+.....+..+...|.+.|++++|...+++.
T Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~a  278 (283)
T 3edt_B          203 EFGSVNGDNKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKV--DSPTVNTTLRSLGALYRRQGKLEAAHTLEDCA  278 (283)
T ss_dssp             HSSSCCSSCCCHHHHHHHHHHTTCCCCC------------CCCC--CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             cCCCcchhHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHHhcCC--CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence               12233222 222222222222      23333333333221  11112456777788888888888888887754

>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=99.10  E-value=2.1e-09  Score=108.52  Aligned_cols=154  Identities=10%  Similarity=0.070  Sum_probs=114.6

Q ss_pred             ccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHH
Q 040371           74 LNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLL  149 (410)
Q Consensus        74 ~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll  149 (410)
                      -+...++.|...|.+.|++++|++.|++..+  | +..+|+.+...|.+.|++++|++.|++..+.  .| +...+..+.
T Consensus         7 ~~a~al~nLG~~~~~~G~~~eAi~~~~kAl~l~P~~~~a~~nLg~~l~~~g~~~eA~~~~~~Al~l--~P~~~~a~~nLg   84 (723)
T 4gyw_A            7 THADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI--SPTFADAYSNMG   84 (723)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHH
Confidence            3467888888888888888888888887653  3 5678888888888888888888888888764  45 466788888


Q ss_pred             HHHHccCCHHHHHHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCch
Q 040371          150 TACSHCGLVEEGRKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRL  226 (410)
Q Consensus       150 ~a~~~~g~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~  226 (410)
                      .++...|++++|.+.|++..+.   .| +...|+.+...|.+.|++++|++.|++. .+.| +...|..+...+...|++
T Consensus        85 ~~l~~~g~~~~A~~~~~kAl~l---~P~~~~a~~~Lg~~~~~~g~~~eAi~~~~~Al~l~P~~~~a~~~L~~~l~~~g~~  161 (723)
T 4gyw_A           85 NTLKEMQDVQGALQCYTRAIQI---NPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDW  161 (723)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHhhhhhHHHhcccH
Confidence            8888888888888888887743   33 3677888888888888888888887775 3444 345555666666666666


Q ss_pred             hHHHHH
Q 040371          227 ELGEVA  232 (410)
Q Consensus       227 ~~a~~~  232 (410)
                      ++|.+.
T Consensus       162 ~~A~~~  167 (723)
T 4gyw_A          162 TDYDER  167 (723)
T ss_dssp             TTHHHH
T ss_pred             HHHHHH
Confidence            666555

>1qqe_A Vesicular transport protein SEC17; helix-turn-helix TPR-like repeat, protein transport; 2.90A {Saccharomyces cerevisiae} SCOP: a.118.8.1

Probab=99.08  E-value=1.6e-08  Score=91.02  Aligned_cols=198  Identities=11%  Similarity=0.016  Sum_probs=139.9

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHC----CCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHc----CCCc-cHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSS----KVEPD-KFTFASVIYGCARLGALNHAYWVHNLIIEK----KIEL-NFI   77 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~----g~~pd-~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~~~-~~~   77 (410)
                      .|+.....|...|++++|++.|.+....    |-+++ ..+|..+..++...|++++|...+++.++.    |-.. -..
T Consensus        39 ~~~~a~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~  118 (292)
T 1qqe_A           39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGAN  118 (292)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            5777788888899999999988877542    32222 457888888899999999999988888764    2111 145


Q ss_pred             HHHHHHHHHHhc-CCHHHHHHHHHhccc--C---C----hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHH----
Q 040371           78 LSAALIDMYSKC-GKIQMAKEVFDTVQR--N---D----VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSI----  143 (410)
Q Consensus        78 ~~~~li~~y~~~-g~~~~A~~~f~~m~~--~---~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~----  143 (410)
                      +++.+...|.+. |++++|...|++..+  |   +    ..+|+.+...|.+.|++++|+..|++...........    
T Consensus       119 ~~~~lg~~~~~~lg~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  198 (292)
T 1qqe_A          119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSL  198 (292)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGH
T ss_pred             HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcCCcccHHH
Confidence            788888889886 999999988887653  1   1    3467888888999999999999999888754322221    


Q ss_pred             --HHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCCh------hHHHHHHHHHH--hcCCHHHHHHHHHhC-CCCC
Q 040371          144 --TFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQL------EHYGAMVDLLG--RAGHIEEAYGLITSM-TMEP  208 (410)
Q Consensus       144 --t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~------~~~~~li~~~~--~~g~~~~A~~~~~~m-~~~p  208 (410)
                        ++..+..++...|++++|...|+...+   +.|+.      ..+..++..|.  ..+++++|++.|+++ .+.|
T Consensus       199 ~~~~~~lg~~~~~~g~~~~A~~~~~~al~---l~p~~~~~~~~~~l~~l~~~~~~~~~~~~~~A~~~~~~~~~l~~  271 (292)
T 1qqe_A          199 KDYFLKKGLCQLAATDAVAAARTLQEGQS---EDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRLDK  271 (292)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHGGGC---C---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCCCH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHh---hCCCCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCccHH
Confidence              466677778888999999999988763   33331      12344555554  356788888888776 3444

>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=99.08  E-value=9.3e-09  Score=79.86  Aligned_cols=127  Identities=14%  Similarity=0.194  Sum_probs=97.5

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      .+|..+...|...|++++|+.+|+++.+.. +.+...+..+...+...|+++.|...++.+.+.+ +.+..++..+...|
T Consensus         2 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~   79 (136)
T 2fo7_A            2 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAY   79 (136)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHC-CCchHHHHHHHHHH
Confidence            357888888889999999999998887653 3466777888888888888888888888887764 44566777788888


Q ss_pred             HhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      .+.|++++|.+.|+++..   .+...|..+...|.+.|++++|...|+++..
T Consensus        80 ~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~  131 (136)
T 2fo7_A           80 YKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALE  131 (136)
T ss_dssp             HTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHH
T ss_pred             HHhcCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHccHHHHHHHHHHHHc
Confidence            888888888888877653   2456677777777777777777777777765

>4i17_A Hypothetical protein; TPR repeats protein, structural genomics, joint center for S genomics, JCSG, protein structure initiative; HET: MSE; 1.83A {Bacteroides fragilis}

Probab=99.06  E-value=1.7e-08  Score=86.99  Aligned_cols=200  Identities=9%  Similarity=0.007  Sum_probs=150.7

Q ss_pred             CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHH
Q 040371           39 PDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMIS  115 (410)
Q Consensus        39 pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~  115 (410)
                      .|+..+......+...|++++|...|+..++...+++...+..+...|.+.|++++|.+.|++..+  | +...|..+..
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            466788888999999999999999999999987547778888899999999999999999998764  3 4568999999


Q ss_pred             HHHHcCChHHHHHHHHHHHHCCCCCC-H-------HHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC---hhHHHHH
Q 040371          116 GVAIHGLAADASAIFTKMEMFNVLPD-S-------ITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ---LEHYGAM  184 (410)
Q Consensus       116 ~~~~~g~~~~A~~l~~~m~~~g~~p~-~-------~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~---~~~~~~l  184 (410)
                      .|...|++++|++.|++..+.  .|+ .       ..|..+...+...|++++|...|+...+   +.|+   ...|..+
T Consensus        85 ~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~---~~p~~~~~~~~~~l  159 (228)
T 4i17_A           85 AYRDMKNNQEYIATLTEGIKA--VPGNATIEKLYAIYYLKEGQKFQQAGNIEKAEENYKHATD---VTSKKWKTDALYSL  159 (228)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHTT---SSCHHHHHHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHHh---cCCCcccHHHHHHH
Confidence            999999999999999999874  343 3       4577777888899999999999999884   3554   4677777


Q ss_pred             HHHHHhcCCHHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHH
Q 040371          185 VDLLGRAGHIEEAYGLITSM-T-MEPDVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNM  250 (410)
Q Consensus       185 i~~~~~~g~~~~A~~~~~~m-~-~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~  250 (410)
                      ...|...|+.     .++++ . ...+...+....  ....+.+++|...   ..++.|.++.+...+..+
T Consensus       160 ~~~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~--~~~~~~~~~A~~~~~~a~~l~p~~~~~~~~l~~i  223 (228)
T 4i17_A          160 GVLFYNNGAD-----VLRKATPLASSNKEKYASEK--AKADAAFKKAVDYLGEAVTLSPNRTEIKQMQDQV  223 (228)
T ss_dssp             HHHHHHHHHH-----HHHHHGGGTTTCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHH-----HHHHHHhcccCCHHHHHHHH--HHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Confidence            7777666543     22222 1 112344444433  2345667888887   566778876666555443

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.04  E-value=3.5e-08  Score=92.21  Aligned_cols=225  Identities=8%  Similarity=0.026  Sum_probs=130.1

Q ss_pred             HHHHHcCCHhHHHHHHHHHHHCC-CCCC----HHHHHHHHHHHHhhCCHHHHHHHHHHHHHc----C-CCc-cHHHHHHH
Q 040371           14 GGFVRNARFDEALRFFREMLSSK-VEPD----KFTFASVIYGCARLGALNHAYWVHNLIIEK----K-IEL-NFILSAAL   82 (410)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~g-~~pd----~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g-~~~-~~~~~~~l   82 (410)
                      ..+...|++++|+..|++..+.. -.+|    ..++..+..++...|+++.|...+.+.++.    + ..+ ...+++.+
T Consensus       109 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~l  188 (378)
T 3q15_A          109 MYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVI  188 (378)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHH
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHH
Confidence            34567788888888888776531 1122    345666777777788888887777776653    1 111 24556677


Q ss_pred             HHHHHhcCCHHHHHHHHHhccc-----CC----hhhHHHHHHHHHHcCChHHHHHHHHHHHHC----CCCCCHHHHHHHH
Q 040371           83 IDMYSKCGKIQMAKEVFDTVQR-----ND----VSVWNAMISGVAIHGLAADASAIFTKMEMF----NVLPDSITFLGLL  149 (410)
Q Consensus        83 i~~y~~~g~~~~A~~~f~~m~~-----~~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p~~~t~~~ll  149 (410)
                      ...|...|++++|.+.|++..+     ++    ..+++.+...|...|++++|++.|++....    +.+....++..+.
T Consensus       189 g~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la  268 (378)
T 3q15_A          189 AGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLS  268 (378)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHH
Confidence            7777777777777777765542     11    235666667777777777777777766551    1111245566666


Q ss_pred             HHHHccCCHHHHHHHHHHhhhhcCCCCC---hhHHHHHHHHHHhcCC---HHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 040371          150 TACSHCGLVEEGRKYFDHMRSRYSIQPQ---LEHYGAMVDLLGRAGH---IEEAYGLITSMTMEPDVVVWRALLSACRTF  223 (410)
Q Consensus       150 ~a~~~~g~~~~a~~~~~~m~~~~~~~~~---~~~~~~li~~~~~~g~---~~~A~~~~~~m~~~p~~~~~~~li~~~~~~  223 (410)
                      ..+.+.|++++|...++...+...-..+   ...+..+...|...++   +.+|+..+++.+..|+.             
T Consensus       269 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~l~~ly~~~~~~~~~~~al~~~~~~~~~~~~-------------  335 (378)
T 3q15_A          269 WTLCKAGQTQKAFQFIEEGLDHITARSHKFYKELFLFLQAVYKETVDERKIHDLLSYFEKKNLHAYI-------------  335 (378)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHCCTTCCSCHHHHHHHHHHHHSSSCCHHHHHHHHHHHHHTTCHHHH-------------
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhCCChhHH-------------
Confidence            6667777777777777666543111111   2233444444445555   55555555554322211             


Q ss_pred             CchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHH
Q 040371          224 KRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMK  268 (410)
Q Consensus       224 g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~  268 (410)
                                       ...+..+...|.+.|++++|...+++..
T Consensus       336 -----------------~~~~~~la~~y~~~g~~~~A~~~~~~al  363 (378)
T 3q15_A          336 -----------------EACARSAAAVFESSCHFEQAAAFYRKVL  363 (378)
T ss_dssp             -----------------HHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             -----------------HHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence                             1234456666666677777666666553

>3q15_A PSP28, response regulator aspartate phosphatase H; tetratricopeptide repeat, 3-helix bundle, phosphorelay signa transduction, phosphatase; 2.19A {Bacillus subtilis}

Probab=99.01  E-value=3.1e-08  Score=92.54  Aligned_cols=156  Identities=8%  Similarity=-0.066  Sum_probs=107.2

Q ss_pred             HHHHhhCCHHHHHHHHHHHHHcC--CC---ccHHHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC-----hhhHHHH
Q 040371           49 YGCARLGALNHAYWVHNLIIEKK--IE---LNFILSAALIDMYSKCGKIQMAKEVFDTVQR-----ND-----VSVWNAM  113 (410)
Q Consensus        49 ~a~~~~~~~~~a~~~~~~~~~~g--~~---~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~~-----~~~~~~l  113 (410)
                      ..+...|+++.|...+..+.+..  .+   ....++..+...|...|+++.|...|++..+     ++     ..+++.+
T Consensus       109 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~l  188 (378)
T 3q15_A          109 MYEFDQKEYVEAIGYYREAEKELPFVSDDIEKAEFHFKVAEAYYHMKQTHVSMYHILQALDIYQNHPLYSIRTIQSLFVI  188 (378)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHTTGGGCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHH
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHHhhCCChHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhCCCchhhHHHHHHHH
Confidence            34467788888888888887641  11   1245677788888888888888877776531     11     3467778


Q ss_pred             HHHHHHcCChHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhc---CCCCChhHHHHHH
Q 040371          114 ISGVAIHGLAADASAIFTKMEMF----NVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRY---SIQPQLEHYGAMV  185 (410)
Q Consensus       114 i~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~---~~~~~~~~~~~li  185 (410)
                      ...|...|++++|++.|++..+.    +..+ ...++..+...+...|++++|...|+...+-.   +.+....++..+.
T Consensus       189 g~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~la  268 (378)
T 3q15_A          189 AGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLLNIANSYDRSGDDQMAVEHFQKAAKVSREKVPDLLPKVLFGLS  268 (378)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHCGGGHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCChhHHHHHHHHH
Confidence            88888888888888888777652    1111 12456677778888888888888888776410   1122255677777


Q ss_pred             HHHHhcCCHHHHHHHHHhC
Q 040371          186 DLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       186 ~~~~~~g~~~~A~~~~~~m  204 (410)
                      ..|.+.|++++|...+++.
T Consensus       269 ~~~~~~g~~~~A~~~~~~a  287 (378)
T 3q15_A          269 WTLCKAGQTQKAFQFIEEG  287 (378)
T ss_dssp             HHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHH
Confidence            8888888888888887765

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.96  E-value=2.6e-08  Score=89.04  Aligned_cols=174  Identities=13%  Similarity=0.072  Sum_probs=117.8

Q ss_pred             HHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccC-----ChhhHHHHHHHHHHcCChHHHHHHHHHHH
Q 040371           60 AYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRN-----DVSVWNAMISGVAIHGLAADASAIFTKME  134 (410)
Q Consensus        60 a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~-----~~~~~~~li~~~~~~g~~~~A~~l~~~m~  134 (410)
                      +...++..+..+ .++......+...|...|++++|++++.+....     +...+-.++..|.+.|+.+.|.+.+++|.
T Consensus        85 a~~~l~~l~~~~-~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~~  163 (310)
T 3mv2_B           85 NIEELENLLKDK-QNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNYT  163 (310)
T ss_dssp             CCHHHHHTTTTS-CCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            566677666655 445555567888888889999998888876432     45577778888888999999999998887


Q ss_pred             HCCCCC-----CHHHHHHHHHHHHc----cCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-
Q 040371          135 MFNVLP-----DSITFLGLLTACSH----CGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-  204 (410)
Q Consensus       135 ~~g~~p-----~~~t~~~ll~a~~~----~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-  204 (410)
                      +.  .|     +..+...+..++..    .++.++|..+|+++.++   .|+..+-..++.++.+.|++++|.+.++.+ 
T Consensus       164 ~~--~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~---~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~  238 (310)
T 3mv2_B          164 NA--IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQT---FPTWKTQLGLLNLHLQQRNIAEAQGIVELLL  238 (310)
T ss_dssp             HH--SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTT---SCSHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             hc--CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHh---CCCcccHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            73  56     35566666666332    33888889999988754   344333444455788889999998888765 


Q ss_pred             CC----------CC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCC
Q 040371          205 TM----------EP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMG  241 (410)
Q Consensus       205 ~~----------~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~  241 (410)
                      ..          .| |..+...+|......|+  .|.++   +.+..|.++
T Consensus       239 ~~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~P~hp  287 (310)
T 3mv2_B          239 SDYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKLDHEHA  287 (310)
T ss_dssp             SHHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHTTCCCH
T ss_pred             HhcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHhCCCCh
Confidence            21          25 44555466655555665  56666   455556554

>1hz4_A MALT regulatory protein; two-helix bundles, helix repeats, protein superhelix, transc activator; 1.45A {Escherichia coli} SCOP: a.118.8.2

Probab=98.95  E-value=3.7e-07  Score=84.75  Aligned_cols=267  Identities=10%  Similarity=0.035  Sum_probs=179.9

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHHHHcCCCccH----HHHHHHHHHHHhcCCHHHHHHHHHhccc-----CCh----hhHHH
Q 040371           46 SVIYGCARLGALNHAYWVHNLIIEKKIELNF----ILSAALIDMYSKCGKIQMAKEVFDTVQR-----NDV----SVWNA  112 (410)
Q Consensus        46 ~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~----~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~~~----~~~~~  112 (410)
                      .....+...|+++.|...++..+...-..+.    .+++.+...|...|++++|...+++...     .+.    .+++.
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            3444566789999999999998876433332    2567778889999999999999987653     222    34667


Q ss_pred             HHHHHHHcCChHHHHHHHHHHHHC----CCC--CC-HHHHHHHHHHHHccCCHHHHHHHHHHhhhhc---CCCCChhHHH
Q 040371          113 MISGVAIHGLAADASAIFTKMEMF----NVL--PD-SITFLGLLTACSHCGLVEEGRKYFDHMRSRY---SIQPQLEHYG  182 (410)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~~----g~~--p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~---~~~~~~~~~~  182 (410)
                      +...+...|++++|...+++....    +..  |. ..++..+...+...|++++|...++...+..   +.......+.
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            788899999999999999988653    222  32 3456667788899999999999999877531   1111235677


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhC----CCCCCHHHHHH-----HHHHHHhcCchhHHHHHHHhhccCCC-------chHHH
Q 040371          183 AMVDLLGRAGHIEEAYGLITSM----TMEPDVVVWRA-----LLSACRTFKRLELGEVAIVNISRLMG-------GDYVL  246 (410)
Q Consensus       183 ~li~~~~~~g~~~~A~~~~~~m----~~~p~~~~~~~-----li~~~~~~g~~~~a~~~~~~~~~~~~-------~~~~~  246 (410)
                      .+...+...|++++|...+++.    +...+...|..     .+..+...|+++.|...+.+.....+       ..+..
T Consensus       179 ~la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~  258 (373)
T 1hz4_A          179 MLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRN  258 (373)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHHHHHCCCHHHHHHHHHhCCCCCCCcchhhHHHHHH
Confidence            8888999999999999998876    11112122322     23347789999999998554432221       13456


Q ss_pred             HHHHHHhcCChhHHHHHHHHHHhC----CCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHHHCCc
Q 040371          247 LSNMYCYLKRWDTAENVREIMKKK----GVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEGF  319 (410)
Q Consensus       247 l~~~~~~~g~~~~a~~~~~~m~~~----g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g~  319 (410)
                      +..++...|++++|...++.....    |........+..       +...+...|+.++|...+++....-...|+
T Consensus       259 la~~~~~~g~~~~A~~~l~~a~~~~~~~~~~~~~~~~~~~-------la~~~~~~g~~~~A~~~l~~al~~~~~~g~  328 (373)
T 1hz4_A          259 IARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLL-------LNQLYWQAGRKSDAQRVLLDALKLANRTGF  328 (373)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH-------HHHHHHHHTCHHHHHHHHHHHHHHHHHHCC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHhCcchhhHHHHHHH-------HHHHHHHhCCHHHHHHHHHHHHHHhccccH
Confidence            788999999999999999877542    211111000100       111223457788888888876666555554

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.91  E-value=1.1e-07  Score=83.78  Aligned_cols=99  Identities=11%  Similarity=-0.025  Sum_probs=73.1

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC---HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCC--CccHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD---KFTFASVIYGCARLGALNHAYWVHNLIIEKKI--ELNFILS   79 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd---~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~--~~~~~~~   79 (410)
                      +...+-.+...+.+.|++++|+..|+++.+.. +-+   ...+..+..++...|+++.|...++.+++...  +....++
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~   92 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG-RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAE   92 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHH
Confidence            45566677778888888888888888887642 222   55777778888888888888888888887632  2235567


Q ss_pred             HHHHHHHHh--------cCCHHHHHHHHHhccc
Q 040371           80 AALIDMYSK--------CGKIQMAKEVFDTVQR  104 (410)
Q Consensus        80 ~~li~~y~~--------~g~~~~A~~~f~~m~~  104 (410)
                      ..+...|.+        .|++++|...|++..+
T Consensus        93 ~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~  125 (261)
T 3qky_A           93 YERAMCYYKLSPPYELDQTDTRKAIEAFQLFID  125 (261)
T ss_dssp             HHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHH
Confidence            777777877        8888888888887753

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.91  E-value=1.1e-07  Score=80.86  Aligned_cols=93  Identities=13%  Similarity=0.169  Sum_probs=50.1

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC-HHHHHH----------------HHHHHHhhCCHHHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD-KFTFAS----------------VIYGCARLGALNHAYWVHNLIIE   69 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-~~t~~~----------------ll~a~~~~~~~~~a~~~~~~~~~   69 (410)
                      ..+-.....+.+.|++++|+..|++..+.  .|+ ...|..                +..++...|++++|...++..++
T Consensus         5 ~~~~~~g~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~   82 (208)
T 3urz_A            5 DEMLQKVSAAIEAGQNGQAVSYFRQTIAL--NIDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQ   82 (208)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHh--CCCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            34444556677889999999999888764  443 333443                44444444444444444444444


Q ss_pred             cCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040371           70 KKIELNFILSAALIDMYSKCGKIQMAKEVFDTV  102 (410)
Q Consensus        70 ~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m  102 (410)
                      .. +.+...+..+...|.+.|++++|...|++.
T Consensus        83 ~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~a  114 (208)
T 3urz_A           83 KA-PNNVDCLEACAEMQVCRGQEKDALRMYEKI  114 (208)
T ss_dssp             HC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            32 223444444444444444444444444443

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.91  E-value=7.9e-08  Score=97.05  Aligned_cols=165  Identities=11%  Similarity=0.033  Sum_probs=96.5

Q ss_pred             HhhCCHHHHHHHHHHHH--------HcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHc
Q 040371           52 ARLGALNHAYWVHNLII--------EKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIH  120 (410)
Q Consensus        52 ~~~~~~~~a~~~~~~~~--------~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~  120 (410)
                      ...|++++|.+.+++.+        +. .+.+...+..+...|.+.|++++|...|++..+   .+...|+.+...|.+.
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~-~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~  480 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVD-FSESVELPLMEVRALLDLGDVAKATRKLDDLAERVGWRWRLVWYRAVAELLT  480 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------C-CTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccc-cccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccCcchHHHHHHHHHHHHHc
Confidence            45566666666666665        22 133455566666666666666666666665542   2455666666666666


Q ss_pred             CChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHH
Q 040371          121 GLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYG  199 (410)
Q Consensus       121 g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~  199 (410)
                      |++++|++.|++..+.  .| +...+..+..++.+.|++++ ...|+...+.  -+.+...|..+..+|.+.|++++|.+
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            6666666666666553  23 34455566666666666666 6666666532  12234566666666667777777776


Q ss_pred             HHHhC-CCCCC-HHHHHHHHHHHHh
Q 040371          200 LITSM-TMEPD-VVVWRALLSACRT  222 (410)
Q Consensus       200 ~~~~m-~~~p~-~~~~~~li~~~~~  222 (410)
                      .|++. ...|+ ...|..+..++..
T Consensus       556 ~~~~al~l~P~~~~a~~~~~~~~~~  580 (681)
T 2pzi_A          556 TLDEVPPTSRHFTTARLTSAVTLLS  580 (681)
T ss_dssp             HHHTSCTTSTTHHHHHHHHHHHTC-
T ss_pred             HHHhhcccCcccHHHHHHHHHHHHc
Confidence            66665 44554 3445444444433

>2fo7_A Synthetic consensus TPR protein; tetratricopeptide repeat, consensus protein, superhelix, de novo protein; 2.30A {Synthetic} SCOP: k.38.1.1 PDB: 2hyz_A

Probab=98.89  E-value=1.4e-07  Score=73.05  Aligned_cols=124  Identities=15%  Similarity=0.125  Sum_probs=61.9

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHc
Q 040371           44 FASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIH  120 (410)
Q Consensus        44 ~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~  120 (410)
                      |..+...+...|++++|..+++.+.+.. +.+..++..+...|...|++++|...|+++..   .+...|..+...+...
T Consensus         4 ~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~   82 (136)
T 2fo7_A            4 WYNLGNAYYKQGDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQ   82 (136)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHcCcHHHHHHHHHHHHHcC-CcchhHHHHHHHHHHHhcCHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHh
Confidence            4444555555556666665555555543 22444555555555555555555555554431   2334445555555555


Q ss_pred             CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          121 GLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       121 g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      |++++|.+.|+++.... +.+..++..+...+...|++++|...|+.+.
T Consensus        83 ~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~  130 (136)
T 2fo7_A           83 GDYDEAIEYYQKALELD-PRSAEAWYNLGNAYYKQGDYDEAIEYYQKAL  130 (136)
T ss_dssp             TCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHHccHHHHHHHHHHHH
Confidence            55555555555554431 1233444444455555555555555555444

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.88  E-value=1.8e-07  Score=89.72  Aligned_cols=217  Identities=8%  Similarity=0.008  Sum_probs=150.3

Q ss_pred             HHHHHHHHHHhcC----CHHHHHHHHHhcccCChhhHHHHHHHHHHcC---ChHHHHHHHHHHHHCCCCCCHHHHHHHHH
Q 040371           78 LSAALIDMYSKCG----KIQMAKEVFDTVQRNDVSVWNAMISGVAIHG---LAADASAIFTKMEMFNVLPDSITFLGLLT  150 (410)
Q Consensus        78 ~~~~li~~y~~~g----~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g---~~~~A~~l~~~m~~~g~~p~~~t~~~ll~  150 (410)
                      ....|..+|...+    ..+++..++......+..++..+...|...|   +.++|++.|++..+.| .++...+..+..
T Consensus       143 a~~~Lg~~y~~~~~~~~~~~~a~~~~~~a~~~~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g-~~~a~~~~~Lg~  221 (452)
T 3e4b_A          143 AGLAQVLLYRTQGTYDQHLDDVERICKAALNTTDICYVELATVYQKKQQPEQQAELLKQMEAGVSRG-TVTAQRVDSVAR  221 (452)
T ss_dssp             HHHHHHHHHHHHTCGGGGHHHHHHHHHHHTTTCTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTT-CSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcccCHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCC-CHHHHHHHHHHH
Confidence            4445555666655    3455666666666677778999999999999   8999999999998876 345554455666


Q ss_pred             HHHcc----CCHHHHHHHHHHhhhhcCCCCChhHHHHHHHH-H--HhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Q 040371          151 ACSHC----GLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDL-L--GRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTF  223 (410)
Q Consensus       151 a~~~~----g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~-~--~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~  223 (410)
                      .|...    ++.++|...|+... . |   +...+..|..+ |  ...+++++|.++|++.-..-+...+..|-..|. .
T Consensus       222 ~y~~g~~~~~d~~~A~~~~~~aa-~-g---~~~a~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~-~  295 (452)
T 3e4b_A          222 VLGDATLGTPDEKTAQALLEKIA-P-G---YPASWVSLAQLLYDFPELGDVEQMMKYLDNGRAADQPRAELLLGKLYY-E  295 (452)
T ss_dssp             HHTCGGGSSCCHHHHHHHHHHHG-G-G---STHHHHHHHHHHHHSGGGCCHHHHHHHHHHHHHTTCHHHHHHHHHHHH-H
T ss_pred             HHhCCCCCCCCHHHHHHHHHHHc-C-C---CHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH-c
Confidence            66554    78999999999876 2 2   56677777776 4  468899999999998722226666666666665 5


Q ss_pred             C-----chhHHHHHHHhhccCCCchHHHHHHHHHh----cCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCC
Q 040371          224 K-----RLELGEVAIVNISRLMGGDYVLLSNMYCY----LKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGD  294 (410)
Q Consensus       224 g-----~~~~a~~~~~~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~  294 (410)
                      |     ++++|...+.+--+.++..+..|..+|..    ..+.++|...|++..+.|...    ....+...   +..|.
T Consensus       296 G~g~~~d~~~A~~~~~~Aa~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~~----A~~~Lg~~---y~~G~  368 (452)
T 3e4b_A          296 GKWVPADAKAAEAHFEKAVGREVAADYYLGQIYRRGYLGKVYPQKALDHLLTAARNGQNS----ADFAIAQL---FSQGK  368 (452)
T ss_dssp             CSSSCCCHHHHHHHHHTTTTTCHHHHHHHHHHHHTTTTSSCCHHHHHHHHHHHHTTTCTT----HHHHHHHH---HHSCT
T ss_pred             CCCCCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHhhChHH----HHHHHHHH---HHhCC
Confidence            5     89999998544436677788888888877    348999999999988877521    11100000   12333


Q ss_pred             CCCccHHHHHHHHH
Q 040371          295 RSHPEAQAIDKILG  308 (410)
Q Consensus       295 ~~~~~~~~~~~~l~  308 (410)
                      .......+++..++
T Consensus       369 g~~~d~~~A~~~~~  382 (452)
T 3e4b_A          369 GTKPDPLNAYVFSQ  382 (452)
T ss_dssp             TBCCCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHH
Confidence            34456777877776

>3mv2_B Coatomer subunit epsilon; vesicular membrane coat COAT protein complex I, protein TRAN; 2.90A {Saccharomyces cerevisiae} PDB: 3mv3_B

Probab=98.87  E-value=4.6e-07  Score=81.02  Aligned_cols=237  Identities=10%  Similarity=-0.024  Sum_probs=163.1

Q ss_pred             HHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCH
Q 040371           13 IGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKI   92 (410)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~   92 (410)
                      |.-..-.|++..++.-..++.  ... ....-.-+.+++..+|+++..         ..-.|.......+... ...+  
T Consensus        20 ikn~fy~G~yq~~i~e~~~~~--~~~-~~~~~~~~~Rs~iAlg~~~~~---------~~~~~~~~a~~~la~~-~~~~--   84 (310)
T 3mv2_B           20 IKQNYYTGNFVQCLQEIEKFS--KVT-DNTLLFYKAKTLLALGQYQSQ---------DPTSKLGKVLDLYVQF-LDTK--   84 (310)
T ss_dssp             HHHHHTTTCHHHHTHHHHTSS--CCC-CHHHHHHHHHHHHHTTCCCCC---------CSSSTTHHHHHHHHHH-HTTT--
T ss_pred             HHHHHHhhHHHHHHHHHHhcC--ccc-hHHHHHHHHHHHHHcCCCccC---------CCCCHHHHHHHHHHHH-hccc--
Confidence            344455788888887333221  112 223444456778777776532         1123343344444333 3332  


Q ss_pred             HHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040371           93 QMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHM  168 (410)
Q Consensus        93 ~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m  168 (410)
                        |...|++...   ++..++..+..+|...|+.++|++++.+-...+..+ +...+...+..+.+.|+.+.|.+.++.|
T Consensus        85 --a~~~l~~l~~~~~~~~~~~~~la~i~~~~g~~eeAL~~l~~~i~~~~~~~~lea~~l~vqi~L~~~r~d~A~k~l~~~  162 (310)
T 3mv2_B           85 --NIEELENLLKDKQNSPYELYLLATAQAILGDLDKSLETCVEGIDNDEAEGTTELLLLAIEVALLNNNVSTASTIFDNY  162 (310)
T ss_dssp             --CCHHHHHTTTTSCCCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTSSCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             --HHHHHHHHHhcCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHhccCCCcCcHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence              7788887653   455666788889999999999999999987655322 4566778889999999999999999999


Q ss_pred             hhhcCCCC-----ChhHHHHHHHHHH--h--cCCHHHHHHHHHhC-CCCCCHHHHHHHHHHHHhcCchhHHHHHHH---h
Q 040371          169 RSRYSIQP-----QLEHYGAMVDLLG--R--AGHIEEAYGLITSM-TMEPDVVVWRALLSACRTFKRLELGEVAIV---N  235 (410)
Q Consensus       169 ~~~~~~~~-----~~~~~~~li~~~~--~--~g~~~~A~~~~~~m-~~~p~~~~~~~li~~~~~~g~~~~a~~~~~---~  235 (410)
                      .+.   .|     +..+...|..++.  .  .+++.+|..+|+++ ...|+..+-..++.++...|++++|+..+.   +
T Consensus       163 ~~~---~~d~~~~~d~~l~~Laea~v~l~~g~~~~q~A~~~f~El~~~~p~~~~~~lLln~~~~~g~~~eAe~~L~~l~~  239 (310)
T 3mv2_B          163 TNA---IEDTVSGDNEMILNLAESYIKFATNKETATSNFYYYEELSQTFPTWKTQLGLLNLHLQQRNIAEAQGIVELLLS  239 (310)
T ss_dssp             HHH---SCHHHHHHHHHHHHHHHHHHHHHHTCSTTTHHHHHHHHHHTTSCSHHHHHHHHHHHHHHTCHHHHHHHHHHHHS
T ss_pred             Hhc---CccccccchHHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhCCCcccHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            854   55     2455566665533  2  34899999999999 444664444556668899999999999943   2


Q ss_pred             h----------ccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCC
Q 040371          236 I----------SRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKG  271 (410)
Q Consensus       236 ~----------~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g  271 (410)
                      .          +|.++.+...++..+...|+  +|.++++++++..
T Consensus       240 ~~p~~~~k~~~~p~~~~~LaN~i~l~~~lgk--~a~~l~~qL~~~~  283 (310)
T 3mv2_B          240 DYYSVEQKENAVLYKPTFLANQITLALMQGL--DTEDLTNQLVKLD  283 (310)
T ss_dssp             HHHHTTTCHHHHSSHHHHHHHHHHHHHHTTC--TTHHHHHHHHHTT
T ss_pred             hcccccccccCCCCCHHHHHHHHHHHHHhCh--HHHHHHHHHHHhC
Confidence            3          36677788778877888887  8899999998764

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.86  E-value=1.9e-07  Score=83.69  Aligned_cols=164  Identities=10%  Similarity=-0.033  Sum_probs=122.5

Q ss_pred             CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--CChhhHHH-HH
Q 040371           38 EPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--NDVSVWNA-MI  114 (410)
Q Consensus        38 ~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~~~~~~~-li  114 (410)
                      +.+...+..+...+...|++++|.+.++++++.. +.+...+..|...|.+.|++++|...|++...  |+...+.. ..
T Consensus       114 p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~~p~~~~~~~~~~  192 (287)
T 3qou_A          114 PREEELXAQQAMQLMQESNYTDALPLLXDAWQLS-NQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQDQDTRYQGLVAQ  192 (287)
T ss_dssp             CCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-TSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGGGCSHHHHHHHHH
T ss_pred             CCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHhC-CcchhHHHHHHHHHHHCCCHHHHHHHHHhCchhhcchHHHHHHHH
Confidence            4455667777788888999999999999888875 44677888888999999999999999998864  44332222 22


Q ss_pred             HHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCH
Q 040371          115 SGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHI  194 (410)
Q Consensus       115 ~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~  194 (410)
                      ..+.+.++.++|+..|++..... +.+...+..+..++...|++++|...|..+.+...-..+...+..+...|...|+.
T Consensus       193 ~~l~~~~~~~~a~~~l~~al~~~-P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~~~l~~~~~~~g~~  271 (287)
T 3qou_A          193 IELLXQAADTPEIQQLQQQVAEN-PEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTRXTFQEILAALGTG  271 (287)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHHHHHHHHHHHHCTT
T ss_pred             HHHHhhcccCccHHHHHHHHhcC-CccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHHHHHHHHHHHcCCC
Confidence            33666778888888888887752 33567778888888899999999999998886411112256788888888888888


Q ss_pred             HHHHHHHHh
Q 040371          195 EEAYGLITS  203 (410)
Q Consensus       195 ~~A~~~~~~  203 (410)
                      ++|...+++
T Consensus       272 ~~a~~~~r~  280 (287)
T 3qou_A          272 DALASXYRR  280 (287)
T ss_dssp             CHHHHHHHH
T ss_pred             CcHHHHHHH
Confidence            888777765

>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=98.78  E-value=3.7e-07  Score=77.38  Aligned_cols=128  Identities=11%  Similarity=-0.024  Sum_probs=109.3

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      .+...+..+...+...|++++|+..|++.    +.|+...+..+..++...|++++|...++..++.. +.+...+..+.
T Consensus         4 ~~~~~~~~~g~~~~~~~~~~~A~~~~~~a----~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-~~~~~~~~~lg   78 (213)
T 1hh8_A            4 VEAISLWNEGVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRG   78 (213)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----cCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-ccchHHHHHHH
Confidence            34556777888899999999999999876    46788899999999999999999999999998875 55788899999


Q ss_pred             HHHHhcCCHHHHHHHHHhcccC---Ch----------------hhHHHHHHHHHHcCChHHHHHHHHHHHHC
Q 040371           84 DMYSKCGKIQMAKEVFDTVQRN---DV----------------SVWNAMISGVAIHGLAADASAIFTKMEMF  136 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~~---~~----------------~~~~~li~~~~~~g~~~~A~~l~~~m~~~  136 (410)
                      .+|.+.|++++|...|++..+.   +.                ..|..+...|.+.|++++|.+.|++..+.
T Consensus        79 ~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~  150 (213)
T 1hh8_A           79 MLYYQTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSM  150 (213)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHcccHHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHc
Confidence            9999999999999999887642   22                67888888999999999999999998874

>3urz_A Uncharacterized protein; tetratricopeptide repeats (TPR) containing protein, structur genomics, joint center for structural genomics, JCSG; HET: PG4; 2.19A {Bacteroides ovatus}

Probab=98.77  E-value=6.2e-07  Score=76.13  Aligned_cols=168  Identities=12%  Similarity=-0.028  Sum_probs=115.7

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHH----------------HHHHHHhcCCHHHHHHHHHhccc--
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAA----------------LIDMYSKCGKIQMAKEVFDTVQR--  104 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~----------------li~~y~~~g~~~~A~~~f~~m~~--  104 (410)
                      .+......+...|++++|...|+..++.. +.+...+..                +...|.+.|++++|...|++..+  
T Consensus         6 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~   84 (208)
T 3urz_A            6 EMLQKVSAAIEAGQNGQAVSYFRQTIALN-IDRTEMYYWTNVDKNSEISSKLATELALAYKKNRNYDKAYLFYKELLQKA   84 (208)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-HHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCChHHHHHhhhcchhhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHC
Confidence            34445566778999999999999998864 334556666                88888999999999999987763  


Q ss_pred             -CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCC--HHHHHHHHHHhhhhcCCCCChhH
Q 040371          105 -NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGL--VEEGRKYFDHMRSRYSIQPQLEH  180 (410)
Q Consensus       105 -~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~--~~~a~~~~~~m~~~~~~~~~~~~  180 (410)
                       .+...|..+...|...|++++|+..|++..+.  .| +..++..+...+...|.  .+.+...+....   ...|....
T Consensus        85 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~lg~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~a  159 (208)
T 3urz_A           85 PNNVDCLEACAEMQVCRGQEKDALRMYEKILQL--EADNLAANIFLGNYYYLTAEQEKKKLETDYKKLS---SPTKMQYA  159 (208)
T ss_dssp             TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHHHHHHC------CCCHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc--CCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHHh---CCCchhHH
Confidence             36678888888899999999999999988874  34 45667777766655543  333444444432   11222223


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHH
Q 040371          181 YGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRAL  216 (410)
Q Consensus       181 ~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~l  216 (410)
                      +..+..++...|++++|...|++. ...|+......+
T Consensus       160 ~~~~g~~~~~~~~~~~A~~~~~~al~l~P~~~~~~~l  196 (208)
T 3urz_A          160 RYRDGLSKLFTTRYEKARNSLQKVILRFPSTEAQKTL  196 (208)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHTTTSCCHHHHHHH
T ss_pred             HHHHHHHHHHccCHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            344455666778899999888876 677876554443

>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition, kinase-INH complex, rubredoxin fold, TPR domain, transferase; HET: AXX; 2.40A {Mycobacterium tuberculosis}

Probab=98.77  E-value=3.8e-07  Score=92.09  Aligned_cols=181  Identities=13%  Similarity=0.009  Sum_probs=144.5

Q ss_pred             HHcCCHhHHHHHHHHHH--------HCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh
Q 040371           17 VRNARFDEALRFFREML--------SSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK   88 (410)
Q Consensus        17 ~~~g~~~~a~~l~~~m~--------~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~   88 (410)
                      ...|++++|++.|++..        +. -+.+...+..+..++...|++++|.+.++++++.. +.+...+..+...|.+
T Consensus       402 ~~~~~~~~A~~~~~~al~~~~~~~~~~-~p~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~  479 (681)
T 2pzi_A          402 TVLSQPVQTLDSLRAARHGALDADGVD-FSESVELPLMEVRALLDLGDVAKATRKLDDLAERV-GWRWRLVWYRAVAELL  479 (681)
T ss_dssp             TTTCCHHHHHHHHHHHHTC-------C-CTTCSHHHHHHHHHHHHHTCHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHhhhhcccccccc-cccchhHHHHHHHHHHhcCCHHHHHHHHHHHhccC-cchHHHHHHHHHHHHH
Confidence            67899999999999987        32 23456788888999999999999999999999874 4578899999999999


Q ss_pred             cCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHH
Q 040371           89 CGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYF  165 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~  165 (410)
                      .|++++|.+.|++..+  | +...|..+...|.+.|++++ ++.|++..+.. +-+...+..+..++.+.|++++|...|
T Consensus       480 ~g~~~~A~~~~~~al~l~P~~~~~~~~lg~~~~~~g~~~~-~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~  557 (681)
T 2pzi_A          480 TGDYDSATKHFTEVLDTFPGELAPKLALAATAELAGNTDE-HKFYQTVWSTN-DGVISAAFGLARARSAEGDRVGAVRTL  557 (681)
T ss_dssp             HTCHHHHHHHHHHHHHHSTTCSHHHHHHHHHHHHHTCCCT-TCHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCChHH-HHHHHHHHHhC-CchHHHHHHHHHHHHHcCCHHHHHHHH
Confidence            9999999999998763  3 66789999999999999999 99999988753 225677888999999999999999999


Q ss_pred             HHhhhhcCCCCC-hhHHHHHHHHHHhcCC--------HHHHHHHHHhC
Q 040371          166 DHMRSRYSIQPQ-LEHYGAMVDLLGRAGH--------IEEAYGLITSM  204 (410)
Q Consensus       166 ~~m~~~~~~~~~-~~~~~~li~~~~~~g~--------~~~A~~~~~~m  204 (410)
                      +.+.+   +.|+ ...|..+..+|...+.        +++|.+.+..+
T Consensus       558 ~~al~---l~P~~~~a~~~~~~~~~~~~~~~~~~~~~~~~A~~~l~~~  602 (681)
T 2pzi_A          558 DEVPP---TSRHFTTARLTSAVTLLSGRSTSEVTEEQIRDAARRVEAL  602 (681)
T ss_dssp             HTSCT---TSTTHHHHHHHHHHHTC-------CCHHHHHHHHHHHHTS
T ss_pred             Hhhcc---cCcccHHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHhhC
Confidence            98873   3555 5667777777755444        55666666655

>3e4b_A ALGK; tetratricopeptide repeat, superhelix, alginate biosynt pseudomonas, protein binding; 2.50A {Pseudomonas fluorescens}

Probab=98.76  E-value=1.1e-06  Score=84.08  Aligned_cols=188  Identities=13%  Similarity=0.029  Sum_probs=143.1

Q ss_pred             cHHHHHHHHHHHHhcC---CHHHHHHHHHhcccC---ChhhHHHHHHHHHHc----CChHHHHHHHHHHHHCCCCCCHHH
Q 040371           75 NFILSAALIDMYSKCG---KIQMAKEVFDTVQRN---DVSVWNAMISGVAIH----GLAADASAIFTKMEMFNVLPDSIT  144 (410)
Q Consensus        75 ~~~~~~~li~~y~~~g---~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~----g~~~~A~~l~~~m~~~g~~p~~~t  144 (410)
                      ++..+..|..+|.+.|   +.++|.+.|++..+.   +...+..+...|...    ++.++|+..|++.. .|   +...
T Consensus       175 ~~~a~~~Lg~~~~~~g~~~~~~~A~~~~~~aa~~g~~~a~~~~~Lg~~y~~g~~~~~d~~~A~~~~~~aa-~g---~~~a  250 (452)
T 3e4b_A          175 TDICYVELATVYQKKQQPEQQAELLKQMEAGVSRGTVTAQRVDSVARVLGDATLGTPDEKTAQALLEKIA-PG---YPAS  250 (452)
T ss_dssp             CTTHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCSCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHG-GG---STHH
T ss_pred             CHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHc-CC---CHHH
Confidence            3448889999999999   899999999987643   344446677777554    68999999999987 33   3445


Q ss_pred             HHHHHHH-H--HccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcC-----CHHHHHHHHHhCCCCCCHHHHHHH
Q 040371          145 FLGLLTA-C--SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAG-----HIEEAYGLITSMTMEPDVVVWRAL  216 (410)
Q Consensus       145 ~~~ll~a-~--~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g-----~~~~A~~~~~~m~~~p~~~~~~~l  216 (410)
                      +..+... +  ...++.++|...|+...+. |   +...+..|..+|. .|     ++++|.++|++.- .-+...+..|
T Consensus       251 ~~~Lg~~~~~~~~~~d~~~A~~~~~~Aa~~-g---~~~A~~~Lg~~y~-~G~g~~~d~~~A~~~~~~Aa-~g~~~A~~~L  324 (452)
T 3e4b_A          251 WVSLAQLLYDFPELGDVEQMMKYLDNGRAA-D---QPRAELLLGKLYY-EGKWVPADAKAAEAHFEKAV-GREVAADYYL  324 (452)
T ss_dssp             HHHHHHHHHHSGGGCCHHHHHHHHHHHHHT-T---CHHHHHHHHHHHH-HCSSSCCCHHHHHHHHHTTT-TTCHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHHC-C---CHHHHHHHHHHHH-cCCCCCCCHHHHHHHHHHHh-CCCHHHHHHH
Confidence            5555555 3  5689999999999998854 4   6778888888887 55     9999999999987 4466677666


Q ss_pred             HHHHHh----cCchhHHHHHHH-hhccCCCchHHHHHHHHHh----cCChhHHHHHHHHHHhCCC
Q 040371          217 LSACRT----FKRLELGEVAIV-NISRLMGGDYVLLSNMYCY----LKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       217 i~~~~~----~g~~~~a~~~~~-~~~~~~~~~~~~l~~~~~~----~g~~~~a~~~~~~m~~~g~  272 (410)
                      -..|..    ..++++|...+. ...+.++.....|..+|..    ..+.++|...++...+.|.
T Consensus       325 g~~y~~G~g~~~d~~~A~~~~~~Aa~~g~~~A~~~Lg~~y~~G~g~~~d~~~A~~~~~~A~~~g~  389 (452)
T 3e4b_A          325 GQIYRRGYLGKVYPQKALDHLLTAARNGQNSADFAIAQLFSQGKGTKPDPLNAYVFSQLAKAQDT  389 (452)
T ss_dssp             HHHHHTTTTSSCCHHHHHHHHHHHHTTTCTTHHHHHHHHHHSCTTBCCCHHHHHHHHHHHHTTCC
T ss_pred             HHHHHCCCCCCcCHHHHHHHHHHHHhhChHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHCCC
Confidence            666654    348899998843 3456677788889999875    4589999999999888775

>3qky_A Outer membrane assembly lipoprotein YFIO; membrane protein; 2.15A {Rhodothermus marinus}

Probab=98.75  E-value=7.5e-07  Score=78.36  Aligned_cols=96  Identities=7%  Similarity=-0.110  Sum_probs=69.7

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc---HHHHHHHHHHHHhcCCHHHHHHHHHhccc--CC----hhhH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN---FILSAALIDMYSKCGKIQMAKEVFDTVQR--ND----VSVW  110 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~---~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~----~~~~  110 (410)
                      +...+-.....+...|++++|...|+.+++.. +.+   ...+..+..+|.+.|++++|...|++..+  |+    ..+|
T Consensus        14 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~l~~~-p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~   92 (261)
T 3qky_A           14 SPQEAFERAMEFYNQGKYDRAIEYFKAVFTYG-RTHEWAADAQFYLARAYYQNKEYLLAASEYERFIQIYQIDPRVPQAE   92 (261)
T ss_dssp             SHHHHHHHHHHHHHTTCHHHHHHHHHHHGGGC-SCSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             CHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CCCcchHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHCCCCchhHHHH
Confidence            45566677777778888888888888887763 223   56777778888888888888888887653  21    2356


Q ss_pred             HHHHHHHHH--------cCChHHHHHHHHHHHHC
Q 040371          111 NAMISGVAI--------HGLAADASAIFTKMEMF  136 (410)
Q Consensus       111 ~~li~~~~~--------~g~~~~A~~l~~~m~~~  136 (410)
                      ..+..+|..        .|++++|+..|++....
T Consensus        93 ~~lg~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~  126 (261)
T 3qky_A           93 YERAMCYYKLSPPYELDQTDTRKAIEAFQLFIDR  126 (261)
T ss_dssp             HHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcccccccchhHHHHHHHHHHHHHH
Confidence            666777777        78888888888887764

>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=98.71  E-value=1.3e-06  Score=74.38  Aligned_cols=171  Identities=9%  Similarity=-0.076  Sum_probs=122.7

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC----CHHHHHHHH
Q 040371           24 EALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG----KIQMAKEVF   99 (410)
Q Consensus        24 ~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g----~~~~A~~~f   99 (410)
                      +|+..|++..+.|   +...+..+...+...+++++|.+.|++..+.|   +...+..|..+|.. |    +.++|.+.|
T Consensus         4 eA~~~~~~aa~~g---~~~a~~~lg~~~~~~~~~~~A~~~~~~a~~~g---~~~a~~~lg~~y~~-~g~~~~~~~A~~~~   76 (212)
T 3rjv_A            4 EPGSQYQQQAEAG---DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQG---DGDALALLAQLKIR-NPQQADYPQARQLA   76 (212)
T ss_dssp             CTTHHHHHHHHTT---CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHTT---CHHHHHHHHHHTTS-STTSCCHHHHHHHH
T ss_pred             hHHHHHHHHHHCC---CHHHHHHHHHHHhcCCCHHHHHHHHHHHHHcC---CHHHHHHHHHHHHc-CCCCCCHHHHHHHH
Confidence            4667777777655   66777777778888888888888888888765   56677777777777 6    788888888


Q ss_pred             HhcccC-ChhhHHHHHHHHHH----cCChHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHc----cCCHHHHHHHHHHhh
Q 040371          100 DTVQRN-DVSVWNAMISGVAI----HGLAADASAIFTKMEMFNVL-PDSITFLGLLTACSH----CGLVEEGRKYFDHMR  169 (410)
Q Consensus       100 ~~m~~~-~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~-p~~~t~~~ll~a~~~----~g~~~~a~~~~~~m~  169 (410)
                      ++..++ +..++..|...|..    .++.++|++.|++..+.|.. .+...+..|-..|..    .++.++|...|+...
T Consensus        77 ~~A~~~g~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~~~~~~~~~~~a~~~Lg~~y~~g~g~~~d~~~A~~~~~~A~  156 (212)
T 3rjv_A           77 EKAVEAGSKSGEIVLARVLVNRQAGATDVAHAITLLQDAARDSESDAAVDAQMLLGLIYASGVHGPEDDVKASEYFKGSS  156 (212)
T ss_dssp             HHHHHTTCHHHHHHHHHHHTCGGGSSCCHHHHHHHHHHHTSSTTSHHHHHHHHHHHHHHHHTSSSSCCHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHHcCCCCccCHHHHHHHHHHHHHcCCCcchHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence            877544 56677777777766    67888888888887765432 014566666677766    678888888888877


Q ss_pred             hhcCCCCChhHHHHHHHHHHhc-C-----CHHHHHHHHHhC
Q 040371          170 SRYSIQPQLEHYGAMVDLLGRA-G-----HIEEAYGLITSM  204 (410)
Q Consensus       170 ~~~~~~~~~~~~~~li~~~~~~-g-----~~~~A~~~~~~m  204 (410)
                      +.   ..+...+..|..+|.+. |     ++++|..+|++.
T Consensus       157 ~~---~~~~~a~~~Lg~~y~~g~gg~~~~d~~~A~~~~~~A  194 (212)
T 3rjv_A          157 SL---SRTGYAEYWAGMMFQQGEKGFIEPNKQKALHWLNVS  194 (212)
T ss_dssp             HT---SCTTHHHHHHHHHHHHCBTTTBCCCHHHHHHHHHHH
T ss_pred             Hc---CCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHH
Confidence            43   23455667777777653 2     778888877765

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.71  E-value=1.5e-06  Score=74.66  Aligned_cols=182  Identities=10%  Similarity=-0.042  Sum_probs=109.3

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCC-CCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCc-c-HHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKV-EPD-KFTFASVIYGCARLGALNHAYWVHNLIIEKKIEL-N-FILSA   80 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~-~pd-~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~-~-~~~~~   80 (410)
                      +...+..+...+.+.|++++|+..|+++.+... .|. ...+..+..++.+.|+++.|...++.+++..... . ...+.
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            345566677888999999999999999987421 111 3567778889999999999999999998864221 1 12344


Q ss_pred             HHHHHHHh------------------cCCHHHHHHHHHhcccCC---hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCC
Q 040371           81 ALIDMYSK------------------CGKIQMAKEVFDTVQRND---VSVWNAMISGVAIHGLAADASAIFTKMEMFNVL  139 (410)
Q Consensus        81 ~li~~y~~------------------~g~~~~A~~~f~~m~~~~---~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  139 (410)
                      .+...|.+                  .|+.++|...|+++.+.+   ..++.+.....          .+...+.     
T Consensus        83 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~~P~~~~a~~a~~~l~----------~~~~~~~-----  147 (225)
T 2yhc_A           83 MRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRGYPNSQYTTDATKRLV----------FLKDRLA-----  147 (225)
T ss_dssp             HHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTTCTTCTTHHHHHHHHH----------HHHHHHH-----
T ss_pred             HHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHHCcCChhHHHHHHHHH----------HHHHHHH-----
Confidence            44444443                  456666666666665421   12222111000          0000000     


Q ss_pred             CCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          140 PDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       140 p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                         .....+...+.+.|++++|...|+.+.+.+.-.|. ...+..+..+|.+.|++++|.+.++.+
T Consensus       148 ---~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l  210 (225)
T 2yhc_A          148 ---KYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKII  210 (225)
T ss_dssp             ---HHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             ---HHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence               01123455666777777777777777754211111 245667777777777777777777765

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.69  E-value=6.4e-07  Score=73.79  Aligned_cols=151  Identities=13%  Similarity=0.033  Sum_probs=75.0

Q ss_pred             HHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--CChhhHHHHHHH-HHHcCCh
Q 040371           47 VIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--NDVSVWNAMISG-VAIHGLA  123 (410)
Q Consensus        47 ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~~~~~~~li~~-~~~~g~~  123 (410)
                      ....+...|++++|...++..++.. +.+...+..+...|.+.|++++|...|++...  |+...+..+... +...+..
T Consensus        12 ~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~   90 (176)
T 2r5s_A           12 QVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSYKSLIAKLELHQQAAE   90 (176)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGCCHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccCChHHHHHHHHHHHHhhccc
Confidence            3344445555555555555544432 22445555555556666666666666655542  222222111111 1122222


Q ss_pred             HHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC---hhHHHHHHHHHHhcCCHHHHHH
Q 040371          124 ADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ---LEHYGAMVDLLGRAGHIEEAYG  199 (410)
Q Consensus       124 ~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~---~~~~~~li~~~~~~g~~~~A~~  199 (410)
                      .+|+..|++..+.  .| +...+..+...+...|++++|...|+.+.+.   .|+   ...+..+...|...|+.++|..
T Consensus        91 ~~a~~~~~~al~~--~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~---~p~~~~~~a~~~l~~~~~~~g~~~~A~~  165 (176)
T 2r5s_A           91 SPELKRLEQELAA--NPDNFELACELAVQYNQVGRDEEALELLWNILKV---NLGAQDGEVKKTFMDILSALGQGNAIAS  165 (176)
T ss_dssp             CHHHHHHHHHHHH--STTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT---CTTTTTTHHHHHHHHHHHHHCSSCHHHH
T ss_pred             chHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHh---CcccChHHHHHHHHHHHHHhCCCCcHHH
Confidence            3455556555542  23 3455555566666666666666666665532   222   3455666666666666666665


Q ss_pred             HHHh
Q 040371          200 LITS  203 (410)
Q Consensus       200 ~~~~  203 (410)
                      .|++
T Consensus       166 ~y~~  169 (176)
T 2r5s_A          166 KYRR  169 (176)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5543

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.68  E-value=5.8e-07  Score=81.33  Aligned_cols=16  Identities=13%  Similarity=0.133  Sum_probs=12.3

Q ss_pred             cCCHhHHHHHHHHHHH
Q 040371           19 NARFDEALRFFREMLS   34 (410)
Q Consensus        19 ~g~~~~a~~l~~~m~~   34 (410)
                      .|++++|.+++++..+
T Consensus         4 ~~~~~eA~~~~~~a~k   19 (307)
T 2ifu_A            4 AQKISEAHEHIAKAEK   19 (307)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHH
Confidence            5678888888887764

>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=98.68  E-value=3e-06  Score=84.67  Aligned_cols=229  Identities=11%  Similarity=-0.006  Sum_probs=172.5

Q ss_pred             hHHHHHHHHHHHcC-------CHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHH-HHHHHHHHcCCCccHHH
Q 040371            7 VSWNSMIGGFVRNA-------RFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAY-WVHNLIIEKKIELNFIL   78 (410)
Q Consensus         7 ~~~n~li~~~~~~g-------~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~-~~~~~~~~~g~~~~~~~   78 (410)
                      ..|...|.---.++       ..+.+..+|++.+.. ++-+...|.....-+...|+.+.|. +++++.+.. .+.+..+
T Consensus       303 ~lW~~yi~fEk~~~~~l~~~~~~~Rv~~~Ye~aL~~-~p~~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s~~L  380 (679)
T 4e6h_A          303 LIWLEWIRWESDNKLELSDDLHKARMTYVYMQAAQH-VCFAPEIWFNMANYQGEKNTDSTVITKYLKLGQQC-IPNSAVL  380 (679)
T ss_dssp             HHHHHHHHHHHTCTTCCCHHHHHHHHHHHHHHHHHH-TTTCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTCHHH
T ss_pred             HHHHHHHHHHHhCCccccchhhHHHHHHHHHHHHHH-cCCCHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCCHHH
Confidence            45777766544433       134466788888875 3557788888888888899999996 999999875 4667888


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhccc-------------CC------------hhhHHHHHHHHHHcCChHHHHHHHHHH
Q 040371           79 SAALIDMYSKCGKIQMAKEVFDTVQR-------------ND------------VSVWNAMISGVAIHGLAADASAIFTKM  133 (410)
Q Consensus        79 ~~~li~~y~~~g~~~~A~~~f~~m~~-------------~~------------~~~~~~li~~~~~~g~~~~A~~l~~~m  133 (410)
                      |-.++...-+.|+++.|+++|+++..             |+            ...|-..+....+.|..+.|..+|.+.
T Consensus       381 wl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A  460 (679)
T 4e6h_A          381 AFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDPTNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKC  460 (679)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccCcchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            99999999999999999999998763             21            236888888888899999999999999


Q ss_pred             HHC-CCCCCHHHHHHHHHHHHcc-CCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC--
Q 040371          134 EMF-NVLPDSITFLGLLTACSHC-GLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP--  208 (410)
Q Consensus       134 ~~~-g~~p~~~t~~~ll~a~~~~-g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p--  208 (410)
                      .+. +. +....|......-.+. ++.+.|..+|+...+.+  +-+...|...++.....|+.+.|..+|++. ...|  
T Consensus       461 ~~~~~~-~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~~--p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~~~~~  537 (679)
T 4e6h_A          461 RRLKKL-VTPDIYLENAYIEYHISKDTKTACKVLELGLKYF--ATDGEYINKYLDFLIYVNEESQVKSLFESSIDKISDS  537 (679)
T ss_dssp             HHTGGG-SCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHHH--TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTTSSST
T ss_pred             HHhcCC-CChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC--CCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCH
Confidence            875 21 1223343322222333 45999999999998753  335667788999899999999999999997 3333  


Q ss_pred             --CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCC
Q 040371          209 --DVVVWRALLSACRTFKRLELGEVA---IVNISRLM  240 (410)
Q Consensus       209 --~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~  240 (410)
                        ....|...+.--..+|+.+.+..+   +.+..|.+
T Consensus       538 ~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~~  574 (679)
T 4e6h_A          538 HLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPEV  574 (679)
T ss_dssp             THHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTTC
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCC
Confidence              346899999988999999999998   55556655

>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=98.68  E-value=3.6e-06  Score=71.61  Aligned_cols=159  Identities=10%  Similarity=-0.016  Sum_probs=132.8

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC----CHHHHHHHHHHHHHcCCCccHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLG----ALNHAYWVHNLIIEKKIELNFILS   79 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~----~~~~a~~~~~~~~~~g~~~~~~~~   79 (410)
                      .|..++..|-..|...+++++|+..|++..+.|   +...+..+...+.. +    ++++|.+.|++..+.|   +...+
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            467788899999999999999999999998876   56777777777777 6    8999999999998876   67788


Q ss_pred             HHHHHHHHh----cCCHHHHHHHHHhcccCC-----hhhHHHHHHHHHH----cCChHHHHHHHHHHHHCCCCCCHHHHH
Q 040371           80 AALIDMYSK----CGKIQMAKEVFDTVQRND-----VSVWNAMISGVAI----HGLAADASAIFTKMEMFNVLPDSITFL  146 (410)
Q Consensus        80 ~~li~~y~~----~g~~~~A~~~f~~m~~~~-----~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~  146 (410)
                      ..|..+|..    .+++++|.+.|++..+.+     ..+++.|-..|..    .++.++|+..|++..+.  .++...+.
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            889999987    889999999999887643     5889999999998    88999999999999876  23444566


Q ss_pred             HHHHHHHcc-C-----CHHHHHHHHHHhhhh
Q 040371          147 GLLTACSHC-G-----LVEEGRKYFDHMRSR  171 (410)
Q Consensus       147 ~ll~a~~~~-g-----~~~~a~~~~~~m~~~  171 (410)
                      .|...|... |     +.++|...|+...+.
T Consensus       167 ~Lg~~y~~g~gg~~~~d~~~A~~~~~~A~~~  197 (212)
T 3rjv_A          167 WAGMMFQQGEKGFIEPNKQKALHWLNVSCLE  197 (212)
T ss_dssp             HHHHHHHHCBTTTBCCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCCCCCHHHHHHHHHHHHHc
Confidence            666666543 3     899999999998864

>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=98.67  E-value=1.4e-06  Score=73.80  Aligned_cols=131  Identities=9%  Similarity=-0.045  Sum_probs=95.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC
Q 040371           78 LSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGL  157 (410)
Q Consensus        78 ~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~  157 (410)
                      .+..+...|.+.|++++|...|++...++...|..+...|.+.|++++|++.|++..... +.+...+..+..++...|+
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            345566777888888888888888877788888888888888888888888888877653 3356677778888888888


Q ss_pred             HHHHHHHHHHhhhhcCC-------------CC-ChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC
Q 040371          158 VEEGRKYFDHMRSRYSI-------------QP-QLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD  209 (410)
Q Consensus       158 ~~~a~~~~~~m~~~~~~-------------~~-~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~  209 (410)
                      +++|...|+...+...-             .| ....+..+...|.+.|++++|...|++. ...|+
T Consensus        87 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~  153 (213)
T 1hh8_A           87 YDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSE  153 (213)
T ss_dssp             HHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCS
T ss_pred             HHHHHHHHHHHHHhCCCccHHHHHHhccccCccchHHHHHHHHHHHHccCHHHHHHHHHHHHHcCcc
Confidence            88888888887753111             11 1256677777777777777777777765 44443

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.67  E-value=1e-06  Score=86.89  Aligned_cols=150  Identities=10%  Similarity=-0.036  Sum_probs=110.2

Q ss_pred             cCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHH
Q 040371           19 NARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEV   98 (410)
Q Consensus        19 ~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~   98 (410)
                      .|++++|++.|++..+.. +-+...+..+..++...|++++|.+.+++.++.. +.+...+..+...|.+.|++++|.+.
T Consensus         2 ~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~   79 (568)
T 2vsy_A            2 TADGPRELLQLRAAVRHR-PQDFVAWLMLADAELGMGDTTAGEMAVQRGLALH-PGHPEAVARLGRVRWTQQRHAEAAVL   79 (568)
T ss_dssp             --------------------CCHHHHHHHHHHHHHHTCHHHHHHHHHHHHTTS-TTCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             CccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence            478899999999887642 3357788889999999999999999999998874 44688899999999999999999999


Q ss_pred             HHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc---CCHHHHHHHHHHhhhh
Q 040371           99 FDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHC---GLVEEGRKYFDHMRSR  171 (410)
Q Consensus        99 f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~---g~~~~a~~~~~~m~~~  171 (410)
                      |++..+   .+...|..+...|.+.|++++|.+.|++..+.. +.+...+..+...+...   |+.++|.+.++...+.
T Consensus        80 ~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~al~~  157 (568)
T 2vsy_A           80 LQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLL-PEEPYITAQLLNWRRRLCDWRALDVLSAQVRAAVAQ  157 (568)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhhccccHHHHHHHHHHHHhc
Confidence            987753   356788899999999999999999999988753 23567788888888888   9999999999988754

>3qou_A Protein YBBN; thioredoxin-like fold, tetratricopeptide repeat, lysine dimethylation, protein binding; HET: MLY; 1.80A {Escherichia coli} PDB: 3qdn_A*

Probab=98.66  E-value=8.8e-07  Score=79.34  Aligned_cols=169  Identities=10%  Similarity=-0.015  Sum_probs=105.8

Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhc
Q 040371           94 MAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRY  172 (410)
Q Consensus        94 ~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~  172 (410)
                      .....+......+...+..+...+.+.|++++|...|++....  .| +...+..+...+...|++++|...++.+... 
T Consensus       104 ~l~~~l~~~lp~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~--~P~~~~a~~~la~~~~~~g~~~~A~~~l~~~~~~-  180 (287)
T 3qou_A          104 AIRALLDXVLPREEELXAQQAMQLMQESNYTDALPLLXDAWQL--SNQNGEIGLLLAETLIALNRSEDAEAVLXTIPLQ-  180 (287)
T ss_dssp             HHHHHHHHHSCCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TTSCHHHHHHHHHHHHHTTCHHHHHHHHTTSCGG-
T ss_pred             HHHHHHHHHcCCchhhHHHHHHHHHhCCCHHHHHHHHHHHHHh--CCcchhHHHHHHHHHHHCCCHHHHHHHHHhCchh-
Confidence            3344444444334455666666677777777777777777664  33 4456666777777777777777777776543 


Q ss_pred             CCCCChhHHHHH-HHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCC--CchH
Q 040371          173 SIQPQLEHYGAM-VDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLM--GGDY  244 (410)
Q Consensus       173 ~~~~~~~~~~~l-i~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~--~~~~  244 (410)
                        .|+....... ...+.+.++.++|...+++. ...| +...+..+...+...|++++|...   ..+..|.+  ...+
T Consensus       181 --~p~~~~~~~~~~~~l~~~~~~~~a~~~l~~al~~~P~~~~~~~~la~~l~~~g~~~~A~~~l~~~l~~~p~~~~~~a~  258 (287)
T 3qou_A          181 --DQDTRYQGLVAQIELLXQAADTPEIQQLQQQVAENPEDAALATQLALQLHQVGRNEEALELLFGHLRXDLTAADGQTR  258 (287)
T ss_dssp             --GCSHHHHHHHHHHHHHHHHTSCHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTGGGGHHH
T ss_pred             --hcchHHHHHHHHHHHHhhcccCccHHHHHHHHhcCCccHHHHHHHHHHHHHcccHHHHHHHHHHHHhcccccccchHH
Confidence              3443322222 22355556666666666655 3334 456677777777777777777777   34445555  5567


Q ss_pred             HHHHHHHHhcCChhHHHHHHHHH
Q 040371          245 VLLSNMYCYLKRWDTAENVREIM  267 (410)
Q Consensus       245 ~~l~~~~~~~g~~~~a~~~~~~m  267 (410)
                      ..|+.+|...|+.++|...+++-
T Consensus       259 ~~l~~~~~~~g~~~~a~~~~r~a  281 (287)
T 3qou_A          259 XTFQEILAALGTGDALASXYRRQ  281 (287)
T ss_dssp             HHHHHHHHHHCTTCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHH
Confidence            78888888888888887777653

>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein structure initiative, PSI, center for eukaryotic structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}

Probab=98.65  E-value=1e-06  Score=79.68  Aligned_cols=182  Identities=10%  Similarity=-0.066  Sum_probs=98.4

Q ss_pred             HHHHhhCCHHHHHHHHHHHHHc----CCCc-cHHHHHHHHHHHHhcCCHHHHHHHHHhccc-------C--ChhhHHHHH
Q 040371           49 YGCARLGALNHAYWVHNLIIEK----KIEL-NFILSAALIDMYSKCGKIQMAKEVFDTVQR-------N--DVSVWNAMI  114 (410)
Q Consensus        49 ~a~~~~~~~~~a~~~~~~~~~~----g~~~-~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-------~--~~~~~~~li  114 (410)
                      ..+...|++++|...|.+..+.    +-.+ -..+++.+...|.+.|++++|...|++..+       +  -..+|+.+.
T Consensus        44 ~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~Al~l~~~~g~~~~~a~~~~~lg  123 (307)
T 2ifu_A           44 VAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGMMLKDLQRMPEAVQYIEKASVMYVENGTPDTAAMALDRAG  123 (307)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCGGGGHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            3455566666666666655443    1111 134556666666666666666666654321       1  123566666


Q ss_pred             HHHHHcCChHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhc---CCCCC-hhHHHHHH
Q 040371          115 SGVAIHGLAADASAIFTKMEMF----NVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRY---SIQPQ-LEHYGAMV  185 (410)
Q Consensus       115 ~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~---~~~~~-~~~~~~li  185 (410)
                      ..|.. |++++|+..|++....    |..+ ...++..+...+...|++++|...|+...+..   +..+. ...+..+.
T Consensus       124 ~~~~~-g~~~~A~~~~~~Al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~g  202 (307)
T 2ifu_A          124 KLMEP-LDLSKAVHLYQQAAAVFENEERLRQAAELIGKASRLLVRQQKFDEAAASLQKEKSMYKEMENYPTCYKKCIAQV  202 (307)
T ss_dssp             HHHTT-TCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHc-CCHHHHHHHHHHHHHHHHhCCChhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHcCChhHHHHHHHHHH
Confidence            66666 7777777777665542    1100 12456666677777777777777777665421   11111 22555666


Q ss_pred             HHHHhcCCHHHHHHHHHhCCCCCC------HHHHHHHHHHHHhcCchhHHHHH
Q 040371          186 DLLGRAGHIEEAYGLITSMTMEPD------VVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       186 ~~~~~~g~~~~A~~~~~~m~~~p~------~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      ..+...|++++|...|++.-..|+      ......++.++ ..|+.+....+
T Consensus       203 ~~~~~~g~~~~A~~~~~~al~~p~~~~~~e~~~l~~l~~~~-~~~d~~~~~~~  254 (307)
T 2ifu_A          203 LVQLHRADYVAAQKCVRESYSIPGFSGSEDCAALEDLLQAY-DEQDEEQLLRV  254 (307)
T ss_dssp             HHHHHTTCHHHHHHHHHHHTTSTTSTTSHHHHHHHHHHHHH-HTTCHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHH-HhcCHHHHHHH
Confidence            666667777777777766422231      12334444444 45666655553

>2yhc_A BAMD, UPF0169 lipoprotein YFIO; essential BAM component, membrane protein; 1.80A {Escherichia coli} PDB: 3tgo_A 3q5m_A

Probab=98.63  E-value=2e-06  Score=73.90  Aligned_cols=178  Identities=11%  Similarity=-0.045  Sum_probs=114.0

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhccc--CC----hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHH----H
Q 040371           75 NFILSAALIDMYSKCGKIQMAKEVFDTVQR--ND----VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSI----T  144 (410)
Q Consensus        75 ~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~----t  144 (410)
                      +...+..+...+.+.|++++|...|+++..  |+    ...+..+..+|.+.|++++|+..|++..+.  .|+..    .
T Consensus         3 ~~~~~~~~a~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~a~~~lg~~~~~~~~~~~A~~~~~~~l~~--~P~~~~~~~a   80 (225)
T 2yhc_A            3 PPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRL--NPTHPNIDYV   80 (225)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCTTHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--CcCCCcHHHH
Confidence            345566677788889999999999998764  32    246777888899999999999999998874  33321    3


Q ss_pred             HHHHHHHHHc------------------cCCHHHHHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040371          145 FLGLLTACSH------------------CGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSMT  205 (410)
Q Consensus       145 ~~~ll~a~~~------------------~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~  205 (410)
                      +..+..++..                  .|+.++|...|+.+.+.   .|+ ...+.+.....    ......       
T Consensus        81 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~l~~---~P~~~~a~~a~~~l~----~~~~~~-------  146 (225)
T 2yhc_A           81 MYMRGLTNMALDDSALQGFFGVDRSDRDPQQARAAFSDFSKLVRG---YPNSQYTTDATKRLV----FLKDRL-------  146 (225)
T ss_dssp             HHHHHHHHHHHHC--------------CCHHHHHHHHHHHHHHTT---CTTCTTHHHHHHHHH----HHHHHH-------
T ss_pred             HHHHHHHHHhhhhhhhhhhhccchhhcCcHHHHHHHHHHHHHHHH---CcCChhHHHHHHHHH----HHHHHH-------
Confidence            3333344433                  45667777777776643   222 22222111100    000000       


Q ss_pred             CCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCC---chHHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 040371          206 MEPDVVVWRALLSACRTFKRLELGEVA---IVNISRLMG---GDYVLLSNMYCYLKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       206 ~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~---~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  272 (410)
                          ......+...+...|+++.|...   +.+..|.++   ..+..+..+|.+.|++++|.+.++.+...+.
T Consensus       147 ----~~~~~~~a~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~l~~~~~~~g~~~~A~~~~~~l~~~~~  215 (225)
T 2yhc_A          147 ----AKYEYSVAEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSS  215 (225)
T ss_dssp             ----HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCCS
T ss_pred             ----HHHHHHHHHHHHHcCcHHHHHHHHHHHHHHCcCCCccHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhCC
Confidence                00112344557788888888888   444556554   4577889999999999999999999888754

>2r5s_A Uncharacterized protein VP0806; APC090868.1, vibrio parahaemolyticus RIMD 22 structural genomics, PSI-2, protein structure initiative; HET: MES; 2.14A {Vibrio parahaemolyticus}

Probab=98.62  E-value=3.4e-07  Score=75.50  Aligned_cols=161  Identities=6%  Similarity=-0.048  Sum_probs=123.7

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH-
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM-   85 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~-   85 (410)
                      ..+..+...+.+.|++++|+..|++..+.. +-+...+..+..++...|++++|...++.+.+...  +......+... 
T Consensus         7 ~~~~~~a~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~la~~~~~~g~~~~A~~~~~~a~~~~p--~~~~~~~~~~~~   83 (176)
T 2r5s_A            7 EQLLKQVSELLQQGEHAQALNVIQTLSDEL-QSRGDVKLAKADCLLETKQFELAQELLATIPLEYQ--DNSYKSLIAKLE   83 (176)
T ss_dssp             TTHHHHHHHHHHTTCHHHHHHHHHTSCHHH-HTSHHHHHHHHHHHHHTTCHHHHHHHHTTCCGGGC--CHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHhhhccC--ChHHHHHHHHHH
Confidence            345667788999999999999999887642 33677899999999999999999999999877542  44444333222 


Q ss_pred             HHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHH
Q 040371           86 YSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a  161 (410)
                      +.+.+....|...|++..+  | +...|..+...|...|++++|...|++..+....+ +...+..+...+...|+.++|
T Consensus        84 ~~~~~~~~~a~~~~~~al~~~P~~~~~~~~la~~~~~~g~~~~A~~~~~~~l~~~p~~~~~~a~~~l~~~~~~~g~~~~A  163 (176)
T 2r5s_A           84 LHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAI  163 (176)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCTTTTTTHHHHHHHHHHHHHCSSCHH
T ss_pred             HHhhcccchHHHHHHHHHHhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHhCCCCcH
Confidence            2232333456778877653  3 57889999999999999999999999998864332 355788889999999999999


Q ss_pred             HHHHHHhhh
Q 040371          162 RKYFDHMRS  170 (410)
Q Consensus       162 ~~~~~~m~~  170 (410)
                      ...|+....
T Consensus       164 ~~~y~~al~  172 (176)
T 2r5s_A          164 ASKYRRQLY  172 (176)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999987653

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.61  E-value=1.9e-06  Score=65.59  Aligned_cols=96  Identities=16%  Similarity=0.217  Sum_probs=58.6

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      ...|..+...|.+.|++++|++.|+++.... +.+..++..+..++...|++++|...++.+.+.. +.+..++..+...
T Consensus         9 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~   86 (125)
T 1na0_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNA   86 (125)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHH
Confidence            4566667777777777777777777766542 3345556666666666666666666666666543 3345555555666


Q ss_pred             HHhcCCHHHHHHHHHhcc
Q 040371           86 YSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~  103 (410)
                      |.+.|++++|...|+++.
T Consensus        87 ~~~~~~~~~A~~~~~~~~  104 (125)
T 1na0_A           87 YYKQGDYDEAIEYYQKAL  104 (125)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHHH
Confidence            666666666666655543

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.57  E-value=1.1e-07  Score=76.32  Aligned_cols=113  Identities=8%  Similarity=-0.119  Sum_probs=70.5

Q ss_pred             HHHHHHhcCCHHHHHHHHHhcccC---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCC
Q 040371           82 LIDMYSKCGKIQMAKEVFDTVQRN---DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGL  157 (410)
Q Consensus        82 li~~y~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~  157 (410)
                      |..+|...|++++|+..|+.....   +...|..+...|.+.|++++|++.|++..+.  .| +..++..+...+...|+
T Consensus         3 LG~~~~~~~~~e~ai~~~~~a~~~~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~--~p~~~~a~~~lg~~~~~~~~   80 (150)
T 4ga2_A            3 LGSMRRSKADVERYIASVQGSTPSPRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINV--QERDPKAHRFLGLLYELEEN   80 (150)
T ss_dssp             ----CCCHHHHHHHHHHHHHHSCSHHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHcChHHHHHHHHHHhcccCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCc
Confidence            344555667777777777665543   3345666677777777777777777777663  33 45566667777777777


Q ss_pred             HHHHHHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHHH
Q 040371          158 VEEGRKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAYG  199 (410)
Q Consensus       158 ~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~  199 (410)
                      +++|...|+...+.   .| +...|..+...|.+.|++++|.+
T Consensus        81 ~~~A~~~~~~al~~---~p~~~~~~~~la~~~~~~~~~~~aa~  120 (150)
T 4ga2_A           81 TDKAVECYRRSVEL---NPTQKDLVLKIAELLCKNDVTDGRAK  120 (150)
T ss_dssp             HHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHCSSSSHHH
T ss_pred             hHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHcCChHHHHH
Confidence            77777777776642   33 35566666666777776655443

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.56  E-value=4.4e-06  Score=74.86  Aligned_cols=164  Identities=12%  Similarity=-0.045  Sum_probs=106.9

Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc-----HHHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----
Q 040371           41 KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN-----FILSAALIDMYSKCGKIQMAKEVFDTVQR-----ND----  106 (410)
Q Consensus        41 ~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~-----~~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~~----  106 (410)
                      ...+...+..+...|++++|.+.+...++......     ...+..+...|...|++++|...|++..+     .+    
T Consensus        75 ~~~l~~~~~~~~~~~~y~~A~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~  154 (293)
T 2qfc_A           75 KKQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQN  154 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHTSSCHHHHHHHHHHHHTTCCCSSCTTHH
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHHHHHHhccccCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcCCchHHH
Confidence            44566667777777888888777777766432211     12344566667777888888888776532     11    


Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHHHHC-CCCCC-----HHHHHHHHHHHHccCCHHHHHHHHHHhhhh---cCCCCC
Q 040371          107 VSVWNAMISGVAIHGLAADASAIFTKMEMF-NVLPD-----SITFLGLLTACSHCGLVEEGRKYFDHMRSR---YSIQPQ  177 (410)
Q Consensus       107 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~-----~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~---~~~~~~  177 (410)
                      ..+|+.+...|...|++++|+..|++.... ...|+     ..++..+...|...|++++|..+++...+-   .+....
T Consensus       155 ~~~~~~lg~~y~~~~~~~~A~~~~~kal~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~Al~~~~kal~~~~~~~~~~~  234 (293)
T 2qfc_A          155 LYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMAL  234 (293)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCSS
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcCccccchHHHHHhHHHHHHHHhhHHHHHHHHHHHHHHHHhcCcHHH
Confidence            347777888888888888888888877621 01112     146777788888888888888888876532   111111


Q ss_pred             -hhHHHHHHHHHHhcCCHHHH-HHHHHhC
Q 040371          178 -LEHYGAMVDLLGRAGHIEEA-YGLITSM  204 (410)
Q Consensus       178 -~~~~~~li~~~~~~g~~~~A-~~~~~~m  204 (410)
                       ..+|..+...|.+.|++++| ...+++.
T Consensus       235 ~~~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          235 IGQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence             45677888888888888888 5555543

>1a17_A Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, S helix; 2.45A {Homo sapiens} SCOP: a.118.8.1 PDB: 2bug_A

Probab=98.56  E-value=3.5e-06  Score=67.87  Aligned_cols=125  Identities=11%  Similarity=0.073  Sum_probs=74.5

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      ..|..+...+...|++++|+..|++..+.. +.+..++..+..++...|++++|...+...++.. +.+..++..+...|
T Consensus        14 ~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~   91 (166)
T 1a17_A           14 EELKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASN   91 (166)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHH
Confidence            456666777777777777777777766542 3345566666666677777777777777666653 33455666666666


Q ss_pred             HhcCCHHHHHHHHHhccc--C-ChhhHHHH--HHHHHHcCChHHHHHHHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQR--N-DVSVWNAM--ISGVAIHGLAADASAIFTKM  133 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~--~-~~~~~~~l--i~~~~~~g~~~~A~~l~~~m  133 (410)
                      .+.|++++|...|++..+  | +...|..+  ...+...|++++|++.+.+.
T Consensus        92 ~~~~~~~~A~~~~~~a~~~~p~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~~  143 (166)
T 1a17_A           92 MALGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHK  143 (166)
T ss_dssp             HHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHcccch
Confidence            666666666666665542  1 23333222  22244555566666555543

>2vsy_A XCC0866; transferase, glycosyl transferase, GT-B, OGT, protein O-GLCN; HET: NHE; 2.10A {Xanthomonas campestris PV} PDB: 2jlb_A* 2xgm_A* 2xgo_A* 2xgs_A* 2vsn_A*

Probab=98.56  E-value=1.4e-06  Score=85.91  Aligned_cols=147  Identities=8%  Similarity=-0.010  Sum_probs=98.9

Q ss_pred             hCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHH
Q 040371           54 LGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIF  130 (410)
Q Consensus        54 ~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~  130 (410)
                      .|++++|.+.++++++.. +.+...+..+...|.+.|++++|.+.|++..+   .+...|..+...|.+.|++++|++.|
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            367788888888877653 34577888888888888888888888887654   25667888888888888888888888


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhc---CCHHHHHHHHHhC
Q 040371          131 TKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRA---GHIEEAYGLITSM  204 (410)
Q Consensus       131 ~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~---g~~~~A~~~~~~m  204 (410)
                      ++..+.. +.+...+..+..++...|++++|.+.|+...+.  -+.+...+..+...|...   |++++|.+.+++.
T Consensus        81 ~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~g~~~~A~~~~~~a  154 (568)
T 2vsy_A           81 QQASDAA-PEHPGIALWLGHALEDAGQAEAAAAAYTRAHQL--LPEEPYITAQLLNWRRRLCDWRALDVLSAQVRAA  154 (568)
T ss_dssp             HHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCCTTHHHHHHHHHHH
T ss_pred             HHHHhcC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHhhccccHHHHHHHHHHH
Confidence            8887742 224667777888888888888888888887753  123466777888888888   8888888888776

>4ga2_A E3 SUMO-protein ligase ranbp2; TPR motif, nuclear pore complex component nucleocytoplasmic transport, transport protein; 0.95A {Pan troglodytes} PDB: 4ga0_A 4ga1_A*

Probab=98.56  E-value=3.4e-07  Score=73.42  Aligned_cols=118  Identities=8%  Similarity=-0.096  Sum_probs=72.7

Q ss_pred             HHHHcCCHhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHH
Q 040371           15 GFVRNARFDEALRFFREMLSSKVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQ   93 (410)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~   93 (410)
                      .+...|++++|++.|++....  .| +...+..+...+...|++++|.+.+++.++.. +.+..++..+..+|.+.|+++
T Consensus         6 ~~~~~~~~e~ai~~~~~a~~~--~p~~~~~~~~la~~y~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~   82 (150)
T 4ga2_A            6 MRRSKADVERYIASVQGSTPS--PRQKSIKGFYFAKLYYEAKEYDLAKKYICTYINVQ-ERDPKAHRFLGLLYELEENTD   82 (150)
T ss_dssp             -CCCHHHHHHHHHHHHHHSCS--HHHHHTTHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHcChHHHHHHHHHHhccc--CcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCchH
Confidence            344456677777777665432  23 23345556666777777777777777776664 345666777777777777777


Q ss_pred             HHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHH-HHHHHH
Q 040371           94 MAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAI-FTKMEM  135 (410)
Q Consensus        94 ~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l-~~~m~~  135 (410)
                      +|...|++..+  | +..+|..+...|.+.|+.++|.+. +++..+
T Consensus        83 ~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~~~~aa~~~~~~al~  128 (150)
T 4ga2_A           83 KAVECYRRSVELNPTQKDLVLKIAELLCKNDVTDGRAKYWVERAAK  128 (150)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCSSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence            77777766542  2 455666666667666766655544 355544

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.54  E-value=2.4e-06  Score=75.32  Aligned_cols=198  Identities=11%  Similarity=-0.011  Sum_probs=139.2

Q ss_pred             HHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHH-------HHHHHhhCCHHHHHHHHHHHHH------------cCC---
Q 040371           15 GFVRNARFDEALRFFREMLSSKVEPDKFTFASV-------IYGCARLGALNHAYWVHNLIIE------------KKI---   72 (410)
Q Consensus        15 ~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~l-------l~a~~~~~~~~~a~~~~~~~~~------------~g~---   72 (410)
                      ++ +.++..+|.+.|.+..+.. +-....|..+       ..++.+.+...++...+...++            .|+   
T Consensus        16 ~~-~~~d~~~A~~~F~~a~~~d-P~~~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~l~p~~l~a~~~~~g~y~~   93 (282)
T 4f3v_A           16 SM-LPMSEARSLDLFTEITNYD-ESACDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQISMSTLNARIAIGGLYGD   93 (282)
T ss_dssp             HH-TTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTTCCGGGGCCEEECCTTTCC
T ss_pred             cc-cCCCHHHHHHHHHHHHHhC-hhhhHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhccCCcccc
Confidence            45 6899999999999998753 2245677776       4555555554444444444433            121   


Q ss_pred             -----CccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC--HH
Q 040371           73 -----ELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD--SI  143 (410)
Q Consensus        73 -----~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~--~~  143 (410)
                           ..-..+.-.+..++...|++++|.++|+.+..  |+-.....+...+.+.+++++|+..|+...... .|.  ..
T Consensus        94 ~~~~v~~r~dl~LayA~~L~~~g~y~eA~~~l~~~~~~~p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~-d~~~~~~  172 (282)
T 4f3v_A           94 ITYPVTSPLAITMGFAACEAAQGNYADAMEALEAAPVAGSEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWP-DKFLAGA  172 (282)
T ss_dssp             CEEECSSHHHHHHHHHHHHHHHTCHHHHHHHHTSSCCTTCHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCS-CHHHHHH
T ss_pred             cccccCCHhHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCchHHHHHHHHHHHHcCCHHHHHHHHHHhhccC-CcccHHH
Confidence                 01134556778889999999999999999864  433366667778899999999999998554321 121  23


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC--hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHHHH
Q 040371          144 TFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ--LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWRAL  216 (410)
Q Consensus       144 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~--~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~~l  216 (410)
                      .+..+-.++...|++++|+..|++.... ...|.  .........++.+.|+.++|..+|+++ ...|+...+..|
T Consensus       173 a~~~LG~al~~LG~~~eAl~~l~~a~~g-~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~~P~~~~~~aL  247 (282)
T 4f3v_A          173 AGVAHGVAAANLALFTEAERRLTEANDS-PAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTTHPEPKVAAAL  247 (282)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHTS-TTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSCCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHhcC-CCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHH
Confidence            5777888999999999999999998742 33254  346677788899999999999999998 456774444433

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.50  E-value=0.00011  Score=65.97  Aligned_cols=180  Identities=8%  Similarity=-0.022  Sum_probs=109.5

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhhC--CHHHHHHHHHHHHHcCCCccHHHHHHHHHHH----Hhc-
Q 040371           18 RNARFDEALRFFREMLSSKVEP-DKFTFASVIYGCARLG--ALNHAYWVHNLIIEKKIELNFILSAALIDMY----SKC-   89 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~~~~--~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y----~~~-   89 (410)
                      +....++|++++.+++..  .| +...|+.--.++...+  +++++.++++.++... +.+..+|+.--..+    .+. 
T Consensus        45 ~~e~s~~aL~~t~~~L~~--nP~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~n-Pk~y~aW~~R~~iL~~~~~~l~  121 (306)
T 3dra_A           45 AEEYSERALHITELGINE--LASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDN-EKNYQIWNYRQLIIGQIMELNN  121 (306)
T ss_dssp             TTCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHC-TTCCHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCHHHHHHHHHHHHH--CcHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHC-cccHHHHHHHHHHHHHHHHhcc
Confidence            334456788888888764  34 4456777667777777  7888888888887764 34555665544444    444 


Q ss_pred             --CCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChH--HHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC-----
Q 040371           90 --GKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAA--DASAIFTKMEMFNVLPDSITFLGLLTACSHCGL-----  157 (410)
Q Consensus        90 --g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~--~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~-----  157 (410)
                        ++++++..+++++.+   +|-.+|+--.-.+.+.|.++  ++++.++++.+... -|...++.-.....+.+.     
T Consensus       122 ~~~~~~~EL~~~~~~l~~~pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~d~-~N~sAW~~R~~ll~~l~~~~~~~  200 (306)
T 3dra_A          122 NDFDPYREFDILEAMLSSDPKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDTDL-KNNSAWSHRFFLLFSKKHLATDN  200 (306)
T ss_dssp             TCCCTHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHSSGGGCCHH
T ss_pred             ccCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhccccchhh
Confidence              677777777777764   35566666666666677776  77777777776532 245555554444455444     


Q ss_pred             -HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHH-HHHHHHh
Q 040371          158 -VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEE-AYGLITS  203 (410)
Q Consensus       158 -~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~-A~~~~~~  203 (410)
                       ++++.+.++.+...  -+-|...|+-+-..+.+.|+..+ +..+..+
T Consensus       201 ~~~eEl~~~~~aI~~--~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~  246 (306)
T 3dra_A          201 TIDEELNYVKDKIVK--CPQNPSTWNYLLGIHERFDRSITQLEEFSLQ  246 (306)
T ss_dssp             HHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHTTCCGGGGHHHHHT
T ss_pred             hHHHHHHHHHHHHHh--CCCCccHHHHHHHHHHhcCCChHHHHHHHHH
Confidence             56666666665532  12345566666666666555332 3334444

>3dra_A Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha; geranylgeranyltrasferase, ggtase, ggtase-I, PGGT, prenyltransferase, farnesyltransferase; HET: B3P GRG; 1.80A {Candida albicans}

Probab=98.50  E-value=3.7e-05  Score=69.07  Aligned_cols=210  Identities=12%  Similarity=0.127  Sum_probs=161.6

Q ss_pred             CHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC--CHHHHHHHHHhccc---CChhhHHHHHHHH----HHc---CCh
Q 040371           56 ALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG--KIQMAKEVFDTVQR---NDVSVWNAMISGV----AIH---GLA  123 (410)
Q Consensus        56 ~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g--~~~~A~~~f~~m~~---~~~~~~~~li~~~----~~~---g~~  123 (410)
                      ..++|.+..+.++..+ +-+..+|+.--......|  ++++++++++.+..   .+..+|+.--..+    ...   +++
T Consensus        48 ~s~~aL~~t~~~L~~n-P~~~taWn~R~~~L~~l~~~~~~eeL~~~~~~L~~nPk~y~aW~~R~~iL~~~~~~l~~~~~~  126 (306)
T 3dra_A           48 YSERALHITELGINEL-ASHYTIWIYRFNILKNLPNRNLYDELDWCEEIALDNEKNYQIWNYRQLIIGQIMELNNNDFDP  126 (306)
T ss_dssp             CSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCTTSCHHHHHHHHHHHHHHCTTCCHHHHHHHHHHHHHHHHTTTCCCT
T ss_pred             CCHHHHHHHHHHHHHC-cHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHhccccCCH
Confidence            4468999999999875 456788998888888888  99999999998874   3556777765555    555   789


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHH--HHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCC------HH
Q 040371          124 ADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVE--EGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGH------IE  195 (410)
Q Consensus       124 ~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~--~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~------~~  195 (410)
                      ++++++++++.+.. +-|...+..-.-...+.|.++  ++.++++.+.+. . .-|-..|+.-...+.+.|.      ++
T Consensus       127 ~~EL~~~~~~l~~~-pkny~aW~~R~~vl~~l~~~~~~~EL~~~~~~i~~-d-~~N~sAW~~R~~ll~~l~~~~~~~~~~  203 (306)
T 3dra_A          127 YREFDILEAMLSSD-PKNHHVWSYRKWLVDTFDLHNDAKELSFVDKVIDT-D-LKNNSAWSHRFFLLFSKKHLATDNTID  203 (306)
T ss_dssp             HHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHHSSGGGCCHHHHH
T ss_pred             HHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhcccChHHHHHHHHHHHHh-C-CCCHHHHHHHHHHHHhccccchhhhHH
Confidence            99999999999853 336777877777777888888  999999999864 2 3356677766666777776      88


Q ss_pred             HHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhH-HHHHHH---hhc---cCCCchHHHHHHHHHhcCChhHHHHHHHH
Q 040371          196 EAYGLITSM-TMEP-DVVVWRALLSACRTFKRLEL-GEVAIV---NIS---RLMGGDYVLLSNMYCYLKRWDTAENVREI  266 (410)
Q Consensus       196 ~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~-a~~~~~---~~~---~~~~~~~~~l~~~~~~~g~~~~a~~~~~~  266 (410)
                      ++++.++++ ...| |...|+-+-..+...|+... ...+..   ...   +.++.....+..+|.+.|+.++|.++++.
T Consensus       204 eEl~~~~~aI~~~p~n~SaW~y~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~s~~al~~la~~~~~~~~~~~A~~~~~~  283 (306)
T 3dra_A          204 EELNYVKDKIVKCPQNPSTWNYLLGIHERFDRSITQLEEFSLQFVDLEKDQVTSSFALETLAKIYTQQKKYNESRTVYDL  283 (306)
T ss_dssp             HHHHHHHHHHHHCSSCHHHHHHHHHHHHHTTCCGGGGHHHHHTTEEGGGTEESCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCccHHHHHHHHHHhcCCChHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Confidence            899888876 4445 78889888888888877444 333422   233   55666788899999999999999999999


Q ss_pred             HHh
Q 040371          267 MKK  269 (410)
Q Consensus       267 m~~  269 (410)
                      +.+
T Consensus       284 l~~  286 (306)
T 3dra_A          284 LKS  286 (306)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            876

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.48  E-value=4.3e-06  Score=64.47  Aligned_cols=115  Identities=7%  Similarity=-0.025  Sum_probs=82.2

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +...|..+...|.+.|++++|+..|++..+.. +.+...+..+..++...|++++|.+.++.+.+.. +.+..++..+..
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~   92 (133)
T 2lni_A           15 LALMVKNKGNECFQKGDYPQAMKHYTEAIKRN-PKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAA   92 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHH
Confidence            45678888888888888888888888887642 3366677777788888888888888888887764 345677777777


Q ss_pred             HHHhcCCHHHHHHHHHhcccC---ChhhHHHHHHHHHHcC
Q 040371           85 MYSKCGKIQMAKEVFDTVQRN---DVSVWNAMISGVAIHG  121 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~g  121 (410)
                      .|.+.|++++|.+.|++..+.   +...|..+...+.+.|
T Consensus        93 ~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~  132 (133)
T 2lni_A           93 ALEAMKDYTKAMDVYQKALDLDSSCKEAADGYQRCMMAQY  132 (133)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCGGGTHHHHHHHHHHHHHT
T ss_pred             HHHHHhhHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhc
Confidence            788888888888877765432   3345555555554443

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.47  E-value=2.6e-06  Score=71.26  Aligned_cols=116  Identities=12%  Similarity=0.003  Sum_probs=56.8

Q ss_pred             HHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc----CCC-ccHHHHHHHHHHHHhcCC
Q 040371           17 VRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK----KIE-LNFILSAALIDMYSKCGK   91 (410)
Q Consensus        17 ~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~~-~~~~~~~~li~~y~~~g~   91 (410)
                      ...|++++|.+.++..... ......++..+...+...|+++.|...+++.++.    +.. ....+++.+...|...|+
T Consensus         3 ~~~g~~~~A~~~~~~~~~~-~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~   81 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLAH-PATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGN   81 (203)
T ss_dssp             ----CHHHHHHHHHHHHTS-TTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             cccccHHHHHHHHHHhcCC-hHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCC
Confidence            3567777777744444321 1223446666666666667777776666665542    111 123445555555666666


Q ss_pred             HHHHHHHHHhccc-----C-C----hhhHHHHHHHHHHcCChHHHHHHHHHH
Q 040371           92 IQMAKEVFDTVQR-----N-D----VSVWNAMISGVAIHGLAADASAIFTKM  133 (410)
Q Consensus        92 ~~~A~~~f~~m~~-----~-~----~~~~~~li~~~~~~g~~~~A~~l~~~m  133 (410)
                      +++|...|++...     + +    ..+++.+...|...|++++|...|++.
T Consensus        82 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~a  133 (203)
T 3gw4_A           82 WDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKS  133 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence            6665555554321     1 1    123444444444455555555555444

>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=98.47  E-value=2.2e-06  Score=76.50  Aligned_cols=97  Identities=6%  Similarity=-0.036  Sum_probs=58.7

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +...|..+...|.+.|++++|+..|++..... +.+...|..+..++...|++++|...++..++.. +.+...+..+..
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~   80 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQ   80 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence            34556666666667777777777776666532 2245566666666666666666666666666543 334555666666


Q ss_pred             HHHhcCCHHHHHHHHHhcc
Q 040371           85 MYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~  103 (410)
                      +|.+.|++++|...|++..
T Consensus        81 ~~~~~g~~~~A~~~~~~al   99 (281)
T 2c2l_A           81 CQLEMESYDEAIANLQRAY   99 (281)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHH
Confidence            6666666666666665543

>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=98.47  E-value=9.1e-06  Score=72.76  Aligned_cols=163  Identities=10%  Similarity=-0.064  Sum_probs=87.8

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcC-CCccH----HHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----h
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKK-IELNF----ILSAALIDMYSKCGKIQMAKEVFDTVQR-----ND----V  107 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g-~~~~~----~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~~----~  107 (410)
                      ..+...+..+...|+++.|..+++...+.. ..|+.    ..+..+...|...|++++|...|++...     .+    .
T Consensus        76 ~~l~~~i~~~~~~~~y~~a~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~  155 (293)
T 3u3w_A           76 KQFKDQVIMLCKQKRYKEIYNKVWNELKKEEYHPEFQQFLQWQYYVAAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNL  155 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHHHhccccCChHHHHHHHHHHHHHHHHHcccCHHHHHHHHHHHHHHhcccccHHHHH
Confidence            344444555566666666666666655532 12221    1233455555566666666666665432     12    1


Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHHHHC-----CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhhhh---cCCCCC-
Q 040371          108 SVWNAMISGVAIHGLAADASAIFTKMEMF-----NVLPD-SITFLGLLTACSHCGLVEEGRKYFDHMRSR---YSIQPQ-  177 (410)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~---~~~~~~-  177 (410)
                      .+|+.+...|...|++++|+..|++..+.     +..|. ..++..+...|.+.|++++|..+++...+-   .+..+. 
T Consensus       156 ~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~nlg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~  235 (293)
T 3u3w_A          156 YIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYNHAKALYLDSRYEESLYQVNKAIEISCRINSMALI  235 (293)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHH
Confidence            24666666666666666666666666531     11222 225566666666777777777766665431   122222 


Q ss_pred             hhHHHHHHHHHHhcCC-HHHHHHHHHhC
Q 040371          178 LEHYGAMVDLLGRAGH-IEEAYGLITSM  204 (410)
Q Consensus       178 ~~~~~~li~~~~~~g~-~~~A~~~~~~m  204 (410)
                      ...|..+...|.+.|+ +++|.+.+++.
T Consensus       236 ~~~~~~lg~~~~~~g~~~~~A~~~~~~A  263 (293)
T 3u3w_A          236 GQLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence            4566666667777773 46665555543

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.45  E-value=7.7e-06  Score=62.63  Aligned_cols=115  Identities=10%  Similarity=0.007  Sum_probs=73.6

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      ...|..+...+...|++++|+..|++..... +.+...+..+..++...|++++|.+.+....+.. +.+..++..+...
T Consensus        12 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~   89 (131)
T 2vyi_A           12 AERLKTEGNEQMKVENFEAAVHFYGKAIELN-PANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLA   89 (131)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHccCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHH
Confidence            4466677777777777777777777776542 3355666667777777777777777777776653 3345666666666


Q ss_pred             HHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCC
Q 040371           86 YSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGL  122 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~  122 (410)
                      |.+.|++++|...|++..+   .+...|..+...+.+.|+
T Consensus        90 ~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           90 LSSLNKHVEAVAYYKKALELDPDNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             HHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTT
T ss_pred             HHHhCCHHHHHHHHHHHHhcCccchHHHHHHHHHHHHHhc
Confidence            7777777777776665542   244455555555555544

>3gw4_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, no structural genomics consortium, NESG, DRR162B; 2.49A {Deinococcus radiodurans R1}

Probab=98.44  E-value=6.7e-06  Score=68.71  Aligned_cols=152  Identities=13%  Similarity=0.045  Sum_probs=109.8

Q ss_pred             HhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc------C---ChhhHHHHHHHHHHcCC
Q 040371           52 ARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR------N---DVSVWNAMISGVAIHGL  122 (410)
Q Consensus        52 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~------~---~~~~~~~li~~~~~~g~  122 (410)
                      ...|++++|.++++.+.. .......+++.+...|...|++++|...|++...      .   ...+++.+...|...|+
T Consensus         3 ~~~g~~~~A~~~~~~~~~-~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~   81 (203)
T 3gw4_A            3 FEAHDYALAERQAQALLA-HPATASGARFMLGYVYAFMDRFDEARASFQALQQQAQKSGDHTAEHRALHQVGMVERMAGN   81 (203)
T ss_dssp             ----CHHHHHHHHHHHHT-STTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTC
T ss_pred             cccccHHHHHHHHHHhcC-ChHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHcCC
Confidence            457889999986655543 2234678889999999999999999999987653      1   34578888889999999


Q ss_pred             hHHHHHHHHHHHHC----CCCC--CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC----hhHHHHHHHHHHhcC
Q 040371          123 AADASAIFTKMEMF----NVLP--DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ----LEHYGAMVDLLGRAG  192 (410)
Q Consensus       123 ~~~A~~l~~~m~~~----g~~p--~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~----~~~~~~li~~~~~~g  192 (410)
                      +++|...|++....    +-.|  ....+..+...+...|++++|...+++..+...-..+    ...+..+...|...|
T Consensus        82 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g  161 (203)
T 3gw4_A           82 WDAARRCFLEERELLASLPEDPLAASANAYEVATVALHFGDLAGARQEYEKSLVYAQQADDQVAIACAFRGLGDLAQQEK  161 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHCc
Confidence            99999999887653    2122  1345777888888999999999999887642111112    234678888899999


Q ss_pred             CHHHHHHHHHhC
Q 040371          193 HIEEAYGLITSM  204 (410)
Q Consensus       193 ~~~~A~~~~~~m  204 (410)
                      ++++|.+.+++.
T Consensus       162 ~~~~A~~~~~~a  173 (203)
T 3gw4_A          162 NLLEAQQHWLRA  173 (203)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH
Confidence            999998887765

>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=98.42  E-value=5.6e-05  Score=67.53  Aligned_cols=120  Identities=14%  Similarity=0.003  Sum_probs=58.9

Q ss_pred             HHHHHccCCHHHHHHHHHHhhhhcCCCCC----hhHHHHHHHHHHhcCCHHHHHHHHHhCC-------C-CCC-HHHHHH
Q 040371          149 LTACSHCGLVEEGRKYFDHMRSRYSIQPQ----LEHYGAMVDLLGRAGHIEEAYGLITSMT-------M-EPD-VVVWRA  215 (410)
Q Consensus       149 l~a~~~~g~~~~a~~~~~~m~~~~~~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~m~-------~-~p~-~~~~~~  215 (410)
                      ...+...|++++|...|+...+...-.++    ...++.+...|...|++++|...|++.-       . .+. ..++..
T Consensus       122 ~~~~~~~~~~~~Ai~~~~~al~~~~~~~~~~~~~~~~~~lg~~y~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~n  201 (293)
T 3u3w_A          122 AAYVLKKVDYEYCILELKKLLNQQLTGIDVYQNLYIENAIANIYAENGYLKKGIDLFEQILKQLEALHDNEEFDVKVRYN  201 (293)
T ss_dssp             HHHHTTSSCHHHHHHHHHHHHHTCCCCSCTTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHH
T ss_pred             HHHHHcccCHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcccchhHHHHHHHH
Confidence            33334444555555555554431111111    1134555555555555555555444430       0 111 124445


Q ss_pred             HHHHHHhcCchhHHHHHH---HhhccC------CCchHHHHHHHHHhcCC-hhHHHHHHHHHH
Q 040371          216 LLSACRTFKRLELGEVAI---VNISRL------MGGDYVLLSNMYCYLKR-WDTAENVREIMK  268 (410)
Q Consensus       216 li~~~~~~g~~~~a~~~~---~~~~~~------~~~~~~~l~~~~~~~g~-~~~a~~~~~~m~  268 (410)
                      +...|...|++++|...+   .++.+.      -..+|..+..+|.+.|+ +++|.+.+++..
T Consensus       202 lg~~y~~~~~y~~A~~~~~~al~~~~~~~~~~~~~~~~~~lg~~~~~~g~~~~~A~~~~~~Al  264 (293)
T 3u3w_A          202 HAKALYLDSRYEESLYQVNKAIEISCRINSMALIGQLYYQRGECLRKLEYEEAEIEDAYKKAS  264 (293)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTBCTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHH
Confidence            555555555555555551   111111      13467778888888884 588888877654

>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=98.39  E-value=8.1e-06  Score=65.71  Aligned_cols=89  Identities=7%  Similarity=-0.025  Sum_probs=38.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC
Q 040371           80 AALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCG  156 (410)
Q Consensus        80 ~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g  156 (410)
                      ..+...|...|++++|...|++...   .+..+|..+...|...|++++|+..|++..... +.+...+..+..++...|
T Consensus        17 ~~~a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~   95 (166)
T 1a17_A           17 KTQANDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALG   95 (166)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHccCHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHHHHHHHHHhc
Confidence            3333444444444444444443321   133344444444444444444444444444321 112333444444444444


Q ss_pred             CHHHHHHHHHHhh
Q 040371          157 LVEEGRKYFDHMR  169 (410)
Q Consensus       157 ~~~~a~~~~~~m~  169 (410)
                      ++++|...|+...
T Consensus        96 ~~~~A~~~~~~a~  108 (166)
T 1a17_A           96 KFRAALRDYETVV  108 (166)
T ss_dssp             CHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHH
Confidence            4444444444444

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=98.39  E-value=2e-05  Score=70.52  Aligned_cols=26  Identities=12%  Similarity=-0.011  Sum_probs=18.2

Q ss_pred             chHHHHHHHHHhcCChhHH-HHHHHHH
Q 040371          242 GDYVLLSNMYCYLKRWDTA-ENVREIM  267 (410)
Q Consensus       242 ~~~~~l~~~~~~~g~~~~a-~~~~~~m  267 (410)
                      .+|..+..+|.+.|++++| ...+++.
T Consensus       237 ~~~~~lg~~y~~~g~~~~Ai~~~~~~A  263 (293)
T 2qfc_A          237 QLYYQRGECLRKLEYEEAEIEDAYKKA  263 (293)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence            3566677788888888888 6656554

>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=98.39  E-value=3.5e-06  Score=69.11  Aligned_cols=118  Identities=12%  Similarity=0.129  Sum_probs=85.0

Q ss_pred             HHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH-HHhcCCH--H
Q 040371           17 VRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM-YSKCGKI--Q   93 (410)
Q Consensus        17 ~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~-y~~~g~~--~   93 (410)
                      ...|++++|+..|++..... +.+...|..+..++...|+++.|...++.+++.. +.+..++..+..+ |.+.|++  +
T Consensus        21 ~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~l~~~~~~~~~~   98 (177)
T 2e2e_A           21 ASQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLR-GENAELYAALATVLYYQASQHMTA   98 (177)
T ss_dssp             C-----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHH-CSCHHHHHHHHHHHHHHTTTCCCH
T ss_pred             hhccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHhcCCcchH
Confidence            45677888888888877643 3466778888888888888888888888887764 3466677777777 7778887  8


Q ss_pred             HHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHC
Q 040371           94 MAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMF  136 (410)
Q Consensus        94 ~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  136 (410)
                      +|...|++...   .+...|..+...|...|++++|...|++....
T Consensus        99 ~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~  144 (177)
T 2e2e_A           99 QTRAMIDKALALDSNEITALMLLASDAFMQANYAQAIELWQKVMDL  144 (177)
T ss_dssp             HHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCcHHHHHHHHHHHHHcccHHHHHHHHHHHHhh
Confidence            88888877653   24567777777888888888888888887764

>1na0_A Designed protein CTPR3; de novo protein; HET: IPT; 1.60A {Unidentified} SCOP: k.38.1.1 PDB: 2wqh_A 3kd7_A

Probab=98.38  E-value=1.5e-05  Score=60.33  Aligned_cols=93  Identities=16%  Similarity=0.104  Sum_probs=48.9

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHH
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVA  118 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~  118 (410)
                      ..+..+...+...|+++.|.+.++.+.+.. +.+..++..+...|.+.|++++|...|+++..   .+..+|..+...|.
T Consensus        10 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~la~~~~   88 (125)
T 1na0_A           10 EAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYY   88 (125)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHHC-cCcHHHHHHHHHHHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHH
Confidence            345555555555666666666665555543 23444555555555555555555555554432   23444555555555


Q ss_pred             HcCChHHHHHHHHHHHH
Q 040371          119 IHGLAADASAIFTKMEM  135 (410)
Q Consensus       119 ~~g~~~~A~~l~~~m~~  135 (410)
                      ..|++++|...|+++..
T Consensus        89 ~~~~~~~A~~~~~~~~~  105 (125)
T 1na0_A           89 KQGDYDEAIEYYQKALE  105 (125)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HhcCHHHHHHHHHHHHH
Confidence            55555555555555544

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.38  E-value=4.7e-06  Score=66.79  Aligned_cols=123  Identities=12%  Similarity=0.023  Sum_probs=97.0

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYS   87 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~   87 (410)
                      .+.+.......+.++++++         +.| +...+..+..++.+.|++++|...|+++++.. +.+...|..+..+|.
T Consensus        12 ~~~l~~~~~~~~~l~~al~---------l~p~~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~-P~~~~~~~~lg~~~~   81 (151)
T 3gyz_A           12 STAVIDAINSGATLKDINA---------IPDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYD-FYNVDYIMGLAAIYQ   81 (151)
T ss_dssp             HHHHHHHHHTSCCTGGGCC---------SCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHhC---------CCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Confidence            3555555555555544432         345 34577888888999999999999999999875 557889999999999


Q ss_pred             hcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHH
Q 040371           88 KCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSI  143 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~  143 (410)
                      +.|++++|...|++...  | +...|..+..+|.+.|++++|+..|++..+.  .||..
T Consensus        82 ~~g~~~~Ai~~~~~al~l~P~~~~~~~~lg~~~~~lg~~~eA~~~~~~al~l--~~~~~  138 (151)
T 3gyz_A           82 IKEQFQQAADLYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECFELVIQH--SNDEK  138 (151)
T ss_dssp             HTTCHHHHHHHHHHHHHHSSSCCHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CCCHH
T ss_pred             HHccHHHHHHHHHHHHhhCCCCcHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCHH
Confidence            99999999999998753  3 6778999999999999999999999999874  45543

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.37  E-value=9.7e-06  Score=62.66  Aligned_cols=91  Identities=14%  Similarity=-0.004  Sum_probs=39.4

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHc
Q 040371           44 FASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIH  120 (410)
Q Consensus        44 ~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~  120 (410)
                      +......+.+.|++++|.+.|++.++.. +.+..++..+..+|.+.|++++|+..|++..+   .+...|..+..+|...
T Consensus        16 ~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~   94 (126)
T 4gco_A           16 EKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLDSKFIKGYIRKAACLVAM   94 (126)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHC
Confidence            3334444444444444444444444432 22344444444444444444444444443321   2233444444444444


Q ss_pred             CChHHHHHHHHHHHH
Q 040371          121 GLAADASAIFTKMEM  135 (410)
Q Consensus       121 g~~~~A~~l~~~m~~  135 (410)
                      |++++|++.|++..+
T Consensus        95 ~~~~~A~~~~~~al~  109 (126)
T 4gco_A           95 REWSKAQRAYEDALQ  109 (126)
T ss_dssp             TCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH
Confidence            444444444444443

>4gco_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; 1.60A {Caenorhabditis elegans}

Probab=98.37  E-value=1.3e-05  Score=61.90  Aligned_cols=105  Identities=7%  Similarity=0.051  Sum_probs=90.0

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      ..|...-..|.+.|++++|++.|++.++.. +.+...|..+..++...|++++|.+.+++.++.. +.+...|..+..+|
T Consensus        14 ~~~~~~G~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~   91 (126)
T 4gco_A           14 QEEKNKGNEYFKKGDYPTAMRHYNEAVKRD-PENAILYSNRAACLTKLMEFQRALDDCDTCIRLD-SKFIKGYIRKAACL   91 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHhhHHHhhccHHHHHHHHHHHHHhh-hhhhHHHHHHHHHH
Confidence            468888999999999999999999998753 4478899999999999999999999999999975 55788999999999


Q ss_pred             HhcCCHHHHHHHHHhccc--C-ChhhHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQR--N-DVSVWNAM  113 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~--~-~~~~~~~l  113 (410)
                      .+.|++++|.+.|++..+  | +...+..+
T Consensus        92 ~~~~~~~~A~~~~~~al~l~P~~~~a~~~l  121 (126)
T 4gco_A           92 VAMREWSKAQRAYEDALQVDPSNEEAREGV  121 (126)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHH
T ss_pred             HHCCCHHHHHHHHHHHHHHCcCCHHHHHHH
Confidence            999999999999998763  3 34444443

>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=98.36  E-value=1e-05  Score=74.17  Aligned_cols=125  Identities=13%  Similarity=-0.052  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc--------------HHHHHHHHHHHHhcCCHHHHHHHHHhccc---C
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELN--------------FILSAALIDMYSKCGKIQMAKEVFDTVQR---N  105 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~--------------~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~  105 (410)
                      .+..+...+.+.|++++|...|++.++......              ..++..+..+|.+.|++++|...|++..+   .
T Consensus       149 ~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~  228 (336)
T 1p5q_A          149 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSN  228 (336)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTT
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCC
Confidence            444444444444444444444444444321111              35566666666666666666666665542   2


Q ss_pred             ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHH-HHHHHHhh
Q 040371          106 DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEG-RKYFDHMR  169 (410)
Q Consensus       106 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a-~~~~~~m~  169 (410)
                      +..+|..+..+|...|++++|+..|++..+.  .| +...+..+..++...|+.+++ ...+..|.
T Consensus       229 ~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~~  292 (336)
T 1p5q_A          229 NEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVCQQRIRRQLAREKKLYANMF  292 (336)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4456666666666666666666666666553  23 344555555566666666655 33444443

>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=98.36  E-value=2.3e-05  Score=78.31  Aligned_cols=213  Identities=7%  Similarity=-0.005  Sum_probs=156.6

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHH-HHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC----------CC
Q 040371            5 DVVSWNSMIGGFVRNARFDEAL-RFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKK----------IE   73 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~-~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g----------~~   73 (410)
                      +...|-..+.-+.+.|+.++|. ++|++.... ++.+...|...+...-+.|+++.|+++|+.+++..          .+
T Consensus       342 ~~~lW~~ya~~~~~~~~~~~a~r~il~rAi~~-~P~s~~Lwl~~a~~ee~~~~~e~aR~iyek~l~~l~~~~~~~~~~~p  420 (679)
T 4e6h_A          342 APEIWFNMANYQGEKNTDSTVITKYLKLGQQC-IPNSAVLAFSLSEQYELNTKIPEIETTILSCIDRIHLDLAALMEDDP  420 (679)
T ss_dssp             CHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHH-CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHHST
T ss_pred             CHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHh-CCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhhhhhccC
Confidence            3456777777788889999997 999999864 45566677788888889999999999999998742          12


Q ss_pred             c-----------cHHHHHHHHHHHHhcCCHHHHHHHHHhcccC-Ch---hhHHHHHHHHHHc-CChHHHHHHHHHHHHCC
Q 040371           74 L-----------NFILSAALIDMYSKCGKIQMAKEVFDTVQRN-DV---SVWNAMISGVAIH-GLAADASAIFTKMEMFN  137 (410)
Q Consensus        74 ~-----------~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~-~~---~~~~~li~~~~~~-g~~~~A~~l~~~m~~~g  137 (410)
                      .           ...+|...+....+.|.++.|+++|.+..+. ..   ..|-..+..-.+. ++.+.|..+|+...+. 
T Consensus       421 ~~~~~~~~~~~~~~~vWi~y~~~erR~~~l~~AR~vf~~A~~~~~~~~~~lyi~~A~lE~~~~~d~e~Ar~ife~~Lk~-  499 (679)
T 4e6h_A          421 TNESAINQLKSKLTYVYCVYMNTMKRIQGLAASRKIFGKCRRLKKLVTPDIYLENAYIEYHISKDTKTACKVLELGLKY-  499 (679)
T ss_dssp             TCHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTGGGSCTHHHHHHHHHHHTTTSCCHHHHHHHHHHHHH-
T ss_pred             cchhhhhhhccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhcCCCChHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH-
Confidence            1           2457889999999999999999999987643 22   2332222222233 4589999999998875 


Q ss_pred             CCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCC--ChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHH
Q 040371          138 VLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP--QLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWR  214 (410)
Q Consensus       138 ~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~--~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~  214 (410)
                      .+-+...+...+......|+.+.|+.+|+..... ...+  ....|...++.-.+.|..+.+.++.+++ ...|+.....
T Consensus       500 ~p~~~~~w~~y~~fe~~~~~~~~AR~lferal~~-~~~~~~~~~lw~~~~~fE~~~G~~~~~~~v~~R~~~~~P~~~~~~  578 (679)
T 4e6h_A          500 FATDGEYINKYLDFLIYVNEESQVKSLFESSIDK-ISDSHLLKMIFQKVIFFESKVGSLNSVRTLEKRFFEKFPEVNKLE  578 (679)
T ss_dssp             HTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHTTT-SSSTTHHHHHHHHHHHHHHHTCCSHHHHHHHHHHHHHSTTCCHHH
T ss_pred             CCCchHHHHHHHHHHHhCCCHHHHHHHHHHHHHh-cCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCcHHH
Confidence            3334555567777777889999999999998853 2111  3468999999999999999999999998 3345544444


Q ss_pred             HHHHHH
Q 040371          215 ALLSAC  220 (410)
Q Consensus       215 ~li~~~  220 (410)
                      .++.-|
T Consensus       579 ~f~~ry  584 (679)
T 4e6h_A          579 EFTNKY  584 (679)
T ss_dssp             HHHHHT
T ss_pred             HHHHHh
Confidence            444444

>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide repeat, TPR, chapero virulence; 2.15A {Shigella flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A

Probab=98.30  E-value=1.2e-05  Score=64.44  Aligned_cols=100  Identities=9%  Similarity=-0.015  Sum_probs=83.7

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHH
Q 040371           75 NFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLT  150 (410)
Q Consensus        75 ~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~  150 (410)
                      +...+..+...|.+.|++++|...|++...  | +...|..+..+|...|++++|+..|++....  .| +...+..+..
T Consensus        35 ~~~~~~~lg~~~~~~g~~~eA~~~~~~al~~~P~~~~~~~~lg~~~~~~g~~~~Ai~~~~~al~l--~P~~~~~~~~lg~  112 (151)
T 3gyz_A           35 MMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAADLYAVAFAL--GKNDYTPVFHTGQ  112 (151)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--SSSCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHccHHHHHHHHHHHHhh--CCCCcHHHHHHHH
Confidence            466788888899999999999999998763  3 6778999999999999999999999999874  34 4677888889


Q ss_pred             HHHccCCHHHHHHHHHHhhhhcCCCCChh
Q 040371          151 ACSHCGLVEEGRKYFDHMRSRYSIQPQLE  179 (410)
Q Consensus       151 a~~~~g~~~~a~~~~~~m~~~~~~~~~~~  179 (410)
                      ++...|++++|...|+...+.   .|+..
T Consensus       113 ~~~~lg~~~eA~~~~~~al~l---~~~~~  138 (151)
T 3gyz_A          113 CQLRLKAPLKAKECFELVIQH---SNDEK  138 (151)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHH---CCCHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHh---CCCHH
Confidence            999999999999999998854   45554

>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=98.30  E-value=3.2e-06  Score=75.43  Aligned_cols=95  Identities=9%  Similarity=-0.145  Sum_probs=58.6

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISG  116 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~  116 (410)
                      +...+..+...+...|++++|...+...++.. +.+...+..+...|.+.|++++|...|++..+   .+...|+.+..+
T Consensus         3 ~a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~   81 (281)
T 2c2l_A            3 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQC   81 (281)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            34455666666666667777766666666653 33556666666666666666666666665543   234556666666


Q ss_pred             HHHcCChHHHHHHHHHHHH
Q 040371          117 VAIHGLAADASAIFTKMEM  135 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~  135 (410)
                      |...|++++|+..|++..+
T Consensus        82 ~~~~g~~~~A~~~~~~al~  100 (281)
T 2c2l_A           82 QLEMESYDEAIANLQRAYS  100 (281)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHH
Confidence            6666666666666666554

>2vyi_A SGTA protein; chaperone, TPR repeat, phosphoprotein, tetratricopeptide repeat protein, HOST-virus interaction; 2.4A {Homo sapiens} SCOP: k.38.1.1

Probab=98.27  E-value=2e-05  Score=60.18  Aligned_cols=114  Identities=9%  Similarity=-0.085  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACS  153 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~  153 (410)
                      ..+..+...+...|++++|...|++...   .+...|..+...|...|++++|++.+++..... +.+...+..+...+.
T Consensus        13 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~~~~~~   91 (131)
T 2vyi_A           13 ERLKTEGNEQMKVENFEAAVHFYGKAIELNPANAVYFCNRAAAYSKLGNYAGAVQDCERAICID-PAYSKAYGRMGLALS   91 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchHHHHHHHHHHHhcC-ccCHHHHHHHHHHHH
Confidence            3444444555555555555555554331   233445555555555555555555555554431 112344444555555


Q ss_pred             ccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCC
Q 040371          154 HCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGH  193 (410)
Q Consensus       154 ~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~  193 (410)
                      ..|++++|...|+...+.  -+.+...+..+...+.+.|+
T Consensus        92 ~~~~~~~A~~~~~~~~~~--~p~~~~~~~~l~~~~~~~~~  129 (131)
T 2vyi_A           92 SLNKHVEAVAYYKKALEL--DPDNETYKSNLKIAELKLRE  129 (131)
T ss_dssp             HTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHTT
T ss_pred             HhCCHHHHHHHHHHHHhc--CccchHHHHHHHHHHHHHhc
Confidence            555555555555555432  11133444444444444443

>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=98.25  E-value=1e-05  Score=64.55  Aligned_cols=91  Identities=11%  Similarity=0.013  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040371           78 LSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSH  154 (410)
Q Consensus        78 ~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~  154 (410)
                      .+..+...+.+.|++++|...|++...   .+...|..+..+|.+.|++++|+..|++..... +.+...+..+..++..
T Consensus        23 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~  101 (148)
T 2vgx_A           23 QLYSLAFNQYQSGXYEDAHXVFQALCVLDHYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD-IXEPRFPFHAAECLLQ  101 (148)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCChHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCchHHHHHHHHHHH
Confidence            333444444444444444444444321   133344444444444444444444444444321 1123334444444444


Q ss_pred             cCCHHHHHHHHHHhh
Q 040371          155 CGLVEEGRKYFDHMR  169 (410)
Q Consensus       155 ~g~~~~a~~~~~~m~  169 (410)
                      .|++++|...|+...
T Consensus       102 ~g~~~~A~~~~~~al  116 (148)
T 2vgx_A          102 XGELAEAESGLFLAQ  116 (148)
T ss_dssp             TTCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH
Confidence            444444444444443

>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=98.24  E-value=1.6e-05  Score=63.33  Aligned_cols=106  Identities=9%  Similarity=-0.011  Sum_probs=77.9

Q ss_pred             HHHHHHHCCCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--
Q 040371           28 FFREMLSSKVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--  104 (410)
Q Consensus        28 l~~~m~~~g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--  104 (410)
                      .|++...  +.| +...+..+...+...|++++|...|+.+++.. +.+...+..+..+|.+.|++++|...|++...  
T Consensus         9 ~~~~al~--~~p~~~~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~   85 (148)
T 2vgx_A            9 TIAMLNE--ISSDTLEQLYSLAFNQYQSGXYEDAHXVFQALCVLD-HYDSRFFLGLGACRQAMGQYDLAIHSYSYGAVMD   85 (148)
T ss_dssp             SHHHHTT--CCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             hHHHHHc--CCHhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHcC-cccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC
Confidence            3444443  234 34466667777788888888888888887764 44677788888888888888888888887652  


Q ss_pred             -CChhhHHHHHHHHHHcCChHHHHHHHHHHHHC
Q 040371          105 -NDVSVWNAMISGVAIHGLAADASAIFTKMEMF  136 (410)
Q Consensus       105 -~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  136 (410)
                       .+...|..+..+|...|++++|+..|++..+.
T Consensus        86 p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~  118 (148)
T 2vgx_A           86 IXEPRFPFHAAECLLQXGELAEAESGLFLAQEL  118 (148)
T ss_dssp             TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence             35667788888888888888888888887663

>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=98.24  E-value=4.7e-05  Score=56.89  Aligned_cols=98  Identities=12%  Similarity=0.070  Sum_probs=68.0

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      ++..|..+...+...|++++|+..|++..... +.+...+..+..++...|+++.|...++...+.. +.+..++..+..
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~   80 (118)
T 1elw_A            3 QVNELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAA   80 (118)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhC-cccHHHHHHHHH
Confidence            34567777788888888888888888877642 3356667777777777777777777777777653 335666666666


Q ss_pred             HHHhcCCHHHHHHHHHhccc
Q 040371           85 MYSKCGKIQMAKEVFDTVQR  104 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~  104 (410)
                      +|.+.|++++|.+.|++..+
T Consensus        81 ~~~~~~~~~~A~~~~~~~~~  100 (118)
T 1elw_A           81 ALEFLNRFEEAKRTYEEGLK  100 (118)
T ss_dssp             HHHHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHhhHHHHHHHHHHHHH
Confidence            77777777777777666543

>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=98.24  E-value=1.2e-05  Score=65.78  Aligned_cols=116  Identities=9%  Similarity=-0.001  Sum_probs=79.9

Q ss_pred             hhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHH-HHHcCCh--HHH
Q 040371           53 RLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISG-VAIHGLA--ADA  126 (410)
Q Consensus        53 ~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~-~~~~g~~--~~A  126 (410)
                      ..|+++.|...+...++.. +.+..++..+...|...|++++|...|++..+   .+...|..+... |...|++  ++|
T Consensus        22 ~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~l~~~~~~~~~~~A  100 (177)
T 2e2e_A           22 SQQNPEAQLQALQDKIRAN-PQNSEQWALLGEYYLWQNDYSNSLLAYRQALQLRGENAELYAALATVLYYQASQHMTAQT  100 (177)
T ss_dssp             -----CCCCHHHHHHHHHC-CSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHCSCHHHHHHHHHHHHHHTTTCCCHHH
T ss_pred             hccCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCCcchHHH
Confidence            4566777777777777664 44677788888888888888888888877652   355667777777 6677777  888


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhh
Q 040371          127 SAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRS  170 (410)
Q Consensus       127 ~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~  170 (410)
                      +..|++..... +.+...+..+...+...|++++|...|+.+.+
T Consensus       101 ~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~  143 (177)
T 2e2e_A          101 RAMIDKALALD-SNEITALMLLASDAFMQANYAQAIELWQKVMD  143 (177)
T ss_dssp             HHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCcHHHHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence            88888777642 22455666677777778888888888877764

>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=98.23  E-value=3.1e-05  Score=60.16  Aligned_cols=96  Identities=6%  Similarity=-0.030  Sum_probs=56.7

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      +...|..+...|...|++++|+..|++..... +.+...|..+..++...|+++.|...++..++.. +.+...+..+..
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~   85 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLGQ   85 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-chhHHHHHHHHH
Confidence            45566666666666666666666666665532 2244556666666666666666666666666553 234555555555


Q ss_pred             HHHhcCCHHHHHHHHHhc
Q 040371           85 MYSKCGKIQMAKEVFDTV  102 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m  102 (410)
                      .|.+.|++++|...|++.
T Consensus        86 ~~~~~~~~~~A~~~~~~a  103 (137)
T 3q49_B           86 CQLEMESYDEAIANLQRA  103 (137)
T ss_dssp             HHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHhhHHHHHHHHHHH
Confidence            666666666665555544

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.22  E-value=1.4e-05  Score=59.40  Aligned_cols=97  Identities=14%  Similarity=-0.009  Sum_probs=63.7

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCc--cHHHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIEL--NFILSAAL   82 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~--~~~~~~~l   82 (410)
                      +...|..+...|.+.|++++|+..|++..+.. +.+...+..+..++...|++++|.+.+++.++.. +.  +..++..+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l   82 (112)
T 2kck_A            5 NPEEYYLEGVLQYDAGNYTESIDLFEKAIQLD-PEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAK   82 (112)
T ss_dssp             STTGGGGHHHHHHSSCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhC-cCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHH
Confidence            45566777777777777777777777776542 3345566666667777777777777777766653 22  45566666


Q ss_pred             HHHHHhc-CCHHHHHHHHHhcc
Q 040371           83 IDMYSKC-GKIQMAKEVFDTVQ  103 (410)
Q Consensus        83 i~~y~~~-g~~~~A~~~f~~m~  103 (410)
                      ...|.+. |++++|.+.|++..
T Consensus        83 ~~~~~~~~~~~~~A~~~~~~~~  104 (112)
T 2kck_A           83 ADALRYIEGKEVEAEIAEARAK  104 (112)
T ss_dssp             HHHHTTCSSCSHHHHHHHHHHG
T ss_pred             HHHHHHHhCCHHHHHHHHHHHh
Confidence            6666666 66666666666554

>2lni_A Stress-induced-phosphoprotein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, chaperone; NMR {Homo sapiens}

Probab=98.21  E-value=2.7e-05  Score=59.81  Aligned_cols=92  Identities=5%  Similarity=-0.091  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACS  153 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~  153 (410)
                      ..+..+...|.+.|++++|...|++..+   .+...|..+...|...|++++|+..|++..... +.+...+..+...+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~   95 (133)
T 2lni_A           17 LMVKNKGNECFQKGDYPQAMKHYTEAIKRNPKDAKLYSNRAACYTKLLEFQLALKDCEECIQLE-PTFIKGYTRKAAALE   95 (133)
T ss_dssp             HHHHHHHHHHHHTTCSHHHHHHHHHHHTTCTTCHHHHHHHHHHHTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhccHHHHHHHHHHHHHhC-CCchHHHHHHHHHHH
Confidence            3344444444444444444444443321   123344444444444444444444444444321 112333444444444


Q ss_pred             ccCCHHHHHHHHHHhh
Q 040371          154 HCGLVEEGRKYFDHMR  169 (410)
Q Consensus       154 ~~g~~~~a~~~~~~m~  169 (410)
                      ..|++++|...|+...
T Consensus        96 ~~~~~~~A~~~~~~~~  111 (133)
T 2lni_A           96 AMKDYTKAMDVYQKAL  111 (133)
T ss_dssp             HTTCHHHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHHH
Confidence            4444444444444443

>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=98.20  E-value=0.0012  Score=60.06  Aligned_cols=180  Identities=6%  Similarity=-0.036  Sum_probs=119.4

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHcCCCccHHHHHHHHHHHH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLG-ALNHAYWVHNLIIEKKIELNFILSAALIDMYS   87 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~-~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~   87 (410)
                      |+.+-....+.+..++|++++.+++..+ +-+...|+.--.++...+ .++++.++++.+++.. +.+..+|+.-...+.
T Consensus        57 ~~~~r~~~~~~e~se~AL~lt~~~L~~n-P~~ytaWn~R~~iL~~l~~~l~eEL~~~~~~L~~n-PKny~aW~hR~wlL~  134 (349)
T 3q7a_A           57 MDYFRAIAAKEEKSERALELTEIIVRMN-PAHYTVWQYRFSLLTSLNKSLEDELRLMNEFAVQN-LKSYQVWHHRLLLLD  134 (349)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTT-CCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHHhC-chhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHH
Confidence            4444444455566678999999988753 224556777777777777 5889999999888775 457788887777777


Q ss_pred             hc-C-CHHHHHHHHHhcccC---ChhhHHHHHHHHHHcCChH--------HHHHHHHHHHHCCCCCCHHHHHHHHHHHHc
Q 040371           88 KC-G-KIQMAKEVFDTVQRN---DVSVWNAMISGVAIHGLAA--------DASAIFTKMEMFNVLPDSITFLGLLTACSH  154 (410)
Q Consensus        88 ~~-g-~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~--------~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~  154 (410)
                      +. + ++++++++++++.+.   |-.+|+--.-.+.+.|.++        ++++.++++.+... -|...++.....+.+
T Consensus       135 ~l~~~~~~~EL~~~~k~L~~dpkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~dp-~N~SAW~~R~~lL~~  213 (349)
T 3q7a_A          135 RISPQDPVSEIEYIHGSLLPDPKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRVDG-RNNSAWGWRWYLRVS  213 (349)
T ss_dssp             HHCCSCCHHHHHHHHHHTSSCTTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHTT
T ss_pred             HhcCCChHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHh
Confidence            76 6 788888888888754   4456666555555555555        77888887777532 255666666666666


Q ss_pred             cCC-------HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCC
Q 040371          155 CGL-------VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGH  193 (410)
Q Consensus       155 ~g~-------~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~  193 (410)
                      .+.       ++++.+.++.+...  -+-|...|+-+-..+.+.|+
T Consensus       214 l~~~~~~~~~~~eELe~~~~aI~~--~P~n~SaW~Ylr~Ll~~~~~  257 (349)
T 3q7a_A          214 RPGAETSSRSLQDELIYILKSIHL--IPHNVSAWNYLRGFLKHFSL  257 (349)
T ss_dssp             STTCCCCHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTC
T ss_pred             ccccccchHHHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHhcCC
Confidence            654       56666666666532  23345666666655555554

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.20  E-value=1.8e-05  Score=62.43  Aligned_cols=92  Identities=10%  Similarity=-0.039  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHH
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAI  119 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~  119 (410)
                      .+..+...+...|++++|...|+.+++.. +.+...|..+..+|.+.|++++|...|++...   .+...|..+..+|..
T Consensus        20 ~~~~~a~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~   98 (142)
T 2xcb_A           20 QLYALGFNQYQAGKWDDAQKIFQALCMLD-HYDARYFLGLGACRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECHLQ   98 (142)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHH
Confidence            44555556666677777777776666654 34566666666677777777777777766542   244566666667777


Q ss_pred             cCChHHHHHHHHHHHH
Q 040371          120 HGLAADASAIFTKMEM  135 (410)
Q Consensus       120 ~g~~~~A~~l~~~m~~  135 (410)
                      .|++++|+..|++...
T Consensus        99 ~g~~~~A~~~~~~al~  114 (142)
T 2xcb_A           99 LGDLDGAESGFYSARA  114 (142)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            7777777777776655

>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=98.19  E-value=4.1e-05  Score=70.10  Aligned_cols=127  Identities=11%  Similarity=-0.036  Sum_probs=100.5

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-C---------------hhhHHHHHHHHHHcCChHHHHHHHHHHHHC
Q 040371           75 NFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-D---------------VSVWNAMISGVAIHGLAADASAIFTKMEMF  136 (410)
Q Consensus        75 ~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~---------------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~  136 (410)
                      +...+..+...|.+.|++++|...|++...  | +               ..+|+.+..+|.+.|++++|+..|++..+.
T Consensus       146 ~a~~~~~~g~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~  225 (336)
T 1p5q_A          146 QSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALEL  225 (336)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCCCSHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhhccccCChHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence            567788888899999999999999987652  3 2               478888889999999999999999988875


Q ss_pred             CCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHH-HHHHHhC
Q 040371          137 NVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEA-YGLITSM  204 (410)
Q Consensus       137 g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A-~~~~~~m  204 (410)
                      . +.+...+..+..++...|++++|...|+...+.  -+.+...+..+..++.+.|+.++| ...+++|
T Consensus       226 ~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  291 (336)
T 1p5q_A          226 D-SNNEKGLSRRGEAHLAVNDFELARADFQKVLQL--YPNNKAAKTQLAVCQQRIRRQLAREKKLYANM  291 (336)
T ss_dssp             C-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             C-CCcHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3 235677888888999999999999999988753  123467788888888888988888 3455555

>3upv_A Heat shock protein STI1; TPR-fold, adaptor protein for HSP70 and HSP90, C-terminal PA HSP70, peptide binding protein; 1.60A {Saccharomyces cerevisiae}

Probab=98.18  E-value=3.8e-05  Score=58.87  Aligned_cols=94  Identities=15%  Similarity=0.063  Sum_probs=53.1

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      ..|..+...+.+.|++++|+..|++..+.. +.+...|..+..++...|++++|...++..++.. +.+...+..+..+|
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~   82 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKD-PNFVRAYIRKATAQ   82 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHH
Confidence            345556666666666666666666665532 2244555555666666666666666666655543 23344555555555


Q ss_pred             HhcCCHHHHHHHHHhc
Q 040371           87 SKCGKIQMAKEVFDTV  102 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m  102 (410)
                      .+.|++++|...|++.
T Consensus        83 ~~~~~~~~A~~~~~~a   98 (126)
T 3upv_A           83 IAVKEYASALETLDAA   98 (126)
T ss_dssp             HHTTCHHHHHHHHHHH
T ss_pred             HHHhCHHHHHHHHHHH
Confidence            5555555555555544

>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=98.17  E-value=5.4e-05  Score=58.01  Aligned_cols=93  Identities=9%  Similarity=-0.157  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHH
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVA  118 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~  118 (410)
                      ..|......+...|++++|...+...++.. +.+..++..+..+|.+.|++++|...|++..+   .+...|..+..+|.
T Consensus         5 ~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~   83 (126)
T 3upv_A            5 EEARLEGKEYFTKSDWPNAVKAYTEMIKRA-PEDARGYSNRAAALAKLMSFPEAIADCNKAIEKDPNFVRAYIRKATAQI   83 (126)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCChHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHH
Confidence            345555666666677777777777666653 33566666666666666666666666665542   24456666666666


Q ss_pred             HcCChHHHHHHHHHHHH
Q 040371          119 IHGLAADASAIFTKMEM  135 (410)
Q Consensus       119 ~~g~~~~A~~l~~~m~~  135 (410)
                      ..|++++|+..|++..+
T Consensus        84 ~~~~~~~A~~~~~~al~  100 (126)
T 3upv_A           84 AVKEYASALETLDAART  100 (126)
T ss_dssp             HTTCHHHHHHHHHHHHH
T ss_pred             HHhCHHHHHHHHHHHHH
Confidence            66666666666666654

>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, tetratricopeptide repeat domain; HET: PGE; 1.85A {Caenorhabditis elegans}

Probab=98.17  E-value=4.4e-05  Score=58.92  Aligned_cols=26  Identities=8%  Similarity=-0.125  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371          110 WNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus       110 ~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      |..+...|...|++++|++.|++.+.
T Consensus        86 ~~~lg~~~~~~~~~~~A~~~~~kal~  111 (127)
T 4gcn_A           86 MSRAGNAFQKQNDLSLAVQWFHRSLS  111 (127)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            44444455555555555555555444

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.17  E-value=5.5e-05  Score=71.38  Aligned_cols=192  Identities=11%  Similarity=-0.003  Sum_probs=138.4

Q ss_pred             HHHHHHcCCHhHHHHHHHHHHHCCCCC-C---------------HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC-CCcc
Q 040371           13 IGGFVRNARFDEALRFFREMLSSKVEP-D---------------KFTFASVIYGCARLGALNHAYWVHNLIIEKK-IELN   75 (410)
Q Consensus        13 i~~~~~~g~~~~a~~l~~~m~~~g~~p-d---------------~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g-~~~~   75 (410)
                      ...+.+.|++++|++.|.+..+..... +               ...+..+...|...|++++|.+.+..+.+.- -.++
T Consensus        11 a~~l~~~~~y~eA~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~al~~l~~~y~~~~~~~~a~~~~~~~~~~~~~~~~   90 (434)
T 4b4t_Q           11 ARRLVNEKQYNEAEQVYLSLLDKDSSQSSAAAGASVDDKRRNEQETSILELGQLYVTMGAKDKLREFIPHSTEYMMQFAK   90 (434)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHSCCCSSSBSSSSSBCSHHHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHTHHHHHTSCH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhhCcccchhHHHHHHHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence            355778999999999999998743211 1               1247788999999999999999998876531 1112


Q ss_pred             H----HHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----hhhHHHHHHHHHHcCChHHHHHHHHHHHHC--C--C
Q 040371           76 F----ILSAALIDMYSKCGKIQMAKEVFDTVQR-----ND----VSVWNAMISGVAIHGLAADASAIFTKMEMF--N--V  138 (410)
Q Consensus        76 ~----~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~--g--~  138 (410)
                      .    .+.+.+-..+...|+.+.|..+++....     .+    ..++..+...|...|++++|..++++....  +  -
T Consensus        91 ~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~~~  170 (434)
T 4b4t_Q           91 SKTVKVLKTLIEKFEQVPDSLDDQIFVCEKSIEFAKREKRVFLKHSLSIKLATLHYQKKQYKDSLALINDLLREFKKLDD  170 (434)
T ss_dssp             HHHHHHHHHHHHHHCSCCSCHHHHHHHHHHHHHHHHHSSCCSSHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSSC
T ss_pred             hHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHhccc
Confidence            2    2344455556667899999999887642     11    347788899999999999999999988653  1  1


Q ss_pred             CCC-HHHHHHHHHHHHccCCHHHHHHHHHHhhhhc-CCC-C-C--hhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          139 LPD-SITFLGLLTACSHCGLVEEGRKYFDHMRSRY-SIQ-P-Q--LEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       139 ~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~-~~~-~-~--~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      +|. ..++..+...|...|++++|..+++...... .+. | .  ...+..+...+...|++++|...|.+.
T Consensus       171 ~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~~~~a  242 (434)
T 4b4t_Q          171 KPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSYFFES  242 (434)
T ss_dssp             STHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence            222 3467888899999999999999998876421 111 1 1  245677777788889999997776554

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.16  E-value=8.1e-05  Score=58.34  Aligned_cols=95  Identities=13%  Similarity=0.053  Sum_probs=58.2

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPD----KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSA   80 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd----~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (410)
                      +...|..+...+.+.|++++|+..|++..+.  .|+    ...+..+..++...|++++|...++..++.. +.+...+.
T Consensus        27 ~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~  103 (148)
T 2dba_A           27 SVEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEKD-GGDVKALY  103 (148)
T ss_dssp             CHHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHT-SCCHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhhC-ccCHHHHH
Confidence            4556677777777777777777777776653  344    4455556666666666666666666665543 23455555


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhc
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTV  102 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m  102 (410)
                      .+..+|.+.|++++|...|++.
T Consensus       104 ~~a~~~~~~~~~~~A~~~~~~a  125 (148)
T 2dba_A          104 RRSQALEKLGRLDQAVLDLQRC  125 (148)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH
Confidence            5555666666666666665554

>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=98.15  E-value=3.7e-05  Score=58.75  Aligned_cols=95  Identities=14%  Similarity=0.064  Sum_probs=57.7

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCC--Ccc----HHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKI--ELN----FILSA   80 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~--~~~----~~~~~   80 (410)
                      .+|..+...|...|++++|+..|++..... +.+...+..+..++...|+++.|...+..+.+...  .++    ..++.
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            456677777777777777777777776542 33555666666666677777777777666655421  111    44455


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhc
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTV  102 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m  102 (410)
                      .+...|.+.|++++|.+.|++.
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~  105 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKS  105 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHH
Confidence            5555555555555555555544

>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=98.14  E-value=4.7e-05  Score=63.66  Aligned_cols=127  Identities=13%  Similarity=0.034  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCC-c--------------cHHHHHHHHHHHHhcCCHHHHHHHHHhccc-
Q 040371           41 KFTFASVIYGCARLGALNHAYWVHNLIIEKKIE-L--------------NFILSAALIDMYSKCGKIQMAKEVFDTVQR-  104 (410)
Q Consensus        41 ~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~-~--------------~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-  104 (410)
                      ...+..+...+...|++++|...+...++.... +              ...++..+..+|.+.|++++|...|++..+ 
T Consensus        38 ~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~  117 (198)
T 2fbn_A           38 AFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEISCNLNLATCYNKNKDYPKAIDHASKVLKI  117 (198)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence            344555555555566666666666655553211 0              025666666777777777777777766542 


Q ss_pred             --CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHH-HHHHHhh
Q 040371          105 --NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGR-KYFDHMR  169 (410)
Q Consensus       105 --~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~-~~~~~m~  169 (410)
                        .+..+|..+..+|...|++++|+..|++....  .| +...+..+...+...++.+++. ..|..+.
T Consensus       118 ~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~f  184 (198)
T 2fbn_A          118 DKNNVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLDIRNSYELCVNKLKEARKKDKLTFGGMF  184 (198)
T ss_dssp             STTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHHHHHC----------
T ss_pred             CcccHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence              34556666777777777777777777776653  23 3445555555555555555555 3344433

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.14  E-value=3.8e-05  Score=62.02  Aligned_cols=96  Identities=11%  Similarity=-0.000  Sum_probs=56.3

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      ...|..+...|.+.|++++|+..|++..+.. +-+...|..+..++...|++++|...+++.++.. +.+...+..+..+
T Consensus        11 a~~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~   88 (164)
T 3sz7_A           11 SDKLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVD-PKYSKAWSRLGLA   88 (164)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            3456666666666666666666666666532 2245556666666666666666666666666553 3345555555556


Q ss_pred             HHhcCCHHHHHHHHHhcc
Q 040371           86 YSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~  103 (410)
                      |.+.|++++|...|++..
T Consensus        89 ~~~~g~~~~A~~~~~~al  106 (164)
T 3sz7_A           89 RFDMADYKGAKEAYEKGI  106 (164)
T ss_dssp             HHHTTCHHHHHHHHHHHH
T ss_pred             HHHccCHHHHHHHHHHHH
Confidence            666666666665555543

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=98.12  E-value=1.9e-05  Score=60.53  Aligned_cols=93  Identities=13%  Similarity=-0.071  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK   88 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~   88 (410)
                      |..+...+.+.|++++|+..|++..+.. +.+...|..+..++...|++++|...+++.++.. +.+...+..+...|.+
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~-P~~~~~~~~la~~~~~   97 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTN   97 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHH
Confidence            3444455555566666666665555431 2244455555555555555555555555555543 2234455555555555


Q ss_pred             cCCHHHHHHHHHhcc
Q 040371           89 CGKIQMAKEVFDTVQ  103 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~  103 (410)
                      .|++++|...|++..
T Consensus        98 ~g~~~~A~~~~~~al  112 (121)
T 1hxi_A           98 EHNANAALASLRAWL  112 (121)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH
Confidence            555555555555443

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=98.11  E-value=2.4e-05  Score=62.20  Aligned_cols=95  Identities=11%  Similarity=0.003  Sum_probs=51.5

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCC-CCC----HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC----CCc-cH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKV-EPD----KFTFASVIYGCARLGALNHAYWVHNLIIEKK----IEL-NF   76 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~-~pd----~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g----~~~-~~   76 (410)
                      .+|..+...|...|++++|+..|++..+... .++    ..++..+...+...|++++|...++...+..    ..+ ..
T Consensus        10 ~~~~~l~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~   89 (164)
T 3ro3_A           10 RAFGNLGNTHYLLGNFRDAVIAHEQRLLIAKEFGDKAAERIAYSNLGNAYIFLGEFETASEYYKKTLLLARQLKDRAVEA   89 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhCCcHHHH
Confidence            4567777777788888888888777654210 011    1245555556666666666666665554321    000 12


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371           77 ILSAALIDMYSKCGKIQMAKEVFDT  101 (410)
Q Consensus        77 ~~~~~li~~y~~~g~~~~A~~~f~~  101 (410)
                      .++..+...|...|++++|...|++
T Consensus        90 ~~~~~l~~~~~~~~~~~~A~~~~~~  114 (164)
T 3ro3_A           90 QSCYSLGNTYTLLQDYEKAIDYHLK  114 (164)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            3344444555555555555555443

>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=98.11  E-value=0.0005  Score=62.58  Aligned_cols=215  Identities=12%  Similarity=0.082  Sum_probs=152.7

Q ss_pred             HhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC-CHHHHHHHHHhcccC---ChhhHHHHHHHHHHc-C-ChHH
Q 040371           52 ARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG-KIQMAKEVFDTVQRN---DVSVWNAMISGVAIH-G-LAAD  125 (410)
Q Consensus        52 ~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g-~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~-g-~~~~  125 (410)
                      .+.+..++|.++.+.++..+ +-+..+|+.--..+...| .+++++++++.+...   +..+|+.-...+.+. + ++++
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            33445568999999999876 457788988888888888 599999999998753   566888877777776 7 8999


Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHH--------HHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCC----
Q 040371          126 ASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVE--------EGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGH----  193 (410)
Q Consensus       126 A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~--------~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~----  193 (410)
                      ++++++++.+.. .-|...++.-.-...+.|..+        ++.++++.+.+. . .-|...|+.....+.+.+.    
T Consensus       144 EL~~~~k~L~~d-pkNy~AW~~R~wvl~~l~~~~~~~~~~~~eELe~~~k~I~~-d-p~N~SAW~~R~~lL~~l~~~~~~  220 (349)
T 3q7a_A          144 EIEYIHGSLLPD-PKNYHTWAYLHWLYSHFSTLGRISEAQWGSELDWCNEMLRV-D-GRNNSAWGWRWYLRVSRPGAETS  220 (349)
T ss_dssp             HHHHHHHHTSSC-TTCHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHTTSTTCCCC
T ss_pred             HHHHHHHHHHhC-CCCHHHHHHHHHHHHHhccccccchhhHHHHHHHHHHHHHh-C-CCCHHHHHHHHHHHHhccccccc
Confidence            999999998753 236666665555555555555        889999988864 2 3367788888877877776    


Q ss_pred             ---HHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCch--------------------hHHHHHHHhhc---------cC
Q 040371          194 ---IEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRL--------------------ELGEVAIVNIS---------RL  239 (410)
Q Consensus       194 ---~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~--------------------~~a~~~~~~~~---------~~  239 (410)
                         ++++++.+++. ...| |...|+-+-..+...|..                    ........++.         +.
T Consensus       221 ~~~~~eELe~~~~aI~~~P~n~SaW~Ylr~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  300 (349)
T 3q7a_A          221 SRSLQDELIYILKSIHLIPHNVSAWNYLRGFLKHFSLPLVPILPAILPYTASKLNPDIETVEAFGFPMPSDPLPEDTPLP  300 (349)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCSGGGHHHHGGGTC--------------CCCCC-CCCSSCCSC
T ss_pred             hHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCCcccccccccccccccccccchhHHHHHHHHHhcccccccCCC
Confidence               68888888776 4455 677887766666665553                    12222222221         12


Q ss_pred             CCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          240 MGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       240 ~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      .+.....|+++|...|+.++|.++++.+.++
T Consensus       301 s~~al~~l~d~~~~~~~~~~a~~~~~~l~~~  331 (349)
T 3q7a_A          301 VPLALEYLADSFIEQNRVDDAAKVFEKLSSE  331 (349)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHHHHhh
Confidence            3334566899999999999999999998654

>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=98.07  E-value=0.00011  Score=56.81  Aligned_cols=95  Identities=9%  Similarity=-0.145  Sum_probs=58.0

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISG  116 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~  116 (410)
                      +...+..+...+...|+++.|...+...++.. +.+..++..+..+|.+.|++++|...|++..+   .+...|..+...
T Consensus         8 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~   86 (137)
T 3q49_B            8 SAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQC   86 (137)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHhCcHHHHHHHHHHHHhhC-cCcHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCchhHHHHHHHHHH
Confidence            45566666666666666666666666666653 33455666666666666666666666665442   234556666666


Q ss_pred             HHHcCChHHHHHHHHHHHH
Q 040371          117 VAIHGLAADASAIFTKMEM  135 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~  135 (410)
                      |...|++++|+..|++...
T Consensus        87 ~~~~~~~~~A~~~~~~a~~  105 (137)
T 3q49_B           87 QLEMESYDEAIANLQRAYS  105 (137)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhhHHHHHHHHHHHHH
Confidence            6666666666666665544

>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=98.06  E-value=0.00024  Score=52.87  Aligned_cols=92  Identities=13%  Similarity=0.031  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHH
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAI  119 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~  119 (410)
                      .+..+...+...|+++.|...++...+.. +.+...+..+...|.+.|++++|...|++..+   .+...|..+...|..
T Consensus         6 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~a~~~~~   84 (118)
T 1elw_A            6 ELKEKGNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEF   84 (118)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcccHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHhhccHHHHHHHHHHHHHhCcccHHHHHHHHHHHHH
Confidence            44444555555555555555555555442 22444555555555555555555555554331   133344444455555


Q ss_pred             cCChHHHHHHHHHHHH
Q 040371          120 HGLAADASAIFTKMEM  135 (410)
Q Consensus       120 ~g~~~~A~~l~~~m~~  135 (410)
                      .|++++|.+.|++..+
T Consensus        85 ~~~~~~A~~~~~~~~~  100 (118)
T 1elw_A           85 LNRFEEAKRTYEEGLK  100 (118)
T ss_dssp             TTCHHHHHHHHHHHHT
T ss_pred             HhhHHHHHHHHHHHHH
Confidence            5555555555554443

>3sz7_A HSC70 cochaperone (SGT); TPR domain, GET4, GET5, GET3, MDY2, SSA1, SSE1, chaperone regulator; 1.72A {Aspergillus fumigatus}

Probab=98.06  E-value=0.00011  Score=59.33  Aligned_cols=92  Identities=13%  Similarity=-0.011  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHH
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAI  119 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~  119 (410)
                      .+..+...+...|++++|.+.|+..++.. +.+..++..+..+|.+.|++++|...|++..+   .+...|..+...|.+
T Consensus        13 ~~~~~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~   91 (164)
T 3sz7_A           13 KLKSEGNAAMARKEYSKAIDLYTQALSIA-PANPIYLSNRAAAYSASGQHEKAAEDAELATVVDPKYSKAWSRLGLARFD   91 (164)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CcCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence            44444444455555555555555544442 22344444444444444444444444444331   123344444444444


Q ss_pred             cCChHHHHHHHHHHHH
Q 040371          120 HGLAADASAIFTKMEM  135 (410)
Q Consensus       120 ~g~~~~A~~l~~~m~~  135 (410)
                      .|++++|+..|++..+
T Consensus        92 ~g~~~~A~~~~~~al~  107 (164)
T 3sz7_A           92 MADYKGAKEAYEKGIE  107 (164)
T ss_dssp             TTCHHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHH
Confidence            4444444444444433

>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=98.06  E-value=8e-05  Score=57.45  Aligned_cols=97  Identities=6%  Similarity=0.028  Sum_probs=81.3

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCC--Ccc----HHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKI--ELN----FILS   79 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~--~~~----~~~~   79 (410)
                      ..+|..+-..|.+.|++++|++.|++.++.. +-+...|..+..++...|++++|.+.+++.++...  .++    ..++
T Consensus         8 A~a~~~lG~~~~~~~~~~~A~~~y~~Al~~~-p~~~~~~~nlg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~   86 (127)
T 4gcn_A            8 AIAEKDLGNAAYKQKDFEKAHVHYDKAIELD-PSNITFYNNKAAVYFEEKKFAECVQFCEKAVEVGRETRADYKLIAKAM   86 (127)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHHHhhhHHHHHHHHHHHHHhCcccchhhHHHHHHH
Confidence            3578889999999999999999999998753 34677899999999999999999999999987521  111    3467


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           80 AALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        80 ~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      ..+...|.+.|++++|++.|++..
T Consensus        87 ~~lg~~~~~~~~~~~A~~~~~kal  110 (127)
T 4gcn_A           87 SRAGNAFQKQNDLSLAVQWFHRSL  110 (127)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHH
Confidence            888899999999999999998764

>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin, type III secretion, protein binding; 1.85A {Pseudomonas aeruginosa} PDB: 2xcc_A

Probab=98.05  E-value=7e-05  Score=58.89  Aligned_cols=90  Identities=14%  Similarity=0.085  Sum_probs=40.3

Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc
Q 040371           79 SAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHC  155 (410)
Q Consensus        79 ~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~  155 (410)
                      +..+...+.+.|++++|...|++...   .+...|..+..+|.+.|++++|+..|++..... +.+...+..+..++...
T Consensus        21 ~~~~a~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~   99 (142)
T 2xcb_A           21 LYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGACRQSLGLYEQALQSYSYGALMD-INEPRFPFHAAECHLQL   99 (142)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHccHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCcHHHHHHHHHHHHc
Confidence            33344444445555555555544331   133444444444445555555555554444421 11233344444444445


Q ss_pred             CCHHHHHHHHHHhh
Q 040371          156 GLVEEGRKYFDHMR  169 (410)
Q Consensus       156 g~~~~a~~~~~~m~  169 (410)
                      |++++|...|+...
T Consensus       100 g~~~~A~~~~~~al  113 (142)
T 2xcb_A          100 GDLDGAESGFYSAR  113 (142)
T ss_dssp             TCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            55555555554444

>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=98.04  E-value=7.2e-05  Score=57.06  Aligned_cols=93  Identities=10%  Similarity=0.037  Sum_probs=54.5

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccC---C-------hhhHH
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRN---D-------VSVWN  111 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~---~-------~~~~~  111 (410)
                      ..+..+...+...|+++.|...+....+.. +.+..++..+...|.+.|++++|...|++....   +       ..+|.
T Consensus         5 ~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (131)
T 1elr_A            5 LKEKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYA   83 (131)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHHHhcC-CccHHHHHHHHHHHHHhccHHHHHHHHHHHHhhccccchhHHHHHHHHH
Confidence            345555566666666666666666666553 334556666666666666666666666654321   1       34555


Q ss_pred             HHHHHHHHcCChHHHHHHHHHHHH
Q 040371          112 AMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus       112 ~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      .+...|...|++++|.+.|++...
T Consensus        84 ~la~~~~~~~~~~~A~~~~~~~~~  107 (131)
T 1elr_A           84 RIGNSYFKEEKYKDAIHFYNKSLA  107 (131)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccHHHHHHHHHHHHH
Confidence            555555666666666666655554

>4f3v_A ESX-1 secretion system protein ECCA1; tetratricopeptide repeat, TPR domain, ATPase, protein secret protein transport; 2.00A {Mycobacterium tuberculosis}

Probab=98.04  E-value=0.00014  Score=64.06  Aligned_cols=171  Identities=9%  Similarity=-0.042  Sum_probs=123.2

Q ss_pred             hhHHHHH-------HHHHHHcCCHhHHHHHHHHHHHCCCCCCH----------------------HHHHHHHHHHHhhCC
Q 040371            6 VVSWNSM-------IGGFVRNARFDEALRFFREMLSSKVEPDK----------------------FTFASVIYGCARLGA   56 (410)
Q Consensus         6 ~~~~n~l-------i~~~~~~g~~~~a~~l~~~m~~~g~~pd~----------------------~t~~~ll~a~~~~~~   56 (410)
                      ...|+.+       ...+.+.++..+++..++.-..  +.|+.                      ........++...|+
T Consensus        40 ~Daw~g~~a~g~~~~~~L~~~~r~~~a~~~~~~~l~--l~p~~l~a~~~~~g~y~~~~~~v~~r~dl~LayA~~L~~~g~  117 (282)
T 4f3v_A           40 CDAWIGRIRCGDTDRVTLFRAWYSRRNFGQLSGSVQ--ISMSTLNARIAIGGLYGDITYPVTSPLAITMGFAACEAAQGN  117 (282)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHHHTGGGTTHHHHTTT--CCGGGGCCEEECCTTTCCCEEECSSHHHHHHHHHHHHHHHTC
T ss_pred             hHHHHhHHHccCCcHHHHHHHHHHHHHHHHHHHHhc--CChhhhhhhhccCCcccccccccCCHhHHHHHHHHHHHHCCC
Confidence            3567777       4666666666666666655433  33322                      123345677789999


Q ss_pred             HHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCC-----hhhHHHHHHHHHHcCChHHHHHHHH
Q 040371           57 LNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRND-----VSVWNAMISGVAIHGLAADASAIFT  131 (410)
Q Consensus        57 ~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~-----~~~~~~li~~~~~~g~~~~A~~l~~  131 (410)
                      +++|.++++.+...+  |+......+...|.+.|++++|+..|+......     ...+..+-.++.+.|++++|+..|+
T Consensus       118 y~eA~~~l~~~~~~~--p~~~~~~~~a~l~~~~~r~~dA~~~l~~a~~~~d~~~~~~a~~~LG~al~~LG~~~eAl~~l~  195 (282)
T 4f3v_A          118 YADAMEALEAAPVAG--SEHLVAWMKAVVYGAAERWTDVIDQVKSAGKWPDKFLAGAAGVAHGVAAANLALFTEAERRLT  195 (282)
T ss_dssp             HHHHHHHHTSSCCTT--CHHHHHHHHHHHHHHTTCHHHHHHHHTTGGGCSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcC--CchHHHHHHHHHHHHcCCHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence            999999999887754  443377777789999999999999999776532     2367778889999999999999999


Q ss_pred             HHHHCCCCCC--HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHH
Q 040371          132 KMEMFNVLPD--SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGA  183 (410)
Q Consensus       132 ~m~~~g~~p~--~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~  183 (410)
                      +.......|.  .........++.+.|+.++|..+|+++...   .|+...+..
T Consensus       196 ~a~~g~~~P~~~~da~~~~glaL~~lGr~deA~~~l~~a~a~---~P~~~~~~a  246 (282)
T 4f3v_A          196 EANDSPAGEACARAIAWYLAMARRSQGNESAAVALLEWLQTT---HPEPKVAAA  246 (282)
T ss_dssp             HHHTSTTTTTTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---SCCHHHHHH
T ss_pred             HHhcCCCCccccHHHHHHHHHHHHHcCCHHHHHHHHHHHHhc---CCcHHHHHH
Confidence            9875443254  234556677888999999999999999864   454333333

>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=98.04  E-value=0.0018  Score=58.52  Aligned_cols=233  Identities=10%  Similarity=0.032  Sum_probs=149.2

Q ss_pred             HHHHHHHHH---HHcCCHh-HHHHHHHHHHHCCCCCC-HHHHHHHHHHHHhhCC----------HHHHHHHHHHHHHcCC
Q 040371            8 SWNSMIGGF---VRNARFD-EALRFFREMLSSKVEPD-KFTFASVIYGCARLGA----------LNHAYWVHNLIIEKKI   72 (410)
Q Consensus         8 ~~n~li~~~---~~~g~~~-~a~~l~~~m~~~g~~pd-~~t~~~ll~a~~~~~~----------~~~a~~~~~~~~~~g~   72 (410)
                      .|..+....   .+.|.+. +|++++..++..  .|+ ...|+.=-.++...+.          ++++..+++.++... 
T Consensus        28 ~y~~~~~~~~~~~~~~e~s~eaL~~t~~~L~~--nP~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~-  104 (331)
T 3dss_A           28 LYQSATQAVFQKRQAGELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-  104 (331)
T ss_dssp             HHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTT--CTTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH--CchhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhC-
Confidence            444444433   3556654 799999999874  454 4455553333333332          678888888888865 


Q ss_pred             CccHHHHHHHHHHHHhcCC--HHHHHHHHHhccc---CChhhHHHHHHHHHHcCC-hHHHHHHHHHHHHCCCCCCHHHHH
Q 040371           73 ELNFILSAALIDMYSKCGK--IQMAKEVFDTVQR---NDVSVWNAMISGVAIHGL-AADASAIFTKMEMFNVLPDSITFL  146 (410)
Q Consensus        73 ~~~~~~~~~li~~y~~~g~--~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~-~~~A~~l~~~m~~~g~~p~~~t~~  146 (410)
                      +.+..+|+.-.-.+.+.|+  ++++..+++++.+   +|-.+|+--.-.....|. ++++++.++++.+..+ -|...++
T Consensus       105 PKny~aW~hR~wlL~~l~~~~~~~EL~~~~k~l~~dprNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~~p-~N~SAW~  183 (331)
T 3dss_A          105 PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNF-SNYSSWH  183 (331)
T ss_dssp             TTCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCS-CCHHHHH
T ss_pred             CCCHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHCC-CCHHHHH
Confidence            5588889888888888884  8999999998874   466788877777777887 5899999999988642 3556666


Q ss_pred             HHHHHHHcc--------------CCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhc-----------CCHHHHHHHH
Q 040371          147 GLLTACSHC--------------GLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRA-----------GHIEEAYGLI  201 (410)
Q Consensus       147 ~ll~a~~~~--------------g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~-----------g~~~~A~~~~  201 (410)
                      .....+.+.              +.++++.+.+......  -+-|...|+-+--.+.+.           +.++++++.+
T Consensus       184 ~R~~ll~~l~~~~~~~~~~~~~~~~~~eEle~~~~ai~~--~P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~  261 (331)
T 3dss_A          184 YRSCLLPQLHPQPDSGPQGRLPENVLLKELELVQNAFFT--DPNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESC  261 (331)
T ss_dssp             HHHHHHHHHSCCC------CCCHHHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhccccccccccchHHHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHH
Confidence            555544443              4577888888887743  234567777666666655           4567777777


Q ss_pred             HhC-CCCCCHHHHHHHHH-----HHHhcCchhHHHHH---HHhhccCCCchHHHH
Q 040371          202 TSM-TMEPDVVVWRALLS-----ACRTFKRLELGEVA---IVNISRLMGGDYVLL  247 (410)
Q Consensus       202 ~~m-~~~p~~~~~~~li~-----~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l  247 (410)
                      +++ ...||. .|..+-.     +....+..++....   +.+++|....-|.-+
T Consensus       262 ~elle~~pd~-~w~l~~~~~~~~~~~~~~~~~~~~~~l~~l~~~Dp~r~~~y~d~  315 (331)
T 3dss_A          262 KELQELEPEN-KWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDDL  315 (331)
T ss_dssp             HHHHHHCTTC-HHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHCGGGHHHHHHH
T ss_pred             HHHHhhCccc-chHHHHHHHHHHhhcccccHHHHHHHHHHHHHhCcchhhHHHHH
Confidence            776 455654 3432111     11134444555444   455566554444443

>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=98.02  E-value=1.5e-05  Score=66.78  Aligned_cols=121  Identities=9%  Similarity=-0.085  Sum_probs=59.8

Q ss_pred             HHHHHHhcCCHHHHHHHHHhcccC---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCC-CCC--------------HH
Q 040371           82 LIDMYSKCGKIQMAKEVFDTVQRN---DVSVWNAMISGVAIHGLAADASAIFTKMEMFNV-LPD--------------SI  143 (410)
Q Consensus        82 li~~y~~~g~~~~A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~-~p~--------------~~  143 (410)
                      .+.+....|++++|.+.|+.-...   ....|..+...+.+.|++++|+..|++...... .|+              ..
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~   89 (198)
T 2fbn_A           10 HSSGRENLYFQGAKKSIYDYTDEEKVQSAFDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDKKKNIEIS   89 (198)
T ss_dssp             ------------CCCSGGGCCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhccccCchhhCCHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhcccccchhhHHHHHHHHHHH
Confidence            334444555666666555533321   334566666667777777777777777665311 110              14


Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          144 TFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       144 t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      .+..+..++...|++++|...++...+.  -+.+...+..+..+|...|++++|.+.|++.
T Consensus        90 ~~~~la~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~a  148 (198)
T 2fbn_A           90 CNLNLATCYNKNKDYPKAIDHASKVLKI--DKNNVKALYKLGVANMYFGFLEEAKENLYKA  148 (198)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHh--CcccHHHHHHHHHHHHHcccHHHHHHHHHHH
Confidence            4555555556666666666666665532  1223455555555566666666666555554

>2kck_A TPR repeat; tetratricopeptide repeat, structural genomics, unknown function, PSI-2, protein structure initiative; NMR {Methanococcus maripaludis}

Probab=98.01  E-value=5.6e-05  Score=55.93  Aligned_cols=92  Identities=8%  Similarity=-0.050  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC--CHHHHHHHHHHH
Q 040371           78 LSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP--DSITFLGLLTAC  152 (410)
Q Consensus        78 ~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p--~~~t~~~ll~a~  152 (410)
                      ++..+...|.+.|++++|...|++..+   .+...|..+...|...|++++|++.|++..+.. +.  +...+..+...+
T Consensus         8 ~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~~~l~~~~   86 (112)
T 2kck_A            8 EYYLEGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLERYEEAVDCYNYVINVI-EDEYNKDVWAAKADAL   86 (112)
T ss_dssp             GGGGHHHHHHSSCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTS-CCTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHccCHHHHHHHHHHHHHhC-cccchHHHHHHHHHHH
Confidence            334444445555555555555544331   233445555555555555555555555555432 11  244455555555


Q ss_pred             Hcc-CCHHHHHHHHHHhhh
Q 040371          153 SHC-GLVEEGRKYFDHMRS  170 (410)
Q Consensus       153 ~~~-g~~~~a~~~~~~m~~  170 (410)
                      ... |++++|.+.+.....
T Consensus        87 ~~~~~~~~~A~~~~~~~~~  105 (112)
T 2kck_A           87 RYIEGKEVEAEIAEARAKL  105 (112)
T ss_dssp             TTCSSCSHHHHHHHHHHGG
T ss_pred             HHHhCCHHHHHHHHHHHhh
Confidence            555 666666666655553

>3ro3_A PINS homolog, G-protein-signaling modulator 2; asymmetric cell division, protein binding; 1.10A {Mus musculus}

Probab=97.96  E-value=8.8e-05  Score=58.80  Aligned_cols=95  Identities=9%  Similarity=0.027  Sum_probs=41.4

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhc---CCCC-Chh
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMF----NVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRY---SIQP-QLE  179 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~---~~~~-~~~  179 (410)
                      ++..+...|...|++++|.+.|++....    +..+ ....+..+...+...|++++|...++...+..   +..+ ...
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            3444444444445555555544443321    0000 02234444445555555555555555443210   1000 123


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHh
Q 040371          180 HYGAMVDLLGRAGHIEEAYGLITS  203 (410)
Q Consensus       180 ~~~~li~~~~~~g~~~~A~~~~~~  203 (410)
                      .+..+...|...|++++|.+.+++
T Consensus       131 ~~~~la~~~~~~g~~~~A~~~~~~  154 (164)
T 3ro3_A          131 ACWSLGNAYTALGNHDQAMHFAEK  154 (164)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHH
Confidence            344555555566666666555544

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.90  E-value=0.00015  Score=69.42  Aligned_cols=92  Identities=14%  Similarity=0.031  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHH
Q 040371           76 FILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTA  151 (410)
Q Consensus        76 ~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a  151 (410)
                      ..+|..+..+|.+.|++++|+..|++..+   .+..+|..+..+|...|++++|+..|++..+.  .| +...+..+..+
T Consensus       317 ~~~~~nla~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~l--~P~~~~a~~~l~~~  394 (457)
T 1kt0_A          317 LAAFLNLAMCYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQISMC  394 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTT--C----CHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHH
Confidence            34555666666666666666666665442   24455666666666666666666666666553  33 33445555555


Q ss_pred             HHccCCHHHHH-HHHHHhh
Q 040371          152 CSHCGLVEEGR-KYFDHMR  169 (410)
Q Consensus       152 ~~~~g~~~~a~-~~~~~m~  169 (410)
                      +.+.++.+++. ..+..|.
T Consensus       395 ~~~~~~~~~a~~~~~~~~f  413 (457)
T 1kt0_A          395 QKKAKEHNERDRRIYANMF  413 (457)
T ss_dssp             HHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            55556555544 2344443

>2dba_A Smooth muscle cell associated protein-1, isoform 2; tetratricopeptide repeat, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.88  E-value=0.00024  Score=55.54  Aligned_cols=94  Identities=9%  Similarity=-0.046  Sum_probs=46.4

Q ss_pred             hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC----HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHH
Q 040371          107 VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD----SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYG  182 (410)
Q Consensus       107 ~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~----~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~  182 (410)
                      ...|..+...+...|++++|++.|++..+.  .|+    ...+..+...+...|++++|...++...+.  .+.+...+.
T Consensus        28 ~~~~~~~a~~~~~~~~~~~A~~~~~~a~~~--~~~~~~~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~--~~~~~~~~~  103 (148)
T 2dba_A           28 VEQLRKEGNELFKCGDYGGALAAYTQALGL--DATPQDQAVLHRNRAACHLKLEDYDKAETEASKAIEK--DGGDVKALY  103 (148)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHHHHHTS--CCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--TSCCHHHHH
T ss_pred             HHHHHHHHHHHHHhCCHHHHHHHHHHHHHH--cccchHHHHHHHHHHHHHHHHccHHHHHHHHHHHHhh--CccCHHHHH
Confidence            344444555555555555555555555442  233    344444445555555555555555554432  111344455


Q ss_pred             HHHHHHHhcCCHHHHHHHHHhC
Q 040371          183 AMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       183 ~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      .+..+|...|++++|...|++.
T Consensus       104 ~~a~~~~~~~~~~~A~~~~~~a  125 (148)
T 2dba_A          104 RRSQALEKLGRLDQAVLDLQRC  125 (148)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH
Confidence            5555555555555555555544

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=97.85  E-value=5.2e-05  Score=72.96  Aligned_cols=121  Identities=12%  Similarity=0.076  Sum_probs=95.0

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK   88 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~   88 (410)
                      |..+...|.+.|++++|++.|++..+.. +-+..+|..+..++.+.|++++|.+.+++.++.. +.+...+..+..+|.+
T Consensus         9 ~~~lg~~~~~~g~~~~A~~~~~~Al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~   86 (477)
T 1wao_1            9 LKTQANDYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMA   86 (477)
T ss_dssp             SSSSSSSTTTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHH
Confidence            4444556778899999999999998752 3357889999999999999999999999999874 4568889999999999


Q ss_pred             cCCHHHHHHHHHhccc--C-ChhhHHHHHHH--HHHcCChHHHHHHHH
Q 040371           89 CGKIQMAKEVFDTVQR--N-DVSVWNAMISG--VAIHGLAADASAIFT  131 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~--~-~~~~~~~li~~--~~~~g~~~~A~~l~~  131 (410)
                      .|++++|.+.|++..+  | +...|..+..+  +.+.|++++|++.++
T Consensus        87 ~g~~~eA~~~~~~al~~~p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           87 LGKFRAALRDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HTCHHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             cCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999998753  3 45566666666  788899999999988

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.85  E-value=0.00046  Score=64.91  Aligned_cols=186  Identities=9%  Similarity=-0.061  Sum_probs=132.5

Q ss_pred             HHHHHHhhCCHHHHHHHHHHHHHcCCCcc----------------HHHHHHHHHHHHhcCCHHHHHHHHHhcccC-----
Q 040371           47 VIYGCARLGALNHAYWVHNLIIEKKIELN----------------FILSAALIDMYSKCGKIQMAKEVFDTVQRN-----  105 (410)
Q Consensus        47 ll~a~~~~~~~~~a~~~~~~~~~~g~~~~----------------~~~~~~li~~y~~~g~~~~A~~~f~~m~~~-----  105 (410)
                      -...+.+.|++++|.+.+..+++......                ......|...|.+.|++++|.+.+......     
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            34566788999999999999987532211                134678899999999999999999877531     


Q ss_pred             Ch----hhHHHHHHHHHHcCChHHHHHHHHHHHH----CCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCC-
Q 040371          106 DV----SVWNAMISGVAIHGLAADASAIFTKMEM----FNVLPD-SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQ-  175 (410)
Q Consensus       106 ~~----~~~~~li~~~~~~g~~~~A~~l~~~m~~----~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~-  175 (410)
                      +.    ...+.+-..+...|+.++|.+++++...    .+..+. ..++..+...+...|++++|..+++.......-. 
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    2334444444556899999999988754    233343 3567788899999999999999999876432211 


Q ss_pred             --C-ChhHHHHHHHHHHhcCCHHHHHHHHHhC-----CC-CC-C--HHHHHHHHHHHHhcCchhHHHHH
Q 040371          176 --P-QLEHYGAMVDLLGRAGHIEEAYGLITSM-----TM-EP-D--VVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       176 --~-~~~~~~~li~~~~~~g~~~~A~~~~~~m-----~~-~p-~--~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                        + ....+..++..|...|++++|..++++.     .. .| .  ...+..+...+...++++.|...
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~~g~~~~~~~~y~~A~~~  238 (434)
T 4b4t_Q          170 DKPSLVDVHLLESKVYHKLRNLAKSKASLTAARTAANSIYCPTQTVAELDLMSGILHCEDKDYKTAFSY  238 (434)
T ss_dssp             CSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHTTSSSCHHHHHHH
T ss_pred             cchhHHHHHHHHHHHHHHhCcHHHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence              1 1457888999999999999999988775     11 12 1  23455555667788899988877

>1hxi_A PEX5, peroxisome targeting signal 1 receptor PEX5; alpha helical, transport protein; 1.60A {Trypanosoma brucei} SCOP: a.118.8.1

Probab=97.84  E-value=0.00018  Score=54.86  Aligned_cols=91  Identities=14%  Similarity=-0.009  Sum_probs=58.4

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHc
Q 040371           44 FASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIH  120 (410)
Q Consensus        44 ~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~  120 (410)
                      +..+...+.+.|++++|...++..++.. +.+...+..+..+|.+.|++++|+..|++..+  | +...|..+...|.+.
T Consensus        20 ~~~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l~P~~~~~~~~la~~~~~~   98 (121)
T 1hxi_A           20 PMEEGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNE   98 (121)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence            3444555666777777777777776653 33566666666777777777777777766542  2 445666666666667


Q ss_pred             CChHHHHHHHHHHHH
Q 040371          121 GLAADASAIFTKMEM  135 (410)
Q Consensus       121 g~~~~A~~l~~~m~~  135 (410)
                      |++++|+..|++..+
T Consensus        99 g~~~~A~~~~~~al~  113 (121)
T 1hxi_A           99 HNANAALASLRAWLL  113 (121)
T ss_dssp             HHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHHH
Confidence            777777777766654

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=97.82  E-value=0.0088  Score=57.55  Aligned_cols=175  Identities=6%  Similarity=-0.096  Sum_probs=96.7

Q ss_pred             HHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCCh---------------------------
Q 040371          126 ASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQL---------------------------  178 (410)
Q Consensus       126 A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~---------------------------  178 (410)
                      +..+|+++... .+-+...+...+.-+...|+++.|..+|++....   +.+.                           
T Consensus       198 v~~~ye~al~~-~p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~---P~~~~l~~~y~~~~e~~~~~~~l~~~~~~~~  273 (493)
T 2uy1_A          198 MHFIHNYILDS-FYYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM---SDGMFLSLYYGLVMDEEAVYGDLKRKYSMGE  273 (493)
T ss_dssp             HHHHHHHHHHH-TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CCSSHHHHHHHHHTTCTHHHHHHHHHTC---
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC---CCcHHHHHHHHhhcchhHHHHHHHHHHHhhc
Confidence            44455555443 1223444555555555667777777777666532   1111                           


Q ss_pred             -------------hHHHHHHHHHHhcCCHHHHHHHHHhCCCCC--CHHHHHHHHHHH-HhcCchhHHHHHH---HhhccC
Q 040371          179 -------------EHYGAMVDLLGRAGHIEEAYGLITSMTMEP--DVVVWRALLSAC-RTFKRLELGEVAI---VNISRL  239 (410)
Q Consensus       179 -------------~~~~~li~~~~~~g~~~~A~~~~~~m~~~p--~~~~~~~li~~~-~~~g~~~~a~~~~---~~~~~~  239 (410)
                                   ..|...++.+.+.+.++.|..+|++. ..|  +...|......- ...++.+.|..++   .+..|.
T Consensus       274 ~~~~~~~~~~~~~~lw~~y~~~~~r~~~~~~AR~i~~~A-~~~~~~~~v~i~~A~lE~~~~~d~~~ar~ife~al~~~~~  352 (493)
T 2uy1_A          274 AESAEKVFSKELDLLRINHLNYVLKKRGLELFRKLFIEL-GNEGVGPHVFIYCAFIEYYATGSRATPYNIFSSGLLKHPD  352 (493)
T ss_dssp             -------CHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHH-TTSCCCHHHHHHHHHHHHHHHCCSHHHHHHHHHHHHHCTT
T ss_pred             cchhhhhcccccHHHHHHHHHHHHHcCCHHHHHHHHHHh-hCCCCChHHHHHHHHHHHHHCCChHHHHHHHHHHHHHCCC
Confidence                         22334444444567788888888887 223  334443222221 2233688888883   333455


Q ss_pred             CCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHHHHHHHHHCC
Q 040371          240 MGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGSLIQRTKSEG  318 (410)
Q Consensus       240 ~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~m~~~g  318 (410)
                      ++..+...++...+.|+.+.|+.+|++..+      ...-|..       ++.-...+|..+.+.+++++....++..+
T Consensus       353 ~~~~~~~yid~e~~~~~~~~aR~l~er~~k------~~~lw~~-------~~~fE~~~G~~~~~r~v~~~~~~~~~~~~  418 (493)
T 2uy1_A          353 STLLKEEFFLFLLRIGDEENARALFKRLEK------TSRMWDS-------MIEYEFMVGSMELFRELVDQKMDAIKADA  418 (493)
T ss_dssp             CHHHHHHHHHHHHHHTCHHHHHHHHHHSCC------BHHHHHH-------HHHHHHHHSCHHHHHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHH------HHHHHHH-------HHHHHHHCCCHHHHHHHHHHHHHHhcccc
Confidence            554555567777788899999988888621      0011211       11112346788888888887776666443

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.79  E-value=0.00039  Score=53.02  Aligned_cols=91  Identities=12%  Similarity=-0.017  Sum_probs=51.5

Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHHHCCCCCCH---HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc---HHHHHHHHH
Q 040371           11 SMIGGFVRNARFDEALRFFREMLSSKVEPDK---FTFASVIYGCARLGALNHAYWVHNLIIEKKIELN---FILSAALID   84 (410)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~---~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~---~~~~~~li~   84 (410)
                      .+...+.+.|++++|+..|++..+.. +.+.   ..+..+..++...|++++|...++.+++.. +.+   ..++..+..
T Consensus         7 ~~a~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~-p~~~~~~~~~~~la~   84 (129)
T 2xev_A            7 NVAFDALKNGKYDDASQLFLSFLELY-PNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY-PTHDKAAGGLLKLGL   84 (129)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHC-SSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTSTTHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHC-CCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC-CCCcccHHHHHHHHH
Confidence            34556666777777777777766532 1122   355555566666666666666666666543 112   344555555


Q ss_pred             HHHhcCCHHHHHHHHHhcc
Q 040371           85 MYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~  103 (410)
                      +|.+.|++++|...|++..
T Consensus        85 ~~~~~g~~~~A~~~~~~~~  103 (129)
T 2xev_A           85 SQYGEGKNTEAQQTLQQVA  103 (129)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHH
Confidence            5555555555555555543

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.77  E-value=4.9e-05  Score=57.56  Aligned_cols=84  Identities=11%  Similarity=0.044  Sum_probs=50.2

Q ss_pred             cCCHhHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHH
Q 040371           19 NARFDEALRFFREMLSSKV--EPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAK   96 (410)
Q Consensus        19 ~g~~~~a~~l~~~m~~~g~--~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~   96 (410)
                      .|++++|+..|++.++.+.  +-+...+..+..++...|++++|...+++.++.. +.+..++..+..+|.+.|++++|.
T Consensus         3 ~g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            3 LGLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQF-PNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             ----CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCchHHHHHHHHHHHHcCCHHHHH
Confidence            5667777777777765421  2234456666666667777777777777766654 334566666666666667776666


Q ss_pred             HHHHhcc
Q 040371           97 EVFDTVQ  103 (410)
Q Consensus        97 ~~f~~m~  103 (410)
                      ..|++..
T Consensus        82 ~~~~~al   88 (117)
T 3k9i_A           82 ELLLKII   88 (117)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            6666543

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.71  E-value=0.00019  Score=68.96  Aligned_cols=63  Identities=8%  Similarity=-0.089  Sum_probs=30.2

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHC---CCCCC----HHHHHHHHHHHHccCCHHHHHHHHHHhhhh
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMF---NVLPD----SITFLGLLTACSHCGLVEEGRKYFDHMRSR  171 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~---g~~p~----~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~  171 (410)
                      +++.|...|...|++++|+.++++..+-   -..||    ..+...+-.++...+.+++|+.++..+.+.
T Consensus       395 ~l~nLa~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~~~~  464 (490)
T 3n71_A          395 AVMRAGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKMREA  464 (490)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4555555555555555555555444321   11122    122333444445556666666666666543

>2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris}

Probab=97.71  E-value=0.00051  Score=52.36  Aligned_cols=85  Identities=16%  Similarity=0.025  Sum_probs=37.7

Q ss_pred             HHHHHhcCCHHHHHHHHHhccc--CC-h---hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC----HHHHHHHHHHH
Q 040371           83 IDMYSKCGKIQMAKEVFDTVQR--ND-V---SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD----SITFLGLLTAC  152 (410)
Q Consensus        83 i~~y~~~g~~~~A~~~f~~m~~--~~-~---~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~----~~t~~~ll~a~  152 (410)
                      ...+.+.|++++|...|++..+  |+ .   ..|..+...|.+.|++++|+..|++.....  |+    ...+..+..++
T Consensus         9 a~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~~~~~~--p~~~~~~~~~~~la~~~   86 (129)
T 2xev_A            9 AFDALKNGKYDDASQLFLSFLELYPNGVYTPNALYWLGESYYATRNFQLAEAQFRDLVSRY--PTHDKAAGGLLKLGLSQ   86 (129)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHCSSSTTHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC--TTSTTHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHC--CCCcccHHHHHHHHHHH
Confidence            3344445555555555544432  21 1   244444444445555555555555444421  21    23333444444


Q ss_pred             HccCCHHHHHHHHHHhh
Q 040371          153 SHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       153 ~~~g~~~~a~~~~~~m~  169 (410)
                      ...|++++|...|+.+.
T Consensus        87 ~~~g~~~~A~~~~~~~~  103 (129)
T 2xev_A           87 YGEGKNTEAQQTLQQVA  103 (129)
T ss_dssp             HHTTCHHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHH
Confidence            44455555555554444

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.71  E-value=5.2e-05  Score=56.34  Aligned_cols=97  Identities=10%  Similarity=0.146  Sum_probs=67.0

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCcc------HHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELN------FIL   78 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~------~~~   78 (410)
                      +...|..+...+.+.|++++|++.|++..+.. +.+...+..+..++...|++++|.+.++..++... .+      ...
T Consensus         3 ~~~~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p-~~~~~~~~~~~   80 (111)
T 2l6j_A            3 QFEKQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLRYTS-TAEHVAIRSKL   80 (111)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTSCS-STTSHHHHHHH
T ss_pred             hHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhCC-CccHHHHHHHH
Confidence            45677788888888888888888888877642 33566777777888888888888888888877532 22      445


Q ss_pred             HHHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           79 SAALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        79 ~~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      +..+..++...|+.+.|...|++++
T Consensus        81 ~~~~~~~~~~~~~~~~a~~~~~~~~  105 (111)
T 2l6j_A           81 QYRLELAQGAVGSVQIPVVEVDELP  105 (111)
T ss_dssp             HHHHHHHHHHHHCCCCCSSSSSSCS
T ss_pred             HHHHHHHHHHHHhHhhhHhHHHHhH
Confidence            5556666666666666655555443

>1kt0_A FKBP51, 51 kDa FK506-binding protein; FKBP-like ppiase, TPR repeats, isomerase; 2.70A {Homo sapiens} SCOP: a.118.8.1 d.26.1.1 d.26.1.1 PDB: 1kt1_A 3o5d_A

Probab=97.71  E-value=0.00059  Score=65.15  Aligned_cols=125  Identities=11%  Similarity=0.026  Sum_probs=75.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-C---------------hhhHHHHHHHHHHcCChHHHHHHHHHHHHCC
Q 040371           76 FILSAALIDMYSKCGKIQMAKEVFDTVQR--N-D---------------VSVWNAMISGVAIHGLAADASAIFTKMEMFN  137 (410)
Q Consensus        76 ~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~---------------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g  137 (410)
                      ...+..+...|.+.|++++|...|++..+  | +               ...|+.+..+|.+.|++++|+..|++..+..
T Consensus       268 a~~~~~~G~~~~~~g~~~~A~~~y~~Al~~~p~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~  347 (457)
T 1kt0_A          268 AAIVKEKGTVYFKGGKYMQAVIQYGKIVSWLEMEYGLSEKESKASESFLLAAFLNLAMCYLKLREYTKAVECCDKALGLD  347 (457)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHHHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHhcC
Confidence            44566667777777777777777776542  2 2               3566666667777777777777777666542


Q ss_pred             CCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHH-HHHHhC
Q 040371          138 VLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAY-GLITSM  204 (410)
Q Consensus       138 ~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~-~~~~~m  204 (410)
                       +.+...+..+..++...|++++|...|+.+.+   +.| +...+..+..++.+.++.+++. .++++|
T Consensus       348 -p~~~~a~~~~g~a~~~~g~~~~A~~~~~~al~---l~P~~~~a~~~l~~~~~~~~~~~~a~~~~~~~~  412 (457)
T 1kt0_A          348 -SANEKGLYRRGEAQLLMNEFESAKGDFEKVLE---VNPQNKAARLQISMCQKKAKEHNERDRRIYANM  412 (457)
T ss_dssp             -TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---TC----CHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred             -CccHHHHHHHHHHHHHccCHHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence             22455566666666677777777777766653   223 3455666666666666666554 244444

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.71  E-value=0.00069  Score=54.30  Aligned_cols=60  Identities=13%  Similarity=0.057  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           76 FILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        76 ~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      ..++..+..+|.+.|++++|...+++...   .+...|..+..+|...|++++|+..|++...
T Consensus        63 ~~~~~nla~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A           63 IPLYANMSQCYLNIGDLHEAEETSSEVLKREETNEKALFRRAKARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             HHHHHHHHHHHHHHTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCcHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHhcHHHHHHHHHHHHh
Confidence            34555666666666666666666665442   2445566666666666666666666666655

>3dss_A Geranylgeranyl transferase type-2 subunit alpha; protein prenylation, metal-binding, prenyltransferase, zinc, phosphoprotein; 1.80A {Rattus norvegicus} PDB: 3dst_A* 3dsu_A* 3dsv_A* 3dsw_A* 3dsx_A* 3hxb_A* 3hxc_A* 3hxd_A* 3hxe_A* 3hxf_A* 3pz1_A* 3pz2_A* 3pz3_A* 3c72_A* 4gtv_A* 4gts_A* 4ehm_A* 4gtt_A*

Probab=97.70  E-value=0.0076  Score=54.44  Aligned_cols=215  Identities=9%  Similarity=-0.007  Sum_probs=146.6

Q ss_pred             HhhCCH-HHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCC----------HHHHHHHHHhccc---CChhhHHHHHHHH
Q 040371           52 ARLGAL-NHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK----------IQMAKEVFDTVQR---NDVSVWNAMISGV  117 (410)
Q Consensus        52 ~~~~~~-~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~----------~~~A~~~f~~m~~---~~~~~~~~li~~~  117 (410)
                      .+.|.+ ++|..+.+.++..+ +-+..+|+.--......|.          ++++..+++.+..   ++..+|+.-.-.+
T Consensus        40 ~~~~e~s~eaL~~t~~~L~~n-P~~ytaWn~Rr~iL~~l~~~~~~~~~~~~l~~EL~~~~~~L~~~PKny~aW~hR~wlL  118 (331)
T 3dss_A           40 RQAGELDESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNPKSYGTWHHRCWLL  118 (331)
T ss_dssp             HHTTCCSHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHH
T ss_pred             HHcCCCCHHHHHHHHHHHHHC-chhHHHHHHHHHHHHHhcccccchhhhHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            345555 47899999998875 4456677755444444333          6788888888764   3667888877777


Q ss_pred             HHcCC--hHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCC-HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhc---
Q 040371          118 AIHGL--AADASAIFTKMEMFNVLPDSITFLGLLTACSHCGL-VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRA---  191 (410)
Q Consensus       118 ~~~g~--~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~-~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~---  191 (410)
                      .+.|+  +++++++++++.+.. +-|...++.-.-.+.+.|. ++++.+.++.+.+. . +-|...|+.....+.+.   
T Consensus       119 ~~l~~~~~~~EL~~~~k~l~~d-prNy~AW~~R~~vl~~l~~~~~eel~~~~~~I~~-~-p~N~SAW~~R~~ll~~l~~~  195 (331)
T 3dss_A          119 SRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITR-N-FSNYSSWHYRSCLLPQLHPQ  195 (331)
T ss_dssp             HHCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH-C-SCCHHHHHHHHHHHHHHSCC
T ss_pred             hccCcccHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHH-C-CCCHHHHHHHHHHHHHhhhc
Confidence            77774  899999999999864 3367777777777777887 68999999999864 2 34667787766666655   


Q ss_pred             -----------CCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhc-----------CchhHHHHH---HHhhccCCCchH
Q 040371          192 -----------GHIEEAYGLITSM-TMEP-DVVVWRALLSACRTF-----------KRLELGEVA---IVNISRLMGGDY  244 (410)
Q Consensus       192 -----------g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~-----------g~~~~a~~~---~~~~~~~~~~~~  244 (410)
                                 +.++++++.+++. ...| |...|+-+-..+...           +.++++.+.   +.++.|++...+
T Consensus       196 ~~~~~~~~~~~~~~~eEle~~~~ai~~~P~d~SaW~Y~r~ll~~~~~~~~~~~~~~~~l~~el~~~~elle~~pd~~w~l  275 (331)
T 3dss_A          196 PDSGPQGRLPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGAGSGRCELSVEKSTVLQSELESCKELQELEPENKWCL  275 (331)
T ss_dssp             C------CCCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHSSSCGGGCCHHHHHHHHHHHHHHHHHHHHCTTCHHHH
T ss_pred             cccccccccchHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccCccccchHHHHHHHHHHHHHHHHHhhCcccchHH
Confidence                       4578888888876 4455 677787554444433           345566665   667778775444


Q ss_pred             HHHHH---HHHhcCChhHHHHHHHHHHhC
Q 040371          245 VLLSN---MYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       245 ~~l~~---~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      ..++.   .....|..+++...+.++.+-
T Consensus       276 ~~~~~~~~~~~~~~~~~~~~~~l~~l~~~  304 (331)
T 3dss_A          276 LTIILLMRALDPLLYEKETLQYFSTLKAV  304 (331)
T ss_dssp             HHHHHHHHHHCTTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcccccHHHHHHHHHHHHHh
Confidence            33332   222456777888888887753

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.70  E-value=0.00014  Score=66.58  Aligned_cols=142  Identities=13%  Similarity=0.076  Sum_probs=67.5

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      ..|..+-..|.+.|++++|+..|++....  .|+...+       ...++.+.+...+          ....++.+..+|
T Consensus       180 ~~~~~~g~~~~~~g~~~~A~~~y~~Al~~--~p~~~~~-------~~~~~~~~~~~~l----------~~~~~~nla~~~  240 (338)
T 2if4_A          180 DRRKMDGNSLFKEEKLEEAMQQYEMAIAY--MGDDFMF-------QLYGKYQDMALAV----------KNPCHLNIAACL  240 (338)
T ss_dssp             HHHHHHHHHTCSSSCCHHHHHHHHHHHHH--SCHHHHH-------TCCHHHHHHHHHH----------HTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHHHHH--hccchhh-------hhcccHHHHHHHH----------HHHHHHHHHHHH
Confidence            45667777778888888888888887653  3443311       1112222221111          012566677777


Q ss_pred             HhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH-HHHHHHHHH-HHccCCHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS-ITFLGLLTA-CSHCGLVEEG  161 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~a-~~~~g~~~~a  161 (410)
                      .+.|++++|...|++..+   .+..+|..+..+|...|++++|+..|++..+  +.|+. ..+..+... ....+..+.+
T Consensus       241 ~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~--l~p~~~~a~~~L~~l~~~~~~~~~~a  318 (338)
T 2if4_A          241 IKLKRYDEAIGHCNIVLTEEEKNPKALFRRGKAKAELGQMDSARDDFRKAQK--YAPDDKAIRRELRALAEQEKALYQKQ  318 (338)
T ss_dssp             HTTTCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC----------------------------
T ss_pred             HHcCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            777777777777776542   2556677777777777777777777777654  23432 222222222 1234556666


Q ss_pred             HHHHHHhh
Q 040371          162 RKYFDHMR  169 (410)
Q Consensus       162 ~~~~~~m~  169 (410)
                      ...|..|.
T Consensus       319 ~~~~~~~l  326 (338)
T 2if4_A          319 KEMYKGIF  326 (338)
T ss_dssp             --------
T ss_pred             HHHHHHhh
Confidence            66776665

>2uy1_A Cleavage stimulation factor 77; RNA-binding protein; 2.0A {Encephalitozoon cuniculi} PDB: 2uy1_B

Probab=97.69  E-value=0.0081  Score=57.80  Aligned_cols=46  Identities=15%  Similarity=-0.085  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc
Q 040371           24 EALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus        24 ~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~   70 (410)
                      .+..+|++++.. .+.+...|...+.-+.+.|+++.|+.++++.++.
T Consensus       197 Rv~~~ye~al~~-~p~~~~lW~~ya~~~~~~~~~~~ar~i~erAi~~  242 (493)
T 2uy1_A          197 RMHFIHNYILDS-FYYAEEVYFFYSEYLIGIGQKEKAKKVVERGIEM  242 (493)
T ss_dssp             HHHHHHHHHHHH-TTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC
Confidence            345566665553 2334555555555566666666666666666665

>3rkv_A Putative peptidylprolyl isomerase; structural genomics, APC102156, PSI-biology, midwest center structural genomics, MCSG; 2.41A {Caenorhabditis elegans}

Probab=97.68  E-value=0.00069  Score=54.28  Aligned_cols=98  Identities=15%  Similarity=0.145  Sum_probs=83.5

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHC-------CC---------CC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSS-------KV---------EP-DKFTFASVIYGCARLGALNHAYWVHNLII   68 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~-------g~---------~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~   68 (410)
                      +..|...-..+.+.|++++|+..|.+.+..       .-         .| +...|..+..++.+.|+++.|...+...+
T Consensus        11 a~~~~~~G~~~~~~~~~~~A~~~y~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~~~~~~A~~~~~~al   90 (162)
T 3rkv_A           11 VEALRQKGNELFVQKDYKEAIDAYRDALTRLDTLILREKPGEPEWVELDRKNIPLYANMSQCYLNIGDLHEAEETSSEVL   90 (162)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHTSCTTSHHHHHHHHTHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence            456888899999999999999999998763       00         12 23578888999999999999999999999


Q ss_pred             HcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc
Q 040371           69 EKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR  104 (410)
Q Consensus        69 ~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~  104 (410)
                      +.. +.+...+..+..+|...|++++|...|++...
T Consensus        91 ~~~-p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  125 (162)
T 3rkv_A           91 KRE-ETNEKALFRRAKARIAAWKLDEAEEDLKLLLR  125 (162)
T ss_dssp             HHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hcC-CcchHHHHHHHHHHHHHhcHHHHHHHHHHHHh
Confidence            975 55788999999999999999999999998764

>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=97.68  E-value=0.00044  Score=64.05  Aligned_cols=134  Identities=11%  Similarity=0.009  Sum_probs=77.0

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYS   87 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~   87 (410)
                      .|..+...|.+.|++++|+..|++.++.  .|+..          .....+...+       . -+.+..++..+..+|.
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~--~~~~~----------~~~~~~~~~~-------~-~~~~~~~~~nla~~~~  284 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRY--VEGSR----------AAAEDADGAK-------L-QPVALSCVLNIGACKL  284 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHH--HHHHH----------HHSCHHHHGG-------G-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHH--hhcCc----------cccChHHHHH-------H-HHHHHHHHHHHHHHHH
Confidence            4666777777777777777777776541  00000          0001111000       1 1224556667777777


Q ss_pred             hcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHH
Q 040371           88 KCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRK  163 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~  163 (410)
                      +.|++++|+..+++..+   .+..+|..+..+|...|++++|++.|++..+.  .| +...+..+...+...++.+++.+
T Consensus       285 ~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l--~P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          285 KMSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             HTTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            77777777777776553   24556677777777777777777777776653  33 34455555555555665555543

>1wao_1 Serine/threonine protein phosphatase 5; hydrolase, protein-protein interactions, TPR, super-helix,; 2.9A {Homo sapiens} SCOP: a.118.8.1 d.159.1.3

Probab=97.67  E-value=0.00021  Score=68.66  Aligned_cols=115  Identities=7%  Similarity=-0.053  Sum_probs=63.6

Q ss_pred             HHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEG  161 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a  161 (410)
                      .|.+.|++++|.+.|++..+   .+..+|+.+..+|.+.|++++|++.|++..+.. +.+..++..+..++...|++++|
T Consensus        15 ~~~~~g~~~~A~~~~~~Al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~l~-p~~~~~~~~lg~~~~~~g~~~eA   93 (477)
T 1wao_1           15 DYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRAA   93 (477)
T ss_dssp             STTTTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHHTCHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHH
Confidence            34455666666666665432   235566666666666666666666666666542 12345566666666677777777


Q ss_pred             HHHHHHhhhhcCCCCChhHHHHHHHH--HHhcCCHHHHHHHHH
Q 040371          162 RKYFDHMRSRYSIQPQLEHYGAMVDL--LGRAGHIEEAYGLIT  202 (410)
Q Consensus       162 ~~~~~~m~~~~~~~~~~~~~~~li~~--~~~~g~~~~A~~~~~  202 (410)
                      .+.|++..+..  +.+...+..+..+  +.+.|++++|.+.++
T Consensus        94 ~~~~~~al~~~--p~~~~~~~~l~~~~~~~~~g~~~~A~~~~~  134 (477)
T 1wao_1           94 LRDYETVVKVK--PHDKDAKMKYQECNKIVKQKAFERAIAGDE  134 (477)
T ss_dssp             HHHHHHHHHHS--TTCTTHHHHHHHHHHHHHHHHHCCC-----
T ss_pred             HHHHHHHHHhC--CCCHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            77776666431  1123344444444  666677777777766

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.67  E-value=0.00074  Score=53.84  Aligned_cols=60  Identities=17%  Similarity=0.107  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCC-------------HHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPD-------------KFTFASVIYGCARLGALNHAYWVHNLIIE   69 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd-------------~~t~~~ll~a~~~~~~~~~a~~~~~~~~~   69 (410)
                      .|...-..+.+.|++++|+..|++.++.  .|+             ...|.....++.++|++++|...+++.++
T Consensus        13 ~~~~~G~~l~~~g~~eeAi~~Y~kAL~l--~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~kAL~   85 (159)
T 2hr2_A           13 LALSDAQRQLVAGEYDEAAANCRRAMEI--SHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKALH   85 (159)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHH--HTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHhh--CCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3555566666777777777777776653  222             11444444555555555555555444444

>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=97.64  E-value=0.00056  Score=63.33  Aligned_cols=118  Identities=7%  Similarity=-0.041  Sum_probs=73.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhccc-------------------CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCC
Q 040371           78 LSAALIDMYSKCGKIQMAKEVFDTVQR-------------------NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNV  138 (410)
Q Consensus        78 ~~~~li~~y~~~g~~~~A~~~f~~m~~-------------------~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~  138 (410)
                      .+..+...|.+.|++++|.+.|++..+                   .+..+|+.+..+|.+.|++++|++.+++..+.. 
T Consensus       225 ~~~~~g~~~~~~g~~~~Ai~~y~kAl~~~~~~~~~~~~~~~~~~~~~~~~~~~nla~~~~~~g~~~~A~~~~~~al~~~-  303 (370)
T 1ihg_A          225 DLKNIGNTFFKSQNWEMAIKKYTKVLRYVEGSRAAAEDADGAKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEID-  303 (370)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHSCHHHHGGGHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcCccccChHHHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC-
Confidence            355566667777777777776665442                   134566677777777777777777777776532 


Q ss_pred             CCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCCHHHHHH
Q 040371          139 LPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGHIEEAYG  199 (410)
Q Consensus       139 ~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~~~~A~~  199 (410)
                      +.+...+..+..++...|++++|...|+...+.   .| +...+..+...+.+.++.+++.+
T Consensus       304 p~~~~a~~~lg~~~~~~g~~~eA~~~l~~Al~l---~P~~~~~~~~l~~~~~~~~~~~~a~k  362 (370)
T 1ihg_A          304 PSNTKALYRRAQGWQGLKEYDQALADLKKAQEI---APEDKAIQAELLKVKQKIKAQKDKEK  362 (370)
T ss_dssp             TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH---CTTCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHccCHHHHHHHHHHHHHh---CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            124556666667777777777777777776642   23 34555566666666666655543

>3k9i_A BH0479 protein; putative protein binding protein, structural genomics, joint for structural genomics, JCSG; 2.71A {Bacillus halodurans}

Probab=97.63  E-value=8.8e-05  Score=56.12  Aligned_cols=82  Identities=16%  Similarity=0.128  Sum_probs=36.5

Q ss_pred             CChHHHHHHHHHHHHCCC-CC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHH
Q 040371          121 GLAADASAIFTKMEMFNV-LP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAY  198 (410)
Q Consensus       121 g~~~~A~~l~~~m~~~g~-~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~  198 (410)
                      |++++|+..|++..+.+. .| +...+..+...+...|++++|...|+...+.  .+-+...+..+..+|.+.|++++|.
T Consensus         4 g~~~~A~~~~~~al~~~~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~g~~~~A~   81 (117)
T 3k9i_A            4 GLEAQAVPYYEKAIASGLQGKDLAECYLGLGSTFRTLGEYRKAEAVLANGVKQ--FPNHQALRVFYAMVLYNLGRYEQGV   81 (117)
T ss_dssp             ---CCCHHHHHHHHSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCchHHHHHHHHHHHHcCCHHHHH
Confidence            445555555555544321 12 2233444445555555555555555555432  1112344445555555555555555


Q ss_pred             HHHHhC
Q 040371          199 GLITSM  204 (410)
Q Consensus       199 ~~~~~m  204 (410)
                      ..+++.
T Consensus        82 ~~~~~a   87 (117)
T 3k9i_A           82 ELLLKI   87 (117)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            555443

>3n71_A Histone lysine methyltransferase SMYD1; heart development, transcription; HET: SFG MES; 2.30A {Mus musculus}

Probab=97.63  E-value=0.00037  Score=66.91  Aligned_cols=119  Identities=8%  Similarity=-0.032  Sum_probs=82.1

Q ss_pred             HHhcCCHHHHHHHHHhccc-------C----ChhhHHHHHHHHHHcCChHHHHHHHHHHHHC-----C-CCCC-HHHHHH
Q 040371           86 YSKCGKIQMAKEVFDTVQR-------N----DVSVWNAMISGVAIHGLAADASAIFTKMEMF-----N-VLPD-SITFLG  147 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~-------~----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g-~~p~-~~t~~~  147 (410)
                      +...|++++|+.++++..+       +    -..+++.|...|...|++++|+.++++.++-     | -.|+ ..+++.
T Consensus       319 ~~~qg~~~eA~~l~~~aL~~~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~n  398 (490)
T 3n71_A          319 ARSEGLYHEVVKLCRECLEKQEPVFADTNLYVLRLLSIASEVLSYLQAYEEASHYARRMVDGYMKLYHHNNAQLGMAVMR  398 (490)
T ss_dssp             HHTTTCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCTTCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            3456777777777665431       1    1246777888888888888888887776542     2 1232 456888


Q ss_pred             HHHHHHccCCHHHHHHHHHHhhh----hcCCC-CC-hhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          148 LLTACSHCGLVEEGRKYFDHMRS----RYSIQ-PQ-LEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       148 ll~a~~~~g~~~~a~~~~~~m~~----~~~~~-~~-~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      |...|...|++++|+.++++..+    .+|-. |+ ..+.+.+-.++...+.+++|+.++.++
T Consensus       399 La~~~~~~G~~~eA~~~~~~Al~i~~~~lG~~Hp~~~~~~~~l~~~~~e~~~~~~ae~~~~~~  461 (490)
T 3n71_A          399 AGLTNWHAGHIEVGHGMICKAYAILLVTHGPSHPITKDLEAMRMQTEMELRMFRQNEFMYHKM  461 (490)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHTCTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999998887653    22322 22 345566777788888899999888887

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=97.53  E-value=0.0011  Score=46.73  Aligned_cols=82  Identities=13%  Similarity=0.193  Sum_probs=52.9

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      ...|..+...|.+.|++++|+..|++..+.. +.+...+..+..++...|++++|...+++..+.. +.+..++..+...
T Consensus         9 ~~~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~a~~~~-p~~~~~~~~l~~~   86 (91)
T 1na3_A            9 AEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAKQNLGNA   86 (91)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Confidence            4566777777777777777777777776542 3345566667777777777777777777776653 3345555555555


Q ss_pred             HHhc
Q 040371           86 YSKC   89 (410)
Q Consensus        86 y~~~   89 (410)
                      +.+.
T Consensus        87 ~~~~   90 (91)
T 1na3_A           87 KQKQ   90 (91)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            5443

>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=97.52  E-value=0.00088  Score=52.35  Aligned_cols=110  Identities=11%  Similarity=-0.016  Sum_probs=73.6

Q ss_pred             CCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh----cCCHHHH
Q 040371           20 ARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK----CGKIQMA   95 (410)
Q Consensus        20 g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~----~g~~~~A   95 (410)
                      +++++|++.|++..+.| .|+..    +-..+...+.++.|.+.|++..+.|   +......|..+|..    .++.++|
T Consensus         9 ~d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A   80 (138)
T 1klx_A            9 KDLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKA   80 (138)
T ss_dssp             HHHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHH
T ss_pred             cCHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCC---CHHHHHHHHHHHHcCCCCCccHHHH
Confidence            45677778887777766 33333    5555556666777777777777765   55666777777776    6777777


Q ss_pred             HHHHHhccc-CChhhHHHHHHHHHH----cCChHHHHHHHHHHHHCC
Q 040371           96 KEVFDTVQR-NDVSVWNAMISGVAI----HGLAADASAIFTKMEMFN  137 (410)
Q Consensus        96 ~~~f~~m~~-~~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g  137 (410)
                      .+.|++..+ .+..++..|-..|..    .++.++|...|++..+.|
T Consensus        81 ~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~g  127 (138)
T 1klx_A           81 AQYYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  127 (138)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHCC
Confidence            777776543 355666666666666    667777777777766655

>2if4_A ATFKBP42; FKBP-like, alpha-beta, TPR-like, alpha, signaling protein; 2.85A {Arabidopsis thaliana}

Probab=97.40  E-value=0.00045  Score=63.16  Aligned_cols=92  Identities=8%  Similarity=0.005  Sum_probs=38.8

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-hhHHHHHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAMVDL  187 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~  187 (410)
                      .|+.+..+|.+.|++++|+..|++..+.. +.+...+..+..++...|++++|...|+...+   +.|+ ...+..+...
T Consensus       232 ~~~nla~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~a~~~~g~~~~A~~~l~~al~---l~p~~~~a~~~L~~l  307 (338)
T 2if4_A          232 CHLNIAACLIKLKRYDEAIGHCNIVLTEE-EKNPKALFRRGKAKAELGQMDSARDDFRKAQK---YAPDDKAIRRELRAL  307 (338)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHTTC------------------
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH---HCCCCHHHHHHHHHH
Confidence            56666666666777777777776666532 22455666666666777777777777766652   2332 3333333333


Q ss_pred             -HHhcCCHHHHHHHHHhC
Q 040371          188 -LGRAGHIEEAYGLITSM  204 (410)
Q Consensus       188 -~~~~g~~~~A~~~~~~m  204 (410)
                       ....+..+++.++|.+|
T Consensus       308 ~~~~~~~~~~a~~~~~~~  325 (338)
T 2if4_A          308 AEQEKALYQKQKEMYKGI  325 (338)
T ss_dssp             ------------------
T ss_pred             HHHHHHHHHHHHHHHHHh
Confidence             22234455555555555

>2l6j_A TPR repeat-containing protein associated with HSP; tetratricopeptide repeat (TPR), HSP90 CO-factor, protein BIN; NMR {Saccharomyces cerevisiae}

Probab=97.37  E-value=0.00029  Score=52.14  Aligned_cols=92  Identities=8%  Similarity=0.012  Sum_probs=45.2

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-------hhHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-------LEHY  181 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-------~~~~  181 (410)
                      .|..+...+...|++++|++.|++..... +.+...+..+..++...|++++|...|+...+   +.|+       ...+
T Consensus         6 ~~~~~g~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~---~~p~~~~~~~~~~~~   81 (111)
T 2l6j_A            6 KQKEQGNSLFKQGLYREAVHCYDQLITAQ-PQNPVGYSNKAMALIKLGEYTQAIQMCQQGLR---YTSTAEHVAIRSKLQ   81 (111)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT---SCSSTTSHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHH---hCCCccHHHHHHHHH
Confidence            44445555555555555555555555431 12344455555555556666666666655552   2232       2333


Q ss_pred             HHHHHHHHhcCCHHHHHHHHHhC
Q 040371          182 GAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       182 ~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      ..+..++...|++++|...++++
T Consensus        82 ~~~~~~~~~~~~~~~a~~~~~~~  104 (111)
T 2l6j_A           82 YRLELAQGAVGSVQIPVVEVDEL  104 (111)
T ss_dssp             HHHHHHHHHHHCCCCCSSSSSSC
T ss_pred             HHHHHHHHHHHhHhhhHhHHHHh
Confidence            44444444445554444444433

>2hr2_A Hypothetical protein; alpha-alpha superhelix fold, structural genomics, joint CENT structural genomics, JCSG, protein structure initiative; 2.54A {Chlorobium tepidum} SCOP: a.118.8.8

Probab=97.34  E-value=0.0038  Score=49.69  Aligned_cols=60  Identities=13%  Similarity=0.005  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCc------c-----HHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIEL------N-----FILSAALIDMYSKCGKIQMAKEVFDT  101 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~------~-----~~~~~~li~~y~~~g~~~~A~~~f~~  101 (410)
                      ..+......+...|++++|...|++.++.....      +     ...|+.+..++.+.|++++|+..|++
T Consensus        12 ~~~~~~G~~l~~~g~~eeAi~~Y~kAL~l~p~~~~~~a~~~~~~~a~a~~n~g~al~~Lgr~~eAl~~~~k   82 (159)
T 2hr2_A           12 YLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADK   82 (159)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCCCCcchhhhhhccchHHHHHHHHHHHHHCCCHHHHHHHHHH
Confidence            345556666777788888888888777653220      1     12455555555555555555544443

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=97.34  E-value=0.0025  Score=47.58  Aligned_cols=78  Identities=9%  Similarity=-0.042  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           24 EALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        24 ~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      +|++.|++..+.. +.+...+..+..++...|++++|...++..++.. +.+...+..+..+|.+.|++++|...|++..
T Consensus         3 ~a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~g~~~~A~~~~~~al   80 (115)
T 2kat_A            3 AITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFD-PTYSVAWKWLGKTLQGQGDRAGARQAWESGL   80 (115)
T ss_dssp             CHHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            4667777776642 3356677777888888888888888888887764 3456677778888888888888888877654

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.25  E-value=0.015  Score=56.98  Aligned_cols=112  Identities=8%  Similarity=-0.023  Sum_probs=59.5

Q ss_pred             HhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCC----------HHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC-
Q 040371           22 FDEALRFFREMLSSKVEPDKFTFASVIYGCARLGA----------LNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG-   90 (410)
Q Consensus        22 ~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~----------~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g-   90 (410)
                      .++|++.+.++.... +-+...|+.--.++...++          ++++.+.++.+++.. +-+..+|+.-.-.+.+.| 
T Consensus        45 ~eeal~~~~~~l~~n-P~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~-pK~y~aW~hR~w~l~~l~~  122 (567)
T 1dce_A           45 DESVLELTSQILGAN-PDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPE  122 (567)
T ss_dssp             SHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSS
T ss_pred             CHHHHHHHHHHHHHC-chhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHccc
Confidence            345566666666532 1133345544444444444          566666666665553 335555555555555555 


Q ss_pred             -CHHHHHHHHHhccc---CChhhHHHHHHHHHHcC-ChHHHHHHHHHHHH
Q 040371           91 -KIQMAKEVFDTVQR---NDVSVWNAMISGVAIHG-LAADASAIFTKMEM  135 (410)
Q Consensus        91 -~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g-~~~~A~~l~~~m~~  135 (410)
                       +++++.+.++++.+   +|-.+|+--...+.+.| .++++++.++++.+
T Consensus       123 ~~~~~el~~~~k~l~~d~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~  172 (567)
T 1dce_A          123 PNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLIT  172 (567)
T ss_dssp             CCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTT
T ss_pred             ccHHHHHHHHHHHHhhccccccHHHHHHHHHHHcCCChHHHHHHHHHHHH
Confidence             44666666665543   24445555555555555 55555555555554

>1dce_A Protein (RAB geranylgeranyltransferase alpha subunit); 2.0 A resolution, N-formylmethionine, alpha subunit; HET: FME; 2.00A {Rattus norvegicus} SCOP: a.118.6.1 b.7.4.1 c.10.2.2 PDB: 1ltx_A*

Probab=97.23  E-value=0.026  Score=55.23  Aligned_cols=164  Identities=8%  Similarity=-0.047  Sum_probs=92.1

Q ss_pred             HHHHHHHHhccc--C-ChhhHHHHHHHHHHcCC----------hHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccC--C
Q 040371           93 QMAKEVFDTVQR--N-DVSVWNAMISGVAIHGL----------AADASAIFTKMEMFNVLPDSITFLGLLTACSHCG--L  157 (410)
Q Consensus        93 ~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~----------~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g--~  157 (410)
                      ++|.+.++++..  | +..+|+.--..+...|+          ++++++.++++.+... -+..+|..-.-++.+.|  +
T Consensus        46 eeal~~~~~~l~~nP~~~taW~~R~~~l~~l~~~~~~~~~~~~~~~eL~~~~~~l~~~p-K~y~aW~hR~w~l~~l~~~~  124 (567)
T 1dce_A           46 ESVLELTSQILGANPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVNP-KSYGTWHHRCWLLSRLPEPN  124 (567)
T ss_dssp             HHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHCT-TCHHHHHHHHHHHHTCSSCC
T ss_pred             HHHHHHHHHHHHHCchhHHHHHHHHHHHHhcccccchhhhhhhHHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHccccc
Confidence            445555555442  2 33445544444444444          5666666666655321 14445555555555555  4


Q ss_pred             HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcC-CHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhc-----------
Q 040371          158 VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAG-HIEEAYGLITSM-TMEP-DVVVWRALLSACRTF-----------  223 (410)
Q Consensus       158 ~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g-~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~-----------  223 (410)
                      ++++.+.++.+.+. . +-+-..|+.-.-.+.+.| .++++++.++++ ...| |...|+..-..+...           
T Consensus       125 ~~~el~~~~k~l~~-d-~~N~~aW~~R~~~l~~l~~~~~~el~~~~~~I~~~p~n~saW~~r~~ll~~l~~~~~~~~~~~  202 (567)
T 1dce_A          125 WARELELCARFLEA-D-ERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGR  202 (567)
T ss_dssp             HHHHHHHHHHHHHH-C-TTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSCCS
T ss_pred             HHHHHHHHHHHHhh-c-cccccHHHHHHHHHHHcCCChHHHHHHHHHHHHHCCCCccHHHHHHHHHHhhccccccccccc
Confidence            56666666666643 1 223445555555555556 566666666665 3344 455565554444432           


Q ss_pred             ---CchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhH
Q 040371          224 ---KRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDT  259 (410)
Q Consensus       224 ---g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~  259 (410)
                         +.++++.+.   .....|.+..+|..+-..+.+.++.++
T Consensus       203 ~~~~~~~eel~~~~~ai~~~P~~~saW~y~~~ll~~~~~~~~  244 (567)
T 1dce_A          203 LPENVLLKELELVQNAFFTDPNDQSAWFYHRWLLGRAEPHDV  244 (567)
T ss_dssp             SCHHHHHHHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCCSC
T ss_pred             ccHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHhcCCCccc
Confidence               345566655   566788898899988888888887544

>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=97.03  E-value=0.012  Score=45.71  Aligned_cols=109  Identities=14%  Similarity=-0.105  Sum_probs=84.5

Q ss_pred             CCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc-CChhhHHHHHHHHHH----cCChHHHHHH
Q 040371           55 GALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR-NDVSVWNAMISGVAI----HGLAADASAI  129 (410)
Q Consensus        55 ~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-~~~~~~~~li~~~~~----~g~~~~A~~l  129 (410)
                      +++++|.+.|++..+.| .++..    |..+|...+.+++|.+.|++..+ .+..+++.+-..|..    .++.++|++.
T Consensus         9 ~d~~~A~~~~~~aa~~g-~~~a~----lg~~y~~g~~~~~A~~~~~~Aa~~g~~~a~~~Lg~~y~~G~g~~~d~~~A~~~   83 (138)
T 1klx_A            9 KDLKKAIQYYVKACELN-EMFGC----LSLVSNSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQY   83 (138)
T ss_dssp             HHHHHHHHHHHHHHHTT-CTTHH----HHHHTCTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHcCC-CHhhh----HHHHHHcCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCccHHHHHHH
Confidence            46788999999998888 33333    77788888888889999987654 467788888888887    7889999999


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHc----cCCHHHHHHHHHHhhhh
Q 040371          130 FTKMEMFNVLPDSITFLGLLTACSH----CGLVEEGRKYFDHMRSR  171 (410)
Q Consensus       130 ~~~m~~~g~~p~~~t~~~ll~a~~~----~g~~~~a~~~~~~m~~~  171 (410)
                      |++..+.|   +...+..|-..|..    .++.++|...|+...+.
T Consensus        84 ~~~Aa~~g---~~~a~~~Lg~~y~~G~g~~~d~~~A~~~~~~Aa~~  126 (138)
T 1klx_A           84 YSKACGLN---DQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRL  126 (138)
T ss_dssp             HHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHcCC---CHHHHHHHHHHHHCCCCCCcCHHHHHHHHHHHHHC
Confidence            98888765   45566667777777    78888888888887753

>2kat_A Uncharacterized protein; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Bordetella parapertussis}

Probab=96.97  E-value=0.007  Score=45.00  Aligned_cols=75  Identities=12%  Similarity=0.066  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           60 AYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        60 a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      +.+.++..++.. +.+...+..+...|.+.|++++|...|++...   .+...|..+...|...|++++|...|++...
T Consensus         4 a~~~~~~al~~~-p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~al~   81 (115)
T 2kat_A            4 ITERLEAMLAQG-TDNMLLRFTLGKTYAEHEQFDAALPHLRAALDFDPTYSVAWKWLGKTLQGQGDRAGARQAWESGLA   81 (115)
T ss_dssp             HHHHHHHHHTTT-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHHHHHHccCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            445555555543 34566677777777777777777777766542   2445666666677777777777777766654

>1na3_A Designed protein CTPR2; de novo protein; HET: IPT; 1.55A {Unidentified} SCOP: k.38.1.1 PDB: 2avp_A

Probab=96.97  E-value=0.01  Score=41.51  Aligned_cols=58  Identities=17%  Similarity=0.080  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDT  101 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~  101 (410)
                      .+..+...+...|++++|...++..++.. +.+..++..+...|.+.|++++|...|++
T Consensus        11 ~~~~la~~~~~~~~~~~A~~~~~~a~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~   68 (91)
T 1na3_A           11 AWYNLGNAYYKQGDYDEAIEYYQKALELD-PNNAEAWYNLGNAYYKQGDYDEAIEYYQK   68 (91)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence            34444444444555555555555444432 22334444444444444444444444443

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.96  E-value=0.0047  Score=44.90  Aligned_cols=65  Identities=17%  Similarity=0.107  Sum_probs=48.7

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~   70 (410)
                      +...|..+...|.+.|++++|+..|++..+.. +.+...|..+..++...|++++|.+.+++.++.
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~l   70 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETD-PDYVGTYYHLGKLYERLDRTDDAIDTYAQGIEV   70 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence            45677888888888888888888888877643 334567777788888888888888888777654

>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=96.93  E-value=0.0025  Score=50.63  Aligned_cols=106  Identities=14%  Similarity=-0.003  Sum_probs=54.2

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      +.+++++|+..+++..+.. +-+...|..+..++...++++.+....                         +.+++|+.
T Consensus        14 r~~~feeA~~~~~~Ai~l~-P~~aea~~n~G~~l~~l~~~~~g~~al-------------------------~~~~eAi~   67 (158)
T 1zu2_A           14 RILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAK-------------------------QMIQEAIT   67 (158)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHH-------------------------HHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHhcccchhhhhH-------------------------hHHHHHHH
Confidence            4455666666666665542 235555555555555555433111100                         01334555


Q ss_pred             HHHhccc--C-ChhhHHHHHHHHHHc-----------CChHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040371           98 VFDTVQR--N-DVSVWNAMISGVAIH-----------GLAADASAIFTKMEMFNVLPDSITFLGLLTA  151 (410)
Q Consensus        98 ~f~~m~~--~-~~~~~~~li~~~~~~-----------g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a  151 (410)
                      .|++..+  | +..+|+.+-.+|...           |++++|++.|++..+  +.|+...|...+..
T Consensus        68 ~le~AL~ldP~~~~A~~~LG~ay~~lg~l~P~~~~a~g~~~eA~~~~~kAl~--l~P~~~~y~~al~~  133 (158)
T 1zu2_A           68 KFEEALLIDPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEM  133 (158)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHH
T ss_pred             HHHHHHHhCcCcHHHHHHHHHHHHHhcccCcchhhhhccHHHHHHHHHHHHH--hCCCCHHHHHHHHH
Confidence            5544431  2 334455555555443           467777777777776  46666655554443

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.88  E-value=0.014  Score=59.70  Aligned_cols=101  Identities=14%  Similarity=0.025  Sum_probs=48.8

Q ss_pred             HccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCC----------CCCHHHHHHHHHHHHh
Q 040371          153 SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTM----------EPDVVVWRALLSACRT  222 (410)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~----------~p~~~~~~~li~~~~~  222 (410)
                      ...|++++|.++.+.+.       +...|..|..++.+.|+++.|.+.|.+++-          .-+...+..+...+..
T Consensus       663 l~~~~~~~A~~~~~~~~-------~~~~W~~la~~al~~~~~~~A~~~y~~~~d~~~l~~l~~~~~~~~~~~~~~~~a~~  735 (814)
T 3mkq_A          663 LKVGQLTLARDLLTDES-------AEMKWRALGDASLQRFNFKLAIEAFTNAHDLESLFLLHSSFNNKEGLVTLAKDAET  735 (814)
T ss_dssp             HHHTCHHHHHHHHTTCC-------CHHHHHHHHHHHHHTTCHHHHHHHHHHHTCHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHhhC-------cHhHHHHHHHHHHHcCCHHHHHHHHHHccChhhhHHHHHHcCCHHHHHHHHHHHHH
Confidence            34556666655543321       345566666666666666666666655530          0112222233333444


Q ss_pred             cCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHH
Q 040371          223 FKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVRE  265 (410)
Q Consensus       223 ~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  265 (410)
                      .|+++.|..++.+.     .-+...+++|.+.++|++|..+-+
T Consensus       736 ~~~~~~A~~~~~~~-----g~~~~a~~~~~~~~~~~~A~~lA~  773 (814)
T 3mkq_A          736 TGKFNLAFNAYWIA-----GDIQGAKDLLIKSQRFSEAAFLGS  773 (814)
T ss_dssp             TTCHHHHHHHHHHH-----TCHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             cCchHHHHHHHHHc-----CCHHHHHHHHHHcCChHHHHHHHH
Confidence            44444444443322     123344555666666666666543

>3ma5_A Tetratricopeptide repeat domain protein; NESG, structural genomics, PSI-2, protein structure initiative; 2.80A {Salinibacter ruber} PDB: 2kcl_A 2kcv_A

Probab=96.87  E-value=0.0045  Score=44.98  Aligned_cols=60  Identities=13%  Similarity=0.019  Sum_probs=33.4

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHH
Q 040371           75 NFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKME  134 (410)
Q Consensus        75 ~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~  134 (410)
                      +..++..+...|.+.|++++|...|++..+  | +...|..+..+|...|++++|++.|++..
T Consensus         6 ~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al   68 (100)
T 3ma5_A            6 DPFTRYALAQEHLKHDNASRALALFEELVETDPDYVGTYYHLGKLYERLDRTDDAIDTYAQGI   68 (100)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            445555555566666666666666655432  2 34455555555556666666666555544

>3mkq_A Coatomer beta'-subunit; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae} PDB: 2ynp_A

Probab=96.76  E-value=0.058  Score=54.99  Aligned_cols=154  Identities=14%  Similarity=0.114  Sum_probs=101.3

Q ss_pred             HHHHcCCHhHHHH-HHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHH
Q 040371           15 GFVRNARFDEALR-FFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQ   93 (410)
Q Consensus        15 ~~~~~g~~~~a~~-l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~   93 (410)
                      .....+++++|.+ ++..     ++ +......++..+.+.|..+.|.++.+.       +.     .-.+....+|+++
T Consensus       608 ~~~~~~~~~~a~~~~l~~-----i~-~~~~~~~~~~~l~~~~~~~~a~~~~~~-------~~-----~~f~~~l~~~~~~  669 (814)
T 3mkq_A          608 TLTLRGEIEEAIENVLPN-----VE-GKDSLTKIARFLEGQEYYEEALNISPD-------QD-----QKFELALKVGQLT  669 (814)
T ss_dssp             HHHHTTCHHHHHHHTGGG-----CC-CHHHHHHHHHHHHHTTCHHHHHHHCCC-------HH-----HHHHHHHHHTCHH
T ss_pred             HHHHhCCHHHHHHHHHhc-----CC-chHHHHHHHHHHHhCCChHHheecCCC-------cc-----hheehhhhcCCHH
Confidence            3446788888877 4421     22 122337777888888998888876531       11     1134567899999


Q ss_pred             HHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcC
Q 040371           94 MAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYS  173 (410)
Q Consensus        94 ~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~  173 (410)
                      .|.++.+.+.  +...|..+...+.+.|+++.|.+.|.++..         |..+...+...|+.+...++-+..... |
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            9999987774  567999999999999999999999998743         334444555566666655554444322 2


Q ss_pred             CCCChhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          174 IQPQLEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       174 ~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                            -++....+|.+.|++++|.+++.++
T Consensus       738 ------~~~~A~~~~~~~g~~~~a~~~~~~~  762 (814)
T 3mkq_A          738 ------KFNLAFNAYWIAGDIQGAKDLLIKS  762 (814)
T ss_dssp             ------CHHHHHHHHHHHTCHHHHHHHHHHT
T ss_pred             ------chHHHHHHHHHcCCHHHHHHHHHHc
Confidence                  2344444566666666666666665

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.70  E-value=0.0047  Score=58.25  Aligned_cols=26  Identities=15%  Similarity=0.026  Sum_probs=12.8

Q ss_pred             HHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          144 TFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       144 t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      +++.|...|...|++++|+.++++..
T Consensus       384 ~l~nLa~~~~~qg~~~eA~~~~~~Al  409 (433)
T 3qww_A          384 MWLKLGRLYMGLENKAAGEKALKKAI  409 (433)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCHHHHHHHHHHHH
Confidence            34445555555555555555544433

>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=96.69  E-value=0.0059  Score=48.52  Aligned_cols=49  Identities=18%  Similarity=0.218  Sum_probs=31.4

Q ss_pred             ChhHHHHHHHHHHHcCCHh----------HHHHHHHHHHHCCCCC-CHHHHHHHHHHHHhhC
Q 040371            5 DVVSWNSMIGGFVRNARFD----------EALRFFREMLSSKVEP-DKFTFASVIYGCARLG   55 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~----------~a~~l~~~m~~~g~~p-d~~t~~~ll~a~~~~~   55 (410)
                      +...|+.+-.++.+.++++          +|+..|++.++.  .| +..+|..+..++...|
T Consensus        35 ~aea~~n~G~~l~~l~~~~~g~~al~~~~eAi~~le~AL~l--dP~~~~A~~~LG~ay~~lg   94 (158)
T 1zu2_A           35 DADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLI--DPKKDEAVWCIGNAYTSFA   94 (158)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHhcccchhhhhHhHHHHHHHHHHHHHHh--CcCcHHHHHHHHHHHHHhc
Confidence            5667877777888877654          666666666653  33 3446666666665553

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.56  E-value=0.056  Score=49.18  Aligned_cols=139  Identities=9%  Similarity=0.021  Sum_probs=85.4

Q ss_pred             CCCCHHHHHHHHHHHHh--h---CCHHHHHHHHHHHHHcCCCcc-HHHHHHHHHHHH----hcC----CH---HHHHHHH
Q 040371           37 VEPDKFTFASVIYGCAR--L---GALNHAYWVHNLIIEKKIELN-FILSAALIDMYS----KCG----KI---QMAKEVF   99 (410)
Q Consensus        37 ~~pd~~t~~~ll~a~~~--~---~~~~~a~~~~~~~~~~g~~~~-~~~~~~li~~y~----~~g----~~---~~A~~~f   99 (410)
                      .+.|...|...+.+...  .   .++.+|+.+|++.++..  |+ ...+..+.-+|.    ..+    ..   ..+.+..
T Consensus       190 ~p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lD--P~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~  267 (372)
T 3ly7_A          190 LPHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSS--PEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNI  267 (372)
T ss_dssp             SCSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHC--TTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhC--CCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHH
Confidence            35566666666665542  2   23567778888887763  33 334433333332    111    11   1122211


Q ss_pred             Hhcc--cCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC
Q 040371          100 DTVQ--RNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ  177 (410)
Q Consensus       100 ~~m~--~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~  177 (410)
                      ..+.  ..+..+|.++...+...|++++|...+++....+  |+...|..+-..+.-.|+.++|.+.|+....   +.|.
T Consensus       268 ~a~~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~Ln--~s~~a~~llG~~~~~~G~~~eA~e~~~~Alr---L~P~  342 (372)
T 3ly7_A          268 VTLPELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDLE--MSWLNYVLLGKVYEMKGMNREAADAYLTAFN---LRPG  342 (372)
T ss_dssp             HTCGGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HSCS
T ss_pred             HhcccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHh---cCCC
Confidence            1121  3366677777777777799999999998888864  7777777777788888999999998888774   3666


Q ss_pred             hhHHH
Q 040371          178 LEHYG  182 (410)
Q Consensus       178 ~~~~~  182 (410)
                      ..+|.
T Consensus       343 ~~t~~  347 (372)
T 3ly7_A          343 ANTLY  347 (372)
T ss_dssp             HHHHH
T ss_pred             cChHH
Confidence            66554

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.53  E-value=0.011  Score=55.60  Aligned_cols=61  Identities=15%  Similarity=0.071  Sum_probs=31.1

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHC-----C-CCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMF-----N-VLPD-SITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~-----g-~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      +++.+...|...|++++|+.++++.+.-     | -.|+ ..+++.|...|...|++++|+.++++..
T Consensus       331 ~~~~L~~~y~~~g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          331 VLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhccHHHHHHHHHHHHHhHHHHcCCCChHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            4555555555555555555555554331     1 1121 2345555555666666666665555544

>3qww_A SET and MYND domain-containing protein 2; methyltransferase, HSP90, transferase-transferase inhibitor; HET: SFG; 1.80A {Mus musculus} PDB: 3qwv_A* 3s7d_A* 3s7b_A* 3s7f_A* 3s7j_A* 3tg4_A* 3tg5_A* 3rib_A*

Probab=96.50  E-value=0.016  Score=54.57  Aligned_cols=81  Identities=10%  Similarity=-0.047  Sum_probs=49.1

Q ss_pred             CCHHHHHHHHHHHHHc-----C--CCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc----------CC-hhhHHHHHHH
Q 040371           55 GALNHAYWVHNLIIEK-----K--IELNFILSAALIDMYSKCGKIQMAKEVFDTVQR----------ND-VSVWNAMISG  116 (410)
Q Consensus        55 ~~~~~a~~~~~~~~~~-----g--~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~----------~~-~~~~~~li~~  116 (410)
                      |++++|..++++.++.     |  .+....+++.|...|...|++++|+.++++...          |+ ..++|.|...
T Consensus       312 g~~~eA~~~~~~~L~i~~~~lg~~Hp~~a~~~~nLa~~y~~~g~~~eA~~~~~~aL~i~~~~lG~~Hp~~a~~l~nLa~~  391 (433)
T 3qww_A          312 KSPSELLEICELSQEKMSSVFEDSNVYMLHMMYQAMGVCLYMQDWEGALKYGQKIIKPYSKHYPVYSLNVASMWLKLGRL  391 (433)
T ss_dssp             SCHHHHHHHHHHHHHHHTTTBCTTSHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHSCSSCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHhhCccChhchHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHcCCCChHHHHHHHHHHHH
Confidence            4556666666555442     1  111235566677777777777777776665541          12 2467777777


Q ss_pred             HHHcCChHHHHHHHHHHHH
Q 040371          117 VAIHGLAADASAIFTKMEM  135 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~  135 (410)
                      |...|++++|+.+|++..+
T Consensus       392 ~~~qg~~~eA~~~~~~Al~  410 (433)
T 3qww_A          392 YMGLENKAAGEKALKKAIA  410 (433)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHhccCHHHHHHHHHHHHH
Confidence            7777777777777776644

>3qwp_A SET and MYND domain-containing protein 3; SMYD3,SET and MYND domain, zinc finger MYND domain-containin 1, structural genomics; HET: SAM; 1.53A {Homo sapiens} PDB: 3mek_A* 3oxg_A* 3oxf_A* 3pdn_A* 3oxl_A* 3ru0_A*

Probab=96.44  E-value=0.014  Score=54.90  Aligned_cols=26  Identities=8%  Similarity=-0.207  Sum_probs=14.6

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHH
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKME  134 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~  134 (410)
                      +++.|...|...|++++|+.++++..
T Consensus       373 ~l~nLa~~~~~~g~~~eA~~~~~~Al  398 (429)
T 3qwp_A          373 QVMKVGKLQLHQGMFPQAMKNLRLAF  398 (429)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHHH
Confidence            45555555555555555555555543

>3ly7_A Transcriptional activator CADC; alpha/beta domain, alpha domain, DNA-binding, transcription regulation, transmembrane; 1.80A {Escherichia coli} PDB: 3lya_A 3ly8_A 3ly9_A

Probab=96.35  E-value=0.08  Score=48.18  Aligned_cols=140  Identities=11%  Similarity=0.019  Sum_probs=86.2

Q ss_pred             CccHHHHHHHHHHHH--hcCC---HHHHHHHHHhccc--CC-hhhHHHHHHHHHH----cCCh-HHHH---HHHHHHHH-
Q 040371           73 ELNFILSAALIDMYS--KCGK---IQMAKEVFDTVQR--ND-VSVWNAMISGVAI----HGLA-ADAS---AIFTKMEM-  135 (410)
Q Consensus        73 ~~~~~~~~~li~~y~--~~g~---~~~A~~~f~~m~~--~~-~~~~~~li~~~~~----~g~~-~~A~---~l~~~m~~-  135 (410)
                      +.+...|...+.+..  ..++   +.+|+.+|++..+  |+ ...|..+.-+|..    .+.. ....   ..++.... 
T Consensus       191 p~~~~Aydl~Lra~~~l~~~~~~~~~~A~~l~e~Al~lDP~~a~A~A~la~a~~~~~~~~~~~~~~~~~l~~a~~a~~a~  270 (372)
T 3ly7_A          191 PHRGALLTNFYQAHDYLLHGDDKSLNRASELLGEIVQSSPEFTYARAEKALVDIVRHSQHPLDEKQLAALNTEIDNIVTL  270 (372)
T ss_dssp             CSSGGGHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHHSCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHHhc
Confidence            455566666554433  3333   5788999988874  43 2344443333321    1111 1111   12221111 


Q ss_pred             CCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCHHHHH
Q 040371          136 FNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDVVVWR  214 (410)
Q Consensus       136 ~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~~~~~  214 (410)
                      .....+..++..+...+...|++++|...++++..- +  |+...|..+...+.-.|++++|.+.|++. .+.|...+|.
T Consensus       271 ~~~~~~a~~~~alal~~l~~gd~d~A~~~l~rAl~L-n--~s~~a~~llG~~~~~~G~~~eA~e~~~~AlrL~P~~~t~~  347 (372)
T 3ly7_A          271 PELNNLSIIYQIKAVSALVKGKTDESYQAINTGIDL-E--MSWLNYVLLGKVYEMKGMNREAADAYLTAFNLRPGANTLY  347 (372)
T ss_dssp             GGGTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH-C--CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHSCSHHHHH
T ss_pred             ccCCcCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc-C--CCHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCcChHH
Confidence            122446677777766667779999999999998864 3  77777888888889999999999888776 5667777654


Q ss_pred             H
Q 040371          215 A  215 (410)
Q Consensus       215 ~  215 (410)
                      .
T Consensus       348 ~  348 (372)
T 3ly7_A          348 W  348 (372)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=96.32  E-value=0.028  Score=40.18  Aligned_cols=59  Identities=19%  Similarity=0.214  Sum_probs=39.3

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHHHCCCCCCHH-HHHHHHHHHHhhCCHHHHHHHHHHHHHcC
Q 040371           12 MIGGFVRNARFDEALRFFREMLSSKVEPDKF-TFASVIYGCARLGALNHAYWVHNLIIEKK   71 (410)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~-t~~~ll~a~~~~~~~~~a~~~~~~~~~~g   71 (410)
                      ....+.+.|++++|+..|++..+.. +.+.. .+..+..++...|++++|.+.+++.++..
T Consensus         6 ~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~   65 (99)
T 2kc7_A            6 TIKELINQGDIENALQALEEFLQTE-PVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIELN   65 (99)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-SSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHC-CCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcC
Confidence            3445667777777777777776642 22445 66666777777777777777777777654

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=96.03  E-value=0.44  Score=38.30  Aligned_cols=105  Identities=18%  Similarity=0.183  Sum_probs=66.1

Q ss_pred             HHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKY  164 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~  164 (410)
                      ...++|+++.|.++-+.+  .+...|..+.....+.|+++-|.+.|.+...         |..+.-.|.-.|+.+.-..+
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            345677777777776665  3566777777777777887777777776532         34445555556666665554


Q ss_pred             HHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCC
Q 040371          165 FDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTME  207 (410)
Q Consensus       165 ~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~  207 (410)
                      -+....+ |      -++.....+...|+++++.+++.+.+.-
T Consensus        83 a~iA~~~-g------~~n~af~~~l~lGdv~~~i~lL~~~~r~  118 (177)
T 3mkq_B           83 QNIAQTR-E------DFGSMLLNTFYNNSTKERSSIFAEGGSL  118 (177)
T ss_dssp             HHHHHHT-T------CHHHHHHHHHHHTCHHHHHHHHHHTTCH
T ss_pred             HHHHHHC-c------cHHHHHHHHHHcCCHHHHHHHHHHCCCh
Confidence            4443322 2      2444555566777777777777776543

>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha, GFT-structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides fragilis}

Probab=95.86  E-value=0.02  Score=40.93  Aligned_cols=51  Identities=12%  Similarity=0.024  Sum_probs=23.5

Q ss_pred             HHHhcCCHHHHHHHHHhccc--C-Chh-hHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           85 MYSKCGKIQMAKEVFDTVQR--N-DVS-VWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~--~-~~~-~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      .|.+.|++++|.+.|++..+  | +.. .|..+...|...|++++|++.|++..+
T Consensus         9 ~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~   63 (99)
T 2kc7_A            9 ELINQGDIENALQALEEFLQTEPVGKDEAYYLMGNAYRKLGDWQKALNNYQSAIE   63 (99)
T ss_dssp             HHHHHTCHHHHHHHHHHHHHHCSSTHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            33444444444444444331  1 233 444444445555555555555555444

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=94.85  E-value=0.24  Score=35.29  Aligned_cols=44  Identities=5%  Similarity=-0.039  Sum_probs=19.9

Q ss_pred             HHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           92 IQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        92 ~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      .++|..+|++...   .++.++..+...+.+.|++++|+..|+++.+
T Consensus        25 ~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~   71 (93)
T 3bee_A           25 TDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLD   71 (93)
T ss_dssp             CHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence            3444444444332   1333444444444455555555555555444

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=94.25  E-value=0.33  Score=38.03  Aligned_cols=79  Identities=9%  Similarity=-0.080  Sum_probs=44.7

Q ss_pred             hHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC---CHHHHHHHHHHHHHcCCCc--cHHHHHHHHHHHHhcCCHHHHHH
Q 040371           23 DEALRFFREMLSSKVEPDKFTFASVIYGCARLG---ALNHAYWVHNLIIEKKIEL--NFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        23 ~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~---~~~~a~~~~~~~~~~g~~~--~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                      ..+.+-|.+....| .++..+.-.+.-++.+..   ++++|..+++.+.+.. .|  +....-.|.-+|.+.|++++|++
T Consensus        15 ~~~~~~y~~e~~~~-~~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~-~p~~~rd~lY~LAv~~~kl~~Y~~A~~   92 (152)
T 1pc2_A           15 LKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKG-SKEEQRDYVFYLAVGNYRLKEYEKALK   92 (152)
T ss_dssp             HHHHHHHHHHHHTT-CCCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHS-CHHHHHHHHHHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHccC-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcC-CccchHHHHHHHHHHHHHccCHHHHHH
Confidence            34445555555444 355555555666666666   4556777777776654 12  23344444555566666666666


Q ss_pred             HHHhcc
Q 040371           98 VFDTVQ  103 (410)
Q Consensus        98 ~f~~m~  103 (410)
                      .|+.+.
T Consensus        93 y~~~lL   98 (152)
T 1pc2_A           93 YVRGLL   98 (152)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            666654

>3bee_A Putative YFRE protein; putaive YFRE protein, structural GE PSI-2, protein structure initiative; 2.15A {Vibrio parahaemolyticus rimd 2210633}

Probab=94.20  E-value=0.26  Score=35.04  Aligned_cols=64  Identities=8%  Similarity=0.020  Sum_probs=47.9

Q ss_pred             CHHHHHHHHHHHHhcCc---hhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCC
Q 040371          209 DVVVWRALLSACRTFKR---LELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       209 ~~~~~~~li~~~~~~g~---~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~  272 (410)
                      |...+..+..++...++   .++|..+   ..+.+|.++.....+...+.+.|++++|...++++.+..-
T Consensus         5 ~~~~~~~~a~al~~~~~~~~~~~A~~~l~~AL~~dp~~~rA~~~lg~~~~~~g~y~~Ai~~w~~~l~~~p   74 (93)
T 3bee_A            5 TATQLAAKATTLYYLHKQAMTDEVSLLLEQALQLEPYNEAALSLIANDHFISFRFQEAIDTWVLLLDSND   74 (93)
T ss_dssp             CHHHHHHHHHHHHHTTTTCCCHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTCCC
T ss_pred             CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCcCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence            45556666666544433   5666666   5667888888889999999999999999999999987643

>1pc2_A Mitochondria fission protein; unknown function; NMR {Homo sapiens} SCOP: a.118.8.1

Probab=94.17  E-value=0.56  Score=36.72  Aligned_cols=84  Identities=6%  Similarity=-0.141  Sum_probs=58.7

Q ss_pred             CHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcC---CHHHHHHHHHhcccCC-----hhhHHHHHHHHHHcCChHHHH
Q 040371           56 ALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCG---KIQMAKEVFDTVQRND-----VSVWNAMISGVAIHGLAADAS  127 (410)
Q Consensus        56 ~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g---~~~~A~~~f~~m~~~~-----~~~~~~li~~~~~~g~~~~A~  127 (410)
                      .+..+++-|....+.|. ++..+.-.+.-+++++.   +++++..+|++..+.+     ...+-.+.-+|.+.|++++|.
T Consensus        13 ~l~~~~~~y~~e~~~~~-~~~~~~F~ya~~Lv~S~~~~~~~~gI~lLe~ll~~~~p~~~rd~lY~LAv~~~kl~~Y~~A~   91 (152)
T 1pc2_A           13 DLLKFEKKFQSEKAAGS-VSKSTQFEYAWCLVRSKYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKAL   91 (152)
T ss_dssp             HHHHHHHHHHHHHHTTC-CCHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHHHHHccCC-CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCccchHHHHHHHHHHHHHccCHHHHH
Confidence            34556666666666653 67777777788888887   5668888888765433     335555666778888888888


Q ss_pred             HHHHHHHHCCCCCCH
Q 040371          128 AIFTKMEMFNVLPDS  142 (410)
Q Consensus       128 ~l~~~m~~~g~~p~~  142 (410)
                      +.++..++  +.|+.
T Consensus        92 ~y~~~lL~--ieP~n  104 (152)
T 1pc2_A           92 KYVRGLLQ--TEPQN  104 (152)
T ss_dssp             HHHHHHHH--HCTTC
T ss_pred             HHHHHHHh--cCCCC
Confidence            88888877  46643

>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=94.03  E-value=0.56  Score=41.03  Aligned_cols=61  Identities=13%  Similarity=0.200  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHhc-----CCHHHHHHHHHhcc--cC--ChhhHHHHHHHHHHc-CChHHHHHHHHHHHHCCC
Q 040371           78 LSAALIDMYSKC-----GKIQMAKEVFDTVQ--RN--DVSVWNAMISGVAIH-GLAADASAIFTKMEMFNV  138 (410)
Q Consensus        78 ~~~~li~~y~~~-----g~~~~A~~~f~~m~--~~--~~~~~~~li~~~~~~-g~~~~A~~l~~~m~~~g~  138 (410)
                      .|..|...|.+.     |+.++|++.|++..  .|  +..++......+++. |+.+++.+.+++.+....
T Consensus       201 A~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd~~~a~~~L~kAL~a~p  271 (301)
T 3u64_A          201 VWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDP  271 (301)
T ss_dssp             HHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTCHHHHHHHHHHHHHCCG
T ss_pred             HHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCC
Confidence            444444444442     45555555554433  22  234444444444442 455555555555554433

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=93.99  E-value=1.5  Score=33.39  Aligned_cols=85  Identities=12%  Similarity=0.060  Sum_probs=58.5

Q ss_pred             hcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040371           88 KCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDH  167 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~  167 (410)
                      +||++......+-.+. .+....+..++.....|+-++-.+++.++.. +.+|+......+..||.+.|+..++.+++.+
T Consensus        73 ~C~NlKrVi~C~~~~n-~~se~vd~ALd~lv~~~KkDqLdki~~~~l~-n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~  150 (172)
T 1wy6_A           73 KCQNLKSVVECGVINN-TLNEHVNKALDILVIQGKRDKLEEIGREILK-NNEVSASILVAIANALRRVGDERDATTLLIE  150 (172)
T ss_dssp             GCSCTHHHHHHHHHTT-CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hhhcHHHHHHHHHHhc-chHHHHHHHHHHHHHhccHhHHHHHHHHHhc-cCCCChHHHHHHHHHHHHhcchhhHHHHHHH
Confidence            4555555555554442 2334456667777888888888888888544 3567777788888888888888888888888


Q ss_pred             hhhhcCCC
Q 040371          168 MRSRYSIQ  175 (410)
Q Consensus       168 m~~~~~~~  175 (410)
                      .-++ |++
T Consensus       151 AC~k-G~k  157 (172)
T 1wy6_A          151 ACKK-GEK  157 (172)
T ss_dssp             HHHT-TCH
T ss_pred             HHHh-hhH
Confidence            8765 653

>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=93.63  E-value=0.72  Score=40.36  Aligned_cols=95  Identities=13%  Similarity=0.088  Sum_probs=67.4

Q ss_pred             cCCHHHHHHHHHhccc--CC---hhhHHHHHHHHHHc-----CChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHc-cCC
Q 040371           89 CGKIQMAKEVFDTVQR--ND---VSVWNAMISGVAIH-----GLAADASAIFTKMEMFNVLPDSITFLGLLTACSH-CGL  157 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~--~~---~~~~~~li~~~~~~-----g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~-~g~  157 (410)
                      .+....|+..+++..+  |+   -..|..+...|.+.     |+.++|.+.|++.++.+..-+..++......++. .|+
T Consensus       176 l~~l~~A~a~lerAleLDP~~~~GsA~~~LG~lY~~vPp~~gGd~ekA~~~ferAL~LnP~~~id~~v~YA~~l~~~~gd  255 (301)
T 3u64_A          176 PDTVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNN  255 (301)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTHHHHHHHHHHHHHHHHSCTTTTCCHHHHHHHHHHHHHHCCTTCSHHHHHHHHHTTTTTTC
T ss_pred             HHhHHHHHHHHHHHHHhCCCcccCHHHHHHHHHHHhCCCccCCCHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHhcCC
Confidence            3445677777776653  33   45899999999994     9999999999999884321135666667777777 499


Q ss_pred             HHHHHHHHHHhhhhcCCC--CChhHHHHH
Q 040371          158 VEEGRKYFDHMRSRYSIQ--PQLEHYGAM  184 (410)
Q Consensus       158 ~~~a~~~~~~m~~~~~~~--~~~~~~~~l  184 (410)
                      .+++.+.++..... ...  |+....+.+
T Consensus       256 ~~~a~~~L~kAL~a-~p~~~P~~~lan~~  283 (301)
T 3u64_A          256 RAGFDEALDRALAI-DPESVPHNKLLVIL  283 (301)
T ss_dssp             HHHHHHHHHHHHHC-CGGGCSSCHHHHHH
T ss_pred             HHHHHHHHHHHHcC-CCCCCCChhHHHHH
Confidence            99999999998853 444  555444443

>1wy6_A Hypothetical protein ST1625; helical repeat protein, structural genomics, unknown function; 2.20A {Sulfolobus tokodaii} SCOP: a.118.20.1

Probab=93.51  E-value=1.9  Score=32.88  Aligned_cols=135  Identities=9%  Similarity=-0.039  Sum_probs=78.0

Q ss_pred             cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHH
Q 040371          120 HGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYG  199 (410)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~  199 (410)
                      .|..++..++..+.....   +..-|+-++.-....-+-+-..+.++.+-+-+.+              ..+|++.....
T Consensus        20 dG~v~qGveii~k~~~ss---ni~E~NW~ICNiiD~a~C~y~v~vLd~IGkiFDi--------------s~C~NlKrVi~   82 (172)
T 1wy6_A           20 DGYIDEGVKIVLEITKSS---TKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDL--------------DKCQNLKSVVE   82 (172)
T ss_dssp             TTCHHHHHHHHHHHHHHS---CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCG--------------GGCSCTHHHHH
T ss_pred             hhhHHHHHHHHHHHcCCC---CccccceeeeecchhhchhHHHHHHHHHhhhcCc--------------HhhhcHHHHHH
Confidence            456666666666655432   2333444444444444445555555554432222              22344444444


Q ss_pred             HHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHh---hccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCc
Q 040371          200 LITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVN---ISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVR  273 (410)
Q Consensus       200 ~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~---~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  273 (410)
                      -+-.++  .+..-+...+......|.-+.-.++...   -.++++.....+.++|.+.|+..+|.+++++.-++|++
T Consensus        83 C~~~~n--~~se~vd~ALd~lv~~~KkDqLdki~~~~l~n~~~~~~~l~kia~Ay~Klg~~r~a~eLl~~AC~kG~k  157 (172)
T 1wy6_A           83 CGVINN--TLNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  157 (172)
T ss_dssp             HHHHTT--CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHhc--chHHHHHHHHHHHHHhccHhHHHHHHHHHhccCCCChHHHHHHHHHHHHhcchhhHHHHHHHHHHhhhH
Confidence            444432  2333344556666677777777777443   34455677778889999999999999999999888874

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=93.18  E-value=0.75  Score=33.20  Aligned_cols=60  Identities=7%  Similarity=-0.129  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcC------CCccHHHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKK------IELNFILSAALIDMYSKCGKIQMAKEVFDTV  102 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g------~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m  102 (410)
                      .+..+...+...++++.|...++.+++.-      -.+...++..|..+|.+.|+++.|...+++.
T Consensus         7 dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~a   72 (104)
T 2v5f_A            7 DCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKL   72 (104)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence            33444555555555555555555554421      1223445555555555555555555555544

>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=92.79  E-value=1.1  Score=34.95  Aligned_cols=95  Identities=12%  Similarity=0.230  Sum_probs=44.6

Q ss_pred             CChhHHHHHHHHHHHcCCH------hHHHHHHHHHHHCCCCCCHH----HHHHHHHHH---HhhCCHHHHHHHHHHHHHc
Q 040371            4 KDVVSWNSMIGGFVRNARF------DEALRFFREMLSSKVEPDKF----TFASVIYGC---ARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~------~~a~~l~~~m~~~g~~pd~~----t~~~ll~a~---~~~~~~~~a~~~~~~~~~~   70 (410)
                      .|..+|=..+.-.-++|++      ++.+++|++.... ++|+..    .|.-+.--|   ...++++.|+++|+.+++.
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            3555666666666666776      6666666666553 555421    111111111   1224555555555555443


Q ss_pred             CCCccHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040371           71 KIELNFILSAALIDMYSKCGKIQMAKEVFD  100 (410)
Q Consensus        71 g~~~~~~~~~~li~~y~~~g~~~~A~~~f~  100 (410)
                      . +.=..+|-.....=.+.|++++|++++.
T Consensus        90 h-KkFAKiwi~~AqFEiRqgnl~kARkILg  118 (161)
T 4h7y_A           90 C-KKFAFVHISFAQFELSQGNVKKSKQLLQ  118 (161)
T ss_dssp             C-TTBHHHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             h-HHHHHHHHHHHHHHHHcccHHHHHHHHH
Confidence            1 1114444444444444444444444444

>2v5f_A Prolyl 4-hydroxylase subunit alpha-1; endoplasmic reticulum, metal-binding, oxidoreductase; 2.03A {Homo sapiens} PDB: 1tjc_A

Probab=92.44  E-value=1.6  Score=31.36  Aligned_cols=66  Identities=11%  Similarity=0.094  Sum_probs=54.2

Q ss_pred             hhHHHHHHHHHHHcCCHhHHHHHHHHHHHC------CCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC
Q 040371            6 VVSWNSMIGGFVRNARFDEALRFFREMLSS------KVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKK   71 (410)
Q Consensus         6 ~~~~n~li~~~~~~g~~~~a~~l~~~m~~~------g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g   71 (410)
                      ..-+-.|...+.+.|++..|..-|+...+.      .-.+....+..+..++.+.|+++.|...++.+.+..
T Consensus         5 a~dc~~lG~~~~~~~~y~~A~~W~~~Al~~~~~~~~~~~~~~~i~~~L~~~~~~~g~~~~A~~~~~~al~l~   76 (104)
T 2v5f_A            5 AEDCFELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD   76 (104)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHccchHHHHHHHHHHHHhhhccCCCcccHHHHHHHHHHHHHHccCHHHHHHHHHHHHhcC
Confidence            344567888999999999999999987653      113356788899999999999999999999999864

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=92.13  E-value=0.0002  Score=66.70  Aligned_cols=239  Identities=12%  Similarity=0.144  Sum_probs=157.9

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      ..|+.|-.++.+.++..+|++-|-+   .   -|+..|..++.++.+.|.++.-...+....+.  ..++.+-+.|+-+|
T Consensus        55 ~VWs~LgkAqL~~~~v~eAIdsyIk---A---~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~--~ke~~IDteLi~ay  126 (624)
T 3lvg_A           55 AVWSQLAKAQLQKGMVKEAIDSYIK---A---DDPSSYMEVVQAANTSGNWEELVKYLQMARKK--ARESYVETELIFAL  126 (624)
T ss_dssp             CCSSSHHHHTTTSSSCTTTTTSSCC---C---SCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTT--CCSTTTTHHHHHHH
T ss_pred             cHHHHHHHHHHccCchHHHHHHHHh---C---CChHHHHHHHHHHHhCCCHHHHHHHHHHHHHH--hcccccHHHHHHHH
Confidence            4688899999999999999887733   1   25667899999999999999988888877665  34566778999999


Q ss_pred             HhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHC--------------------CCCCCHHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMF--------------------NVLPDSITFL  146 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~--------------------g~~p~~~t~~  146 (410)
                      +|.|++.+-.+++.   .||+.--..+.+-+...|.++.|.-+|..+-..                    .-.-+..||-
T Consensus       127 Ak~~rL~elEefl~---~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~ktWK  203 (624)
T 3lvg_A          127 AKTNRLAELEEFIN---GPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRTWK  203 (624)
T ss_dssp             HTSCSSSTTTSTTS---CCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCSHH
T ss_pred             HhhCcHHHHHHHHc---CCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhHHH
Confidence            99998776543332   344444444555555555555555555443211                    1123567888


Q ss_pred             HHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CC-CCCHHHHHHHHHHHHhcC
Q 040371          147 GLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TM-EPDVVVWRALLSACRTFK  224 (410)
Q Consensus       147 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~-~p~~~~~~~li~~~~~~g  224 (410)
                      -+-.+|...+.+..|.-.--.+.-      .......++..|-..|.++|-+.+++.- +. +....+|+-|--.|++..
T Consensus       204 eV~~ACvd~~EfrLAqicGLniIv------hadeL~elv~~YE~~G~f~ELIsLlEaglglErAHmGmFTELaILYsKY~  277 (624)
T 3lvg_A          204 EVCFACVDGKEFRLAQMCGLHIVV------HADELEELINYYQDRGYFEELITMLEAALGLERAHMGMFTELAILYSKFK  277 (624)
T ss_dssp             HHTHHHHHSCTTTTTTHHHHHHHC------CSSCCSGGGSSSSTTCCCTTSTTTHHHHTTSTTCCHHHHHHHHHHHHSSC
T ss_pred             HHHHHHhCchHHHHHHHhcchhcc------cHHHHHHHHHHHHhCCCHHHHHHHHHHHhCCCchhHHHHHHHHHHHHhcC
Confidence            888899988887766654433332      1223345677788888888888888765 43 357788888887887775


Q ss_pred             chhHHHHH---HHhhcc-------CCCchHHHHHHHHHhcCChhHHHH
Q 040371          225 RLELGEVA---IVNISR-------LMGGDYVLLSNMYCYLKRWDTAEN  262 (410)
Q Consensus       225 ~~~~a~~~---~~~~~~-------~~~~~~~~l~~~~~~~g~~~~a~~  262 (410)
                      --..-+.+   ..++.-       .....|.-++-.|.+-..|+.|..
T Consensus       278 PeKlmEHlklf~sriNipKviracE~ahLW~ElvfLY~~ydE~DnA~l  325 (624)
T 3lvg_A          278 PQKMREHLELFWSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAII  325 (624)
T ss_dssp             TTHHHHHHTTSSSSSCCTTTHHHHTTTTCHHHHHHHHHHHTCHHHHHH
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHhhHHHHHHHHhcchhHHHHHH
Confidence            33333333   111111       123457778888888888887754

>3mkq_B Coatomer subunit alpha; beta-propeller, alpha-solenoid, transport protein; 2.50A {Saccharomyces cerevisiae}

Probab=92.12  E-value=3.9  Score=32.80  Aligned_cols=129  Identities=14%  Similarity=0.080  Sum_probs=80.6

Q ss_pred             HHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHH
Q 040371           50 GCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAI  129 (410)
Q Consensus        50 a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l  129 (410)
                      .....|+++.|.++-+.+      .+...|..|.+...+.|+++-|.+.|.+..+     +..+.-.|.-.|+.+....+
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            345678888888876654      3677888888888889999999888888753     34455556667777666555


Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCC
Q 040371          130 FTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMT  205 (410)
Q Consensus       130 ~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~  205 (410)
                      -+.....|      -++.....+.-.|+++++.++|...-+          |.--+-.....|..+.|.++.+.++
T Consensus        83 a~iA~~~g------~~n~af~~~l~lGdv~~~i~lL~~~~r----------~~eA~~~A~t~g~~~~a~~~~~~~~  142 (177)
T 3mkq_B           83 QNIAQTRE------DFGSMLLNTFYNNSTKERSSIFAEGGS----------LPLAYAVAKANGDEAAASAFLEQAE  142 (177)
T ss_dssp             HHHHHHTT------CHHHHHHHHHHHTCHHHHHHHHHHTTC----------HHHHHHHHHHTTCHHHHHHHHHHTT
T ss_pred             HHHHHHCc------cHHHHHHHHHHcCCHHHHHHHHHHCCC----------hHHHHHHHHHcCcHHHHHHHHHHhC
Confidence            54444443      134444555667888888887765432          1111111122455666666666664

>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=91.61  E-value=2.7  Score=29.96  Aligned_cols=87  Identities=14%  Similarity=0.118  Sum_probs=64.4

Q ss_pred             CHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           56 ALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        56 ~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      .-++|..|-+.+...+.  ...+--.-+......|++++|..+.+.+..||++.|-++-.  .+.|..+++..-+.++..
T Consensus        22 ~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~   97 (116)
T 2p58_C           22 YHEEANCIAEWLHLKGE--EEAVQLIRLSSLMNRGDYASALQQGNKLAYPDLEPWLALCE--YRLGLGSALESRLNRLAR   97 (116)
T ss_dssp             CHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHHHHTTSCCGGGHHHHHHHH--HHHTCHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHh
Confidence            56778888777777664  33344444556778999999999999999999999998765  467888888888878877


Q ss_pred             CCCCCCHHHHHH
Q 040371          136 FNVLPDSITFLG  147 (410)
Q Consensus       136 ~g~~p~~~t~~~  147 (410)
                      .| .|....|..
T Consensus        98 sg-~p~~q~Fa~  108 (116)
T 2p58_C           98 SQ-DPRIQTFVN  108 (116)
T ss_dssp             CC-CHHHHHHHH
T ss_pred             CC-CHHHHHHHH
Confidence            66 455555543

>2uwj_G Type III export protein PSCG; virulence, chaperones, coiled coil, needle formation, type III secretion, bacterial pathogenicity; 2.0A {Pseudomonas aeruginosa}

Probab=90.83  E-value=2.5  Score=30.05  Aligned_cols=87  Identities=14%  Similarity=0.069  Sum_probs=64.7

Q ss_pred             CHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           56 ALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        56 ~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      .-++|..|-+.+...+.  ...+--.-+......|++++|..+.+.+..||++.|-++-.  .+.|..+++..-+.++..
T Consensus        21 ~HqEA~tIAdwL~~~~~--~E~v~lIR~sSLmNrG~Yq~Al~l~~~~c~pdlepw~ALce--~rlGl~s~le~rL~~la~   96 (115)
T 2uwj_G           21 CHEEALCIAEWLERLGQ--DEAARLIRISSLANQGRYQEALAFAHGNPWPALEPWFALCE--WHLGLGAALDRRLAGLGG   96 (115)
T ss_dssp             CHHHHHHHHHHHHHTTC--HHHHHHHHHHHHHHTTCHHHHHGGGTTCCCGGGHHHHHHHH--HHTTCHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhCCc--HHHHHHHHHHHHHcchhHHHHHHhcCCCCCchHHHHHHHHH--HhcccHHHHHHHHHHHHh
Confidence            56777778777777664  33343444556778999999999999999999999998765  467888888888878877


Q ss_pred             CCCCCCHHHHHH
Q 040371          136 FNVLPDSITFLG  147 (410)
Q Consensus       136 ~g~~p~~~t~~~  147 (410)
                      .| .|....|..
T Consensus        97 sg-~p~~q~Fa~  107 (115)
T 2uwj_G           97 SS-DPALADFAA  107 (115)
T ss_dssp             CS-SHHHHHHHH
T ss_pred             CC-CHHHHHHHH
Confidence            76 455555543

>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=90.50  E-value=1.9  Score=30.84  Aligned_cols=63  Identities=11%  Similarity=0.191  Sum_probs=50.5

Q ss_pred             ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHH
Q 040371          122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVD  186 (410)
Q Consensus       122 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~  186 (410)
                      +.-+..+-++.+....+.|+.....+.|.||.+..++..|.++|+.++.+.|-  ....|..+++
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K~~~--~~~iY~~~lq   87 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAGP--HKEIYPYVIQ   87 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTT--CTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhcC--chhhHHHHHH
Confidence            45567777777777788999999999999999999999999999999876443  3456777664

>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} PDB: 3lvh_A

Probab=89.76  E-value=0.00029  Score=65.69  Aligned_cols=177  Identities=14%  Similarity=0.113  Sum_probs=103.7

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc
Q 040371           76 FILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHC  155 (410)
Q Consensus        76 ~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~  155 (410)
                      +.+|.-|..++.+.|++.+|+..|-+  ..|...|..+|.+..+.|.+++-+..+...++..-  +...=+.|+-+|++.
T Consensus        54 p~VWs~LgkAqL~~~~v~eAIdsyIk--A~Dps~y~eVi~~A~~~~~~edLv~yL~MaRk~~k--e~~IDteLi~ayAk~  129 (624)
T 3lvg_A           54 PAVWSQLAKAQLQKGMVKEAIDSYIK--ADDPSSYMEVVQAANTSGNWEELVKYLQMARKKAR--ESYVETELIFALAKT  129 (624)
T ss_dssp             CCCSSSHHHHTTTSSSCTTTTTSSCC--CSCCCSSSHHHHHTTTSSCCTTHHHHHHTTSTTCC--STTTTHHHHHHHHTS
T ss_pred             ccHHHHHHHHHHccCchHHHHHHHHh--CCChHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhc--ccccHHHHHHHHHhh
Confidence            45667777777777777776655532  34556666777777777777777666654443322  223334566777777


Q ss_pred             CCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCC-----------------------CCCCHHH
Q 040371          156 GLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMT-----------------------MEPDVVV  212 (410)
Q Consensus       156 g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~-----------------------~~p~~~~  212 (410)
                      +++.+-+++        --.|+......+.+-+...|.++.|.-+|..++                       ...+..|
T Consensus       130 ~rL~elEef--------l~~~N~A~iq~VGDrcf~e~lYeAAKilys~isN~akLAstLV~L~~yq~AVdaArKAns~kt  201 (624)
T 3lvg_A          130 NRLAELEEF--------INGPNNAHIQQVGDRCYDEKMYDAAKLLYNNVSNFGRLASTLVHLGEYQAAVDGARKANSTRT  201 (624)
T ss_dssp             CSSSTTTST--------TSCCSSSCTHHHHHHHHHSCCSTTSSTTGGGSCCCTTTSSSSSSCSGGGSSTTTTTTCCSSCS
T ss_pred             CcHHHHHHH--------HcCCCcccHHHHHHHHHHccCHHHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHhcCChhH
Confidence            665442222        223455455556666666666666665555441                       1246789


Q ss_pred             HHHHHHHHHhcCchhHHHHHHHhhccCCCchHHHHHHHHHhcCChhHHHHHHH
Q 040371          213 WRALLSACRTFKRLELGEVAIVNISRLMGGDYVLLSNMYCYLKRWDTAENVRE  265 (410)
Q Consensus       213 ~~~li~~~~~~g~~~~a~~~~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~  265 (410)
                      |..+-.+|...+.+..|......+-. .+.-...|+.-|.+.|.+++-..+++
T Consensus       202 WKeV~~ACvd~~EfrLAqicGLniIv-hadeL~elv~~YE~~G~f~ELIsLlE  253 (624)
T 3lvg_A          202 WKEVCFACVDGKEFRLAQMCGLHIVV-HADELEELINYYQDRGYFEELITMLE  253 (624)
T ss_dssp             HHHHTHHHHHSCTTTTTTHHHHHHHC-CSSCCSGGGSSSSTTCCCTTSTTTHH
T ss_pred             HHHHHHHHhCchHHHHHHHhcchhcc-cHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            99999999999999999887222210 01122334555555555555555544

>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=88.31  E-value=2.6  Score=38.82  Aligned_cols=60  Identities=12%  Similarity=0.009  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           43 TFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        43 t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      +...++.++...|+.+.+......+.... +.+...+..||.+|.++|+..+|.+.|++..
T Consensus       173 a~~~~~~~~l~~g~~~~a~~~l~~~~~~~-P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r  232 (388)
T 2ff4_A          173 AHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVK  232 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34455666677788888777777776653 4567778888888888888888888777654

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=87.78  E-value=8  Score=30.52  Aligned_cols=61  Identities=5%  Similarity=-0.065  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHC-CCCCCH-------HHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSS-KVEPDK-------FTFASVIYGCARLGALNHAYWVHNLIIE   69 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~-g~~pd~-------~t~~~ll~a~~~~~~~~~a~~~~~~~~~   69 (410)
                      +-.-+..+...|.++.|.-+...+... +..|+.       .++..+.+++...+++..|...|++.++
T Consensus        23 l~dqik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq   91 (167)
T 3ffl_A           23 VIDHVRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQ   91 (167)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHH
Confidence            334466777788888888877765532 123331       2566677788888888888888888643

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=86.63  E-value=4.7  Score=30.26  Aligned_cols=23  Identities=9%  Similarity=-0.138  Sum_probs=12.0

Q ss_pred             HHHHHHHcCChHHHHHHHHHHHH
Q 040371          113 MISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus       113 li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      +.-++.+.|++++|.+.++.+++
T Consensus        80 LAvg~yklg~Y~~A~~~~~~lL~  102 (126)
T 1nzn_A           80 LAVGNYRLKEYEKALKYVRGLLQ  102 (126)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhhHHHHHHHHHHHHH
Confidence            33445555555555555555554

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=86.62  E-value=16  Score=38.90  Aligned_cols=28  Identities=21%  Similarity=0.108  Sum_probs=16.2

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhc
Q 040371           75 NFILSAALIDMYSKCGKIQMAKEVFDTV  102 (410)
Q Consensus        75 ~~~~~~~li~~y~~~g~~~~A~~~f~~m  102 (410)
                      +....-.+..+|..+|++++|...|.+.
T Consensus       841 ~~~~~yl~g~~~L~~ge~~~A~~~F~ka  868 (1139)
T 4fhn_B          841 DPIAVYLKALIYLKSKEAVKAVRCFKTT  868 (1139)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHTC
T ss_pred             CcHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence            3333334455666667777777777654

>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=86.51  E-value=3.1  Score=38.25  Aligned_cols=64  Identities=9%  Similarity=0.108  Sum_probs=40.4

Q ss_pred             HHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC--------CCCCCHHH
Q 040371          147 GLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM--------TMEPDVVV  212 (410)
Q Consensus       147 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m--------~~~p~~~~  212 (410)
                      .++.++...|+.+++...+..+...  -+.+...|..+|.+|.++|+..+|++.|++.        ++.|...+
T Consensus       176 ~~~~~~l~~g~~~~a~~~l~~~~~~--~P~~E~~~~~lm~al~~~Gr~~~Al~~y~~~r~~L~~eLG~~P~~~l  247 (388)
T 2ff4_A          176 AKAEAEIACGRASAVIAELEALTFE--HPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  247 (388)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHH--STTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhCCCCCHHH
Confidence            3455666677777777666666543  1335556777777777777777776666554        66676554

>1nzn_A CGI-135 protein, fission protein FIS1P; TPR, unknown function; 2.00A {Homo sapiens} SCOP: a.118.8.1 PDB: 1iyg_A

Probab=86.21  E-value=8.9  Score=28.74  Aligned_cols=65  Identities=9%  Similarity=-0.118  Sum_probs=28.6

Q ss_pred             CCHHHHHHHHHHHHhhCCHHH---HHHHHHHHHHcCCC-ccHHHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           39 PDKFTFASVIYGCARLGALNH---AYWVHNLIIEKKIE-LNFILSAALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        39 pd~~t~~~ll~a~~~~~~~~~---a~~~~~~~~~~g~~-~~~~~~~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      |+..+--.+.-++.+..+...   |..+++.+.+.+.+ ......-.|.-+|.|.|++++|++.++.+.
T Consensus        33 ~s~~~~F~yAw~Lv~S~~~~d~~~GI~lLe~l~~~~~p~~~Rd~lY~LAvg~yklg~Y~~A~~~~~~lL  101 (126)
T 1nzn_A           33 VSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVGNYRLKEYEKALKYVRGLL  101 (126)
T ss_dssp             CCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence            333333334444444443333   55555555544311 122222333445555555555555555543

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=86.19  E-value=12  Score=37.44  Aligned_cols=124  Identities=14%  Similarity=0.070  Sum_probs=74.5

Q ss_pred             HHHHHHHHhcCC-HHHHHHHHHhcccCChh--h--HHHHHHHHHHcC-ChHHHHHHHHHHHHC------CCCCCHH----
Q 040371           80 AALIDMYSKCGK-IQMAKEVFDTVQRNDVS--V--WNAMISGVAIHG-LAADASAIFTKMEMF------NVLPDSI----  143 (410)
Q Consensus        80 ~~li~~y~~~g~-~~~A~~~f~~m~~~~~~--~--~~~li~~~~~~g-~~~~A~~l~~~m~~~------g~~p~~~----  143 (410)
                      .+|+..+...|+ .+.|..+|+++...+..  .  ..++|..+.+.+ +--+|.+++.+..+.      ...+...    
T Consensus       252 ~~Ll~~~~~t~~~~~~a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~~~  331 (754)
T 4gns_B          252 YSLKSFIAITPSLVDFTIDYLKGLTKKDPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADSAR  331 (754)
T ss_dssp             HHHHHHHHTCGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHHHH
T ss_pred             HHHHHHHcccccHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhccccccccc
Confidence            445555555666 57788888887654332  1  122333222222 233455555544321      1222111    


Q ss_pred             --HH-HHH----HHHHHccCCHHHHHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhCCC
Q 040371          144 --TF-LGL----LTACSHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSMTM  206 (410)
Q Consensus       144 --t~-~~l----l~a~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m~~  206 (410)
                        .+ ..|    ..-|...|+++.|+.+-++...   ..|+ -.+|..|...|...|+++.|+-.++.+|+
T Consensus       332 ~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~---~aPseF~tW~~La~vYi~l~d~e~ALLtLNScPm  399 (754)
T 4gns_B          332 LMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTE---LALDSFESWYNLARCHIKKEEYEKALFAINSMPR  399 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH---HCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSCC
T ss_pred             ccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHh---cCchhhHHHHHHHHHHHHhccHHHHHHHHhcCCC
Confidence              01 112    2335568999999999988874   3454 67999999999999999999999988863

>4fhn_B Nucleoporin NUP120; protein complex,structural protein,nuclear pore complex,mRNA transport,protein transport, WD repeat; 6.99A {Schizosaccharomyces pombe 972h-}

Probab=86.16  E-value=15  Score=39.09  Aligned_cols=186  Identities=8%  Similarity=-0.015  Sum_probs=113.0

Q ss_pred             HHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC-------------------
Q 040371           81 ALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD-------------------  141 (410)
Q Consensus        81 ~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-------------------  141 (410)
                      .++..+.+.|..+-|+++..-.+. +..+--.+..+|...|++++|.+.|.+... |+.++                   
T Consensus       817 ~l~~~l~~~~~~~~~~~l~~~~~~-~~~~~yl~g~~~L~~ge~~~A~~~F~kaa~-~~~~~~~l~~~~~~~~~~~~~~~~  894 (1139)
T 4fhn_B          817 ELVEKLFLFKQYNACMQLIGWLNS-DPIAVYLKALIYLKSKEAVKAVRCFKTTSL-VLYSHTSQFAVLREFQEIAEKYHH  894 (1139)
T ss_dssp             HHHHHHHHHSCTTHHHHHHHHSCC-CHHHHHHHHHHHHHTTCHHHHHHHHHTCCC-SCTTCCCSCSSHHHHHHHHHTTTS
T ss_pred             HHHHHHHHhhhHHHHHHHhhhccC-CcHHHHHHHHHHHhcCCHHHHHHHHHHHhh-hhcccchhhhhhcccccccccccc
Confidence            455566677777777776554443 444334566778889999999999977521 21110                   


Q ss_pred             ----HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC---hhHHHHHHHHHHhcCCHHHHHHHHHhCCC-CCCHHHH
Q 040371          142 ----SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ---LEHYGAMVDLLGRAGHIEEAYGLITSMTM-EPDVVVW  213 (410)
Q Consensus       142 ----~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~---~~~~~~li~~~~~~g~~~~A~~~~~~m~~-~p~~~~~  213 (410)
                          ..-|..++..+.+.+.++.+.++-....+..+-.++   ...|..+.+.+...|++++|...+-.++- .--....
T Consensus       895 ~~~l~~YY~hv~~LFe~~~~~~~vi~fa~lAi~~~~~~~~~~~~~l~~~iFk~~L~l~~ye~Ay~aL~~~pd~~~r~~cL  974 (1139)
T 4fhn_B          895 QNLLSCYYLHLSKKLFEESAYIDALEFSLLADASKETDDEDLSIAITHETLKTACAAGKFDAAHVALMVLSTTPLKKSCL  974 (1139)
T ss_dssp             CCSSHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHCCSGGGGHHHHHHHHSSSCHHHH
T ss_pred             cccHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccCCChhhHHHHHHHHHHHHHhhCCHHHHHHHHHhCCCHHHHHHHH
Confidence                123667778888888888888877666543221111   22688889999999999999888877631 1123455


Q ss_pred             HHHHHHHHhcCchhHHHHH------------HH----hh-ccCCCchHH-HHHHHHHhcCChhHHHHH-HHHHH
Q 040371          214 RALLSACRTFKRLELGEVA------------IV----NI-SRLMGGDYV-LLSNMYCYLKRWDTAENV-REIMK  268 (410)
Q Consensus       214 ~~li~~~~~~g~~~~a~~~------------~~----~~-~~~~~~~~~-~l~~~~~~~g~~~~a~~~-~~~m~  268 (410)
                      ..|+...+..|..+.-..+            +.    .. .+.+...|. .|=.-+...|++..|..+ ++...
T Consensus       975 r~LV~~lce~~~~~~L~~lpf~gl~~~Vd~IL~~kAr~~~~~~~~p~Yy~iLYs~ri~r~dyR~AA~vmYe~~~ 1048 (1139)
T 4fhn_B          975 LDFVNQLTKQGKINQLLNYSMPTLRQDVDNLLERKAFQMINVESQPCWYNILFSWRYKHQNYRDAAAIIYEKLS 1048 (1139)
T ss_dssp             HHHHHHHHHHCCHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCChhhhhCCCCccHHHHHHHHHHHHHHhCCccccCCCHHHHhHhhhhccCChHHHHHHHHHHHH
Confidence            6677666666665444333            11    11 223333344 444445677777777664 45443

>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=85.73  E-value=5.5  Score=28.51  Aligned_cols=50  Identities=14%  Similarity=0.242  Sum_probs=35.1

Q ss_pred             CHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc
Q 040371           21 RFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus        21 ~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~   70 (410)
                      +.-+...-++.+....+.|++....+.|.||-+.+++..|.++++-+...
T Consensus        25 D~~e~rrglN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~iK~K   74 (109)
T 1v54_E           25 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK   74 (109)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            34455555666666667778888888888888888888888877776543

>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=85.71  E-value=4.9  Score=30.44  Aligned_cols=63  Identities=13%  Similarity=0.245  Sum_probs=50.3

Q ss_pred             ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHH
Q 040371          122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVD  186 (410)
Q Consensus       122 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~  186 (410)
                      +..+..+-++.+....+-|+.....+.|.+|.+.+++..|.++|+.++.+.|  +....|..+++
T Consensus        68 D~wElrrglN~l~~~DlVPeP~Ii~AALrAcRRvNDfalAVR~lE~vK~K~~--~~~~iY~y~lq  130 (152)
T 2y69_E           68 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG--PHKEIYPYVIQ  130 (152)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT--TCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcC--CchhhHHHHHH
Confidence            4445666677777778999999999999999999999999999999987543  34556777664

>4gns_B Protein CSD3, chitin biosynthesis protein CHS6; FN3, BRCT, tetratricopeptide repeat, cargo adaptor, transpor; HET: EPE; 2.75A {Saccharomyces cerevisiae}

Probab=84.69  E-value=9.5  Score=38.26  Aligned_cols=124  Identities=10%  Similarity=-0.018  Sum_probs=83.0

Q ss_pred             HHHHHHHHHhhCC-HHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCH-HHHHHHHHhc-----------ccCChhh-
Q 040371           44 FASVIYGCARLGA-LNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKI-QMAKEVFDTV-----------QRNDVSV-  109 (410)
Q Consensus        44 ~~~ll~a~~~~~~-~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~-~~A~~~f~~m-----------~~~~~~~-  109 (410)
                      -.+++..+...++ .+.|..+++.+.+.....+.....+++.+..+.++- -+|.++..+.           +..+... 
T Consensus       251 ~~~Ll~~~~~t~~~~~~a~~~le~L~~~~p~~~~~~~~~~i~~~~~~~~~Ev~av~ll~~~l~~~~~~~~~l~~~~~~~~  330 (754)
T 4gns_B          251 MYSLKSFIAITPSLVDFTIDYLKGLTKKDPIHDIYYKTAMITILDHIETKELDMITILNETLDPLLSLLNDLPPRDADSA  330 (754)
T ss_dssp             HHHHHHHHHTCGGGHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHTTCGGGHHHHHHHHHHHHHHHHHHHHTCSSCCHHHH
T ss_pred             HHHHHHHHcccccHHHHHHHHHHHHHhhCCchhHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhhcccccccc
Confidence            3556666666666 588999999998875433444555666666555532 2344444332           2233211 


Q ss_pred             ----H-HHHH----HHHHHcCChHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          110 ----W-NAMI----SGVAIHGLAADASAIFTKMEMFNVLPD-SITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       110 ----~-~~li----~~~~~~g~~~~A~~l~~~m~~~g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                          + ..|+    .-+...|+++-|+++-++...  ..|+ -.||..|..+|.+.|+++.|+-.++.+.
T Consensus       331 ~~~~~~~~LL~~Qa~FLl~K~~~elAL~~Ak~AV~--~aPseF~tW~~La~vYi~l~d~e~ALLtLNScP  398 (754)
T 4gns_B          331 RLMNCMSDLLNIQTNFLLNRGDYELALGVSNTSTE--LALDSFESWYNLARCHIKKEEYEKALFAINSMP  398 (754)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHH--HCSSCHHHHHHHHHHHHHTTCHHHHHHHHHHSC
T ss_pred             cccCcchHHHHHHHHHHhccCcHHHHHHHHHHHHh--cCchhhHHHHHHHHHHHHhccHHHHHHHHhcCC
Confidence                1 1122    335568999999999999877  4565 5789999999999999999999999874

>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=83.99  E-value=8.3  Score=29.98  Aligned_cols=35  Identities=11%  Similarity=0.044  Sum_probs=22.8

Q ss_pred             CHHHHHHHHHHHHhhCCH------HHHHHHHHHHHHcCCCcc
Q 040371           40 DKFTFASVIYGCARLGAL------NHAYWVHNLIIEKKIELN   75 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~------~~a~~~~~~~~~~g~~~~   75 (410)
                      |..+|-..+...-+.|+.      +..+++|++.... ++|+
T Consensus        12 ~yd~W~~yl~llE~~g~p~~d~~l~rlrd~YerAia~-~Pp~   52 (161)
T 4h7y_A           12 NPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEA-LPPD   52 (161)
T ss_dssp             SHHHHHHHHHHHHHHTCSCCHHHHHHHHHHHHHHHHH-SCGG
T ss_pred             CHHHHHHHHHHHHHcCCCchhhHHHHHHHHHHHHHHc-CCcc
Confidence            555666666666666766      6777777777664 3443

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.92  E-value=30  Score=32.21  Aligned_cols=185  Identities=12%  Similarity=0.081  Sum_probs=120.5

Q ss_pred             CCHhHHHHHHHHHHH-----CCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHH-cCCCccHH--HHHHHHHHHHhcCC
Q 040371           20 ARFDEALRFFREMLS-----SKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIE-KKIELNFI--LSAALIDMYSKCGK   91 (410)
Q Consensus        20 g~~~~a~~l~~~m~~-----~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~-~g~~~~~~--~~~~li~~y~~~g~   91 (410)
                      |++++|++-+..+.+     ............++..|...++++...+.+..+.+ +|..+...  ..+.+++.......
T Consensus        30 ~~~~~a~e~ll~lEK~~r~~~d~~s~~r~l~~iv~l~~~~~~~~~l~e~i~~Lskkr~qlk~ai~~~V~~~~~~l~~~~~  109 (445)
T 4b4t_P           30 NDCNSALDQLLVLEKKTRQASDLASSKEVLAKIVDLLASRNKWDDLNEQLTLLSKKHGQLKLSIQYMIQKVMEYLKSSKS  109 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHSSSCSTTTCHHHHHHHHHHHHHHSCHHHHHHHHHHHHTTTTTSHHHHHHHHHHHHHHHHHHCT
T ss_pred             CCHHHHHHHHHHHHHHhhhccchhhHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhcCCc
Confidence            678888887766653     23444567788899999999999998777766654 34333222  22333444444443


Q ss_pred             HHH--HHHHHHhccc---C-------ChhhHHHHHHHHHHcCChHHHHHHHHHHHHC--CCCCC---HHHHHHHHHHHHc
Q 040371           92 IQM--AKEVFDTVQR---N-------DVSVWNAMISGVAIHGLAADASAIFTKMEMF--NVLPD---SITFLGLLTACSH  154 (410)
Q Consensus        92 ~~~--A~~~f~~m~~---~-------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~--g~~p~---~~t~~~ll~a~~~  154 (410)
                      .+.  -..+.+....   .       .......|...|...|++.+|.+++.++...  |..+.   ...+..-+..|..
T Consensus       110 ~d~~~~~~~i~~l~~vte~kiflE~erarl~~~La~i~e~~g~~~eA~~iL~~l~~Et~~~~~~~~kve~~l~q~rl~l~  189 (445)
T 4b4t_P          110 LDLNTRISVIETIRVVTENKIFVEVERARVTKDLVEIKKEEGKIDEAADILCELQVETYGSMEMSEKIQFILEQMELSIL  189 (445)
T ss_dssp             THHHHHHHHHHCCSSSSSCCCCCCHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHCSSSCHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHHH
Confidence            332  2233333221   1       1123456778899999999999999998754  22221   2356667888999


Q ss_pred             cCCHHHHHHHHHHhhhhc-CCCCC----hhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          155 CGLVEEGRKYFDHMRSRY-SIQPQ----LEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       155 ~g~~~~a~~~~~~m~~~~-~~~~~----~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      .+++..|..++..+..+. ...++    ...|..++..+...+++.+|...|.+.
T Consensus       190 ~~d~~~a~~~~~ki~~~~~~~~~~~~lk~~~~~~~~~~~~~e~~y~~a~~~y~e~  244 (445)
T 4b4t_P          190 KGDYSQATVLSRKILKKTFKNPKYESLKLEYYNLLVKISLHKREYLEVAQYLQEI  244 (445)
T ss_dssp             HTCHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhhcccCCcHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            999999999999875321 12222    245778888899999999998777665

>3ffl_A Anaphase-promoting complex subunit 7; tetratricopeptide repeat motif, helis-turn-helix, cell cycle division, mitosis, TPR repeat; 2.50A {Homo sapiens}

Probab=80.86  E-value=10  Score=29.87  Aligned_cols=110  Identities=5%  Similarity=-0.007  Sum_probs=52.3

Q ss_pred             HHHHHhcCCHHHHHHHHHhcc-----cCCh-------hhHHHHHHHHHHcCChHHHHHHHHHHHHC-CCCCCHH-HHHHH
Q 040371           83 IDMYSKCGKIQMAKEVFDTVQ-----RNDV-------SVWNAMISGVAIHGLAADASAIFTKMEMF-NVLPDSI-TFLGL  148 (410)
Q Consensus        83 i~~y~~~g~~~~A~~~f~~m~-----~~~~-------~~~~~li~~~~~~g~~~~A~~l~~~m~~~-g~~p~~~-t~~~l  148 (410)
                      +......|.++.|+-+.+-+.     ++++       .+...+.+++...|++..|...|++.+.. ..-|... +..++
T Consensus        27 ik~L~d~~LY~sA~~La~lLlSl~~~~~~~~sp~~~~~~l~~ladalf~~~eyrrA~~~y~qALq~~k~l~k~~s~~~~~  106 (167)
T 3ffl_A           27 VRDMAAAGLHSNVRLLSSLLLTLSNNNPELFSPPQKYQLLVYHADSLFHDKEYRNAVSKYTMALQQKKALSKTSKVRPST  106 (167)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHSTTSSCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHCC----------
T ss_pred             HHHHHHhhhHHHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHhcCCCccccc
Confidence            555666777777766655432     2332       13444556666677777777777665332 1111111 11111


Q ss_pred             HHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCC
Q 040371          149 LTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTM  206 (410)
Q Consensus       149 l~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~  206 (410)
                      -.    ......          .....++.+.---+-.+|.+.+++++|+.+++.+|.
T Consensus       107 ~~----~ss~p~----------s~~~~~e~Elkykia~C~~~l~~~~~Ai~~Le~Ip~  150 (167)
T 3ffl_A          107 GN----SASTPQ----------SQCLPSEIEVKYKLAECYTVLKQDKDAIAILDGIPS  150 (167)
T ss_dssp             ------------------------CCCCHHHHHHHHHHHHHHTTCHHHHHHHHHTSCG
T ss_pred             cc----cCCCcc----------cccccchHHHHHHHHHHHHHHCCHHHHHHHHhcCCc
Confidence            00    000000          001122334444566677777888888887777753

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	410
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.71
d1w3ba_	388	O-GlcNAc transferase p110 subunit, OGT {Human (Hom	99.69
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.54
d1fcha_	323	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	99.5
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	99.12
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	99.11
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	99.0
d2onda1	308	Cleavage stimulation factor 77 kDa subunit CSTF3 {	98.99
d2h6fa1	315	Protein farnesyltransferase alpha-subunit {Human (	98.9
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.87
d1xnfa_	259	Lipoprotein NlpI {Escherichia coli [TaxId: 562]}	98.87
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.72
d1hz4a_	366	Transcription factor MalT domain III {Escherichia	98.67
d1dcea1	334	Rab geranylgeranyltransferase alpha-subunit, N-ter	98.62
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.54
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.54
d1hh8a_	192	Neutrophil cytosolic factor 2 (NCF-2, p67-phox) {H	98.5
d1qqea_	290	Vesicular transport protein sec17 {Baker's yeast (	98.48
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.2
d1elwa_	117	Hop {Human (Homo sapiens) [TaxId: 9606]}	98.17
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.16
d2c2la1	201	STIP1 homology and U box-containing protein 1, STU	98.16
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.1
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	98.08
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	98.03
d1a17a_	159	Protein phosphatase 5 {Human (Homo sapiens) [TaxId	98.0
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	97.91
d1hxia_	112	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1	97.87
d1nzna_	122	Mitochondria fission protein Fis1 {Human (Homo sap	97.8
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.63
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.6
d1elra_	128	Hop {Human (Homo sapiens) [TaxId: 9606]}	97.59
d1p5qa1	170	FKBP52 (FKBP4), C-terminal domain {Human (Homo sap	97.56
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	97.49
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.46
d2fbna1	153	Putative 70 kda peptidylprolyl isomerase PFL2275c	97.46
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.42
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.35
d1ihga1	169	Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}	97.24
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.17
d1kt1a1	168	FKBP51, C-terminal domain {Monkey (Saimiri bolivie	97.15
d2ff4a2	179	Probable regulatory protein EmbR, middle domain {M	97.07
d1ouva_	265	Cysteine rich protein C (HcpC) {Helicobacter pylor	97.04
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	97.04
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	97.02
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	97.02
d1zbpa1	264	Hypothetical protein VPA1032 {Vibrio parahaemolyti	96.97
d1b89a_	336	Clathrin heavy chain proximal leg segment {Cow (Bo	96.89
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	96.86
d1zu2a1	145	Mitochondrial import receptor subunit tom20-3 {Tha	96.82
d1ya0a1	497	SMG-7 {Human (Homo sapiens) [TaxId: 9606]}	96.7
d2hr2a1	156	Hypothetical protein CT2138 {Chlorobium tepidum [T	96.68
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	95.47
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	95.1
d1tjca_	95	Prolyl 4-hydroxylase alpha-1 subunit, P4HA1 {Human	94.91
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.99
d1wy6a1	161	Hypothetical protein ST1625 {Archaeon Sulfolobus t	93.67
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	89.2
d1klxa_	133	Cysteine rich protein B (HcpB) {Helicobacter pylor	88.42
d1v54e_	105	Cytochrome c oxidase subunit E {Cow (Bos taurus) [	84.18
d2pqrb1	124	Mitochondria fission protein Fis1 {Baker's yeast (	83.26

>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=99.71  E-value=1.4e-14  Score=132.68  Aligned_cols=262  Identities=11%  Similarity=0.026  Sum_probs=186.8

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCC-----------
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIE-----------   73 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~-----------   73 (410)
                      +...|..+...|.+.|++++|+..|++..+.. +-+..+|..+..++...|++++|...+....+....           
T Consensus        32 ~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~~~  110 (388)
T d1w3ba_          32 NTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQLQEAIEHYRHALRLKPDFIDGYINLAAA  110 (388)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhcccccccccccccccccccccccccccccc
Confidence            45567777777777777777777777776642 224557777777777777777777766665543211           


Q ss_pred             --------------------------------------------------------ccHHHHHHHHHHHHhcCCHHHHHH
Q 040371           74 --------------------------------------------------------LNFILSAALIDMYSKCGKIQMAKE   97 (410)
Q Consensus        74 --------------------------------------------------------~~~~~~~~li~~y~~~g~~~~A~~   97 (410)
                                                                              .+...+..+...+...|++++|..
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~  190 (388)
T d1w3ba_         111 LVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAIETQPNFAVAWSNLGCVFNAQGEIWLAIH  190 (388)
T ss_dssp             HHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhhccCcchhHHHHhhcccccccCcHHHHHH
Confidence                                                                    122344455566666777777777


Q ss_pred             HHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCC
Q 040371           98 VFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSI  174 (410)
Q Consensus        98 ~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~  174 (410)
                      .+++..+   .+..+|..+...|...|++++|+..|++..... ..+...+..+...+.+.|++++|...|+...+.  -
T Consensus       191 ~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~  267 (388)
T d1w3ba_         191 HFEKAVTLDPNFLDAYINLGNVLKEARIFDRAVAAYLRALSLS-PNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL--Q  267 (388)
T ss_dssp             HHHHHHHHCTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHT--C
T ss_pred             HHHHHHHhCcccHHHHHHHhhhhhccccHHHHHHHHHHhHHHh-hhHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh--C
Confidence            7766542   245577777788888888888888888877653 335566777778888888888888888887742  2


Q ss_pred             CCChhHHHHHHHHHHhcCCHHHHHHHHHhC-C-CCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHH
Q 040371          175 QPQLEHYGAMVDLLGRAGHIEEAYGLITSM-T-MEPDVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSN  249 (410)
Q Consensus       175 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~-~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~  249 (410)
                      +-+...|..+...|...|++++|.+.++.. . ...+...+..+...+...|++++|...   ..+..|.++.++..+..
T Consensus       268 p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~  347 (388)
T d1w3ba_         268 PHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLAS  347 (388)
T ss_dssp             SSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHTTSCTTCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            234667888888888888888888888776 2 234667778888888888888888888   34556777778888888


Q ss_pred             HHHhcCChhHHHHHHHHHHhC
Q 040371          250 MYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       250 ~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      +|.+.|++++|.+.+++..+.
T Consensus       348 ~~~~~g~~~~A~~~~~~al~l  368 (388)
T d1w3ba_         348 VLQQQGKLQEALMHYKEAIRI  368 (388)
T ss_dssp             HHHTTTCCHHHHHHHHHHHTT
T ss_pred             HHHHcCCHHHHHHHHHHHHHh
Confidence            888999999998888877653

>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=99.69  E-value=3.1e-15  Score=137.23  Aligned_cols=283  Identities=12%  Similarity=0.037  Sum_probs=227.2

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCC
Q 040371           12 MIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK   91 (410)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~   91 (410)
                      +...+.+.|++++|++.|+++.+.. +-+...+..+..++...|++++|...++.+++.. +.+..++..+...|.+.|+
T Consensus         5 la~~~~~~G~~~~A~~~~~~~l~~~-p~~~~~~~~la~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~l~~~~~~~g~   82 (388)
T d1w3ba_           5 LAHREYQAGDFEAAERHCMQLWRQE-PDNTGVLLLLSSIHFQCRRLDRSAHFSTLAIKQN-PLLAEAYSNLGNVYKERGQ   82 (388)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHhhhhcc
Confidence            3456789999999999999998753 3367788999999999999999999999999875 4568899999999999999


Q ss_pred             HHHHHHHHHhcccC------------------------------------------------------------------
Q 040371           92 IQMAKEVFDTVQRN------------------------------------------------------------------  105 (410)
Q Consensus        92 ~~~A~~~f~~m~~~------------------------------------------------------------------  105 (410)
                      +++|...|......                                                                  
T Consensus        83 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  162 (388)
T d1w3ba_          83 LQEAIEHYRHALRLKPDFIDGYINLAAALVAAGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKALGRLEEAKACYLKAI  162 (388)
T ss_dssp             HHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHSCSSHHHHHHHHHHHHCTTCTHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhhhHHHHHHhh
Confidence            99999988664321                                                                  


Q ss_pred             -----ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChh
Q 040371          106 -----DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLE  179 (410)
Q Consensus       106 -----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~  179 (410)
                           +...+..+...+...|+.++|...+++....  .| +...+..+...+...|++++|...+......  -..+..
T Consensus       163 ~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~al~~--~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~~  238 (388)
T d1w3ba_         163 ETQPNFAVAWSNLGCVFNAQGEIWLAIHHFEKAVTL--DPNFLDAYINLGNVLKEARIFDRAVAAYLRALSL--SPNHAV  238 (388)
T ss_dssp             HHCTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHTTTCTTHHHHHHHHHHHH--CTTCHH
T ss_pred             ccCcchhHHHHhhcccccccCcHHHHHHHHHHHHHh--CcccHHHHHHHhhhhhccccHHHHHHHHHHhHHH--hhhHHH
Confidence                 1234555666777889999999999988774  34 4567888889999999999999999998853  234567


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhc
Q 040371          180 HYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYL  254 (410)
Q Consensus       180 ~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~  254 (410)
                      .+..+...|.+.|++++|...|++. ...| +..+|..+...+...|++++|...   .....|.+...+..+...|.+.
T Consensus       239 ~~~~l~~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~l~~~~~~~  318 (388)
T d1w3ba_         239 VHGNLACVYYEQGLIDLAIDTYRRAIELQPHFPDAYCNLANALKEKGSVAEAEDCYNTALRLCPTHADSLNNLANIKREQ  318 (388)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHcCCHHHHHHHHHhhhccCCccchhhhHHHHHHHHC
Confidence            7888999999999999999999886 5556 567899999999999999999998   4566677778888999999999


Q ss_pred             CChhHHHHHHHHHHhCCCcCCCceeEEEECCEEEEEEeCCCCCccHHHHHHHHHH
Q 040371          255 KRWDTAENVREIMKKKGVRKSQGKSWLELAGVIHQFKAGDRSHPEAQAIDKILGS  309 (410)
Q Consensus       255 g~~~~a~~~~~~m~~~g~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  309 (410)
                      |++++|.+.+++..+.  .|+....|..       +...+...|+.++|...+++
T Consensus       319 ~~~~~A~~~~~~al~~--~p~~~~~~~~-------la~~~~~~g~~~~A~~~~~~  364 (388)
T d1w3ba_         319 GNIEEAVRLYRKALEV--FPEFAAAHSN-------LASVLQQQGKLQEALMHYKE  364 (388)
T ss_dssp             TCHHHHHHHHHHHTTS--CTTCHHHHHH-------HHHHHHTTTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHh--CCCCHHHHHH-------HHHHHHHcCCHHHHHHHHHH
Confidence            9999999999987654  2333222321       22334567888999888874

>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=99.54  E-value=2.2e-12  Score=115.75  Aligned_cols=247  Identities=13%  Similarity=0.051  Sum_probs=188.7

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCC
Q 040371           12 MIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK   91 (410)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~   91 (410)
                      ....|.+.|++++|+..|++.++.. +-+..+|..+..++...|+++.|...+.+.++.. +.+...+..+...|.+.|+
T Consensus        25 ~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~la~~~~~~~~  102 (323)
T d1fcha_          25 EGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELK-PDNQTALMALAVSFTNESL  102 (323)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhccc-ccccccccccccccccccc
Confidence            4566889999999999999999863 3357799999999999999999999999999875 4468889999999999999


Q ss_pred             HHHHHHHHHhcccC--C----------------hhhHHHHHHHHHHcCChHHHHHHHHHHHHCC-CCCCHHHHHHHHHHH
Q 040371           92 IQMAKEVFDTVQRN--D----------------VSVWNAMISGVAIHGLAADASAIFTKMEMFN-VLPDSITFLGLLTAC  152 (410)
Q Consensus        92 ~~~A~~~f~~m~~~--~----------------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g-~~p~~~t~~~ll~a~  152 (410)
                      +++|.+.+++....  +                .......+..+...+...+|.+.|.+..... -.++...+..+...+
T Consensus       103 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~~~  182 (323)
T d1fcha_         103 QRQACEILRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLF  182 (323)
T ss_dssp             HHHHHHHHHHHHHTSTTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHHHH
T ss_pred             ccccccchhhHHHhccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHHHH
Confidence            99999999886532  1                0111122334455677888999998876542 234566778888899


Q ss_pred             HccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHH
Q 040371          153 SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGE  230 (410)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~  230 (410)
                      ...|++++|...|+.....  .+-+...|..+...|.+.|++++|.+.|++. ...| +..+|..+..+|...|++++|.
T Consensus       183 ~~~~~~~~A~~~~~~al~~--~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~  260 (323)
T d1fcha_         183 NLSGEYDKAVDCFTAALSV--RPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAV  260 (323)
T ss_dssp             HHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHhhhhccccccccc--ccccccchhhhhhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHHH
Confidence            9999999999999998753  1234778899999999999999999999886 4456 5678889999999999999999


Q ss_pred             HH---HHhhccCCCch-----------HHHHHHHHHhcCChhHHHH
Q 040371          231 VA---IVNISRLMGGD-----------YVLLSNMYCYLKRWDTAEN  262 (410)
Q Consensus       231 ~~---~~~~~~~~~~~-----------~~~l~~~~~~~g~~~~a~~  262 (410)
                      ..   ..++.|.+...           +..+-.++...|+.+.+..
T Consensus       261 ~~~~~al~l~p~~~~~~~~~~~~~~~~~~~l~~al~~~~~~d~~~~  306 (323)
T d1fcha_         261 EHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGA  306 (323)
T ss_dssp             HHHHHHHHHHHTC------CCCCCHHHHHHHHHHHHHHTCGGGHHH
T ss_pred             HHHHHHHHhCCcChhhhhhhHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence            98   45556655432           3345556666676665543

>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=99.50  E-value=2.3e-12  Score=115.66  Aligned_cols=221  Identities=12%  Similarity=0.037  Sum_probs=179.9

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCC
Q 040371           46 SVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGL  122 (410)
Q Consensus        46 ~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~  122 (410)
                      .....+.+.|++++|...|+.+++.. +.+...|..+..+|...|++++|...|++..+   .+...|..+...|...|+
T Consensus        24 ~~g~~~~~~g~~~~A~~~~~~al~~~-P~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~la~~~~~~~~  102 (323)
T d1fcha_          24 EEGLRRLQEGDLPNAVLLFEAAVQQD-PKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESL  102 (323)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHSC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHHHHHHHHHcCChHHHHHHHHhhhcccccccccccccccccccccc
Confidence            35566789999999999999999875 45688999999999999999999999998753   367789999999999999


Q ss_pred             hHHHHHHHHHHHHCCCCCCHHH----------------HHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHH
Q 040371          123 AADASAIFTKMEMFNVLPDSIT----------------FLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVD  186 (410)
Q Consensus       123 ~~~A~~l~~~m~~~g~~p~~~t----------------~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~  186 (410)
                      +++|.+.+++....  .|+...                ....+..+...+..+++...|....+...-.++..++..+..
T Consensus       103 ~~~A~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~p~~~~~~~~~~l~~  180 (323)
T d1fcha_         103 QRQACEILRDWLRY--TPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGV  180 (323)
T ss_dssp             HHHHHHHHHHHHHT--STTTGGGCC---------------CTTHHHHHHHHHHHHHHHHHHHHHHSTTSCCHHHHHHHHH
T ss_pred             ccccccchhhHHHh--ccchHHHHHhhhhhhhhcccccchhhHHHHHHhhHHHHHHHHHHHHHHHhhcccccccchhhHH
Confidence            99999999998764  232111                111222334456678888888887754333456778889999


Q ss_pred             HHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHH
Q 040371          187 LLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAE  261 (410)
Q Consensus       187 ~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~  261 (410)
                      .+...|++++|...|++. ...| +...|..+-..+...|++++|...   ..++.|.++.++..+..+|.+.|++++|.
T Consensus       181 ~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~  260 (323)
T d1fcha_         181 LFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAV  260 (323)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCHHHHH
T ss_pred             HHHHHHHHhhhhcccccccccccccccchhhhhhcccccccchhHHHHHHHHHHHhhccHHHHHHHHHHHHHCCCHHHHH
Confidence            999999999999999986 4445 577898999999999999999999   56678888889999999999999999999


Q ss_pred             HHHHHHHh
Q 040371          262 NVREIMKK  269 (410)
Q Consensus       262 ~~~~~m~~  269 (410)
                      +.|++..+
T Consensus       261 ~~~~~al~  268 (323)
T d1fcha_         261 EHFLEALN  268 (323)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99998765

>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=99.12  E-value=3.4e-08  Score=88.08  Aligned_cols=257  Identities=13%  Similarity=0.022  Sum_probs=186.2

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHHHCCCCCC-----HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcC----CC-ccHHHHHH
Q 040371           12 MIGGFVRNARFDEALRFFREMLSSKVEPD-----KFTFASVIYGCARLGALNHAYWVHNLIIEKK----IE-LNFILSAA   81 (410)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~g~~pd-----~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g----~~-~~~~~~~~   81 (410)
                      ....+...|++++|+.+|++.++.. +.+     ...+..+..++...|++++|...++...+..    .. .....+..
T Consensus        18 rA~~~~~~g~~~~A~~~~~~aL~~~-~~~~~~~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~   96 (366)
T d1hz4a_          18 RAQVAINDGNPDEAERLAKLALEEL-PPGWFYSRIVATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQ   96 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHTC-CTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhhC-cCCCcHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHH
Confidence            3455678999999999999988752 222     2356677788999999999999999887642    11 12445667


Q ss_pred             HHHHHHhcCCHHHHHHHHHhccc-------C----ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCC----CCCHHHHH
Q 040371           82 LIDMYSKCGKIQMAKEVFDTVQR-------N----DVSVWNAMISGVAIHGLAADASAIFTKMEMFNV----LPDSITFL  146 (410)
Q Consensus        82 li~~y~~~g~~~~A~~~f~~m~~-------~----~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~----~p~~~t~~  146 (410)
                      +...|...|++..|...+.....       +    ....+..+...+...|+++.+...+.+......    .....++.
T Consensus        97 ~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  176 (366)
T d1hz4a_          97 QSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPMHEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLA  176 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHH
Confidence            78889999999999988876531       1    113556677788899999999999988876422    22334555


Q ss_pred             HHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-----hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-----CHHHHHH
Q 040371          147 GLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-----LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-----DVVVWRA  215 (410)
Q Consensus       147 ~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-----~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-----~~~~~~~  215 (410)
                      .....+...+....+...+........-...     ...+..+...+...|++++|...+++. ...|     ....+..
T Consensus       177 ~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~  256 (366)
T d1hz4a_         177 MLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDWISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRN  256 (366)
T ss_dssp             HHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHH
T ss_pred             HHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCchHHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHH
Confidence            6667777889999998888776543221111     234566677888999999999999876 2221     2456667


Q ss_pred             HHHHHHhcCchhHHHHHHHhh---------ccCCCchHHHHHHHHHhcCChhHHHHHHHHHHh
Q 040371          216 LLSACRTFKRLELGEVAIVNI---------SRLMGGDYVLLSNMYCYLKRWDTAENVREIMKK  269 (410)
Q Consensus       216 li~~~~~~g~~~~a~~~~~~~---------~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~  269 (410)
                      +...+...|++++|...+.+.         .|....++..+..+|.+.|++++|.+.+++..+
T Consensus       257 la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~l~~Al~  319 (366)
T d1hz4a_         257 IARAQILLGEFEPAEIVLEELNENARSLRLMSDLNRNLLLLNQLYWQAGRKSDAQRVLLDALK  319 (366)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            788899999999999983322         233445678899999999999999999987644

>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=99.11  E-value=1.3e-08  Score=90.15  Aligned_cols=207  Identities=12%  Similarity=0.034  Sum_probs=155.8

Q ss_pred             HhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh--------------hCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHH
Q 040371           22 FDEALRFFREMLSSKVEPDKFTFASVIYGCAR--------------LGALNHAYWVHNLIIEKKIELNFILSAALIDMYS   87 (410)
Q Consensus        22 ~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~--------------~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~   87 (410)
                      .+.+..+|++++.. ++-+...|...+.-+-.              .+..+.+..++++.++...+.+...|..++..+.
T Consensus        32 ~~Rv~~vyerAl~~-~~~~~~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~ral~~~~p~~~~l~~~ya~~~~  110 (308)
T d2onda1          32 TKRVMFAYEQCLLV-LGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEE  110 (308)
T ss_dssp             HHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHTTTTTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH-CCCCHHHHHHHHHHHHHcCchHHHHHHHhhcccchHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            45577888888764 34455566555543322              2345788999999988766677888999999999


Q ss_pred             hcCCHHHHHHHHHhccc--C-C-hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHH-HHHccCCHHHHH
Q 040371           88 KCGKIQMAKEVFDTVQR--N-D-VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLT-ACSHCGLVEEGR  162 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~~--~-~-~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~-a~~~~g~~~~a~  162 (410)
                      +.|+++.|+.+|+++..  | + ...|...+....+.|+.++|.++|+++.+.+.. +...|..... -+...|+.+.|.
T Consensus       111 ~~~~~~~a~~i~~~~l~~~~~~~~~~w~~~~~~~~~~~~~~~ar~i~~~al~~~~~-~~~~~~~~a~~e~~~~~~~~~a~  189 (308)
T d2onda1         111 SRMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDART-RHHVYVTAALMEYYCSKDKSVAF  189 (308)
T ss_dssp             HTTCHHHHHHHHHHHHTSSSSCTHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSTTC-CTHHHHHHHHHHHHTSCCHHHHH
T ss_pred             hcccHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCC-cHHHHHHHHHHHHHhccCHHHHH
Confidence            99999999999998764  2 3 347999999999999999999999999876432 3333433332 334568999999


Q ss_pred             HHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC----CCCCC--HHHHHHHHHHHHhcCchhHHHHH
Q 040371          163 KYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM----TMEPD--VVVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       163 ~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~p~--~~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      .+|+.+.+.  .+.+...|...++.+.+.|++++|..+|++.    +..|+  ...|...+.--..+|+.+.+..+
T Consensus       190 ~i~e~~l~~--~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~~~~~~iw~~~~~fE~~~G~~~~~~~~  263 (308)
T d2onda1         190 KIFELGLKK--YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFESNIGDLASILKV  263 (308)
T ss_dssp             HHHHHHHHH--HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCGGGCHHHHHHHHHHHHHHSCHHHHHHH
T ss_pred             HHHHHHHHh--hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence            999999864  3445788999999999999999999999986    33442  46788888877788888887777

>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=99.00  E-value=6.6e-08  Score=85.82  Aligned_cols=208  Identities=10%  Similarity=0.056  Sum_probs=150.3

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC-CHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLG-ALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~-~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      -.|+-+-..+.+.+.+++|+++++++++.. +-+...|+....++...+ ++++|...++.+++.. +-+..+|+.+...
T Consensus        44 ~a~~~~~~~~~~~e~~~~Al~~~~~ai~ln-P~~~~a~~~r~~~l~~l~~~~~eal~~~~~al~~~-p~~~~a~~~~~~~  121 (315)
T d2h6fa1          44 DVYDYFRAVLQRDERSERAFKLTRDAIELN-AANYTVWHFRRVLLKSLQKDLHEEMNYITAIIEEQ-PKNYQVWHHRRVL  121 (315)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCchHHHHHHHHHHHHHC-CCChHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH-HhhhhHHHHHhHH
Confidence            357777788888999999999999998852 335567888888888776 5899999999998875 4578889999999


Q ss_pred             HHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCC----
Q 040371           86 YSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGL----  157 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~----  157 (410)
                      +.+.|++++|+..|+++.+   .+..+|+.+...+.+.|++++|++.|+++.+.  .| +...|+.+...+.+.+.    
T Consensus       122 ~~~l~~~~eAl~~~~kal~~dp~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~--~p~n~~a~~~r~~~l~~~~~~~~~  199 (315)
T d2h6fa1         122 VEWLRDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE--DVRNNSVWNQRYFVISNTTGYNDR  199 (315)
T ss_dssp             HHHHTCCTTHHHHHHHHHHHCTTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH--CTTCHHHHHHHHHHHHHTTCSCSH
T ss_pred             HHhhccHHHHHHHHhhhhhhhhcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHH--CCccHHHHHHHHHHHHHccccchh
Confidence            9999999999999998764   46788999999999999999999999999885  34 45566665555555444    


Q ss_pred             --HHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC----CCCCCHHHHHHHHHHHH
Q 040371          158 --VEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM----TMEPDVVVWRALLSACR  221 (410)
Q Consensus       158 --~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m----~~~p~~~~~~~li~~~~  221 (410)
                        +++|...+....+.  -+.+...|+.+...+...| .+++.+.++..    +...+...+..+...+.
T Consensus       200 ~~~~~ai~~~~~al~~--~P~~~~~~~~l~~ll~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~  266 (315)
T d2h6fa1         200 AVLEREVQYTLEMIKL--VPHNESAWNYLKGILQDRG-LSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYE  266 (315)
T ss_dssp             HHHHHHHHHHHHHHHH--STTCHHHHHHHHHHHTTTC-GGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHH
T ss_pred             hhhHHhHHHHHHHHHh--CCCchHHHHHHHHHHHhcC-hHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHH
Confidence              56788777777643  1235666776665554443 45555555444    22224455555555543

>d2onda1 a.118.8.7 (A:242-549) Cleavage stimulation factor 77 kDa subunit CSTF3 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: HAT/Suf repeat
domain: Cleavage stimulation factor 77 kDa subunit CSTF3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.99  E-value=3.9e-08  Score=87.06  Aligned_cols=183  Identities=11%  Similarity=0.048  Sum_probs=146.1

Q ss_pred             CHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHH
Q 040371           21 RFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFD  100 (410)
Q Consensus        21 ~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~  100 (410)
                      ..++|..+|++..+...+.+...|...+....+.|+.+.++.+++.+++........+|..++....+.|+++.|+++|+
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            45788899999887544446667888888889999999999999999987544446689999999999999999999999


Q ss_pred             hcccCC---hhhHHHHHHH-HHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCC
Q 040371          101 TVQRND---VSVWNAMISG-VAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP  176 (410)
Q Consensus       101 ~m~~~~---~~~~~~li~~-~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~  176 (410)
                      +..+..   ...|-..... +...|+.+.|..+|+.+... .+.+...+...+....+.|+++.|+.+|++..+..+..|
T Consensus       159 ~al~~~~~~~~~~~~~a~~e~~~~~~~~~a~~i~e~~l~~-~p~~~~~w~~y~~~~~~~g~~~~aR~~fe~ai~~~~~~~  237 (308)
T d2onda1         159 KAREDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKK-YGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPP  237 (308)
T ss_dssp             HHHTSTTCCTHHHHHHHHHHHHTSCCHHHHHHHHHHHHHH-HTTCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHSSSSCG
T ss_pred             HHHHhCCCcHHHHHHHHHHHHHhccCHHHHHHHHHHHHHh-hhhhHHHHHHHHHHHHHcCChHHHHHHHHHHHHhCCCCh
Confidence            986533   2333333322 33468999999999999875 334567788899999999999999999999886544554


Q ss_pred             C--hhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          177 Q--LEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       177 ~--~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      .  ...|...+..-.+.|+.+.+.++++++
T Consensus       238 ~~~~~iw~~~~~fE~~~G~~~~~~~~~~r~  267 (308)
T d2onda1         238 EKSGEIWARFLAFESNIGDLASILKVEKRR  267 (308)
T ss_dssp             GGCHHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence            3  457899998888999999999999887

>d2h6fa1 a.118.6.1 (A:55-369) Protein farnesyltransferase alpha-subunit {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Protein farnesyltransferase alpha-subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.90  E-value=1.4e-07  Score=83.66  Aligned_cols=206  Identities=10%  Similarity=0.062  Sum_probs=158.8

Q ss_pred             HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCC-HHHHHHHHHhccc---CChhhHHHHHHHH
Q 040371           42 FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK-IQMAKEVFDTVQR---NDVSVWNAMISGV  117 (410)
Q Consensus        42 ~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~-~~~A~~~f~~m~~---~~~~~~~~li~~~  117 (410)
                      ..|+.+...+.+.+..++|.++++.+++.. +-+..+|+.....+.+.|+ +++|...++...+   .+..+|+.+...+
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            456667777888899999999999999985 5578899999999998875 9999999998753   4678999999999


Q ss_pred             HHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCC-ChhHHHHHHHHHHhcCC---
Q 040371          118 AIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP-QLEHYGAMVDLLGRAGH---  193 (410)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~-~~~~~~~li~~~~~~g~---  193 (410)
                      .+.|++++|++.|+++.+.. +-+...|..+...+.+.|++++|.+.|+.+.+.   .| +...|+.+...+.+.+.   
T Consensus       123 ~~l~~~~eAl~~~~kal~~d-p~n~~a~~~~~~~~~~~~~~~~Al~~~~~al~~---~p~n~~a~~~r~~~l~~~~~~~~  198 (315)
T d2h6fa1         123 EWLRDPSQELEFIADILNQD-AKNYHAWQHRQWVIQEFKLWDNELQYVDQLLKE---DVRNNSVWNQRYFVISNTTGYND  198 (315)
T ss_dssp             HHHTCCTTHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCCTTHHHHHHHHHHH---CTTCHHHHHHHHHHHHHTTCSCS
T ss_pred             HhhccHHHHHHHHhhhhhhh-hcchHHHHHHHHHHHHHHhhHHHHHHHHHHHHH---CCccHHHHHHHHHHHHHccccch
Confidence            99999999999999998852 236788999999999999999999999999853   33 56678877777777665   


Q ss_pred             ---HHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCc--hHHHHHHHHHh
Q 040371          194 ---IEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGG--DYVLLSNMYCY  253 (410)
Q Consensus       194 ---~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~--~~~~l~~~~~~  253 (410)
                         +++|++.+.+. ...| +...|..+...+...+ .+++...   +.++.|....  .+..++..|..
T Consensus       199 ~~~~~~ai~~~~~al~~~P~~~~~~~~l~~ll~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~y~~  267 (315)
T d2h6fa1         199 RAVLEREVQYTLEMIKLVPHNESAWNYLKGILQDRG-LSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYED  267 (315)
T ss_dssp             HHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHHTTTC-GGGCHHHHHHHHHHTTTCCCHHHHHHHHHHHHH
T ss_pred             hhhhHHhHHHHHHHHHhCCCchHHHHHHHHHHHhcC-hHHHHHHHHHHHHhCCCcCCHHHHHHHHHHHHH
Confidence               56788777765 4556 5777877766655444 4555555   5555665443  34456666644

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.87  E-value=7.4e-08  Score=82.46  Aligned_cols=113  Identities=13%  Similarity=-0.052  Sum_probs=55.1

Q ss_pred             HhHHHHHHHHHHHCCC-CC--CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHH
Q 040371           22 FDEALRFFREMLSSKV-EP--DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEV   98 (410)
Q Consensus        22 ~~~a~~l~~~m~~~g~-~p--d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~   98 (410)
                      .+.++.-+++...... .+  ...+|..+..++.+.|++++|.+.|++.++.. +.++.+++.+..+|.+.|++++|.+.
T Consensus        15 ~e~al~~~~e~l~~~~~~~~~~a~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A~~~   93 (259)
T d1xnfa_          15 QEVILARMEQILASRALTDDERAQLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEA   93 (259)
T ss_dssp             HHHHHHHHHHHHTSSCCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHhhhh
Confidence            4445555555543311 11  11244444455555555555555555555543 23445555555555555555555555


Q ss_pred             HHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           99 FDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        99 f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      |++..+  | +..+|..+...|...|++++|++.|++..+
T Consensus        94 ~~~al~~~p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~  133 (259)
T d1xnfa_          94 FDSVLELDPTYNYAHLNRGIALYYGGRDKLAQDDLLAFYQ  133 (259)
T ss_dssp             HHHHHHHCTTCTHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             hhHHHHHHhhhhhhHHHHHHHHHHHhhHHHHHHHHHHHHh
Confidence            554432  1 233455555555555555555555555444

>d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Lipoprotein NlpI
species: Escherichia coli [TaxId: 562]

Probab=98.87  E-value=1.1e-07  Score=81.46  Aligned_cols=196  Identities=10%  Similarity=-0.079  Sum_probs=136.3

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      .+|..+-..|.+.|++++|++.|++.++.. +-+..+|..+..++...|++++|...|+++++.. +.+..++..+..+|
T Consensus        38 ~~~~~~G~~y~~~g~~~~A~~~~~~al~l~-p~~~~a~~~lg~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~  115 (259)
T d1xnfa_          38 QLLYERGVLYDSLGLRALARNDFSQALAIR-PDMPEVFNYLGIYLTQAGNFDAAYEAFDSVLELD-PTYNYAHLNRGIAL  115 (259)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHhhccC-CCCHHHHhhhchHHHHHHHHHHhhhhhhHHHHHH-hhhhhhHHHHHHHH
Confidence            467788899999999999999999998752 3367799999999999999999999999999975 44677889999999


Q ss_pred             HhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHcc----CCHH
Q 040371           87 SKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHC----GLVE  159 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~----g~~~  159 (410)
                      ...|++++|...|+...+  | +...+..+..++.+.+..+.+..+..........+  ..+. ++..+...    +..+
T Consensus       116 ~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~-~~~~~~~~~~~~~~~~  192 (259)
T d1xnfa_         116 YYGGRDKLAQDDLLAFYQDDPNDPFRSLWLYLAEQKLDEKQAKEVLKQHFEKSDKEQ--WGWN-IVEFYLGNISEQTLME  192 (259)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHSCCCS--THHH-HHHHHTTSSCHHHHHH
T ss_pred             HHHhhHHHHHHHHHHHHhhccccHHHHHHHHHHHHHhhhHHHHHHHHHHhhccchhh--hhhh-HHHHHHHHHHHHHHHH
Confidence            999999999999998763  2 34444444455566666666666666665543222  2222 22222211    1122


Q ss_pred             HHHHHHHHhhhhcCCCCC-hhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCCH
Q 040371          160 EGRKYFDHMRSRYSIQPQ-LEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPDV  210 (410)
Q Consensus       160 ~a~~~~~~m~~~~~~~~~-~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~~  210 (410)
                      .+...+....   ...|+ ..+|..+...|...|++++|.+.|++. ...|+.
T Consensus       193 ~~~~~~~~~~---~~~~~~~~~~~~lg~~~~~~g~~~~A~~~~~~al~~~p~~  242 (259)
T d1xnfa_         193 RLKADATDNT---SLAEHLSETNFYLGKYYLSLGDLDSATALFKLAVANNVHN  242 (259)
T ss_dssp             HHHHHCCSHH---HHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCTT
T ss_pred             HHHHHHHHhh---hcCcccHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCC
Confidence            2222222211   11122 346777888899999999999999986 566754

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.72  E-value=3.9e-08  Score=88.03  Aligned_cols=252  Identities=6%  Similarity=-0.076  Sum_probs=170.4

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHH-HHHHH---HHHH-------HhhCCHHHHHHHHHHHHHcCCCccHH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKF-TFASV---IYGC-------ARLGALNHAYWVHNLIIEKKIELNFI   77 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~-t~~~l---l~a~-------~~~~~~~~a~~~~~~~~~~g~~~~~~   77 (410)
                      ++.++......+..++|++++++.++.  .|+.. .|+..   +...       ...+.++++..+++.+++.. +.+..
T Consensus        32 ~~~~~~~~~~~~~~~~al~~~~~~l~~--~P~~~~a~~~r~~~l~~l~~~~~~~~~~~~~~~al~~~~~~l~~~-pk~~~  108 (334)
T d1dcea1          32 TQAVFQKRQAGELDESVLELTSQILGA--NPDFATLWNCRREVLQHLETEKSPEESAALVKAELGFLESCLRVN-PKSYG  108 (334)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHHHHHH--CTTCHHHHHHHHHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHHHC-TTCHH
T ss_pred             HHHHHHHHhcccccHHHHHHHHHHHHH--CCCcHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHHHHhC-CCcHH
Confidence            344444444445568999999999874  56544 44332   2222       23445788889999988875 55777


Q ss_pred             HHHHHHHHHHhcCC--HHHHHHHHHhccc---CChhhHHHHH-HHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHH
Q 040371           78 LSAALIDMYSKCGK--IQMAKEVFDTVQR---NDVSVWNAMI-SGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTA  151 (410)
Q Consensus        78 ~~~~li~~y~~~g~--~~~A~~~f~~m~~---~~~~~~~~li-~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a  151 (410)
                      .|..+...+...++  +++|...+++..+   ++...|...+ ..+...|..++|++.+++..... +-+...+..+...
T Consensus       109 ~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~~~~~~~~~~~~~~Al~~~~~~i~~~-p~~~~a~~~l~~~  187 (334)
T d1dcea1         109 TWHHRCWLLSRLPEPNWARELELCARFLEADERNFHCWDYRRFVAAQAAVAPAEELAFTDSLITRN-FSNYSSWHYRSCL  187 (334)
T ss_dssp             HHHHHHHHHHTCSSCCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTCCCHHHHHHHHHTTTTTT-CCCHHHHHHHHHH
T ss_pred             HHHHhhHHHHHhccccHHHHHHHHHHHHhhCchhhhhhhhHHHHHHHhccccHHHHHHHHHHHHcC-CCCHHHHHHHHHH
Confidence            88888777777664  8899999988753   3556665444 56667899999999999887753 2256778888888


Q ss_pred             HHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCC-CCHHHHHHHHHHHHhcCchhHH
Q 040371          152 CSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TME-PDVVVWRALLSACRTFKRLELG  229 (410)
Q Consensus       152 ~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~-p~~~~~~~li~~~~~~g~~~~a  229 (410)
                      +...|++++|...+....+.   .  . ....+...+...+..+++...+.+. ... ++...+..+...+...++.++|
T Consensus       188 ~~~~~~~~~A~~~~~~~~~~---~--~-~~~~~~~~~~~l~~~~~a~~~~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~a  261 (334)
T d1dcea1         188 LPQLHPQPDSGPQGRLPENV---L--L-KELELVQNAFFTDPNDQSAWFYHRWLLGRAEPLFRCELSVEKSTVLQSELES  261 (334)
T ss_dssp             HHHHSCCCCSSSCCSSCHHH---H--H-HHHHHHHHHHHHCSSCSHHHHHHHHHHSCCCCSSSCCCCHHHHHHHHHHHHH
T ss_pred             HHHhcCHHHHHHHHHHhHHh---H--H-HHHHHHHHHHHhcchhHHHHHHHHHHHhCcchhhHHHHHHHHHHHHhhHHHH
Confidence            88888888776655554432   1  1 1122334455666667776666654 122 2344555666667777888888


Q ss_pred             HHHHHhhc---cCCCchHHHHHHHHHhcCChhHHHHHHHHHHhC
Q 040371          230 EVAIVNIS---RLMGGDYVLLSNMYCYLKRWDTAENVREIMKKK  270 (410)
Q Consensus       230 ~~~~~~~~---~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~  270 (410)
                      ...+.+..   |.+..++..+..+|.+.|+.++|.+.++...+.
T Consensus       262 ~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~l  305 (334)
T d1dcea1         262 CKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAV  305 (334)
T ss_dssp             HHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            88855444   444566778899999999999999999988764

>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=98.67  E-value=4.5e-06  Score=73.72  Aligned_cols=226  Identities=10%  Similarity=0.016  Sum_probs=163.5

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHC----CCCC-CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc----CCCc---
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSS----KVEP-DKFTFASVIYGCARLGALNHAYWVHNLIIEK----KIEL---   74 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~----g~~p-d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~~~---   74 (410)
                      ..++.+...|...|++++|+..|++..+.    +..+ ...++..+...+...|++..+...+......    +...   
T Consensus        52 ~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~~~~~~~~~~~  131 (366)
T d1hz4a_          52 VATSVLGEVLHCKGELTRSLALMQQTEQMARQHDVWHYALWSLIQQSEILFAQGFLQTAWETQEKAFQLINEQHLEQLPM  131 (366)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCTTSTH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchhhH
Confidence            46788889999999999999999988652    1111 1235566777888999999999988877642    2221   


Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhcccC--------ChhhHHHHHHHHHHcCChHHHHHHHHHHHHC----CCCCC-
Q 040371           75 NFILSAALIDMYSKCGKIQMAKEVFDTVQRN--------DVSVWNAMISGVAIHGLAADASAIFTKMEMF----NVLPD-  141 (410)
Q Consensus        75 ~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~--------~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~----g~~p~-  141 (410)
                      ....+..+...|...|+++.|...++.....        ...++..+...+...+...++...+.+....    +..+. 
T Consensus       132 ~~~~~~~la~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~~~~~~~~  211 (366)
T d1hz4a_         132 HEFLVRIRAQLLWAWARLDEAEASARSGIEVLSSYQPQQQLQCLAMLIQCSLARGDLDNARSQLNRLENLLGNGKYHSDW  211 (366)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTTTSCGGGGHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCCCHHH
T ss_pred             HHHHHHHHHHHHHHhcchhhhHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcccCch
Confidence            2345667788999999999999999876521        2345666677788889999999988776542    11121 


Q ss_pred             -HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCC--ChhHHHHHHHHHHhcCCHHHHHHHHHhC-------CCCCC-H
Q 040371          142 -SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQP--QLEHYGAMVDLLGRAGHIEEAYGLITSM-------TMEPD-V  210 (410)
Q Consensus       142 -~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~--~~~~~~~li~~~~~~g~~~~A~~~~~~m-------~~~p~-~  210 (410)
                       ...+..+...+...|+.+.|...+....+...-.+  ....+..+...|...|++++|...+++.       +..|+ .
T Consensus       212 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~~~~~~~~  291 (366)
T d1hz4a_         212 ISNANKVRVIYWQMTGDKAAAANWLRHTAKPEFANNHFLQGQWRNIARAQILLGEFEPAEIVLEELNENARSLRLMSDLN  291 (366)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHSCCCCCTTCGGGHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHHHhcccHHHHHHHHHHHHHhccccchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccChHHH
Confidence             23455566778889999999999998764311111  1345666788999999999999988875       33443 3


Q ss_pred             HHHHHHHHHHHhcCchhHHHHH
Q 040371          211 VVWRALLSACRTFKRLELGEVA  232 (410)
Q Consensus       211 ~~~~~li~~~~~~g~~~~a~~~  232 (410)
                      .++..+-..+...|++++|...
T Consensus       292 ~~~~~la~~~~~~g~~~~A~~~  313 (366)
T d1hz4a_         292 RNLLLLNQLYWQAGRKSDAQRV  313 (366)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCHHHHHHH
Confidence            5677777889999999999998

>d1dcea1 a.118.6.1 (A:1-241,A:351-443) Rab geranylgeranyltransferase alpha-subunit, N-terminal domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Protein prenylyltransferase
family: Protein prenylyltransferase
domain: Rab geranylgeranyltransferase alpha-subunit, N-terminal domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.62  E-value=3.2e-08  Score=88.58  Aligned_cols=226  Identities=11%  Similarity=-0.003  Sum_probs=166.8

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC--CHHHHHHHHHHHHHcCCCccHHHHH-HHHHHHHhcCCHHH
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLG--ALNHAYWVHNLIIEKKIELNFILSA-ALIDMYSKCGKIQM   94 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~--~~~~a~~~~~~~~~~g~~~~~~~~~-~li~~y~~~g~~~~   94 (410)
                      ..|++++|+.+|++..+.. +-+...|.....++...+  +.+.+...+..+++.. +++...+. .+...+...|..++
T Consensus        85 ~~~~~~~al~~~~~~l~~~-pk~~~~~~~~~~~~~~~~~~~~~~a~~~~~~al~~~-~~~~~~~~~~~~~~~~~~~~~~~  162 (334)
T d1dcea1          85 SAALVKAELGFLESCLRVN-PKSYGTWHHRCWLLSRLPEPNWARELELCARFLEAD-ERNFHCWDYRRFVAAQAAVAPAE  162 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHTCSSCCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTCCCHHH
T ss_pred             HHHHHHHHHHHHHHHHHhC-CCcHHHHHHhhHHHHHhccccHHHHHHHHHHHHhhC-chhhhhhhhHHHHHHHhccccHH
Confidence            3455889999999998753 336667777777777766  4899999999999875 34555554 45577888999999


Q ss_pred             HHHHHHhcccC---ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhh
Q 040371           95 AKEVFDTVQRN---DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSR  171 (410)
Q Consensus        95 A~~~f~~m~~~---~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~  171 (410)
                      |...++...+.   +..+|+.+...+.+.|++++|...+++....  .|+..   .+...+...+..+++...+..... 
T Consensus       163 Al~~~~~~i~~~p~~~~a~~~l~~~~~~~~~~~~A~~~~~~~~~~--~~~~~---~~~~~~~~l~~~~~a~~~~~~~l~-  236 (334)
T d1dcea1         163 ELAFTDSLITRNFSNYSSWHYRSCLLPQLHPQPDSGPQGRLPENV--LLKEL---ELVQNAFFTDPNDQSAWFYHRWLL-  236 (334)
T ss_dssp             HHHHHHTTTTTTCCCHHHHHHHHHHHHHHSCCCCSSSCCSSCHHH--HHHHH---HHHHHHHHHCSSCSHHHHHHHHHH-
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHHHHHHhcCHHHHHHHHHHhHHh--HHHHH---HHHHHHHHhcchhHHHHHHHHHHH-
Confidence            99999988753   6678999999999999998887766554432  22222   233344556777778887777664 


Q ss_pred             cCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCC-CHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHH
Q 040371          172 YSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEP-DVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVL  246 (410)
Q Consensus       172 ~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p-~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~  246 (410)
                       .-+++...+..+...+...|+.++|...+.+. ...| +..+|..+...+...|+.++|...   +.+++|.+...|..
T Consensus       237 -~~~~~~~~~~~l~~~~~~~~~~~~a~~~~~~~~~~~p~~~~~~~~l~~~~~~~~~~~eA~~~~~~ai~ldP~~~~y~~~  315 (334)
T d1dcea1         237 -GRAEPLFRCELSVEKSTVLQSELESCKELQELEPENKWCLLTIILLMRALDPLLYEKETLQYFSTLKAVDPMRAAYLDD  315 (334)
T ss_dssp             -SCCCCSSSCCCCHHHHHHHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHCTGGGHHHHHHHHHHHHHHCGGGHHHHHH
T ss_pred             -hCcchhhHHHHHHHHHHHHhhHHHHHHHHHHHHhhCchHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCcccHHHHHH
Confidence             33445666777788888899999999988876 5556 456788888889999999999999   66777877666776


Q ss_pred             HHHHHH
Q 040371          247 LSNMYC  252 (410)
Q Consensus       247 l~~~~~  252 (410)
                      |...+.
T Consensus       316 L~~~~~  321 (334)
T d1dcea1         316 LRSKFL  321 (334)
T ss_dssp             HHHHHH
T ss_pred             HHHHHh
Confidence            665554

>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=98.54  E-value=3.8e-06  Score=68.27  Aligned_cols=126  Identities=12%  Similarity=0.011  Sum_probs=99.6

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYS   87 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~   87 (410)
                      .||- -..+...|++++|++.|.++    .+|+..+|..+..++...|+++.|.+.|++.++.. +.+...|..+..+|.
T Consensus         8 l~~~-g~~~~~~~d~~~Al~~~~~i----~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~   81 (192)
T d1hh8a_           8 LWNE-GVLAADKKDWKGALDAFSAV----QDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYY   81 (192)
T ss_dssp             HHHH-HHHHHHTTCHHHHHHHHHTS----SSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHH
T ss_pred             HHHH-HHHHHHCCCHHHHHHHHHhc----CCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHH
Confidence            4665 56678899999999999864    36788889999999999999999999999999876 557889999999999


Q ss_pred             hcCCHHHHHHHHHhccc---CC----------------hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCC
Q 040371           88 KCGKIQMAKEVFDTVQR---ND----------------VSVWNAMISGVAIHGLAADASAIFTKMEMFNVL  139 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~~---~~----------------~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~  139 (410)
                      +.|++++|.+.|++...   .+                ..++..+..+|.+.|++++|.+.|.+.......
T Consensus        82 ~~g~~~~A~~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A~~~~~~  152 (192)
T d1hh8a_          82 QTEKYDLAIKDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALATSMKSE  152 (192)
T ss_dssp             HTTCHHHHHHHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTCCS
T ss_pred             hhccHHHHHHHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC
Confidence            99999999998887531   10                134555667778888888888888877664333

>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=98.54  E-value=6.2e-06  Score=71.70  Aligned_cols=197  Identities=10%  Similarity=-0.010  Sum_probs=97.8

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHC----CCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHc----CC-CccHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSS----KVEPD-KFTFASVIYGCARLGALNHAYWVHNLIIEK----KI-ELNFI   77 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~----g~~pd-~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~-~~~~~   77 (410)
                      .|.-....|...|++++|++.|.+....    +-+|+ ..+|..+..++.+.|++++|.+.++...+.    |. .....
T Consensus        39 ~y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~  118 (290)
T d1qqea_          39 LCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGAN  118 (290)
T ss_dssp             HHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHH
Confidence            3556666666667777777776666431    11121 235666666666667777766666655442    11 11133


Q ss_pred             HHHHHHHHHHh-cCCHHHHHHHHHhccc-----CC----hhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCC-----H
Q 040371           78 LSAALIDMYSK-CGKIQMAKEVFDTVQR-----ND----VSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPD-----S  142 (410)
Q Consensus        78 ~~~~li~~y~~-~g~~~~A~~~f~~m~~-----~~----~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~-----~  142 (410)
                      ++..+...|-. .|++++|.+.|++..+     .+    ..+|..+...|...|++++|++.|++.........     .
T Consensus       119 ~~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~  198 (290)
T d1qqea_         119 FKFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSL  198 (290)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGH
T ss_pred             HHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhH
Confidence            44445555533 4666666666655431     11    22455566666666666666666666554321111     0


Q ss_pred             -HHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC---hhHHHHHHHHHHh--cCCHHHHHHHHHhC
Q 040371          143 -ITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ---LEHYGAMVDLLGR--AGHIEEAYGLITSM  204 (410)
Q Consensus       143 -~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~---~~~~~~li~~~~~--~g~~~~A~~~~~~m  204 (410)
                       ..+...+..+...|+++.|...|+...+...--++   ......++.++-.  .+.+++|+.-|+++
T Consensus       199 ~~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~  266 (290)
T d1qqea_         199 KDYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNF  266 (290)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence             11222333444556666666666665532100011   1123344444443  23456666666554

>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=98.50  E-value=6.3e-06  Score=66.94  Aligned_cols=121  Identities=10%  Similarity=-0.032  Sum_probs=86.2

Q ss_pred             HHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHH
Q 040371           83 IDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGR  162 (410)
Q Consensus        83 i~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~  162 (410)
                      ...+...|+++.|.+.|+++..++..+|..+...|...|++++|++.|++..+.. +-+...|..+..++.+.|++++|.
T Consensus        12 g~~~~~~~d~~~Al~~~~~i~~~~~~~~~nlG~~~~~~g~~~~A~~~~~kAl~ld-p~~~~a~~~~g~~~~~~g~~~~A~   90 (192)
T d1hh8a_          12 GVLAADKKDWKGALDAFSAVQDPHSRICFNIGCMYTILKNMTEAEKAFTRSINRD-KHLAVAYFQRGMLYYQTEKYDLAI   90 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHTSSSCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCchhHHHHHHHHHHHh-hhhhhhHHHHHHHHHhhccHHHHH
Confidence            4456778888888888888888888888888888888888888888888887743 224667777888888888888888


Q ss_pred             HHHHHhhhhc-----------CCCC--C-hhHHHHHHHHHHhcCCHHHHHHHHHhC
Q 040371          163 KYFDHMRSRY-----------SIQP--Q-LEHYGAMVDLLGRAGHIEEAYGLITSM  204 (410)
Q Consensus       163 ~~~~~m~~~~-----------~~~~--~-~~~~~~li~~~~~~g~~~~A~~~~~~m  204 (410)
                      ..|+......           |...  + ..++..+..+|.+.|++++|.+.+.+.
T Consensus        91 ~~~~kAl~~~~~n~~~~~~~~~~~~~~~~~e~~~n~a~~~~~~~~~~~A~~~l~~A  146 (192)
T d1hh8a_          91 KDLKEALIQLRGNQLIDYKILGLQFKLFACEVLYNIAFMYAKKEEWKKAEEQLALA  146 (192)
T ss_dssp             HHHHHHHHTTTTCSEEECGGGTBCCEEEHHHHHHHHHHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCccCchHHHHHhhhhcccchHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence            8888765310           1110  1 234455666677777777777776655

>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=98.48  E-value=9.6e-06  Score=70.44  Aligned_cols=197  Identities=10%  Similarity=-0.077  Sum_probs=124.9

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHc----CCCc-cHHHHHHHHHHHHhcCCHHHHHHHHHhccc-----CC----hhh
Q 040371           44 FASVIYGCARLGALNHAYWVHNLIIEK----KIEL-NFILSAALIDMYSKCGKIQMAKEVFDTVQR-----ND----VSV  109 (410)
Q Consensus        44 ~~~ll~a~~~~~~~~~a~~~~~~~~~~----g~~~-~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-----~~----~~~  109 (410)
                      |......|...+++++|.+.|.++.+.    +-++ -..+++.+..+|.+.|++++|.+.+++..+     .+    ..+
T Consensus        40 y~~aa~~y~~~~~~~~A~~~y~kA~~~~~~~~~~~~~a~~~~~~g~~y~~~~~~~~A~~~~~~a~~~~~~~~~~~~~~~~  119 (290)
T d1qqea_          40 CVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGGNSVNAVDSLENAIQIFTHRGQFRRGANF  119 (290)
T ss_dssp             HHHHHHHHHHTTCTHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCCcHHHHHHHHHhhHHhhhcccchhHHHH
Confidence            444566788888999999888887653    2222 245788888999999999999988886542     11    345


Q ss_pred             HHHHHHHHHH-cCChHHHHHHHHHHHHC----CCCCC-HHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCCh-----
Q 040371          110 WNAMISGVAI-HGLAADASAIFTKMEMF----NVLPD-SITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQL-----  178 (410)
Q Consensus       110 ~~~li~~~~~-~g~~~~A~~l~~~m~~~----g~~p~-~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~-----  178 (410)
                      +..+...|.. .|++++|++.|++..+.    +..+. ..++..+...+...|++++|..+|+.+.....-.+..     
T Consensus       120 ~~~l~~~~~~~~~~~~~A~~~~~~A~~l~~~~~~~~~~~~~~~~la~~~~~~g~y~~A~~~~~~~~~~~~~~~~~~~~~~  199 (290)
T d1qqea_         120 KFELGEILENDLHDYAKAIDCYELAGEWYAQDQSVALSNKCFIKCADLKALDGQYIEASDIYSKLIKSSMGNRLSQWSLK  199 (290)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTSSCTTTGGGHH
T ss_pred             HHHHHHhHhhHHHHHHHHHHHHHHHHHHHHhcCchhhhhhHHHHHHHHHHHcChHHHHHHHHHHHHHhCccchhhhhhHH
Confidence            6666666644 58999999999877542    22221 3456778888889999999999998877532111111     


Q ss_pred             hHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC------HHHHHHHHHHHHhc--CchhHHHHHHHhhccCC
Q 040371          179 EHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD------VVVWRALLSACRTF--KRLELGEVAIVNISRLM  240 (410)
Q Consensus       179 ~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~------~~~~~~li~~~~~~--g~~~~a~~~~~~~~~~~  240 (410)
                      ..+..++..+...|+++.|...+++. .+.|+      ......++.++...  +.+++|...+.+..+.+
T Consensus       200 ~~~~~~~~~~l~~~d~~~A~~~~~~~~~~~~~~~~sre~~~l~~l~~a~~~~d~e~~~eai~~y~~~~~lD  270 (290)
T d1qqea_         200 DYFLKKGLCQLAATDAVAAARTLQEGQSEDPNFADSRESNFLKSLIDAVNEGDSEQLSEHCKEFDNFMRLD  270 (290)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHGGGCC---------HHHHHHHHHHHHTTCTTTHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHHHHHhccHHHHHHHHHHHHHhCCCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhcC
Confidence            22345555677788999999888887 33332      22345555555432  23444444443333333

>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=98.20  E-value=1.3e-05  Score=59.12  Aligned_cols=88  Identities=13%  Similarity=0.080  Sum_probs=41.7

Q ss_pred             HHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHH
Q 040371           14 GGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQ   93 (410)
Q Consensus        14 ~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~   93 (410)
                      ..+.+.|++++|+..|.+.++.. +-+...|..+..++...|+++.|...+...++.+ +.+...|..+..+|...|+++
T Consensus        11 ~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~-p~~~~~~~~~g~~~~~~~~~~   88 (117)
T d1elwa_          11 NKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLK-PDWGKGYSRKAAALEFLNRFE   88 (117)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhc-cchhhHHHHHHHHHHHccCHH
Confidence            34445555555555555554431 2233444444555555555555555555554443 234444444444444444444


Q ss_pred             HHHHHHHhcc
Q 040371           94 MAKEVFDTVQ  103 (410)
Q Consensus        94 ~A~~~f~~m~  103 (410)
                      +|...|++..
T Consensus        89 ~A~~~~~~a~   98 (117)
T d1elwa_          89 EAKRTYEEGL   98 (117)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            4444444443

>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=98.17  E-value=3.5e-05  Score=56.78  Aligned_cols=87  Identities=14%  Similarity=0.032  Sum_probs=48.7

Q ss_pred             HHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChH
Q 040371           48 IYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAA  124 (410)
Q Consensus        48 l~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~  124 (410)
                      ...+...|++++|...|...++.. +.+...|..+..+|.+.|++++|...|++..+   .+...|..+..+|...|+++
T Consensus        10 g~~~~~~g~~~eAi~~~~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~~~p~~~~~~~~~g~~~~~~~~~~   88 (117)
T d1elwa_          10 GNKALSVGNIDDALQCYSEAIKLD-PHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFE   88 (117)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcC-CcchhhhhcccccccccccccccchhhhhHHHhccchhhHHHHHHHHHHHccCHH
Confidence            344555566666666666665553 33455555555666666666666665554432   24455555555555566666


Q ss_pred             HHHHHHHHHHH
Q 040371          125 DASAIFTKMEM  135 (410)
Q Consensus       125 ~A~~l~~~m~~  135 (410)
                      +|+..|++..+
T Consensus        89 ~A~~~~~~a~~   99 (117)
T d1elwa_          89 EAKRTYEEGLK   99 (117)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHH
Confidence            66666655554

>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=98.16  E-value=2.1e-05  Score=63.83  Aligned_cols=95  Identities=11%  Similarity=-0.114  Sum_probs=46.6

Q ss_pred             CCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc--C-ChhhHHHHHH
Q 040371           39 PDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR--N-DVSVWNAMIS  115 (410)
Q Consensus        39 pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~  115 (410)
                      |+...+....+.+.+.|+++.|...|..+++.. +.+...|+.+..+|.+.|++++|...|++..+  | ++.+|..+..
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~p~~~~a~~~lg~   80 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELDGQSVKAHFFLGQ   80 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSCTTCHHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhCCCcHHHHHHHHH
Confidence            334444444444555555555555555544443 33444555555555555555555555554432  2 3344555555


Q ss_pred             HHHHcCChHHHHHHHHHHH
Q 040371          116 GVAIHGLAADASAIFTKME  134 (410)
Q Consensus       116 ~~~~~g~~~~A~~l~~~m~  134 (410)
                      +|.+.|++++|+..|++..
T Consensus        81 ~~~~l~~~~~A~~~~~~al   99 (201)
T d2c2la1          81 CQLEMESYDEAIANLQRAY   99 (201)
T ss_dssp             HHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHHHH
Confidence            5555555555555555443

>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=98.16  E-value=1.4e-05  Score=64.89  Aligned_cols=98  Identities=6%  Similarity=-0.038  Sum_probs=86.7

Q ss_pred             CChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHH
Q 040371            4 KDVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALI   83 (410)
Q Consensus         4 ~~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li   83 (410)
                      |++......-..|.+.|++++|+..|.+.+... +-+...|..+..++.+.|+++.|...+..+++.. +-+...|..+.
T Consensus         2 ~~a~~l~~~Gn~~~~~g~~~~Ai~~~~kal~~~-p~~~~~~~~lg~~y~~~~~~~~Ai~~~~~al~l~-p~~~~a~~~lg   79 (201)
T d2c2la1           2 PSAQELKEQGNRLFVGRKYPEAAACYGRAITRN-PLVAVYYTNRALCYLKMQQPEQALADCRRALELD-GQSVKAHFFLG   79 (201)
T ss_dssp             CCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-SCCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTSC-TTCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhC-CCCHHHHHhHHHHHhhhhhhhhhhHHHHHHHHhC-CCcHHHHHHHH
Confidence            677777788899999999999999999988753 4577889999999999999999999999998764 34688899999


Q ss_pred             HHHHhcCCHHHHHHHHHhcc
Q 040371           84 DMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~  103 (410)
                      .+|.+.|++++|...|++..
T Consensus        80 ~~~~~l~~~~~A~~~~~~al   99 (201)
T d2c2la1          80 QCQLEMESYDEAIANLQRAY   99 (201)
T ss_dssp             HHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHCCCHHHHHHHHHHHH
Confidence            99999999999999998764

>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=98.10  E-value=4.5e-05  Score=59.51  Aligned_cols=85  Identities=11%  Similarity=-0.068  Sum_probs=43.1

Q ss_pred             HHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHH
Q 040371           50 GCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADA  126 (410)
Q Consensus        50 a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A  126 (410)
                      .+.+.|+++.|...|..+++.. +.+...|..+..+|.+.|++++|...|++..+   .+..+|..+..+|...|++++|
T Consensus        19 ~~~~~~~y~~A~~~~~~al~~~-p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~p~~~~a~~~~g~~~~~~g~~~eA   97 (159)
T d1a17a_          19 DYFKAKDYENAIKFYSQAIELN-PSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFRAA   97 (159)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHH
T ss_pred             HHHHcCCHHHHHHHhhhccccc-hhhhhhhhhhHHHHHhccccchHHHHHHHHHHHcccchHHHHHHHHHHHHcCCHHHH
Confidence            4445555555555555555443 33445555555555555555555555554432   2334555555555555555555


Q ss_pred             HHHHHHHHH
Q 040371          127 SAIFTKMEM  135 (410)
Q Consensus       127 ~~l~~~m~~  135 (410)
                      +..|++...
T Consensus        98 ~~~~~~a~~  106 (159)
T d1a17a_          98 LRDYETVVK  106 (159)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555555544

>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=98.08  E-value=1.4e-05  Score=58.59  Aligned_cols=88  Identities=14%  Similarity=-0.033  Sum_probs=53.6

Q ss_pred             HHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCC
Q 040371           12 MIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGK   91 (410)
Q Consensus        12 li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~   91 (410)
                      +...+.+.|++++|+..|++..... +-+...|..+..++.+.+++++|...+++.++.. +.+..++..|...|...|+
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~-p~~~~a~~~la~~y~~~g~   99 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLD-PKDIAVHAALAVSHTNEHN   99 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccc-cccccchHHHHHHHHHCCC
Confidence            4455566666666666666666532 2245566666666666666666666666666653 3345666666666666666


Q ss_pred             HHHHHHHHHh
Q 040371           92 IQMAKEVFDT  101 (410)
Q Consensus        92 ~~~A~~~f~~  101 (410)
                      +++|.+.|++
T Consensus       100 ~~~A~~~l~~  109 (112)
T d1hxia_         100 ANAALASLRA  109 (112)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            6666666654

>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=98.03  E-value=4e-05  Score=56.89  Aligned_cols=96  Identities=5%  Similarity=-0.145  Sum_probs=62.7

Q ss_pred             HHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCH---HHHHHHHHhcccCC-----hhhHHHHHHH
Q 040371           45 ASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKI---QMAKEVFDTVQRND-----VSVWNAMISG  116 (410)
Q Consensus        45 ~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~---~~A~~~f~~m~~~~-----~~~~~~li~~  116 (410)
                      ..+++.+...+++++|++.|+..++.+ +.++.+...+..++.+.++.   ++|+++|++....+     ..+|..+..+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            356666677777777777777777765 44666777777777665543   35777777765422     2256666777


Q ss_pred             HHHcCChHHHHHHHHHHHHCCCCCCHH
Q 040371          117 VAIHGLAADASAIFTKMEMFNVLPDSI  143 (410)
Q Consensus       117 ~~~~g~~~~A~~l~~~m~~~g~~p~~~  143 (410)
                      |.+.|++++|++.|++..+  +.|+..
T Consensus        82 y~~~g~~~~A~~~~~~aL~--~~P~~~  106 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQ--TEPQNN  106 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHH--HCTTCH
T ss_pred             HHHHhhhHHHHHHHHHHHH--hCcCCH
Confidence            7777777777777777776  345543

>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=98.00  E-value=9.8e-05  Score=57.48  Aligned_cols=86  Identities=7%  Similarity=-0.017  Sum_probs=45.5

Q ss_pred             HHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHH
Q 040371           84 DMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEE  160 (410)
Q Consensus        84 ~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~  160 (410)
                      +.|.+.|++++|...|++..+   .+...|..+...|...|++++|+..|++..+.. +-+...|..+..++...|++++
T Consensus        18 n~~~~~~~y~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~~~~~~A~~~~~kal~~~-p~~~~a~~~~g~~~~~~g~~~e   96 (159)
T d1a17a_          18 NDYFKAKDYENAIKFYSQAIELNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELD-KKYIKGYYRRAASNMALGKFRA   96 (159)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHH
T ss_pred             HHHHHcCCHHHHHHHhhhccccchhhhhhhhhhHHHHHhccccchHHHHHHHHHHHc-ccchHHHHHHHHHHHHcCCHHH
Confidence            345555555555555555432   244455555555555555555555555555431 1133455555555555555555


Q ss_pred             HHHHHHHhhh
Q 040371          161 GRKYFDHMRS  170 (410)
Q Consensus       161 a~~~~~~m~~  170 (410)
                      |...++...+
T Consensus        97 A~~~~~~a~~  106 (159)
T d1a17a_          97 ALRDYETVVK  106 (159)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5555555553

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=97.91  E-value=0.0032  Score=52.79  Aligned_cols=93  Identities=11%  Similarity=0.008  Sum_probs=53.9

Q ss_pred             ChhHHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHh----hCCHHHHHHHHHHHHHcCCCccHHHHH
Q 040371            5 DVVSWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCAR----LGALNHAYWVHNLIIEKKIELNFILSA   80 (410)
Q Consensus         5 ~~~~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~----~~~~~~a~~~~~~~~~~g~~~~~~~~~   80 (410)
                      |+..|..|-..+.+.+++++|++.|++..+.|   |...+..|-..+..    ..+...+...+....+.+   +.....
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~---~~~a~~   74 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLN---YSNGCH   74 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT---CHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhccccccc---ccchhh
Confidence            34456666667777778888888887777665   44445455555544    446677777777666655   233333


Q ss_pred             HHHHHHHh----cCCHHHHHHHHHhcc
Q 040371           81 ALIDMYSK----CGKIQMAKEVFDTVQ  103 (410)
Q Consensus        81 ~li~~y~~----~g~~~~A~~~f~~m~  103 (410)
                      .|...+..    ..+.+.|...|+...
T Consensus        75 ~l~~~~~~~~~~~~~~~~a~~~~~~a~  101 (265)
T d1ouva_          75 LLGNLYYSGQGVSQNTNKALQYYSKAC  101 (265)
T ss_dssp             HHHHHHHHTSSSCCCHHHHHHHHHHHH
T ss_pred             ccccccccccccchhhHHHHHHHhhhh
Confidence            44444332    234555655555443

>d1hxia_ a.118.8.1 (A:) Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor) {Trypanosoma brucei [TaxId: 5691]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
species: Trypanosoma brucei [TaxId: 5691]

Probab=97.87  E-value=8.4e-05  Score=54.13  Aligned_cols=86  Identities=15%  Similarity=0.014  Sum_probs=61.6

Q ss_pred             HHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCCh
Q 040371           47 VIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLA  123 (410)
Q Consensus        47 ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~  123 (410)
                      ....+.+.|++++|...++..++.. +-+...|..+..+|.+.|++++|+..|++..+   .+..+|..+...|...|+.
T Consensus        22 ~g~~~~~~g~~~~A~~~~~~al~~~-p~~~~a~~~lg~~~~~~~~~~~A~~~~~~al~~~p~~~~a~~~la~~y~~~g~~  100 (112)
T d1hxia_          22 EGLSMLKLANLAEAALAFEAVCQKE-PEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNA  100 (112)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhHHHHHHHhhhcccc-cccchhhhhhhhhhhhhhhHHHhhcccccccccccccccchHHHHHHHHHCCCH
Confidence            4455667778888888887777764 33577777777777777778777777776542   2456777777777777777


Q ss_pred             HHHHHHHHHH
Q 040371          124 ADASAIFTKM  133 (410)
Q Consensus       124 ~~A~~l~~~m  133 (410)
                      ++|++.|++.
T Consensus       101 ~~A~~~l~~~  110 (112)
T d1hxia_         101 NAALASLRAW  110 (112)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            7777777764

>d1nzna_ a.118.8.1 (A:) Mitochondria fission protein Fis1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondria fission protein Fis1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.80  E-value=3.5e-05  Score=57.20  Aligned_cols=94  Identities=9%  Similarity=-0.025  Sum_probs=77.8

Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhC---CHHHHHHHHHHHHHcCCCcc-HHHHHHHHHH
Q 040371           10 NSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLG---ALNHAYWVHNLIIEKKIELN-FILSAALIDM   85 (410)
Q Consensus        10 n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~---~~~~a~~~~~~~~~~g~~~~-~~~~~~li~~   85 (410)
                      ..+++.+...+++++|.+.|++.+..+ +.+..++..+..++.+.+   ++++|..+++.+++.+..|+ ..++..|..+
T Consensus         3 ~~l~n~~~~~~~l~~Ae~~Y~~aL~~~-p~~~~~~~n~a~~L~~s~~~~d~~~Ai~~l~~~l~~~~~~~~~~~~~~Lg~~   81 (122)
T d1nzna_           3 EAVLNELVSVEDLLKFEKKFQSEKAAG-SVSKSTQFEYAWCLVRTRYNDDIRKGIVLLEELLPKGSKEEQRDYVFYLAVG   81 (122)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHS-CCCHHHHHHHHHHHTTSSSHHHHHHHHHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHHHhhC-CCCHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence            467888999999999999999999864 557788888888887655   45679999999988654444 3478889999


Q ss_pred             HHhcCCHHHHHHHHHhccc
Q 040371           86 YSKCGKIQMAKEVFDTVQR  104 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~  104 (410)
                      |.+.|++++|++.|++..+
T Consensus        82 y~~~g~~~~A~~~~~~aL~  100 (122)
T d1nzna_          82 NYRLKEYEKALKYVRGLLQ  100 (122)
T ss_dssp             HHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHhhhHHHHHHHHHHHH
Confidence            9999999999999998864

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.63  E-value=0.0013  Score=51.57  Aligned_cols=106  Identities=13%  Similarity=0.004  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSK-VEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMY   86 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g-~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y   86 (410)
                      .++..-..|.+.|++++|+..|.+.+..- ..+..              ..+.......        .-..+++.+..+|
T Consensus        15 ~l~~~G~~~~~~~~~~~Ai~~y~~al~~~~~~~~~--------------~~~~~~~~~~--------~~~~~~~nla~~y   72 (170)
T d1p5qa1          15 IVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSF--------------SNEEAQKAQA--------LRLASHLNLAMCH   72 (170)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHHHHHTTTCCCC--------------CSHHHHHHHH--------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHhhhcccc--------------chHHHhhhch--------hHHHHHHHHHHHH
Confidence            45555667888899999999998876521 01100              0000000000        0123466677777


Q ss_pred             HhcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHH
Q 040371           87 SKCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus        87 ~~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      .+.|++++|...++....  | ++.+|..+..+|...|++++|+..|++..+
T Consensus        73 ~k~~~~~~A~~~~~~al~~~p~~~~a~~~~g~~~~~~g~~~~A~~~~~~al~  124 (170)
T d1p5qa1          73 LKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQ  124 (170)
T ss_dssp             HHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HhhhhcccccchhhhhhhccccchhhhHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence            788888888887776552  3 566777777788888888888888887776

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.60  E-value=0.00041  Score=51.63  Aligned_cols=60  Identities=13%  Similarity=0.086  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIE   69 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~   69 (410)
                      +..+-..|.+.|++++|+..|.+.++.+ +.+...|..+..++...|+++.|.+.+.++++
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~   66 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIE   66 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHH
Confidence            3444455555566666666665555432 22444555555555555555555555555543

>d1elra_ a.118.8.1 (A:) Hop {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Hop
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.59  E-value=0.00054  Score=50.93  Aligned_cols=91  Identities=10%  Similarity=0.034  Sum_probs=64.5

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc---CCh-------hhHHHH
Q 040371           44 FASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR---NDV-------SVWNAM  113 (410)
Q Consensus        44 ~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~---~~~-------~~~~~l  113 (410)
                      +-.+...+...|++++|...|...++.+ +.+..++..+..+|.+.|++++|...|++..+   .+.       .+|..+
T Consensus         7 ~k~~G~~~~~~~~y~~Ai~~y~~al~~~-p~~~~~~~~~a~~~~~~~~~~~A~~~~~~al~l~~~~~~~~~~~a~~~~~l   85 (128)
T d1elra_           7 EKELGNDAYKKKDFDTALKHYDKAKELD-PTNMTYITNQAAVYFEKGDYNKCRELCEKAIEVGRENREDYRQIAKAYARI   85 (128)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHHSTTCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHhC-cccHHHHHhHHHHHHHcCchHHHHHHHHHHHHhCcccHHHHHHHHHHHHHH
Confidence            4455667778888888888888888775 44677788888888888888888888877653   121       245556


Q ss_pred             HHHHHHcCChHHHHHHHHHHHH
Q 040371          114 ISGVAIHGLAADASAIFTKMEM  135 (410)
Q Consensus       114 i~~~~~~g~~~~A~~l~~~m~~  135 (410)
                      ...+...+++++|++.|++...
T Consensus        86 g~~~~~~~~~~~A~~~~~kal~  107 (128)
T d1elra_          86 GNSYFKEEKYKDAIHFYNKSLA  107 (128)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHHHh
Confidence            6666667777777777776654

>d1p5qa1 a.118.8.1 (A:258-427) FKBP52 (FKBP4), C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP52 (FKBP4), C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.56  E-value=0.00067  Score=53.21  Aligned_cols=29  Identities=10%  Similarity=0.013  Sum_probs=22.0

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHHHHC
Q 040371          108 SVWNAMISGVAIHGLAADASAIFTKMEMF  136 (410)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~  136 (410)
                      ..+......+.+.|++++|+..|.+....
T Consensus        14 ~~l~~~G~~~~~~~~~~~Ai~~y~~al~~   42 (170)
T d1p5qa1          14 TIVKERGTVYFKEGKYKQALLQYKKIVSW   42 (170)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence            34555667788889999999999887653

>d1b89a_ a.118.1.3 (A:) Clathrin heavy chain proximal leg segment {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: ARM repeat
family: Clathrin heavy chain proximal leg segment
domain: Clathrin heavy chain proximal leg segment
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.49  E-value=0.025  Score=49.05  Aligned_cols=236  Identities=12%  Similarity=-0.013  Sum_probs=117.5

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK   88 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~   88 (410)
                      -..+..-|.+.|.++.|..+|..+.         -|..++..+.+.+++..|.++....   +   +..+|..+...+.+
T Consensus        17 ~~~i~~~c~~~~lye~A~~lY~~~~---------d~~rl~~~~v~l~~~~~avd~~~k~---~---~~~~~k~~~~~l~~   81 (336)
T d1b89a_          17 IQQVGDRCYDEKMYDAAKLLYNNVS---------NFGRLASTLVHLGEYQAAVDGARKA---N---STRTWKEVCFACVD   81 (336)
T ss_dssp             ------------CTTTHHHHHHHTT---------CHHHHHHHHHTTTCHHHHHHHHHHH---T---CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHhCC---------CHHHHHHHHHhhccHHHHHHHHHHc---C---CHHHHHHHHHHHHh
Confidence            3445556667777777777776542         2556667777777777766554422   2   45577777777776


Q ss_pred             cCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHh
Q 040371           89 CGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHM  168 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m  168 (410)
                      ......|.-+ ......+...-..++..|-..|.+++...+++..... -.++...++-++..|++.+ .++-.+.+...
T Consensus        82 ~~e~~la~i~-~~~~~~~~d~l~~~v~~ye~~~~~e~Li~~Le~~~~~-~~~~~~~~~~L~~lyak~~-~~kl~e~l~~~  158 (336)
T d1b89a_          82 GKEFRLAQMC-GLHIVVHADELEELINYYQDRGYFEELITMLEAALGL-ERAHMGMFTELAILYSKFK-PQKMREHLELF  158 (336)
T ss_dssp             TTCHHHHHHT-TTTTTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHTTS-TTCCHHHHHHHHHHHHTTC-HHHHHHHHHHH
T ss_pred             CcHHHHHHHH-HHHhhcCHHHHHHHHHHHHHcCChHHHHHHHHHHHcC-CccchHHHHHHHHHHHHhC-hHHHHHHHHhc
Confidence            6665544221 1111223334456777777778888877777765432 2445556677777777654 34444444333


Q ss_pred             hhhcCCC------CChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHHHHhhccCCCc
Q 040371          169 RSRYSIQ------PQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRLELGEVAIVNISRLMGG  242 (410)
Q Consensus       169 ~~~~~~~------~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~~~~~~~~~~~  242 (410)
                      ...+.++      .....|.-++-.|.+.|++++|..+.-.-+  ++..-....+..+.+..+.+..-+++.-.-...|.
T Consensus       159 s~~y~~~k~~~~c~~~~l~~elv~Ly~~~~~~~~A~~~~i~~~--~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~~~p~  236 (336)
T d1b89a_         159 WSRVNIPKVLRAAEQAHLWAELVFLYDKYEEYDNAIITMMNHP--TDAWKEGQFKDIITKVANVELYYRAIQFYLEFKPL  236 (336)
T ss_dssp             STTSCHHHHHHHHHTTTCHHHHHHHHHHTTCHHHHHHHHHHST--TTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHHCGG
T ss_pred             cccCCHHHHHHHHHHcCChHHHHHHHHhcCCHHHHHHHHHHcc--hhhhhHHHHHHHHHccCChHHHHHHHHHHHHcCHH
Confidence            2111110      011234556666666666666655433321  22222344555566677776666651111111233


Q ss_pred             hHHHHHHHHHhcCChhHHHHHH
Q 040371          243 DYVLLSNMYCYLKRWDTAENVR  264 (410)
Q Consensus       243 ~~~~l~~~~~~~g~~~~a~~~~  264 (410)
                      ....|+......-+..+..+.+
T Consensus       237 ~i~~lL~~v~~~~d~~r~V~~~  258 (336)
T d1b89a_         237 LLNDLLMVLSPRLDHTRAVNYF  258 (336)
T ss_dssp             GHHHHHHHHGGGCCHHHHHHHH
T ss_pred             HHHHHHHHhccCCCHHHHHHHH
Confidence            3444554444444444444433

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.46  E-value=0.0039  Score=47.61  Aligned_cols=112  Identities=15%  Similarity=0.168  Sum_probs=77.0

Q ss_pred             hHHHHHHHHHHHcCCHhHHHHHHHHHHHCC----CCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 040371            7 VSWNSMIGGFVRNARFDEALRFFREMLSSK----VEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAAL   82 (410)
Q Consensus         7 ~~~n~li~~~~~~g~~~~a~~l~~~m~~~g----~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l   82 (410)
                      .++..-...+.+.|++.+|+..|.+.+..-    ..++......                    ..    .....+++.+
T Consensus        18 ~~~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~~~--------------------~~----~~~~~~~~Nl   73 (153)
T d2fbna1          18 FDIKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILLDK--------------------KK----NIEISCNLNL   73 (153)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHHHH--------------------HH----HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHHHh--------------------hh----hHHHHHHhhH
Confidence            456667788889999999999999887531    0111111100                    00    0123467778


Q ss_pred             HHHHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHH
Q 040371           83 IDMYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSIT  144 (410)
Q Consensus        83 i~~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t  144 (410)
                      ..+|.+.|++++|.+.+++..+   .++.+|..+..+|...|++++|+..|++..+.  .|+...
T Consensus        74 a~~~~~l~~~~~Al~~~~~al~~~p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l--~P~n~~  136 (153)
T d2fbna1          74 ATCYNKNKDYPKAIDHASKVLKIDKNNVKALYKLGVANMYFGFLEEAKENLYKAASL--NPNNLD  136 (153)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH--STTCHH
T ss_pred             HHHHHHhcccchhhhhhhccccccchhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh--CCCCHH
Confidence            8888888888888888887652   36678888888888889999999888888773  454433

>d2fbna1 a.118.8.1 (A:22-174) Putative 70 kda peptidylprolyl isomerase PFL2275c {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Putative 70 kda peptidylprolyl isomerase PFL2275c
species: Plasmodium falciparum [TaxId: 5833]

Probab=97.46  E-value=0.0024  Score=48.85  Aligned_cols=119  Identities=14%  Similarity=0.033  Sum_probs=81.0

Q ss_pred             HHHHHHHHHhhCCHHHHHHHHHHHHHcCCC----ccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHH
Q 040371           44 FASVIYGCARLGALNHAYWVHNLIIEKKIE----LNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAI  119 (410)
Q Consensus        44 ~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~----~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~  119 (410)
                      +..-...+.+.|++..|...|..+++.-..    ++....                    .......+.+|+.+..+|.+
T Consensus        20 ~~~~G~~~f~~~~y~~A~~~Y~~al~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~Nla~~~~~   79 (153)
T d2fbna1          20 IKEEGNEFFKKNEINEAIVKYKEALDFFIHTEEWDDQILL--------------------DKKKNIEISCNLNLATCYNK   79 (153)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHTTTTCTTCCCHHHH--------------------HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHhhCcchhhhhhHHHH--------------------HhhhhHHHHHHhhHHHHHHH
Confidence            344445666777777777777776653110    011100                    01111123577889999999


Q ss_pred             cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCC-hhHHHHHHH
Q 040371          120 HGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQ-LEHYGAMVD  186 (410)
Q Consensus       120 ~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~-~~~~~~li~  186 (410)
                      .|++++|++.+++..... +.+..+|..+..++...|++++|...|+...+-   .|+ ......+-.
T Consensus        80 l~~~~~Al~~~~~al~~~-p~~~ka~~~~g~~~~~lg~~~~A~~~~~~al~l---~P~n~~~~~~l~~  143 (153)
T d2fbna1          80 NKDYPKAIDHASKVLKID-KNNVKALYKLGVANMYFGFLEEAKENLYKAASL---NPNNLDIRNSYEL  143 (153)
T ss_dssp             TTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH---STTCHHHHHHHHH
T ss_pred             hcccchhhhhhhcccccc-chhhhhhHHhHHHHHHcCCHHHHHHHHHHHHHh---CCCCHHHHHHHHH
Confidence            999999999999998753 336789999999999999999999999998853   454 444444433

>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=97.42  E-value=0.00089  Score=52.97  Aligned_cols=74  Identities=14%  Similarity=0.086  Sum_probs=52.1

Q ss_pred             ChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhh----hcCCCCChhH
Q 040371          106 DVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRS----RYSIQPQLEH  180 (410)
Q Consensus       106 ~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~----~~~~~~~~~~  180 (410)
                      .+..+..+...+...|++++|+..++++.... +-+...+..++.++...|+.++|.+.|+.+.+    ..|+.|+..+
T Consensus        66 ~~~a~~~la~~~~~~g~~~~Al~~~~~al~~~-P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          66 KVLAHTAKAEAEIACGRASAVIAELEALTFEH-PYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHS-TTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HHHHHHHHHHHHHHCCCchHHHHHHHHHHHhC-CccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            34566777777778888888888888777642 23667777788888888888888887777643    3577776544

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.35  E-value=0.0018  Score=50.48  Aligned_cols=61  Identities=3%  Similarity=-0.166  Sum_probs=33.0

Q ss_pred             hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          108 SVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       108 ~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      ..|+.+..+|.+.|++++|+..|.+..+.. +.+..+|..+..++.+.|++++|...|+...
T Consensus        78 ~~~~nla~~~~~~~~~~~Ai~~~~~al~~~-p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al  138 (169)
T d1ihga1          78 SCVLNIGACKLKMSDWQGAVDSCLEALEID-PSNTKALYRRAQGWQGLKEYDQALADLKKAQ  138 (169)
T ss_dssp             HHHHHHHHHHHHTTCHHHHHHHHHHHHTTC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcccchhhhhhhhhhhhh-hhhhhHHHhHHHHHHHccCHHHHHHHHHHHH
Confidence            344555555555566666666665555432 1234455555555555666666666555555

>d1ihga1 a.118.8.1 (A:197-365) Cyclophilin 40 {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Cyclophilin 40
species: Cow (Bos taurus) [TaxId: 9913]

Probab=97.24  E-value=0.0023  Score=49.78  Aligned_cols=123  Identities=12%  Similarity=0.046  Sum_probs=80.8

Q ss_pred             HHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh
Q 040371            9 WNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK   88 (410)
Q Consensus         9 ~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~   88 (410)
                      +......+.+.|++++|+..|.+.++.            +..............+        -+.+...++.+..+|.+
T Consensus        30 ~~~~~~~~~~~~~y~~Ai~~y~~al~~------------~~~~~~~~~~~~~~~~--------~~~~~~~~~nla~~~~~   89 (169)
T d1ihga1          30 LKNIGNTFFKSQNWEMAIKKYTKVLRY------------VEGSRAAAEDADGAKL--------QPVALSCVLNIGACKLK   89 (169)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHHHHHHH------------HHHHHHHSCHHHHGGG--------HHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHHHHHh------------hhhhhhhhhhHHHHHh--------ChhhHHHHHHHHHHHHh
Confidence            445566677888899898888876531            0001111111111100        02245677788889999


Q ss_pred             cCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHH
Q 040371           89 CGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACS  153 (410)
Q Consensus        89 ~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~  153 (410)
                      .|++++|+..|++..+   .++.+|..+..+|...|++++|++.|++..+.  .| |......+.....
T Consensus        90 ~~~~~~Ai~~~~~al~~~p~~~~a~~~~g~~~~~l~~~~~A~~~~~~al~l--~p~n~~~~~~l~~~~~  156 (169)
T d1ihga1          90 MSDWQGAVDSCLEALEIDPSNTKALYRRAQGWQGLKEYDQALADLKKAQEI--APEDKAIQAELLKVKQ  156 (169)
T ss_dssp             TTCHHHHHHHHHHHHTTCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTCHHHHHHHHHHHH
T ss_pred             hcccchhhhhhhhhhhhhhhhhhHHHhHHHHHHHccCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHH
Confidence            9999999999988764   36678999999999999999999999988874  44 4444444444433

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.17  E-value=0.0045  Score=48.10  Aligned_cols=60  Identities=8%  Similarity=-0.080  Sum_probs=33.3

Q ss_pred             hHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhh
Q 040371          109 VWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMR  169 (410)
Q Consensus       109 ~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~  169 (410)
                      .|+.+..+|.+.|++++|+..+++..... +.+...|..+..++...|++++|...|+.+.
T Consensus        66 ~~~Nla~~~~~l~~~~~Ai~~~~~al~l~-p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al  125 (168)
T d1kt1a1          66 AFLNLAMCYLKLREYTKAVECCDKALGLD-SANEKGLYRRGEAQLLMNEFESAKGDFEKVL  125 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHhHHHHHHHhhhcccchhhhhhhhhcc-cchHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence            34445555556666666666666555432 2244555555556666666666666666655

>d1kt1a1 a.118.8.1 (A:254-421) FKBP51, C-terminal domain {Monkey (Saimiri boliviensis) [TaxId: 27679]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: FKBP51, C-terminal domain
species: Monkey (Saimiri boliviensis) [TaxId: 27679]

Probab=97.15  E-value=0.019  Score=44.24  Aligned_cols=137  Identities=12%  Similarity=0.041  Sum_probs=81.3

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHC---CCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSS---KVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALID   84 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~---g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~   84 (410)
                      .+.-....+.+.|++.+|+..|.+.+..   ...++..                ..... .       .....+++.+..
T Consensus        17 ~~~e~G~~~~~~~~~~~A~~~Y~~al~~~~~~~~~~~~----------------~~~~~-~-------~~~~~~~~Nla~   72 (168)
T d1kt1a1          17 IVKEKGTVYFKGGKYVQAVIQYGKIVSWLEMEYGLSEK----------------ESKAS-E-------SFLLAAFLNLAM   72 (168)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTCCSCCHH----------------HHHHH-H-------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhccchh----------------hhhhc-c-------hhHHHHHHhHHH
Confidence            4455566777788888888888765531   1111110                00000 0       001335666777


Q ss_pred             HHHhcCCHHHHHHHHHhccc---CChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHHccCCH-H
Q 040371           85 MYSKCGKIQMAKEVFDTVQR---NDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS-ITFLGLLTACSHCGLV-E  159 (410)
Q Consensus        85 ~y~~~g~~~~A~~~f~~m~~---~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~-~t~~~ll~a~~~~g~~-~  159 (410)
                      +|.+.|++++|...++....   .+..+|..+..+|...|++++|+..|++....  .|+. .....+-......+.. +
T Consensus        73 ~~~~l~~~~~Ai~~~~~al~l~p~~~~a~~~~~~~~~~l~~~~~A~~~~~~al~l--~P~n~~~~~~l~~~~~~~~~~~e  150 (168)
T d1kt1a1          73 CYLKLREYTKAVECCDKALGLDSANEKGLYRRGEAQLLMNEFESAKGDFEKVLEV--NPQNKAARLQIFMCQKKAKEHNE  150 (168)
T ss_dssp             HHHHTTCHHHHHHHHHHHHHHCTTCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHS--CTTCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhhcccchhhhhhhhhcccchHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh--CCCCHHHHHHHHHHHHHHHhHHH
Confidence            88888888888888887653   36678888888888888999999988888774  4543 3333333333333333 2


Q ss_pred             HHHHHHHHhhh
Q 040371          160 EGRKYFDHMRS  170 (410)
Q Consensus       160 ~a~~~~~~m~~  170 (410)
                      ...++|..|-+
T Consensus       151 ~~kk~~~~~f~  161 (168)
T d1kt1a1         151 RDRRTYANMFK  161 (168)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            34455555443

>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=97.07  E-value=0.0054  Score=48.20  Aligned_cols=119  Identities=13%  Similarity=0.159  Sum_probs=83.8

Q ss_pred             HHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCC-H-HHHHHHHHHHHHcCCCccHHHHHHHHHHHH
Q 040371           10 NSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGA-L-NHAYWVHNLIIEKKIELNFILSAALIDMYS   87 (410)
Q Consensus        10 n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~-~-~~a~~~~~~~~~~g~~~~~~~~~~li~~y~   87 (410)
                      ..........|++++|.+.|.+.+..  -+..+.     ..+ ..+. . .....+-.        .....+..+...+.
T Consensus        15 ~~~g~~~~~~g~~e~A~~~~~~AL~l--~rG~~l-----~~~-~~~~w~~~~r~~l~~--------~~~~a~~~la~~~~   78 (179)
T d2ff4a2          15 KTAGVHAAAAGRFEQASRHLSAALRE--WRGPVL-----DDL-RDFQFVEPFATALVE--------DKVLAHTAKAEAEI   78 (179)
T ss_dssp             HHHHHHHHHTTCHHHHHHHHHHHHTT--CCSSTT-----GGG-TTSTTHHHHHHHHHH--------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHhh--Cccccc-----ccC-cchHHHHHHHHHHHH--------HHHHHHHHHHHHHH
Confidence            34446778899999999999998863  111110     000 0000 0 11111111        13456788999999


Q ss_pred             hcCCHHHHHHHHHhccc--C-ChhhHHHHHHHHHHcCChHHHHHHHHHHHH-----CCCCCCHHH
Q 040371           88 KCGKIQMAKEVFDTVQR--N-DVSVWNAMISGVAIHGLAADASAIFTKMEM-----FNVLPDSIT  144 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~~--~-~~~~~~~li~~~~~~g~~~~A~~l~~~m~~-----~g~~p~~~t  144 (410)
                      +.|++++|...+++...  | +...|..++.+|.+.|+..+|++.|+++..     .|+.|...|
T Consensus        79 ~~g~~~~Al~~~~~al~~~P~~e~~~~~l~~al~~~Gr~~eAl~~y~~~~~~L~~eLG~~P~~~l  143 (179)
T d2ff4a2          79 ACGRASAVIAELEALTFEHPYREPLWTQLITAYYLSDRQSDALGAYRRVKTTLADDLGIDPGPTL  143 (179)
T ss_dssp             HTTCHHHHHHHHHHHHHHSTTCHHHHHHHHHHHHTTTCHHHHHHHHHHHHHHHHHHHSCCCCHHH
T ss_pred             HCCCchHHHHHHHHHHHhCCccHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhCCCcCHHH
Confidence            99999999999998864  3 678999999999999999999999999744     589998765

>d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: HCP-like
family: HCP-like
domain: Cysteine rich protein C (HcpC)
species: Helicobacter pylori [TaxId: 210]

Probab=97.04  E-value=0.062  Score=44.38  Aligned_cols=223  Identities=10%  Similarity=-0.062  Sum_probs=155.1

Q ss_pred             CHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh----cCCHHHHHHHHHhcccC-ChhhHHHHH
Q 040371           40 DKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK----CGKIQMAKEVFDTVQRN-DVSVWNAMI  114 (410)
Q Consensus        40 d~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~----~g~~~~A~~~f~~m~~~-~~~~~~~li  114 (410)
                      |+..+..+...+...+++++|.+.|++..+.|   +......|..+|..    ..+...|...+.....+ +...+..+.
T Consensus         1 ~p~~~~~lG~~~~~~~d~~~A~~~~~kAa~~g---~~~A~~~Lg~~y~~G~~~~~d~~~a~~~~~~a~~~~~~~a~~~l~   77 (265)
T d1ouva_           1 DPKELVGLGAKSYKEKDFTQAKKYFEKACDLK---ENSGCFNLGVLYYQGQGVEKNLKKAASFYAKACDLNYSNGCHLLG   77 (265)
T ss_dssp             CHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC---CHHHHHHHHHHHHcCCCcchhHHHHHHhhcccccccccchhhccc
Confidence            45566777777888999999999999999887   55667778888876    56899999999887654 556666666


Q ss_pred             HHHHH----cCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH----ccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHH
Q 040371          115 SGVAI----HGLAADASAIFTKMEMFNVLPDSITFLGLLTACS----HCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVD  186 (410)
Q Consensus       115 ~~~~~----~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~----~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~  186 (410)
                      ..+..    ..+.+.|...++.....|..+.   ...+...+.    .......+...+.....    ..+...+..|..
T Consensus        78 ~~~~~~~~~~~~~~~a~~~~~~a~~~g~~~a---~~~l~~~~~~~~~~~~~~~~a~~~~~~~~~----~~~~~~~~~L~~  150 (265)
T d1ouva_          78 NLYYSGQGVSQNTNKALQYYSKACDLKYAEG---CASLGGIYHDGKVVTRDFKKAVEYFTKACD----LNDGDGCTILGS  150 (265)
T ss_dssp             HHHHHTSSSCCCHHHHHHHHHHHHHTTCHHH---HHHHHHHHHHCSSSCCCHHHHHHHHHHHHH----TTCHHHHHHHHH
T ss_pred             cccccccccchhhHHHHHHHhhhhhhhhhhH---HHhhcccccCCCcccchhHHHHHHhhhhhc----ccccchhhhhhh
Confidence            65554    4678899999998887764322   222222222    34557777777777654    235677888888


Q ss_pred             HHHh----cCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHh----cCchhHHHHHHHhh-ccCCCchHHHHHHHHHh----
Q 040371          187 LLGR----AGHIEEAYGLITSMTMEPDVVVWRALLSACRT----FKRLELGEVAIVNI-SRLMGGDYVLLSNMYCY----  253 (410)
Q Consensus       187 ~~~~----~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~----~g~~~~a~~~~~~~-~~~~~~~~~~l~~~~~~----  253 (410)
                      .|..    ..+...+..+++...-..+......+-..+..    ..+++.|...+.+. ...++..+..|..+|.+    
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~a~~~g~~~A~~~lg~~y~~g~~~~~d~~~A~~~~~~aa~~g~~~a~~~LG~~y~~G~g~  230 (265)
T d1ouva_         151 LYDAGRGTPKDLKKALASYDKACDLKDSPGCFNAGNMYHHGEGATKNFKEALARYSKACELENGGGCFNLGAMQYNGEGV  230 (265)
T ss_dssp             HHHHTSSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTCSSCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSSS
T ss_pred             hhccCCCcccccccchhhhhccccccccccccchhhhcccCcccccchhhhhhhHhhhhcccCHHHHHHHHHHHHcCCCC
Confidence            8876    45667777777766222355555555444433    56888888884332 33456677888888876    


Q ss_pred             cCChhHHHHHHHHHHhCCC
Q 040371          254 LKRWDTAENVREIMKKKGV  272 (410)
Q Consensus       254 ~g~~~~a~~~~~~m~~~g~  272 (410)
                      ..+.++|.+.|++..+.|.
T Consensus       231 ~~n~~~A~~~~~kAa~~g~  249 (265)
T d1ouva_         231 TRNEKQAIENFKKGCKLGA  249 (265)
T ss_dssp             SCCSTTHHHHHHHHHHHTC
T ss_pred             ccCHHHHHHHHHHHHHCcC
Confidence            3479999999999988775

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=97.04  E-value=0.0027  Score=48.15  Aligned_cols=113  Identities=13%  Similarity=0.009  Sum_probs=66.4

Q ss_pred             HHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhh----------CCHHHHHHHHHHHHHcCCCccHHHHHHHHHH
Q 040371           16 FVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARL----------GALNHAYWVHNLIIEKKIELNFILSAALIDM   85 (410)
Q Consensus        16 ~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~----------~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~   85 (410)
                      |-+.+.+++|+..|+...+.. |.|..++..+..++...          +.+++|...++++++.. +.+...|..+...
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~~~~~~~Ai~~~~kAl~l~-P~~~~a~~~lG~~   84 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDAKQMIQEAITKFEEALLID-PKKDEAVWCIGNA   84 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHhc-chhhHHHhhHHHH
Confidence            456677888999998888753 44666777777777644          33466777777776654 3456666666666


Q ss_pred             HHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
Q 040371           86 YSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTAC  152 (410)
Q Consensus        86 y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~  152 (410)
                      |...|++.           ++..         ...+.+++|.+.|++..+  +.|+..++..-+..+
T Consensus        85 y~~~g~~~-----------~~~~---------~~~~~~~~A~~~~~kal~--l~P~~~~~~~~L~~~  129 (145)
T d1zu2a1          85 YTSFAFLT-----------PDET---------EAKHNFDLATQFFQQAVD--EQPDNTHYLKSLEMT  129 (145)
T ss_dssp             HHHHHHHC-----------CCHH---------HHHHHHHHHHHHHHHHHH--HCTTCHHHHHHHHHH
T ss_pred             HHHcccch-----------hhHH---------HHHHhHHHhhhhhhcccc--cCCCHHHHHHHHHHH
Confidence            65544321           0000         001234566667766665  456666655555544

>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=97.02  E-value=0.0057  Score=46.78  Aligned_cols=62  Identities=16%  Similarity=0.199  Sum_probs=34.9

Q ss_pred             hHHHHH--HHHHHHcCCHhHHHHHHHHHHHCC-CCCC----------HHHHHHHHHHHHhhCCHHHHHHHHHHHH
Q 040371            7 VSWNSM--IGGFVRNARFDEALRFFREMLSSK-VEPD----------KFTFASVIYGCARLGALNHAYWVHNLII   68 (410)
Q Consensus         7 ~~~n~l--i~~~~~~g~~~~a~~l~~~m~~~g-~~pd----------~~t~~~ll~a~~~~~~~~~a~~~~~~~~   68 (410)
                      .+|+.+  ...+.+.|++++|+..|++.++.. -.|+          ...|+.+..++...|+++.|.+.++..+
T Consensus         8 ~a~~~l~~g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~al   82 (156)
T d2hr2a1           8 GAYLALSDAQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADKAL   82 (156)
T ss_dssp             HHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhhhh
Confidence            466666  444556688888888888776521 0111          2345555555555555555555555444

>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=97.02  E-value=0.002  Score=54.27  Aligned_cols=52  Identities=17%  Similarity=0.071  Sum_probs=25.2

Q ss_pred             HcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc
Q 040371           18 RNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus        18 ~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~   70 (410)
                      +.|++++|+..|++.++.. +-|...+..+...++..|++++|.+.++...+.
T Consensus         8 ~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~~l   59 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSIKL   59 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh
Confidence            3455555555555554432 224444555555555555555555555554443

>d1zbpa1 e.61.1.1 (A:2-265) Hypothetical protein VPA1032 {Vibrio parahaemolyticus [TaxId: 670]}

class: Multi-domain proteins (alpha and beta)
fold: ImpE-like
superfamily: ImpE-like
family: ImpE-like
domain: Hypothetical protein VPA1032
species: Vibrio parahaemolyticus [TaxId: 670]

Probab=96.97  E-value=0.00052  Score=58.10  Aligned_cols=50  Identities=18%  Similarity=0.154  Sum_probs=27.1

Q ss_pred             hhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           53 RLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        53 ~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      +.|++++|.+.++..++.. +.|...+..|...|+..|++++|.+.|+...
T Consensus         8 ~~G~l~eAl~~l~~al~~~-P~d~~ar~~La~lL~~~G~~e~A~~~l~~a~   57 (264)
T d1zbpa1           8 SEGQLQQALELLIEAIKAS-PKDASLRSSFIELLCIDGDFERADEQLMQSI   57 (264)
T ss_dssp             TTTCHHHHHHHHHHHHHTC-TTCHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHHHHC-CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3455555555555555543 3345555555555555555555555555543

>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=96.89  E-value=0.11  Score=44.78  Aligned_cols=240  Identities=10%  Similarity=0.066  Sum_probs=140.3

Q ss_pred             HHHHHHHHHHHcCCHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHH
Q 040371            8 SWNSMIGGFVRNARFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYS   87 (410)
Q Consensus         8 ~~n~li~~~~~~g~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~   87 (410)
                      -|..++..|.+.++++.|.+++.+..      +..+|..+..+|........+     .+.......+..-...++..|-
T Consensus        42 d~~rl~~~~v~l~~~~~avd~~~k~~------~~~~~k~~~~~l~~~~e~~la-----~i~~~~~~~~~d~l~~~v~~ye  110 (336)
T d1b89a_          42 NFGRLASTLVHLGEYQAAVDGARKAN------STRTWKEVCFACVDGKEFRLA-----QMCGLHIVVHADELEELINYYQ  110 (336)
T ss_dssp             CHHHHHHHHHTTTCHHHHHHHHHHHT------CHHHHHHHHHHHHHTTCHHHH-----HHTTTTTTTCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhhccHHHHHHHHHHcC------CHHHHHHHHHHHHhCcHHHHH-----HHHHHHhhcCHHHHHHHHHHHH
Confidence            35678888888899999888876541      466888888888877766543     2223333445566678888999


Q ss_pred             hcCCHHHHHHHHHhcc---cCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCH--------HHHHHHHHHHHccC
Q 040371           88 KCGKIQMAKEVFDTVQ---RNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDS--------ITFLGLLTACSHCG  156 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~---~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~--------~t~~~ll~a~~~~g  156 (410)
                      ..|..++...+++...   ..+...++-++..|++.+ .++.++.++.... ...+..        .-|.-++-.|.+.|
T Consensus       111 ~~~~~e~Li~~Le~~~~~~~~~~~~~~~L~~lyak~~-~~kl~e~l~~~s~-~y~~~k~~~~c~~~~l~~elv~Ly~~~~  188 (336)
T d1b89a_         111 DRGYFEELITMLEAALGLERAHMGMFTELAILYSKFK-PQKMREHLELFWS-RVNIPKVLRAAEQAHLWAELVFLYDKYE  188 (336)
T ss_dssp             HTTCHHHHHHHHHHHTTSTTCCHHHHHHHHHHHHTTC-HHHHHHHHHHHST-TSCHHHHHHHHHTTTCHHHHHHHHHHTT
T ss_pred             HcCChHHHHHHHHHHHcCCccchHHHHHHHHHHHHhC-hHHHHHHHHhccc-cCCHHHHHHHHHHcCChHHHHHHHHhcC
Confidence            9999999988888643   346667888888888764 4444444443311 122211        12345777888888


Q ss_pred             CHHHHHHHHHHhhhh----------cCCCCChhHHHHHHHHHHhcCCHHHHHHHHHhCCCCCCHHHHHHHHHHHHhcCch
Q 040371          157 LVEEGRKYFDHMRSR----------YSIQPQLEHYGAMVDLLGRAGHIEEAYGLITSMTMEPDVVVWRALLSACRTFKRL  226 (410)
Q Consensus       157 ~~~~a~~~~~~m~~~----------~~~~~~~~~~~~li~~~~~~g~~~~A~~~~~~m~~~p~~~~~~~li~~~~~~g~~  226 (410)
                      .++.|..+.-.=...          ..-..|+..|-..+..|..+. .+-...++..++-+-|.   ..++.-+.+.+++
T Consensus       189 ~~~~A~~~~i~~~~~~~~~~~f~e~~~k~~N~e~~~~~i~~yL~~~-p~~i~~lL~~v~~~~d~---~r~V~~~~k~~~l  264 (336)
T d1b89a_         189 EYDNAIITMMNHPTDAWKEGQFKDIITKVANVELYYRAIQFYLEFK-PLLLNDLLMVLSPRLDH---TRAVNYFSKVKQL  264 (336)
T ss_dssp             CHHHHHHHHHHSTTTTCCHHHHHHHHHHCSSTHHHHHHHHHHHHHC-GGGHHHHHHHHGGGCCH---HHHHHHHHHTTCT
T ss_pred             CHHHHHHHHHHcchhhhhHHHHHHHHHccCChHHHHHHHHHHHHcC-HHHHHHHHHHhccCCCH---HHHHHHHHhcCCc
Confidence            888876653221100          000123334444444444321 22222222222111122   2344555666666


Q ss_pred             hHHHHHHHhhcc-CCCchHHHHHHHHHhcCChhHHHHHH
Q 040371          227 ELGEVAIVNISR-LMGGDYVLLSNMYCYLKRWDTAENVR  264 (410)
Q Consensus       227 ~~a~~~~~~~~~-~~~~~~~~l~~~~~~~g~~~~a~~~~  264 (410)
                      ......+..... .+..+..+|...|...++++.-++..
T Consensus       265 ~li~p~Le~v~~~n~~~vn~al~~lyie~~d~~~l~~~i  303 (336)
T d1b89a_         265 PLVKPYLRSVQNHNNKSVNESLNNLFITEEDYQALRTSI  303 (336)
T ss_dssp             TTTHHHHHHHHTTCCHHHHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcChHHHHHHHHHHHhCcchhHHHHHHH
Confidence            666666444333 34457888999999999876544433

>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=96.86  E-value=0.00015  Score=67.79  Aligned_cols=217  Identities=10%  Similarity=-0.034  Sum_probs=106.6

Q ss_pred             HHHHHHHHHHHCCCCCCH-HHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccH-HHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371           24 EALRFFREMLSSKVEPDK-FTFASVIYGCARLGALNHAYWVHNLIIEKKIELNF-ILSAALIDMYSKCGKIQMAKEVFDT  101 (410)
Q Consensus        24 ~a~~l~~~m~~~g~~pd~-~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~-~~~~~li~~y~~~g~~~~A~~~f~~  101 (410)
                      +|.+.|++..+  ++||. ..+..+..++...++++++   +++++...  |+. ...+..-..+.  ..+..+.+.++.
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 QSAQYLRQAEV--LKADMTDSKLGPAEVWTSRQALQDL---YQKMLVTD--LEYALDKKVEQDLWN--HAFKNQITTLQG   74 (497)
T ss_dssp             HHHHHHHHHHH--HHGGGTCSSSCSSSSHHHHHHHHHH---HHHHHHHC--HHHHHHHTHHHHHHH--HHTHHHHHHHHH
T ss_pred             HHHHHHHHHHH--cCCCCHHHHhhHHHHHHHHchHHHH---HHHHHHcC--hhhHHHHhHHHHHHH--HHHHHHHHHHHH
Confidence            67788888766  45553 3556666677777777654   66666542  221 11222111111  113445555554


Q ss_pred             ccc----CChhhHHHHHHHH--HHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCC
Q 040371          102 VQR----NDVSVWNAMISGV--AIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSI  174 (410)
Q Consensus       102 m~~----~~~~~~~~li~~~--~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~  174 (410)
                      ..+    ++..-.......+  ...+.++.|+..+.+..  ++.| +...+..+...+.+.|+.++|...+......   
T Consensus        75 ~~k~~~~~~~~~~~~~~~~~l~~a~~~Y~~ai~~l~~~~--~l~~~~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~---  149 (497)
T d1ya0a1          75 QAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVF--NVDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSY---  149 (497)
T ss_dssp             HHSCSSCTTTTHHHHHHHHHHHHHHHHHHHHHHHHTC---------------------------------CCHHHHH---
T ss_pred             hcccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CCChhhHHHHHHhHHHHHhCCCHHHHHHHHHHHhCC---
Confidence            432    1222111111111  12344444444444332  2333 3445666667777788888887776665432   


Q ss_pred             CCChhHHHHHHHHHHhcCCHHHHHHHHHhC-CCCCC-HHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHH
Q 040371          175 QPQLEHYGAMVDLLGRAGHIEEAYGLITSM-TMEPD-VVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSN  249 (410)
Q Consensus       175 ~~~~~~~~~li~~~~~~g~~~~A~~~~~~m-~~~p~-~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~  249 (410)
                      .| ...+..+.+.+...|++++|...|++. .+.|+ ...|+.|-..+...|+..+|...   .....|+.+.++..|..
T Consensus       150 ~~-~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l~P~~~~~~~~Lg~~~~~~~~~~~A~~~y~ral~~~~~~~~a~~nL~~  228 (497)
T d1ya0a1         150 IC-QHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQK  228 (497)
T ss_dssp             HH-HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHCTTBSHHHHHHHHHHHHTTCHHHHHHHHHHHHSSSBCCHHHHHHHHH
T ss_pred             CH-HHHHHHHHHHHHHcccHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence            11 246777888888888888888888876 45564 57888888888888888888877   34445666667777777


Q ss_pred             HHHhcC
Q 040371          250 MYCYLK  255 (410)
Q Consensus       250 ~~~~~g  255 (410)
                      .|.+..
T Consensus       229 ~~~~~~  234 (497)
T d1ya0a1         229 ALSKAL  234 (497)
T ss_dssp             HHHHHT
T ss_pred             HHHHhh
Confidence            776544

>d1zu2a1 a.118.8.1 (A:1-145) Mitochondrial import receptor subunit tom20-3 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: Tetratricopeptide repeat (TPR)
domain: Mitochondrial import receptor subunit tom20-3
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=96.82  E-value=0.0037  Score=47.32  Aligned_cols=113  Identities=10%  Similarity=0.103  Sum_probs=66.7

Q ss_pred             HHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHH
Q 040371           51 CARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIF  130 (410)
Q Consensus        51 ~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~  130 (410)
                      +-+.+.+++|++.++..++.. |.+..++..+..+|...+++..+.+-                     .+.+++|+..|
T Consensus         7 ~~r~~~fe~A~~~~e~al~~~-P~~~~~~~~~g~~l~~~~~~~~~~e~---------------------~~~~~~Ai~~~   64 (145)
T d1zu2a1           7 FDRILLFEQIRQDAENTYKSN-PLDADNLTRWGGVLLELSQFHSISDA---------------------KQMIQEAITKF   64 (145)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHC-TTCHHHHHHHHHHHHHHHHHSCHHHH---------------------HHHHHHHHHHH
T ss_pred             HHHHccHHHHHHHHHHHHhhC-CcchHHHHHHHHHHHHhhhhhhhhHH---------------------HHHHHHHHHHH
Confidence            345566788888888887775 55677777777777655443322211                     12234555555


Q ss_pred             HHHHHCCCCC-CHHHHHHHHHHHHccC-----------CHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHh
Q 040371          131 TKMEMFNVLP-DSITFLGLLTACSHCG-----------LVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGR  190 (410)
Q Consensus       131 ~~m~~~g~~p-~~~t~~~ll~a~~~~g-----------~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~  190 (410)
                      ++..+.  .| +..+|..+..+|...|           .+++|.+.|+...+   +.|+...|..-+..+.+
T Consensus        65 ~kAl~l--~P~~~~a~~~lG~~y~~~g~~~~~~~~~~~~~~~A~~~~~kal~---l~P~~~~~~~~L~~~~k  131 (145)
T d1zu2a1          65 EEALLI--DPKKDEAVWCIGNAYTSFAFLTPDETEAKHNFDLATQFFQQAVD---EQPDNTHYLKSLEMTAK  131 (145)
T ss_dssp             HHHHHH--CTTCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH---HCTTCHHHHHHHHHHHT
T ss_pred             HHHHHh--cchhhHHHhhHHHHHHHcccchhhHHHHHHhHHHhhhhhhcccc---cCCCHHHHHHHHHHHHH
Confidence            555542  23 3444555555554432           35788888888774   47777777666655543

>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=96.70  E-value=0.0043  Score=57.53  Aligned_cols=114  Identities=11%  Similarity=-0.020  Sum_probs=61.6

Q ss_pred             cHHHHHHHHHHHHhcCCHHHHHHHHHhcccCCh-hhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCC-CHHHHHHHHHHH
Q 040371           75 NFILSAALIDMYSKCGKIQMAKEVFDTVQRNDV-SVWNAMISGVAIHGLAADASAIFTKMEMFNVLP-DSITFLGLLTAC  152 (410)
Q Consensus        75 ~~~~~~~li~~y~~~g~~~~A~~~f~~m~~~~~-~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p-~~~t~~~ll~a~  152 (410)
                      +...+..+...+.+.|+.++|...+.....++. .++..+...+...|++++|...|++..+.  .| +...|+.+...+
T Consensus       119 ~~~~~~~lg~~~~~~~~~~~A~~~~~~al~~~~~~~~~~LG~l~~~~~~~~~A~~~y~~A~~l--~P~~~~~~~~Lg~~~  196 (497)
T d1ya0a1         119 CRVKSSQLGIISNKQTHTSAIVKPQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQL--VPSNGQPYNQLAILA  196 (497)
T ss_dssp             ------------------------CCHHHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH--CTTBSHHHHHHHHHH
T ss_pred             hHHHHHHhHHHHHhCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHcccHHHHHHHHHHHHHH--CCCchHHHHHHHHHH
Confidence            455666777777777777777766655443322 35666777777788888888888877763  44 456788888888


Q ss_pred             HccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcC
Q 040371          153 SHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAG  192 (410)
Q Consensus       153 ~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g  192 (410)
                      ...|+..+|...|.+...  --+|-..++..|...|.+..
T Consensus       197 ~~~~~~~~A~~~y~ral~--~~~~~~~a~~nL~~~~~~~~  234 (497)
T d1ya0a1         197 SSKGDHLTTIFYYCRSIA--VKFPFPAASTNLQKALSKAL  234 (497)
T ss_dssp             HHTTCHHHHHHHHHHHHS--SSBCCHHHHHHHHHHHHHHT
T ss_pred             HHcCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHHHHHhh
Confidence            888888888888877763  33556677777777766543

>d2hr2a1 a.118.8.8 (A:2-157) Hypothetical protein CT2138 {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: TPR-like
family: CT2138-like
domain: Hypothetical protein CT2138
species: Chlorobium tepidum [TaxId: 1097]

Probab=96.68  E-value=0.0093  Score=45.49  Aligned_cols=54  Identities=13%  Similarity=-0.023  Sum_probs=28.6

Q ss_pred             HHHHHhhCCHHHHHHHHHHHHHcCCC-c----------cHHHHHHHHHHHHhcCCHHHHHHHHHh
Q 040371           48 IYGCARLGALNHAYWVHNLIIEKKIE-L----------NFILSAALIDMYSKCGKIQMAKEVFDT  101 (410)
Q Consensus        48 l~a~~~~~~~~~a~~~~~~~~~~g~~-~----------~~~~~~~li~~y~~~g~~~~A~~~f~~  101 (410)
                      .......|++++|.+.|.+.++..-. |          ....|+.+..+|.+.|++++|..-+++
T Consensus        16 g~~~~~~g~y~~Ai~~y~~Al~i~~~~~~~~~~~~~~~~a~~~~nlg~~~~~lg~~~~A~~~~~~   80 (156)
T d2hr2a1          16 AQRQLVAGEYDEAAANCRRAMEISHTMPPEEAFDHAGFDAFCHAGLAEALAGLRSFDEALHSADK   80 (156)
T ss_dssp             HHHHHHHTCHHHHHHHHHHHHHHHTTSCTTSCCCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHhChhhhhhhhcccchhHHHHHHHHHHHHHHcCccchhhHhhhh
Confidence            33444556777777777666653110 1          123455555556666666555555444

>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=95.47  E-value=0.11  Score=35.27  Aligned_cols=71  Identities=13%  Similarity=0.105  Sum_probs=41.2

Q ss_pred             HHHHHHHHcCCHhHHHHHHHHHHHC-----CCCCC-HHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHH
Q 040371           11 SMIGGFVRNARFDEALRFFREMLSS-----KVEPD-KFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAAL   82 (410)
Q Consensus        11 ~li~~~~~~g~~~~a~~l~~~m~~~-----g~~pd-~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~l   82 (410)
                      .+-..+.+.|++++|+..|++..+.     ...++ ..++..+..++.+.|++++|...++++++.. |-+..+.+.+
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL~l~-P~~~~a~~Nl   86 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLLELD-PEHQRANGNL   86 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHC-TTCHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHHHhC-cCCHHHHHHH
Confidence            4556666777777777777666532     11122 3456666666677777777777777766653 2234444433

>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=95.10  E-value=0.31  Score=35.28  Aligned_cols=109  Identities=12%  Similarity=0.033  Sum_probs=57.1

Q ss_pred             CHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHh----cCCHHHHH
Q 040371           21 RFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEKKIELNFILSAALIDMYSK----CGKIQMAK   96 (410)
Q Consensus        21 ~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~----~g~~~~A~   96 (410)
                      ++++|++.|++..+.|..   .....+.  .....+.++|.+.+.+..+.|   ++.....|..+|..    ..+.++|.
T Consensus         8 d~~~A~~~~~kaa~~g~~---~a~~~l~--~~~~~~~~~a~~~~~~aa~~g---~~~a~~~Lg~~y~~g~~~~~d~~~A~   79 (133)
T d1klxa_           8 DLKKAIQYYVKACELNEM---FGCLSLV--SNSQINKQKLFQYLSKACELN---SGNGCRFLGDFYENGKYVKKDLRKAA   79 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCT---THHHHHH--TCTTSCHHHHHHHHHHHHHTT---CHHHHHHHHHHHHHCSSSCCCHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCh---hhhhhhc--cccccCHHHHHHHHhhhhccc---chhhhhhHHHhhhhccccchhhHHHH
Confidence            567788888887776622   2222222  223456677777777776665   34444455555543    23455666


Q ss_pred             HHHHhccc-CChhhHHHHHHHHHH----cCChHHHHHHHHHHHHCC
Q 040371           97 EVFDTVQR-NDVSVWNAMISGVAI----HGLAADASAIFTKMEMFN  137 (410)
Q Consensus        97 ~~f~~m~~-~~~~~~~~li~~~~~----~g~~~~A~~l~~~m~~~g  137 (410)
                      +.|++..+ .++.+...|-..|..    ..+.++|.++|++..+.|
T Consensus        80 ~~~~~aa~~g~~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa~~G  125 (133)
T d1klxa_          80 QYYSKACGLNDQDGCLILGYKQYAGKGVVKNEKQAVKTFEKACRLG  125 (133)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHHHTT
T ss_pred             HHHhhhhccCcchHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHCC
Confidence            66655443 233444444444433    234555555555554444

>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=94.91  E-value=0.088  Score=35.89  Aligned_cols=58  Identities=7%  Similarity=-0.125  Sum_probs=28.9

Q ss_pred             HHHHHHHhhCCHHHHHHHHHHHHHcC------CCccHHHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           46 SVIYGCARLGALNHAYWVHNLIIEKK------IELNFILSAALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        46 ~ll~a~~~~~~~~~a~~~~~~~~~~g------~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      .+...+.+.|++++|...|++.++..      ......+++.|..+|.+.|++++|+..|++..
T Consensus        10 ~lG~~~~~~g~y~~A~~~~~~Al~~~~~~~~~~~~~~~~l~~Lg~~~~~~g~~~~A~~~y~~aL   73 (95)
T d1tjca_          10 ELGKVAYTEADYYHTELWMEQALRQLDEGEISTIDKVSVLDYLSYAVYQQGDLDKALLLTKKLL   73 (95)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHTTCCCSSCHHHHHHHHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHhhhhccCccHHHHHHHHhhHHHhcCChHHHHHHHHHHH
Confidence            44555556666666666665554431      01113444555555555555555555555443

>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=93.99  E-value=0.55  Score=33.44  Aligned_cols=137  Identities=9%  Similarity=-0.003  Sum_probs=84.2

Q ss_pred             HHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHHHHHhcCCHHHH
Q 040371          118 AIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVDLLGRAGHIEEA  197 (410)
Q Consensus       118 ~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~~~~~~g~~~~A  197 (410)
                      ...|..++..++..+.....   +..-|+-++.-....-+-+...+.++.+-+-+.+.              .++++...
T Consensus        13 ildG~ve~Gveii~k~~~ss---~~~E~NW~ICNiidt~dC~~v~~~Ld~IG~~FDls--------------~C~Nlk~v   75 (161)
T d1wy6a1          13 LLDGYIDEGVKIVLEITKSS---TKSEYNWFICNLLESIDCRYMFQVLDKIGSYFDLD--------------KCQNLKSV   75 (161)
T ss_dssp             HHTTCHHHHHHHHHHHHHHS---CHHHHTHHHHHHHHHCCHHHHHHHHHHHGGGSCGG--------------GCSCTHHH
T ss_pred             HHhhhHHhHHHHHHHHcccC---CccccceeeeecccccchHHHHHHHHHHhhhcCch--------------hhhcHHHH
Confidence            34566667777776665432   34455656655555666666666666655433322              23333333


Q ss_pred             HHHHHhCCCCCCHHHHHHHHHHHHhcCchhHHHHH---HHhhccCCCchHHHHHHHHHhcCChhHHHHHHHHHHhCCCc
Q 040371          198 YGLITSMTMEPDVVVWRALLSACRTFKRLELGEVA---IVNISRLMGGDYVLLSNMYCYLKRWDTAENVREIMKKKGVR  273 (410)
Q Consensus       198 ~~~~~~m~~~p~~~~~~~li~~~~~~g~~~~a~~~---~~~~~~~~~~~~~~l~~~~~~~g~~~~a~~~~~~m~~~g~~  273 (410)
                      ..-+-.++  .+..-+...++...+.|.-+.-.++   +.+.+..++.....+.++|-+.|...++-+++.+.-++|++
T Consensus        76 v~C~~~~n--~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn~~i~~~~llkia~A~kkig~~re~nell~~ACe~G~K  152 (161)
T d1wy6a1          76 VECGVINN--TLNEHVNKALDILVIQGKRDKLEEIGREILKNNEVSASILVAIANALRRVGDERDATTLLIEACKKGEK  152 (161)
T ss_dssp             HHHHHHTT--CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC--CCSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHTTCH
T ss_pred             HHHHHHhc--chHHHHHHHHHHHHHhccHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhcchhhHHHHHHHHHHHhHH
Confidence            33333332  2333344556666777777777777   44555666777788899999999999999999999999874

>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=93.67  E-value=0.78  Score=32.65  Aligned_cols=85  Identities=11%  Similarity=0.033  Sum_probs=60.4

Q ss_pred             hcCCHHHHHHHHHhcccCChhhHHHHHHHHHHcCChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHH
Q 040371           88 KCGKIQMAKEVFDTVQRNDVSVWNAMISGVAIHGLAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDH  167 (410)
Q Consensus        88 ~~g~~~~A~~~f~~m~~~~~~~~~~li~~~~~~g~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~  167 (410)
                      +|+++......|-.+- .+....+..++...+.|+-+.-.++++.+.+. -+|++.....+..||.+.|...++.+++.+
T Consensus        68 ~C~Nlk~vv~C~~~~n-~~se~vdlALd~lv~~~kkd~Ld~i~~~l~kn-~~i~~~~llkia~A~kkig~~re~nell~~  145 (161)
T d1wy6a1          68 KCQNLKSVVECGVINN-TLNEHVNKALDILVIQGKRDKLEEIGREILKN-NEVSASILVAIANALRRVGDERDATTLLIE  145 (161)
T ss_dssp             GCSCTHHHHHHHHHTT-CCCHHHHHHHHHHHHTTCHHHHHHHHHHHC---CCSCHHHHHHHHHHHHHTTCHHHHHHHHHH
T ss_pred             hhhcHHHHHHHHHHhc-chHHHHHHHHHHHHHhccHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHhcchhhHHHHHHH
Confidence            3444444444443332 23345566778888899999888998887664 467778888899999999999999999988


Q ss_pred             hhhhcCCC
Q 040371          168 MRSRYSIQ  175 (410)
Q Consensus       168 m~~~~~~~  175 (410)
                      .-++ |++
T Consensus       146 ACe~-G~K  152 (161)
T d1wy6a1         146 ACKK-GEK  152 (161)
T ss_dssp             HHHT-TCH
T ss_pred             HHHH-hHH
Confidence            8865 653

>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=89.20  E-value=1.1  Score=30.22  Aligned_cols=63  Identities=13%  Similarity=0.245  Sum_probs=50.4

Q ss_pred             ChHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHccCCHHHHHHHHHHhhhhcCCCCChhHHHHHHH
Q 040371          122 LAADASAIFTKMEMFNVLPDSITFLGLLTACSHCGLVEEGRKYFDHMRSRYSIQPQLEHYGAMVD  186 (410)
Q Consensus       122 ~~~~A~~l~~~m~~~g~~p~~~t~~~ll~a~~~~g~~~~a~~~~~~m~~~~~~~~~~~~~~~li~  186 (410)
                      +.-++.+-++.+....+.|+.....+.|.||.+..++..|.++|+..+.+.|  ++...|..++.
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K~~--~~k~~y~yilq   83 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDKAG--PHKEIYPYVIQ   83 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHTT--TCTTHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHhc--CcHHHHHHHHH
Confidence            5566777777777778899999999999999999999999999999886543  34556776654

>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=88.42  E-value=3.1  Score=29.52  Aligned_cols=106  Identities=12%  Similarity=-0.103  Sum_probs=54.0

Q ss_pred             CHHHHHHHHHHHHHcCCCccHHHHHHHHHHHHhcCCHHHHHHHHHhccc-CChhhHHHHHHHHHH----cCChHHHHHHH
Q 040371           56 ALNHAYWVHNLIIEKKIELNFILSAALIDMYSKCGKIQMAKEVFDTVQR-NDVSVWNAMISGVAI----HGLAADASAIF  130 (410)
Q Consensus        56 ~~~~a~~~~~~~~~~g~~~~~~~~~~li~~y~~~g~~~~A~~~f~~m~~-~~~~~~~~li~~~~~----~g~~~~A~~l~  130 (410)
                      ++++|.+.|.+..+.|...   ....|..  ....+.++|.+.|++.-+ .+..+...|-..|..    ..+.++|+++|
T Consensus         8 d~~~A~~~~~kaa~~g~~~---a~~~l~~--~~~~~~~~a~~~~~~aa~~g~~~a~~~Lg~~y~~g~~~~~d~~~A~~~~   82 (133)
T d1klxa_           8 DLKKAIQYYVKACELNEMF---GCLSLVS--NSQINKQKLFQYLSKACELNSGNGCRFLGDFYENGKYVKKDLRKAAQYY   82 (133)
T ss_dssp             HHHHHHHHHHHHHHTTCTT---HHHHHHT--CTTSCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHCSSSCCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHCCChh---hhhhhcc--ccccCHHHHHHHHhhhhcccchhhhhhHHHhhhhccccchhhHHHHHHH
Confidence            5677888888877776322   2222221  223456666666665543 344455545444443    23456666666


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHc----cCCHHHHHHHHHHhh
Q 040371          131 TKMEMFNVLPDSITFLGLLTACSH----CGLVEEGRKYFDHMR  169 (410)
Q Consensus       131 ~~m~~~g~~p~~~t~~~ll~a~~~----~g~~~~a~~~~~~m~  169 (410)
                      ++..+.|.   ......|-..|.+    ..+.++|..+|+...
T Consensus        83 ~~aa~~g~---~~a~~~Lg~~y~~G~gv~~d~~~A~~~~~~Aa  122 (133)
T d1klxa_          83 SKACGLND---QDGCLILGYKQYAGKGVVKNEKQAVKTFEKAC  122 (133)
T ss_dssp             HHHHHTTC---HHHHHHHHHHHHHTSSSCCCHHHHHHHHHHHH
T ss_pred             hhhhccCc---chHHHHHHHHHHcCCccCCCHHHHHHHHHHHH
Confidence            66665542   2222233333332    234555555555544

>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=84.18  E-value=3.3  Score=27.69  Aligned_cols=50  Identities=14%  Similarity=0.242  Sum_probs=37.0

Q ss_pred             CHhHHHHHHHHHHHCCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHc
Q 040371           21 RFDEALRFFREMLSSKVEPDKFTFASVIYGCARLGALNHAYWVHNLIIEK   70 (410)
Q Consensus        21 ~~~~a~~l~~~m~~~g~~pd~~t~~~ll~a~~~~~~~~~a~~~~~~~~~~   70 (410)
                      +.-++..-++.+....+.|++....+.|.||-+.+++..|.++++-+...
T Consensus        21 D~we~rrgmN~l~~~DlVPeP~Ii~aALrAcRRvND~alAVR~lE~vK~K   70 (105)
T d1v54e_          21 DAWELRKGMNTLVGYDLVPEPKIIDAALRACRRLNDFASAVRILEVVKDK   70 (105)
T ss_dssp             CHHHHHHHHHHHTTSSBCCCHHHHHHHHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence            34455566666666677888888888888888888888888888877543

>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=83.26  E-value=5.6  Score=27.95  Aligned_cols=47  Identities=21%  Similarity=0.006  Sum_probs=26.5

Q ss_pred             CHHHHHHHHHHHHHcCCCcc-HHHHHHHHHHHHhcCCHHHHHHHHHhcc
Q 040371           56 ALNHAYWVHNLIIEKKIELN-FILSAALIDMYSKCGKIQMAKEVFDTVQ  103 (410)
Q Consensus        56 ~~~~a~~~~~~~~~~g~~~~-~~~~~~li~~y~~~g~~~~A~~~f~~m~  103 (410)
                      +.+.|..+++.+.+.+ +.+ ...+-.|.-+|.+.|++++|++.++.+.
T Consensus        53 d~~~gI~lLe~~~~~~-p~~~rd~lY~Lav~yyklgdy~~A~~~~~~~L  100 (124)
T d2pqrb1          53 DERLGVKILTDIYKEA-ESRRRECLYYLTIGCYKLGEYSMAKRYVDTLF  100 (124)
T ss_dssp             HHHHHHHHHHHHHHHC-GGGHHHHHHHHHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcC-chhHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence            4456666666666543 222 2344455555666666666666666654